Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of nitrogen fixation in rhizobia

Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N2 gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.
Retinogenesis of the Human Fetal Retina: An Apical Polarity Perspective

The Crumbs complex has prominent roles in the control of apical cell polarity, in the coupling of cell density sensing to downstream cell signaling pathways, and in regulating junctional structures and cell adhesion. The Crumbs complex acts as a conductor orchestrating multiple downstream signaling pathways in epithelial and neuronal tissue development. These pathways lead to the regulation of cell size, cell fate, cell self-renewal, proliferation, differentiation, migration, mitosis, and apoptosis. In retinogenesis, these are all pivotal processes with important roles for the Crumbs complex to maintain proper spatiotemporal cell processes. Loss of Crumbs function in the retina results in loss of the stratified appearance resulting in retinal degeneration and loss of visual function. In this review, we begin by discussing the physiology of vision. We continue by outlining the processes of retinogenesis and how well this is recapitulated between the human fetal retina and human embryonic stem cell (ESC) or induced pluripotent stem cell (iPSC)-derived retinal organoids. Additionally, we discuss the functionality of in utero and preterm human fetal retina and the current level of functionality as detected in human stem cell-derived organoids. We discuss the roles of apical-basal cell polarity in retinogenesis with a focus on Leber congenital amaurosis which leads to blindness shortly after birth. Finally, we discuss Crumbs homolog (CRB)-based gene augmentation.
Characterization of the Barley Net Blotch Pathosystem at the Center of Origin of Host and Pathogen

Net blotch (NB) is a major disease of barley caused by the fungus Pyrenophora teres f. teres (Ptt), and P. teres f. maculata (Ptm). Ptt and Ptm infect the cultivated crop (Hordeum vulgare) and its wild relatives (H. vulgare ssp. spontaneum and H. murinum ssp. glaucum). The main goal of this research was to study the NB-causing pathogen in the crop center of origin. To address this, we have constructed a Ptt (n = 15) and Ptm (n = 12) collection isolated from three barley species across Israel. Isolates were characterized genetically and phenotypically. Aggressiveness of the isolates was determined based on necrotrophic growth rate on detached leaves of barley. In addition, isolates were genetically characterized by the mating type, followed by phylogenetic analysis, clustering them into seven groups. The analysis showed no significant differentiation of isolates based on either geographic origin, host of origin or form (Ptt vs. Ptm). Nevertheless, there was a significant difference in aggressiveness among the isolates regardless of host species, geographic location or sampling site. Moreover, it was apparent that the isolates derived from wild hosts were more variable in their necrotrophic growth rate, compared to isolates sampled from cultivated hosts, thereby suggesting that NB plays a major role in epidemiology at the center of barley origin where most of the diversity lies. Ptm has significantly higher necrotrophic and saprotrophic growth rates than Ptt, and for both a significant negative correlation was found between light intensity exposure and growth rates.
INSILICO ANALYSIS ON THE EFFECT OF RUTIN BIOFLAVONOID AND CHEMOTHERAPEUTIC DRUG CYCLOPHOSPHAMIDE ON NUCLEAR FACTOR KAPPA-B PROTEIN EXPRESSION

Cancer is medically termed as a malignant neoplasm characterized by uncontrolled growth of abnormal cells. Lung cancer is one of the commonest malignant neoplasms all over the world. Lung cancer is initiated by activation of oncogenes or inactivation of tumor suppressor genes. NF-kB p65 nuclear expression is an early and frequent phenomenon in the pathogenesis of lung cancer. It has been found that NF-kB activation plays a vital role in lung cancer pathogenesis and also identified as molecular link between inflammation and cancer. Rutin is a natural citrus bioflavonoid glycoside found in buckwheat, the leaves and petioles of Rheum species, and asparagus. The scavenging activity of rutin was strongest when compared with other flavonoids such as quercetin and naringin. The present study was undertaken to show the activity of natural therapeutic flavonoid rutin inhibiting the activity of NF-kB in lung cancer. Docking study of rutin was performed against NF-kB activity compared with the already existing chemotherapeutic agent Cyclophosphamide. The study showed a strong interaction between the rutin flavonoid with the hydrogen bonds of the NF-kB protein with a negative score inhibiting the expression of NF-kB which leads to chronic inflammation and progression of lung cancer.
A global analysis of function and conservation of catalytic residues in enzymes

The catalytic residues of an enzyme comprise the amino acids located in the active center responsible for accelerating the enzyme-catalyzed reaction. These residues lower the activation energy of reactions by performing several catalytic functions. Decades of enzymology research has established general themes regarding the roles of specific residues in these catalytic reactions, but it has been more difficult to explore these roles in a more systematic way. Here, we review the data on the catalytic residues of 648 enzymes, as annotated in the Mechanism and Catalytic Site Atlas (M-CSA), and compare our results with those in previous studies. We structured this analysis around three key properties of the catalytic residues: amino acid type, catalytic function, and sequence conservation in homologous proteins. As expected, we observed that catalysis is mostly accomplished by a small set of residues performing a limited number of catalytic functions. Catalytic residues are typically highly conserved, but to a smaller degree in homologues that perform different reactions or are nonenzymes (pseudoenzymes). Cross-analysis yielded further insights revealing which residues perform particular functions and how often. We obtained more detailed specificity rules for certain functions by identifying the chemical group upon which the residue acts. Finally, we show the mutation tolerance of the catalytic residues based on their roles. The characterization of the catalytic residues, their functions, and conservation, as presented here, is key to understanding the impact of mutations in evolution, disease, and enzyme design. The tools developed for this analysis are available at the M-CSA website and allow for user specific analysis of the same data.
Foodborne Pathogenic Microorganisms and Natural Toxins

Staphylococcal species are Gram-positive, non­ motile, catalase-positive, small, spherical bacteria (cocci), which, on microscopic examination, appear in pairs, short chains, or bunched in grape-like clusters. Staphylococci are ubiquitous and impossible to eradicate from the environment. Many of the 32 species and subspecies in the genus Staphylococcus are potentially found in foods due to environmental, human, and animal contamination.
Screening for Autism in Infants and Preschool Children with Developmental Delay

Objective: This study aimed to identify emotional and behavioural problems specific to young children with autism using the Developmental Behaviour Checklist (DBC-P) and thus evaluate the efficacy of this checklist as a screening tool for autism in children with developmental delay aged 18–48 months. Method: Subjects were 60 children with autism and developmental delay and 60 children with developmental delay without autism. Results: Features were identified which differentiated the children with autism from those with developmental delay without autism. Analyses revealed that a 17-item version of the DBC-P performed well as a screening tool for autism, with an ‘area under the curve’ of 0.874, sensitivity of 0.8750, and specificity of 0.6909. Conclusions: The DBC-P offers a potential simple and inexpensive method of screening at risk populations of preschool children with developmental delay for autism, thus facilitating timely referral to scarce specialist autism diagnostic services.
Pattern of Spread of Breast Cancer among Patients attending Cancer Unit of Lagos State University Teaching Hospital

Breast cancer spread usually result in high tumor burden with poor outcome. We aimed to determine the pattern of metastasis, relationship between characteristic of primary breast cancer and extent of subsequent metastasis. Background information and histological type were obtained from the patients records. Clinical, Radiological, Staging (Manchester) and site of metastasis information were obtained during pre-treatment examination and follow-up periods. Data analysis was done using descriptive statistics. The mean age of the respondents was 48.7 years and the peak age was 30-39 years. Evidence of metastatic involvement at presentation for care was lymph node 41.7%, lungs 20.2%, liver 5.4% and spine 4.2%. Site of metastasis after 2 years of follow up revealed that out of stage III patients, distant metastatic involvement observed were: Lymph node 85% (59), 22.2% (2), lungs 11.8% (4), spine 16.7% (1) and anterior chest wall 50% (3). For stage II, 5.9% had metastasis to the lung, 16.7% had spread to the spine and 16.7% had anterior chest wall recurrence. Distant recurrence remains common and incurable. Early recognition of metastatic breast disease will allow rapid institution of effective palliative treatment.
Topical Review: Neuronal Migration Disorders, Genetics, and Epileptogenesis

Several malformation syndromes with abnormal cortical development have been recognized. Specific causative gene defects and characteristic electroclinical patterns have been identified for some. X-linked periventricular nodular heterotopia is mainly seen in female patients and is often associated with focal epilepsy. FLN1 mutations have been reported in all familial cases and in about 25% of sporadic patients. A rare recessive form of periventricular nodular heterotopia owing to ARGEF2 gene mutations has also been reported in children with microcephaly, severe delay, and early-onset seizures. Lissencephaly-pachygyria and subcortical band heterotopia represent a malformative spectrum resulting from mutations of either the LIS1 or the DCX (XLIS) gene. LIS1 mutations cause a more severe malformation posteriorly. Most children have severe developmental delay and infantile spasms, but milder phenotypes are on record, including posterior subcortical band heterotopia owing to mosaic mutations of LIS1. DCX mutations usually cause anteriorly predominant lissencephaly in male patients and subcortical band heterotopia in female patients. Mutations of the coding region of DCX were found in all reported pedigrees and in about 50% of sporadic female patients with subcortical band heterotopia. Mutations of XLIS have also been found in male patients with anterior subcortical band heterotopia and in female patients with normal brain magnetic resonance imaging. The thickness of the band and the severity of pachygyria correlate with the likelihood of developing severe epilepsy. Autosomal recessive lissencephaly with cerebellar hypoplasia, accompanied by severe delay, hypotonia, and seizures, has been associated with mutations of the reelin (RELN) gene. X-linked lissencephaly with corpus callosum agenesis and ambiguous genitalia in genotypic males is associated with mutations of the ARX gene. Affected boys have severe delay and infantile spasms with suppression-burst electroencephalograms. Early death is frequent. Carrier female patients can have isolated corpus callosum agenesis. Schizencephaly has a wide anatomoclinical spectrum, including focal epilepsy in most patients. Familial occurrence is rare. Initial reports of heterozygous mutations in the EMX2 gene have not been confirmed. Among several syndromes featuring polymicrogyria, bilateral perisylvian polymicrogyria shows genetic heterogeneity, including linkage to chromosome Xq28 in some pedigrees, autosomal dominant or recessive inheritance in others, and an association with chromosome 22q11.2 deletion in some patients. About 65% of patients have severe epilepsy. Recessive bilateral frontoparietal polymicrogyria has been associated with mutations of the GPR56 gene. (J Child Neurol 2005;20:287—299).
Architecture of Indoor Air Volatile Organic Compounds Testing System Based on Wireless Sensor Networks

Today, as people's living standard grows better and better, the people’s indoor living environment is also demanding higher and higher. In particular, the concentration of indoor air VOCs is of even greater concern. Given that the traditional system developed for testing indoor air quality has some defects such as monomer node, single detection target and high user threshold, this paper applies wireless sensor network to the test system for indoor air VOCs. The results show that users can easily access the detection results via the Web, and the whole system features wireless, networking, multiple nodes, simple operation and low cost. The holistic equipment works in good condition and never fails. In a specific environment, compared with the traditional wireless sensor network, the detection control system devised herein reaches a constant value in a shorter time. With the test of the system functions, it is proved that the system can work in a truly and stably manner and has a high detection precision.
A Combined Stochastic-Deterministic Solution for Tracking Multiple Objects with an Stereo-Vision System

In this paper, the authors propose the use of a probabilistic algorithm to develop a multi-object tracking task. Different solutions have already been proposed by the scientific community to find a solution for this application, and the particle filter is proven to be the best choice in this case as the multimodality character of this Bayes filter implementation can be well-spent: an only particle filter can be used to track a variable number of objects. On the other hand, the flexibility of the particle filter can become in a lack of robustness for the estimator, so a deterministic algorithm is added to the standard filter to increase it. In the following paragraphs the global combined algorithm is described and different tests based on stereo-vision information are also included, proving the reliability of the proposal tracker. Key-Words: Bayesian estimation, PFs (Particle Filters), Visual tracking, MOT (Multi-Objets Tracking), Multimodal density functions
Deep Learning in Dynamic Scene Understanding

Video understanding is an attractive area in computer vision, which will contribute significantly in the future where artificial intelligence becomes mainstream. This project aims to solve video understanding through deep learning and improve the state-of-art model's performance. The project is divided into two parts. The first part is to learn and understand the basic neural network for video learning and the extraction of temporal features by implementing gesture recognition. This part implements two models, LRCN and 3D-CNN. Compared with the previous researches, the model size has been reduced and the performance has been improved. Finally, the 3D-CNN has achieved an accuracy of 83.37%. The second part is the improvement of the state-of-art model based on previous learning. This paper introduces temporal features into semantic segmentation by using 3D-CNN to extract features from video clips. The memory requirement and calculation time of the state-of-art model are greatly reduced with only little F-measure decreased, and the water puddle detection is realized. This paper provides a brand new way to handle video understanding tasks by using 3D-CNN and shows the importance of temporal features in video understanding area. Table of Content
What impact does an illustrated article have?

Today we use more and more illustrations in printed matter assuming it helps to clarify the meaning. My idea was to find out how people recognize, remember and understand contents in illustrated articles compared to those without pictures. This kind of studies have been made before (for instance Standing 1973, Paivio & Csapo 1973, Paivio 1986 and 1991, Dwyer 1976, Anglin & Levie 1985, Hannus 1996, Mikkilä-Erdmann 2002), but I was especially interested in the overall impact of illustrations over long time periods. Why have so many studies arrived at the conclusion that illustrations interfere or that they are inconsequential? The basic question is how we perceive and think. What is the role of mental images in the process? There are several cognitive theories about it. According to Pylyshyn (1999) all thinking is propositional, while Kosslyn (1996) claims that imagery rather relies on depictive representations. Thinking carries visual images, which are different from the rest of the semantic components. Dual coding theory by Paivio (1986) is an intermediate theory between the two: images may also be coded verbally, if there is enough time. A link may be created between visual and verbal representation in the memory: when one of them is activated, it may arouse the other one, too. Two codes are better than one. In conveying the meaning of an image there are several steps: recognition, understanding and recollection. We can recognize, even if we do not identify, and remember, even if we do not understand. Cognition is not a neutral system of perception, but rather, always embedded in functional contexts, directed and altered by motivation and emotion (Dai, 2004). According to Dake (2004) significant aesthetic perception begins before conscious awareness. I have applied semiotics in my thesis by borrowing some useful concepts like semiotic levels (Morris 1971, Goldsmith 1984), because they offer a good tool in analysing illustrations and their different content levels: material, meaning and context. Syntactic level of the image is the external appearance, which exists regardless of the viewer. Semantic level gives it a meaning and pragmatic level sets it in context. If we can create illustrations that help us understand and create effective imagery, we are a step closer to our goal.
Nonlinear Properties of the Rice Statistical Distribution: Theory and Applications in Stochastic Data Analysis

The paper considers the theoretical basics and the specific mathematical techniques having been developed for solving the tasks of the stochastic data analysis within the Rice statistical model in which the output signal’s amplitude is composed as a sum of the sought-for initial value and a random Gaussian noise. The Rician signal’s characteristics such as the average value and the noise dispersion have been shown to depend upon the Rice distribution’s parameters nonlinearly what has become a prerequisite for the development of a new approach to the stochastic Rician data analysis implying the joint signal and noise accurate evaluation. The joint computing of the Rice distribution’s parameters allows efficient reconstruction of the signal’s in-formative component against the noise background. A meaningful advantage of the proposed approach consists in the absence of restrictions connected with any a priori suppositions inherent to the traditional techniques. The results of the numerical experiments are provided confirming the efficiency of the elaborated approach to stochastic data analysis within the Rice statistical model.
Assertion, expression, experience

ABSTRACT It has been frequently observed in the literature that assertions of plain sentences containing predicates like fun and frightening give rise to an acquaintance inference: they imply that the speaker has first-hand knowledge of the item under consideration. The goal of this paper is to develop and defend a broadly expressivist explanation of this phenomenon: acquaintance inferences arise because plain sentences containing subjective predicates are designed to express distinguished kinds of attitudes that differ from beliefs in that they can only be acquired by undergoing certain experiences. Its guiding hypothesis is that natural language predicate expressions lexically specify what it takes for their use to be properly ‘grounded’ in a speaker's state of mind: what state of mind a speaker must be in for a predication to be in accordance with the norms governing assertion. The resulting framework accounts for a range of data surrounding the acquaintance inference as well as for striking parallels between the evidential requirements on subjective predicate uses and the kind of considerations that fuel motivational internalism about the language of morals. A discussion of how the story can be implemented compositionally and of how it compares with other proposals currently on the market is provided.
Texture Synthesis using Super Fractal

The Texture-Synthesis which recreate the new contents using the existing pictures or video data has mainly two goals. One is the solution for the engeneering technique, for example, like the seamless tiling of picure, and the other goal is to give the new visual expression method. From the view of the latter goals, we introduce the Super Fractal for the texture synthesis and discuss about the its possibility.
Effect of Bacillus cereus and Phytase on the Expression of Musculoskeletal Strength and Gut Health in Japanese Quail (Coturnix japonica)

We conducted a 28-day trial to evaluate the influence of Bacillus cereus and phytase supplementation on the expression of musculoskeletal strength and intestinal histological features in Japanese quail. Two-hundred day-old quail chicks were divided into four groups with five replicates (n=10): the first group served as a control and was fed only a basal diet (BD); the second group was fed BD + 0.1% B. cereus; the third group was fed BD + 0.01% microbial phytase; and the fourth group was fed BD + 0.01% microbial phytase + 0.1% B. cereus. Compared to the control, individual and combined supplementation of probiotic and phytase increased (P<0.05) the tibial weight, length, outside diameter, and weight of bone ash, but decreased (P<0.05) the weight-to-length index. The water-holding capacity, fiber diameter, fiber cross-sectional area, number of fibers per unit area, fascicle diameter, and fascicle cross-sectional area increased significantly (P<0.05) in birds fed on the combination of phytase and B. cereus. The villus height, width, depth, height-to-crypt depth, and surface area increased significantly (P<0.05) in the B. cereus and phytase groups on an individual basis. The strength of the musculoskeletal system was fully expressed when B. cereus and phytase were given synergistically. However, the histological features of the intestines improved in birds fed on an individual basis.