Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous discovery of candidate imprinted genes and Imprinting Control Regions in the mouse genome

In mammals, parent-of-origin-specific gene expression is regulated by specific genomic DNA segments known as Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). In the mouse genome, the known ICRs/gDMRs often include clusters of a set of composite-DNA-elements known as ZFBS-morph overlaps. These elements consist of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes. To improve detection of such clusters, we created density-plots. In genome-wide analyses, peaks in these plots pinpointed ∼90% of the known ICRs/gDMRs and located candidate ICRs within relatively long genomic DNA sections. In several cases, the candidate ICRs mapped to chromatin boundaries, to a subset of gene-transcripts, or to both. By viewing the plots at the UCSC genome browser, we could examine the candidate ICRs in the context of the genes in their vicinity. This strategy uncovered several potential imprinted genes with a broad range of physiologically important functions. Examples include: folliculogenesis; lineage commitment of murine embryonic stem cells; the development of the junctional zone of the placenta; left-right patterning of the body axis; the development of the neocortex, hippocampus, and cerebellum; postnatal vision; self-renewal of mouse spermatogonial stem cells; and histone-to-protamine replacement during spermatogenesis.
Genetic and Cytological Investigation of Genic Male Sterility in Brassica rapa ssp. rapa ‘Kida-aokabu’ and ‘Tennhoji-kabu’

Summary A male sterile (ms) plant was identiﬁed in each of the two turnip ( Brassica rapa ) cultivars ʻ Kida-aokabu ʼ and ʻ Tennhoji-kabu, ʼ which are two of the main domestic varieties in Japan. Morphological analysis of organs constituting the ﬂowers in ʻ Kida-aokabu ʼ and ʻ Tennhoji-kabu ʼ showed differences in the features of ms plants between both cultivars, in addition to the differences in size between ms and male fertile (mf) plants in each cultivar. The results of a cross between an ms plant and two cultivars of B. rapa indicated that male sterility is controlled by a single genic recessive gene without any cytoplasmic effect in both cultivars. Light microscopic observations showed that at an early microspore stage, pollen and tapetum development of the ms plant was different from that of the mf plant in ʻ Kida-aokabu ʼ and ʻ Tennhoji-kabu, ʼ respectively. In ms anthers of both cultivars, microspores and tapetum have degenerated, and then completely disappeared before or during the developmental stage to pollen grains. Although the collapse of microsporogenesis in both cultivars occurred at a similar stage, the modes of collapse differed. This is because the collapse of microspores and the tapetum in the locule did not occur synchronously in the ms anther during early microspore development in ʻ Tennhoji-kabu, ʼ which was different from that in ʻ Kida-aokabu. ʼ Our results suggest that the ms plant of ʻ Kida-aokabu ʼ and ʻ Tennhoji-kabu ʼ may represent a new type of Brassica genic male sterility.
Aislamiento y caracterizacion del gen hoy1 involucrado en la transicion levadura-micelio de yarrowia lipolytica

En el presente trabajo se han aislado y caracterizado mutantes morfologicos de yarrowia lipolytica incapaces de llevar a cabo la transicion levadura-micelio. Las mutaciones manifiestan un caracter recesivo, monogenico y nuclear. Se han clasificado en 3 grupos de complementacion. Se ha aislado y caracterizado un fragmento de dna de 3,6 kb que contiene una fase de lectura abierta de 1527 pb que codifica una proteina de 509 aminoacidos. A la fase de lectura abierta se le denomino hoy1. El homeodominio dentro de la secuencia presenta una alta homologia con el homeodominio de los genes chox 4.8 de pollo y pho2 de saccharomyces cerevisiae. El gen hoy1 esta presente como una copia unica en distintas cepas de yarrowia lipolytica. Cuando se transforman mutantes levaduriformes de cada uno de los grupos de complementacion obtenidos, con el gen hoy1 tanto de forma integrativa como autonoma, se obtiene una complementacion parcial (reversion a pseudomicelio) en todas las cepas. La transcripcion del gen hoy1 da lugar a una especie unica de mrna con un tamano aproximado de 1.5 kb. La interrupcion de la fase de lectura abierta del gen hoy1 induce un crecimiento levaduriforme impidiendo el desarrollo micelial en yarrowia lipolytica. Su sobreexpresion promueve el crecimiento polarizado tanto en mutantes levaduriformes como en cepas con fenotipo silvestre.
How to Cope with Change? - Preserving Validity of Predictive Services over Time

Companies more and more rely on predictive services which are constantly monitoring and analyzing the available data streams for better service offerings. However, sudden or incremental changes in those streams are a challenge for the validity and proper functionality of the predictive service over time. We develop a framework which allows to characterize and differentiate predictive services with regard to their ongoing validity. Furthermore, this work proposes a research agenda of worthwhile research topics to improve the long-term validity of predictive services. In our work, we especially focus on different scenarios of true label availability for predictive services as well as the integration of expert knowledge. With these insights at hand, we lay an important foundation for future research in the field of valid predictive services.
An integrated approach to public’s perception of urban water use and ownership of water companies during a period of economic crisis. Case study in Athens, Greece

ABSTRACT This study applies an integrated approach to investigate public perception of residential water issues during a period of economic crisis. The study investigates the perceptions and practices of Athenians in water conservation, their satisfaction with the supplied water, their opinion on the privatization of Water Company and their willingness for additional payment for the improvement of water services. A survey was conducted using a structured questionnaire. Results indicate that the respondents have adopted water conservation practices, but there is still room for further saving. Most of the respondents declared to be satisfied with the supplied water and do not agree to the privatization of water companies. Women, older participants and those having lower income are less willing for additional payment. Research findings are useful tool for policymakers to design policies and make decisions regarding water management, ownership of water companies and changes in behavior of water use.
Performance Analysis of Wireless Mobile Adhoc Network with Different Types of Antennas

The mobile ad network has become a new area in the communication networks and is being congested due to viability and utility of the ad hoc networks in every area. The wide use has increased the chances of interference and congestion. Use of directional antennas can largely reduce the radio interference, hence improving the utilization of wireless medium and consequently the network throughput. In this paper the Performance of ad-hoc networks has been analysed by using various types of antennas. The result has been analysed for different types and can help in deciding the type of antenna to be used depending on radio noise conditions
High-throughput sequencing analysis reveals different Lactobacillus populations that dominate during “Chorizo de León” cured meat making

“Chorizo de Leon” is a high-value Spanish dry fermented sausage traditionally manufactured without the use of starter cultures, owing to the activity of a house-specific autochthonous microbiota that naturally contaminates the meat from the environment, the equipment and the raw materials. Lactic acid bacteria (particularly Lactobacillus) and coagulase-negative cocci (mainly Staphylococcus) have been reported as the most important bacterial groups regarding the organoleptic and safety properties of the dry fermented sausages. In this study, samples from raw minced meat to final products were taken from five different producers and the microbial diversity was investigated by high-throughput sequencing of 16S rRNA gene amplicons. The diverse microbial composition observed during the first stages of “Chorizo de Leon” evolved during ripening to a microbiota mainly composed by Lactobacillus in the final product. Oligotyping performed on 16S rRNA gene sequences of Lactobacillus and Staphylococcus populations revealed sub-genus level diversity within the different manufacturers, likely responsible of the characteristic organoleptic properties of the products from different companies.
Heritability and Functional Importance of the Setaria viridis Bacterial Seed Microbiome

Seed-associated bacteria represent an important reservoir of microorganisms passed onto progeny plants and have been postulated to be important for early plant development and early plant vigor. According to a few reports, some bacterial taxa seem to be transferred from seed to seed and some seed-associated microorganisms may derive from insect visits during flowering; however, the origin of seed endophytes is poorly understood. To better understand the origin, ecology, and functional role of seed bacterial endophytes, we planted Setaria viridis seeds over several generations in a sterile growth substrate. Seed microbiota of each generation were analyzed by next generation sequencing of 16S rRNA genes and seeds were characterized regarding to their germination and plant growth. Growing plants in a sterile (or highly depleted) substrate resulted in seed microbiota, which were largely less diverse and which had altered community composition, particularly at later generations, indicating that soil is an important reservoir of seed microbiota. Some taxa were inherited to the next generations seeds; however, different subsets of taxa were inherited in different seeds/seed batches and across different generations. This suggests that other factors than the host control the establishment of most seed endophytes and only few, e.g., obligate endophytes, might be consistently inherited. Furthermore, we observed a drastic decline in seed vigor and later generations were particularly affected. Overall, our results demonstrated that the supply of endophytes from external sources such as the soil/rhizosphere environment is highly important for the build-up of a healthy seed microbiome warranting early plant establishment and vigor of next generation plants.
An Explorative Approach to the Quantitative Ranking of Historical Countries in Terms of Prominence Using PageRank

This paper presents a novel algorithmic technique to quantitatively rank the relative importance and power of countries throughout history. The algorithm is based on PageRank, the kernel of Google's webpage ranking algorithm. Changes are suggested to enable PageRank to rank countries based on historic signed political and trade treaties. Relative changes in the ranking of countries can be observed by executing the algorithm on a sliding window over time. The algorithm is demonstrated on a case study period. The results show that the proposed approach does indeed rank countries sensibly in the period under consideration.
Fashion pose machine for fashion landmark detection

Combined with deep learning technologies, fashion landmark detection is an efficient method for visual fashion analysis. Existing works mainly focus on eliminating the effect of scale and background, and require prior knowledge of body structure. In this paper, we propose a fashion pose machine which is based on the location method of the landmark for human posture estimation. To increase the accuracy of fashion detection, we utilize convolutional neural network to learn the spatial structure among fashion landmarks in sequential prediction framework, which can eliminate the effect of the clothing placement and model posture on fashion landmark in the image. Our method does not require any prior knowledge of human body structure to learn the dependencies between different landmarks. We evaluated our model on the dataset of FashionAI, and the result showed that our model is 25% better than the state-of-the-art alternative.
Improving identification algorithms in causal inference

Causal models provide a formal approach to the study of causality. One of the most useful features of causal modeling is that it enables one to make causal claims about a phenomenon using observational data alone under suitable conditions. This feature enables the analysis of interventions that may be infeasible to conduct in the real world for practical or ethical reasons. The uncertainty associated with the variables of interest is taken into account by including a probability distribution in the causal model, making it is possible to study the effects of external interventions by examining how this distribution is changed by the action. The probability distribution of a specific variable in a causal model perturbed by an outside intervention is the causal effect of that intervention on the variable. One of the most fundamental problems of causal inference is determining whether a causal effect can be uniquely expressed in terms of the joint probability distribution over the observed variables in a given causal model. Causal effects that can be expressed in this way are called identifiable and they serve as the link between observational and experimental information. Complete solutions to the identifiability problem take the form of an algorithm that produces an expression in terms of observed quantities whenever the causal effect given as input is identifiable. However, completeness in this context refers only to the correctness and exhaustiveness of the methods. The formulas obtained as output from identifiability algorithms are often impractical and unnecessarily complicated. The thesis augments the pre-existing identifiability methodology by providing a simplification procedure that drastically improves the complicated outputs in many cases. Simplification also has practical benefits when statistical estimation is considered if variables affected by bias or missing data no longer appear in the simplified expression. The thesis also introduces a new method called pruning, which aims to eliminate variables that are unnecessary for the identification task from the causal model itself. Finally, a variety of identification algorithms are implemented more complicated settings, such as when data are available from multiple domains. The methods are provided through the R package “causaleffect”.
Fingerprint image enhancement method based on knowledge

The fingerprint image enhancement method based on knowledge includes the steps: image pre-treatment; direction field estimation to calcualte the direction of each pixel in fingerprint image; binarization to change fingerprint image into black-white image according to pixel direction; fining the binary image; detail post-treatment to eliminate burr, spot and bridge in fined image to avoid pseudo detail; feedback enhacement with the knowledge rules; and extracting detail points including crest line end points. The said technology can be used to extract the details in fingerprint image and has important application value in biological recognition.
THE RECOMMENDATION ALGORITHM FOR AN ONLINE ART GALLERY

The paper discusses the need for recommendations and the basic recommendation systems and algorithms. In the second part the design and implementation of the recommender system for online art gallery (photos, drawings, and paintings) is presented. The designed customized recommendation algorithm is based on collaborative filtering technique using the similarity between objects, improved by information from user profile. At the end conclusions of performed algorithm are formulated.
A Comparative Study of Approaches of Ontology Driven Software Development

Ontology Driven Software Development (ODSD) combines traditional Model Based Software Development (MBSD) techniques with ontology technology in order to provide extensions to and advantages over MBSD. The goal of the paper is to identify current ODSD approaches and to provide qualitative and comparative analysis of the collection of identified approaches. Main research questions of the paper concern the ways of how ontologies are integrated to MBSD process and how their usage advances MBSD. Benefits and challenges of each of the discussed approaches are presented. The analysis is based on literature and projects reviews in the fields of ontology engineering, MBSD and ODSD. The result of the analysis provides understanding of what is the role of ontologies in ODSD and shows whether application of ontology technologies to the MBSD process gives rise to a new paradigm called consistency preserving software development or not.
Knowledge sharing in technology-intensive manufacturing organizations

Purpose This purpose of this paper is to identify and prioritize the critical factors impacting knowledge sharing (KS) in technology-intensive manufacturing organizations in the United Arab Emirates (UAE) and to propose a decision-making framework for KS. Design/methodology/approach Analytical Hierarchical Process method is used to identify these critical factors impacting KS in technology-intensive manufacturing organizations in the UAE. Findings Results show that organizational leadership and culture are the most critical factors impacting KS in the technology-intensive manufacturing organizations. Research limitations/implications The data are collected from technology-intensive manufacturing organizations in the UAE; therefore, these cannot be generalized to other locations. Future research in different countries is required. Practical implications To implement successful KS practices in technology-intensive manufacturing organizations, it is essential that all impacting factors and sub-factors are well understood within the organizations. Originality/value This study is among the first studies in the region that presents a comprehensive framework for KS in manufacturing sector.
Study of acoustoplasma discharge as a technique for synthesis of optically active materials

In this study, plasma discharge in a liquid at intensive ultrasonic field above the cavitation threshold has been proven to be of great interest for initiation of various physical and chemical processes. In such discharge, nanoparticles of tungsten and zinc oxides have been synthesised. Further exploration of synthesised nanoparticles has demonstrated that the factor of ultrasonic cavitation during the synthesis substantially affects physical and chemical characteristics of nanoparticles.
New data on two species of the genus Hemicycliophora de Man, 1921 (Tylenchida)

Species of the genus Hemicycliophora de Man, 1921 are not very often reported from natural or agricultural areas of Bulgaria. Hemicycliophora labiata Colbran 1920 was reported from the region of Blagoevgrad (Choleva-Abadjieva and Budurova 1983) but in later studies no other records of the genus were found. We isolated specimens of Hemicycliophora from intensively irrigated patches with wilt and postponed plants from a strawberry field in the Plovdiv region (30.10.2015) and a golf course in the Dobrich region (27.07.2019). Nematodes were isolated by Oostenbrink elutriator followed by 72 h exposition, killed by gently heating at temperature of 55oC and fixed in FAA. Fifty two specimens from Plovdiv region and 31 specimens from Dobrich were mounted in glycerol after Seinhorst (1959). The specimens from Plovdiv were identified as H. poranga Monteiro & Lordello, 1978. Ther morphology is similar to those of the population described from Pistachino, Italy (Subbotin et al. 2017). According to our knowledge this is the first record of the species on the Balkans. The population from Dobrich was similar morphologically to Polish populations of H. epicharoides Loof, 1968 (Brzeski 1998). It differed by a longer vulvar sleeve in some of the specimens and a generally less stout tail. That is first record of the species in Bulgaria, but it was found on the Balkans in Serbia and Greece (Krnjaic and Krnjaic 1976, Subbotin et al. 2017). Morphometrics and microphotograph for both species were obtained.
Use of Factor Analysis in Pattern Recognition

Pattern recognition deals with obtaining and processing certain data on objects in the real world aimed at characterizing their common properties and classifying them with respect to these properties into classes. This paper deals with a method of pattern recognition with respect to the basic position of images. Factor analysis is used for classification. Factor analysis is a special statistical method using the same features and pattern classes as in discriminant analysis. The m dimensional vector is an input parameter. The method can classify into n groups of patterns. Pattern recognition can work in real time.
The Effects Of Computer-Assisted Cloze Procedure On The Acquisition Of English As A Second Language

The purposes of this study were (1) to determine the effect of computer-assisted cloze exercises on the acquisition of English as a second language of selected community college students, and (2) to determine if computer-assisted cloze exercises were more effective for Spanish as opposed to Chinese native language students. It was hypothesized that (1) students using the CAI exercises would receive higher posttest scores than students not using the exercises, and that (2) within the experimental group, Spanish native language students would receive higher scores on a posttest of grammar proficiency than Chinese native language students. The sample for the study was composed of thirty-eight community college students of various ethnic backgrounds. Measures of achievement were obtained through the administration of the ALFA test of grammar proficiency. The Mann-Whitney U test and the t test were used to determine the retention or rejection of the hypotheses. Statistical analyses indicated that (1) computer-assisted cloze exercises were not, overall, more effective than traditional instruction, , and (2) Spanish and Chinese students did not differ significantly in posttest scores of English language proficiency. Recommendations are made for future research iii concerning teaching methods and materials, language proficiency measurement instruments, and computer-assisted exercises.
Characterization of the complete mitochondrial genome of the Pamir yak (Bos grunniens)

Abstract Pamir yak (Bos grunniens) is a yak breed from Pamir Plateau with strong adaptation to the high-elevation, cold and anoxic environments. Its complete mitochondrial genome was determined to be 16,323 bp long with a moderately asymmetric nucleotide composition, and harbors the typical set of 37 mitochondrial genes and the noncoding control region. The PCGs start with the typical ATA or ATG codons, and end with TAA, TAG or the incomplete termination codon T. Phylogenetic analysis suggests that Pamir yak is most closely related to six other yak breeds (i.e. Datong, Pali, polled, Qilian, Seron and Sunan yaks).