Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin accessibility variations across pancreatic islet maturation

Glucose-induced insulin secretion, a peculiar property of fully mature β-cells, is only achieved after birth and is preceded by a phase of intense proliferation. These events occurring in the neonatal period are decisive for the establishment of an appropriate functional β-cell mass that provides the required insulin throughout life. However, key regulators of gene expression involved in cellular reprogramming along pancreatic islet maturation remain to be elucidated. The present study addressed this issue by mapping open chromatin regions in newborn versus adult rat islets using the ATAC-seq assay. Accessible regions were then correlated with the expression profiles of mRNAs to unveil the regulatory networks governing functional islet maturation. This led to the identification of Scrt1, a novel transcriptional repressor controlling β-cell proliferation.
Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura

While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations (2) interpopulation differences in recombination rate may be the result of local adaptation, and (3) the observed variation among individuals in recombination rate is primarily driven by global regulators of crossover rate, with little detected variation in recombination rate among strains across specific tracts of individual chromosomes.
Studies on the effect of organic manures on growth, yield and quality of chilli (capsicum annuum l.) under northern transition zone of Karnataka

A field experiment was conducted to study the effect of organic manures on growth, yield and quality of chilli (Capsicum annuum L.) at Main Agricultural Research Station, University of Agricultural Sciences, Dharwad during kharif 2005-06. In experiment was laid out in RBD with four organic source and their combinations. The RDF with and without FYM kept as control. Application of FYM + 100 RDF (772.2 kg/ha) recorded significantly higher fruit yield over sole application of organics and RDF alone. However, the different combinations of organics viz., FYM (50%) + poultry manure (50%) (727.6 kg/ha), vermicompost (50%) + FYM (50%) (713.51 kg/ha), FYM (50%) + neem cake (50%) (710.6 kg/ha) and poultrymanure @ 7.5 t/ha (708.2 kg/ha) also recorded yield on par with FYM + 100 per cent RDF. The growth and yield components, NPK uptake at harvest also followed the same trend as that of fruit yield. The quality parameters like oleoresin per cent and yield increased by 13.89, 6.6, 3.7 and 2.3 per cent with application of poultry manure @ 7.5 t/ha, vermicompost 10 t/ha, FYM (50%) + vermicompost (50%), FYM (50%) + neem cake (50%) as compared RDF alone. The extractable similar value also increased by 2.9 to 6.0 with application of FYM (50%) + poultry manure (50%), FYM (50%) + neem cake (50%) over RDF alone. The maximum net returns is higher with application of RDF (Rs.28,614) followed by RDF + FYM @ 10 t ha -1 (Rs.27,996), poultry manure @ 7.5 t ha -1 (Rs.24,952), FYM (50%) + poultry manure (50%) (Rs.24,755).
Hardware Support to Minimize the End-to-End Delay in Ethernet-Based Ring Networks

Ethernet is a popular networking technology in factory automation and industrial embedded systems, frequently using a ring topology for improved fault-tolerance. As many applications demand ever shorter cycle times and a higher number of nodes, the popular ring endure to remain as a valid topology. In this work, we discuss the factors that determine the ring network delay and show how they affect the network cycle time. Since increasing the link capacity has limited reach, we explore a time-triggered protocol that brings the nodes forwarding delay near to the physical layer delay. Additionally, we propose hardware accelerators based on FPGA technology that minimise the packet reception delay from physical reception to delivery to an application handler, preserving Ethernet layers and being compatible with its standard. This paper explains the accelerators concept and implementation, presents measurements using standard Media Access Control implementations, and shows the solution effectiveness with experimental results. We achieved a delay, from physical reception to the triggering of a user-level handler, of 1.1 µs independent of the packet length.
Single and Multi-Domain Adaptive Allocation Algorithms for VNF Forwarding Graph Embedding

Network function virtualization (NFV) will simplify deployment and management of network and telecommunication services. NFV provides flexibility by virtualizing the network functions and moving them to a virtualization platform. In order to achieve its full potential, NFV is being extended to mobile or wireless networks by considering virtualization of radio functions. A typical network service setup requires the allocation of a virtual network function-forwarding graph (VNF-FG). A VNF-FG is allocated considering the resource constraints of the lower infrastructure. This topic has been well-studied in existing literature, however, the effects of variations of networks over time have not been addressed yet. In this paper, we provide a model of the adaptive and dynamic VNF allocation problem considering also VNF migration. Then we formulate the optimization problem as an integer linear programming (ILP) and provide a heuristic algorithm for allocating multiple VNF-FGs. The idea is that VNF-FGs can be reallocated dynamically to obtain the optimal solution over time. First, a centralized optimization approach is proposed to cope with the ILP-resource allocation problem. Next, a decentralized optimization approach is proposed to deal with cooperative multi-operator scenarios. We adopt AD3, an alternating direction method of multipliers-based algorithm, to solve this problem in a distributed way. The results confirm that the proposed algorithms are able to optimize the network utilization, while limiting the number of reallocations of VNFs which could interrupt network services.
Genome-wide mutation profiling and related risk signature for prognosis of papillary renal cell carcinoma.

Background The papillary renal cell carcinoma (pRCC) is a rare subtype of renal cell carcinoma with limited investigation. Our study aimed to explore a robust signature to predict the prognosis of pRCC from the perspective of mutation profiles. Methods In this study, we downloaded the simple nucleotide variation data of 288 pRCC samples from The Cancer Genome Atlas (TCGA) database. "GenVisR" package was utilized to visualize gene mutation profiles in pRCC. The PPI network was conducted based on the STRING database and the modification was performed via Cytoscape software (Version 3.7.1). Top 50 mutant genes were selected and Cox regression method was conducted to identify the hub prognostic mutant signature in pRCC using "survival" package. Mutation Related Signature (MRS) risk score was established by multivariate Cox regression method. Receiver Operating Characteristic (ROC) curve drawn by "timeROC" was conducted to assess the predictive accuracy of overall survival (OS) and Kaplan-Meier analysis was then performed. Relationships between mutants and expression levels were compared by Wilcox rank-sum test. Function enrichment pathway analysis for mutated genes was performed by "org.Hs. eg.db", "clusterProfiler", "ggplot2" and "enrichplot" packages. Gene Set Enrichment Analysis was exploited using the MRS as the phenotypes, which worked based on the JAVA platform. All statistical analyses were achieved by R software (version 3.5.2). P value <0.05 was considered to be significant. Results The mutation landscape in waterfall plot revealed that a list of 49 genes that were mutated in more than 10 samples, of which 6 genes (TTN, MUC16, KMT2C, MET, OBSCN, LRP2) were mutated in more than 20 samples. Besides, non-synonymous was the most frequent mutation effect, and missense mutation was one of the most common mutation types in mutated genes across 248 samples. The AUC of MRS model consisted of 17 prognostic mutant signatures was 0.907 in 3-year OS prediction. Moreover, pRCC patients with high level of MRS showed the worse survival outcomes compared with that in low-level MRS group (P=0). In addition, correlation analysis indicated that 6 mutated genes (BAP1, OBSCN, NF2, SETD2, PBRM1, DNAH1) were significantly associated with corresponding expression levels. Last, functional enriched pathway analysis showed that these mutant genes were involved in multiple cancer-related crosstalk, including PI3K-AKT signaling pathway, JAK-STAT signaling pathway, extracellular matrix (ECM)-receptor interaction or cell cycle. Conclusions In summary, our study was the first attempt to explore the mutation-related signature for predicting survival outcomes of pRCC based on the high-throughput data, which might provide valuable information for further uncovering the molecular pathogenesis in pRCC.
Clonal evaluation and recurrent flowering of ornamental pineapple hybrid for use as miniature potted plant

The objective of this study was to evaluate the cloning and recurrent flowering of the miniature pineapple hybrid ORN-MUT based on quantitative and qualitative morphological descriptors, for possible use as a potted plant. Besides its reduced size, the ORN-MUT hybrid is notable for its pink fruit, absence of thorns and recurrent flowering at the crown, formed after the plant’s complete cycle (562 days). The hybrid was assessed in the experimental field of the Embrapa Cassava and Fruits research unit in two flowering stages (first flowering and recurrent flowering) and was characterized by quantitative and qualitative morphological descriptors. A joint analysis of the data (multivariate analysis) was performed to verify the distinguishability and uniformity of the clones and parents. ORN-MUT presented uniformity in the first flowering, completing the phenological cycle at 75.70 ± 8.01 days (first repetition) and 72.35 ± 6.17 days (second repetition) after floral induction, respectively. The recurrent flowering occurred 170.60 ± 1.85 days after induction. The peduncle is straight, with average length of 19.30 ± 3.83 cm. The syncarp is small and pink, with conical-cylindrical shape. The crown has a moderately sharp tip with greenish central color and pink edges. In the recurrent flowering stage, the plants are smaller, with average size of 24.45 ± 2.52 cm. The syncarp is miniaturized, with average of 1.20 ± 1.15 layers of fruitlets and length of 1.61 ± 0.20 cm. The quantitative and qualitative morphological traits allow classifying the hybrid as a potential potted plant.
User-defined gesture interaction for immersive VR shopping applications

ABSTRACT Gesture elicitation studies, which are a popular technology for collecting requirements and expectations by involving real users in gesture design processes, often suffer from gesture disagreement and legacy bias and may not generate optimal gestures for a target system in practice. This paper reports a research project on user-defined gestures for interacting with immersive VR shopping applications. The main contribution of this work is the proposal of a more practical method for deriving more reliable gestures than traditional gesture elicitation studies. We applied this method to a VR shopping application and obtained empirical evidence for the benefits of deriving two gestures in the a priori stage and selecting the top-two gestures in the a posteriori stage of traditional elicitation studies for each referent. We hope that this research can help lay a theoretical foundation for freehand-gesture-based user interface design and be generalised to all freehand-gesture-based applications.
CYP11B1 and PPARGC1A genes polymorphism controlling reproductive traits and estimation of breeding value of first lactation milk yield in Bos indicus (Deoni) cattle

In the present study, in Deoni, the dual purpose cattle breed of Southern India, maintained in a National Dairy Research Institute herd, Southern Regional Station, Bengaluru, molecular characterization of the putative exon 1 of CYP11B1 and putative intron 9 and 3’UTR of PPARGC1A genes was carried out in 146 animals using the PCR-RFLP technique. Three restriction enzymes, namely PstI, HaeIII and NheI, were used for digestion of the amplicons of the genes, respectively. In the putative exon 1 of the CYP11B1 gene, two genotypes, VV and VA, were detected with frequencies of 0.23 and 0.77, respectively. The frequencies of allele V and A in the population were found to be 0.62 and 0.38, respectively. The allelic frequencies of C and T types were observed as 0.63 and 0.37, with frequencies of CC, TC and TT genotypes as 0.38, 0.51 and 0.11 in the putative intron 9 of the PPARGC1A gene, respectively. Three genotypes, namely AA, AC and CC were detected in 3’UTR of the PPARGC1A gene, with respective frequencies of 0.75, 0.21 and 0.04. The allelic frequencies of A and C types were 0.86 and 0.14, respectively. The locus (c.1892+19T>C) in the putative intron 9 of the PPARGC1A gene was found to be significant (P<0.05), with unadjusted data of age of first calving (AFC). Adjusted data of first lactation milk yield (FLMY) showed a significant (P<0.10) association with the loci of the CYP11B1 (p.Val30Ala) and PPARGC1A (c.3359A>C) genes. No significant (P<0.10) association was observed between the loci of the genes and breeding value of FLMY in the studied cattle population. key words: Deoni; first lactation milk yield; CYP11B1 gene; PPARGC1A gene ________________________________________________________________________________________
A new species of Eirenis (Ophidia: Colubridae) from highland habitats in southern Iran

A new colubrid snake of the genus Eirenis, Eirenis yassujicus sp. n. , is described from highlands of central Zagros in Kohgilouyeh & Boyer-Ahmad Province, southern Iran, and increases the number of Eirenis species to 21. Morphologically, E. yassujicus sp. n. is assigned to the subgenus Eirenis (Eirenis) characterised by 17 mid-body scales. The lowest genetic distance between the new species and its closest relative, E. punc- tatolineatus, is 12% in the mitochondrial Cytb gene. An updated key for the species of Eirenis spp. in Iran is provided. http://www.zoobank.org/urn:lsid:zoobank.org:pub:95943A74-53F8-4D43-B306-3711F9841263
Morphological Processing Before and During Children’s Spelling

ABSTRACT Our understanding of spelling development has largely been gleaned from analysis of children’s accuracy at spelling words under varying conditions and the nature of their errors. Here, we consider whether handwriting durations can inform us about the time course with which children use morphological information to produce accurate spellings of root morphemes. Six- to 7-year-old (n = 23) and 8- to 11-year-old (n = 25) children produced 28 target spellings in a spelling-to-dictation task. Target words were matched quadruplets of base, control, inflected, and derived words beginning with the same letters (e.g., rock, rocket, rocking, rocky). Both groups of children showed evidence of morphological processing as they prepared their spelling; writing onset latencies were shorter for two-morpheme words than control words. The findings are consistent with statistical learning theories of spelling development and theories of lexical quality that include a role of morphology.
EFFECT OF SOME ESSENTIAL OILS ON CUT FLOWERS OF CHRYSANTHEMUM ( Dendranthema grandiflorum Ram. ) cv. "Flyer".

The experiment was carried out at the Laboratory of The Veget. and Floric. Depart. , Fac. of Agric. , Mansoura Univ., Egypt, during the two successive seasons of 2013 and 2014 to study the effect of preservative solutions containing some essential oils of peppermint, caraway and lemon grass with different concentrations (25 and 50 ml /L), on the quality, postharvest characters, water uptake, some chemical constituents and bacterial growth in the vase solution of chrysanthemum (Dendranthema grandiflorum Ram.) cv. Flyer cut flowers. The obtained results revealed that: Chrysanthemum cut flowers held in solution containing 25 mg/ L lemon grass oil recorded the highest longevity, maximum fresh weight %, highest values of relative fresh weight % and the better water balance up to the 2 nd day of the vase life in both seasons. While, the least values of these characters were recorded by using distilled water (control) as a holding solution in the both seasons. The best total water uptake and the highest values of relative fresh weight % were recorded using a preservative solution contained 50 mg/ L caraway oil. The highest value of chlorophyll a and total chlorophyll content were recorded in the 7 th day of the vase life period when preservative solution contained 50 mg/ L lemon grass oil. While, the lowest value of these characters were recorded in control flower in both seasons. The highest value of total sugar recorded in the 7 th day during the vase life period when used preservative solutions contained 25 mg /L caraway oil and 25 mg/ L lemon grass oil, while the lowest value of total sugar were recorded in control flowers and solution containing 25 mg/ L peppermint oil in both seasons. The least average of bacterial count in vase solution resulted by using 25 mg/ L lemon grass oil as compared with other treatments, while the maximum average of bacterial count was recorded in distilled water (control) treatment in both seasons. It could be recommended that the use of preservative solution containing 25 mg /L lemon grass oil + 0.2 % sucrose extend vase life, increase fresh weight, increase water uptake, chlorophyll content, total sugar and bacterial counts of Chrysanthemum cut spikes.
An Investigation on Topic Maps Based Document Classification with Unbalance Classes

— Classification of imbalanced data has become a widespread problem due to the fact that the most real world datasets are imbalanced. In a classification task, one of the challenges is to learn the feature-space of classification under class-imbalance setting. The majority classes generally have good representation of features in the learned classification function and the minority classes lack this representation; subsequently, the classification for these classes failed more often. In this paper, authors investigate the task of document classification with topic map based representation of documents under class imbalance setting. In order to measure of topic-map based representation for classification under imbalance data, authors compare three representations: Bag-of-Words, Phrases and Topic terms for three approaches (i) under-sampling, (ii) cost-adjusting, and (iii) cluster based sampling. A series of experiments are carried out and results are reported.
Examining the Role of Polymorphisms in Exon 25 of the PKD1 Gene in the Pathogenesis of Autosomal Dominant Polycystic Kidney Disease in ranian Patients.

Background Autosomal dominant polycystic kidney disease (ADPKD) is a highly prevalent life-threatening monogenic disorder with high morbidity and mortality. Roughly 1:400-1000 individuals are affected with this disease worldwide. The development of ADPKD is largely attributed to mutations in the polycystic kidney disease (PKD)1 and PKD2 genes. However, the pathogenicity of the different polymorphisms in PDK1 in the development of ADPKD remains unclear. The aim of this study was to further elucidate the role of the polymorphisms in exon 25 of the PDK1 gene in relation to the pathogenesis of ADPKD in Iranian patients. Methods The genomic DNA of 36 Iranian patients with ADPKD was isolated using the standard salting out method. The PCR products were directly sequenced and analyzed. Results The frequencies of CAG>GAG, ATG>GTG, GTC>GTA, and GTG>ATG polymorphisms in exon 25 of the PKD1 gene were 34 (94.44%), 33 (91.67%), 26 (72.22%), and 5 (13.89%), respectively. The most frequent polymorphism associated with ADPKD was the homozygous CAG→GAG which causes an amino acid change of Q[Gln] to E[Glu] at codon 3005. Conclusion Our data suggests that there is potentially a common polymorphism of PDK1 among the Iranian population with ADPKD. This may aid in the diagnosis and genetic screening of at-risk patients for ADPKD.
Genome analysis and engineering of industrial lager brewing yeasts

Lager beer, also referred to as Pilsner, is the most popular alcoholic beverage in the world, with an annual consumption of almost 200 billion litres per year. To make lager beer, brewer’s wort is fermented with the yeast Saccharomyces pastorianus. This microorganism converts wort sugars into ethanol and contributes key flavour compounds to the beer. S.pastorianus is an interspecific hybrid which likely formed about 500 years ago by spontaneous mating between an ale-brewing S. cerevisiae strain and a wild S. eubayanus contaminant. The genome of lager brewing yeast is exceptionally complex: not only does it contain chromosomes from the two parental species, but these have also undergone extensive recombination and are present in varying copy numbers, a situation referred to as aneuploidy. The S. eubayanus ancestor was only discovered in 2011, enabling an improved understanding of the complex genomeand convoluted evolutionary ancestry of S.pastorianus. Furthermore, recent advances in whole-genome sequencing technology and in gene editing tools have simplified the genetic accessibility and amenability of Saccharomycesyeast genomes. The aim of this thesis was to leverage these advances to investigate how the genetic complexity of current S.pastorianus strains emerged and how it contributes to industrial lager brewing performance, and to develop new methods for strain improvement of brewing yeasts.