Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficiency and precision of miRNA biogenesis modes in plants

Many evolutionary conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized an approach to detect intermediates during miRNA biogenesis. We characterized a miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes. Despite the various potential structural determinants present in a single a miRNA precursor, DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, our studies in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative processing determinants. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.
A Mixed-Initiative Planning Approach to Exploratory Data Analysis

Exploratory data analysis (EDA) has come to play an increasingly important role in statistical analysis. Modern computer-based statistics packages contain a rich set of operations, suitable for almost any EDA application. One can fit lines and higher order functions to relationships, identify and describe clusters, transform and reduce data to meet the specific requirements of a domain, among many other possibilities, in seeking to understand patterns in data. Unfortunately, EDA can be difficult. Conventional statistics packages offer the user hundreds of operations, which must often be combined in lengthy sequences to produce useful results. In addition, the application of these operations often depends on the user's knowledge of what the data mean. In other words, EDA is too large a problem for a human analyst to solve alone, but complete automation of the process is not feasible either because domain-specific knowledge is required. This dissertation describes an assistant for intelligent data exploration called A scIDE. A scIDE is mixed-initiative, autonomously pursuing its own goals, but always allowing the user to review and possibly override its decisions. A scIDE's design as a knowledge-based planning system allows it to detect and evaluate suggestive features in the data, identify appropriate strategies for extracting the patterns, apply the strategies incrementally, and combine the results in a coherent whole. An experimental evaluation compared the performance of human subjects analyzing data with and without A scIDE's assistance. Although the subjects worked with A scIDE for only a couple of hours, each, it clearly influenced the efficiency and coherence of their explorations. Analysis of the experimental results turned up suggestive evidence that A scIDE facilitates data analysis primarily by helping users navigate through the space of relations among variables. This research provides a novel look at automated support for data analysis. Conventional systems tend to take over the task completely, or rely on the user for every step of the analysis. A scIDE's mixed-initiative planning approach provides an alternative in which control changes hands flexibly between the user and the system. This arrangement capitalizes on the strengths of both: the system takes over low-level search and statistical computations, while the user remains responsible for strategic, knowledgeable guidance of the process.
Power and Area Efficient Pipelined ADC Stage in Digital CMOS Technology

ABSTRACT A power and area efficient metal-oxide semiconductor field-effect transistor (MOSFET)-only 1.5-bit fully differential pipelined analog-to-digital converter (ADC) stage is proposed and designed in TSMC 0.18 μm digital CMOS technology with supply voltage of 1.8 V. It is based on charge pump based technique to achieve the stage voltage gain of 2. Various capacitances are implemented by MOSCAPs (capacitance offered by the MOSFET), offering compatibility with cheaper digital complimentary metal-oxide semiconductor (CMOS) process in order to reduce the much required manufacturing cost. The proposed stage suffers from only linear gain error with full signal swing of 2 V peak-to-peak (p–p) differential. Using the proposed stage, un-calibrated signal-to-noise and distortion ratio (SNDR) and spurious-free dynamic range (SFDR) for 10-bit, 100 MS/s pipelined ADC are 40.11 and 40.86 dB, respectively, which can be further increased by using a simple digital calibration technique. Comparison between the proposed stage and conventional operational amplifier based stage shows insensitivity towards capacitor mismatch along with power savings and design simplicity.
Molecular insights into the evolution of novel genes

This project generated genomic resources (such as genomes and transcriptomes) to understand the evolution of genes unique to a group of organisms, or novel genes. It was found that these novel genes can be found in all animals and are abundant in sea anemones. In sea anemones, novel genes play an important role in the evolution of venom and its delivery. This includes the toxic compounds found in their venom, as well as the cells that deliver the venom. Overall, this information provides insights into understanding the mechanisms that underpin the formation of novel genes, which is a key research area in molecular evolution.
Solving weighted graph matching problem by modified microgenetic algorithm

Microgenetic algorithm (MGA) is genetic algorithm (GA) using a very small population size (population size<20). The weighted graph matching problem (WGMP) has received much attention in the field of pattern recognition. In this paper, a hybrid MGA with larger population is proposed to solved the weighted graph matching problem. In our hybrid microgenetic algorithm, many modules, such as local search algorithm, biased initial population, a modified selection scheme, and a refining procedure, are embedded to improve the performance of the algorithm. Experimental results show that our method outperforms a well-known method, the symmetric polynomial transform (SPT), on most instances of the weighted graph matching problems.
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

The HepG2 cancer cell line is one of the most widely-used biomedical research and one of the main cell lines of ENCODE. Vast numbers of functional genomics and epigenomics datasets have been produced to characterize its biology. However, the correct interpretation such data requires an understanding of the cell line’s genome sequence and genome structure. Using a variety of sequencing and analysis methods, we identified a wide spectrum of HepG2 genome characteristics: copy numbers of chromosomal segments, SNVs and Indels (corrected for aneuploidy), phased haplotypes extending to entire chromosome arms, loss of heterozygosity, retrotransposon insertions, structural variants (SVs) including complex and somatic genomic rearrangements. We also identified allele-specific expression and DNA methylation genome-wide and assembled an allele-specific CRISPR/Cas9 targeting map. SIGNIFICANCE Haplotype-resolved and comprehensive whole-genome analysis of a widely-used cell line for cancer research and ENCODE, HepG2, serves as an essential resource for unlocking complex cancer gene regulation using a genome-integrated framework and also provides genomic context for the analysis of ~1,000 functional datasets to date on ENCODE for biological discovery. We also demonstrate how deeper insights into genomic regulatory complexity are gained by adopting a genome-integrated framework.
The Impact of Mathematical Writing on Students¡¯ Metacognition in Applied Algebra Test

Students always use their pens and papers from time to time in their daily routine mathematics lesson to perform activities such as taking notes, performing calculation, doing mathematics assignments or examinations. However, students mainly use writing as a mechanism to demonstrate their computational skills rather than their conceptual thinking. Mathematical writing becomes a powerful learning tool only if it combines language and mathematical algorithm. Thus, this paper intends to explore the impact of mathematical writing on studentsi¯ metacognition in an applied algebra test. It attempts to examine the metacognitive behavior of three foundation students in engineering and the qualitative data was the participantsi¯ take-home test after five weeks of mathematical writing intervention. This paper reports the analysis of these studentsi¯ writing responses in the test. The findings revealed the quality of the studentsi¯ metacognition abilities and their mathematical problem solving skills.
A feedback loop between miRNA-155, Programmed cell death 4 and Activation Protein-1 modulates the expression of miR-155 and tumorigenesis in tongue cancer

miR-155 is an oncomir, generated as a non-coding RNA from BIC gene whose promoter activity is mainly controlled via AP-1 and NF-κB transcription factors. We found that the expression levels of miR-155 and Pdcd4 exhibit inverse relationship in tongue cancer cells (SAS and AWL) and tumor tissues compared to normal FBM cells and normal tongue tissues, respectively. Insilco and In-vitro studies with 3’UTR of Pdcd4 via luciferase reporter assays, qPCR and western blots show that miR-155 directly targets Pdcd4 mRNA and blocks its expression. Ectopic expression of Pdcd4 or knockdown of miR-155 in tongue cancer cells predominantly reduces AP-1 dependent transcriptional activity of BIC promoter and decreases miR-155 expression. In this study, we demonstrate that miR-155 expression is modulated by a feedback loop between Pdcd4, AP-1 and miR-155 which results in enhanced expression of miR-155 with a consequent progression of tongue tumorigenesis. Further, miR-155 knockdown increases apoptosis, arrests cell cycle, regresses tumor size in xenograft nude mice and reduces cell viability and colony formation in soft agar and clonogenic assays. Thus, the restoration of Pdcd4 levels by the use of molecular manipulation such as using miR-155 sponge have important role in the therapeutic intervention of cancers, including tongue cancer.
Ovarian cancer prognosis and soft computing

This paper highlights seven applications of various methods in soft computing to the task of ovarian cancer prognosis. Soft computing is described as well as its constituents. The ovarian cancer data is described. The task involves building a series of prognostic classifiers to carry out time-step prognosis. The results from the seven methods described are compared briefly, and also are compared with statistical multilinear regression analysis.
REPORT RAPPORT

The use of constraints for the de(cid:12)nition of graphical user interfaces has been recognized as a great concept. However, often many valuations of the variables will satisfy the constraints, and which particular valuation matches best with the expectation of the user cannot be decided without further information. Three typical examples ofuser interfacesare presentedwhere this occurs,and fromthese, requirementson a more cooperative constraint solver are derived. A new method for the de(cid:12)nition and implementation of the strategy to decide which variables to adapt is presented. The model is based on two notions: hierarchy and grouping. Variables are divided into groups, and for each group three parametersare set. These are used to determine the level of variables, dependent on which group they belong, and which variables are modi(cid:12)ed. These levels are used in turn to select the variables to be adapted. An implementation of this method is described, as part of the Computational Steering Environment (CSE) developed at CWI. The resulting constraint solver can handle simultaneous sets of non-linear, multi-way constraints; and can handle a high-level de(cid:12)nition of the strategy to be followed. Finally, the results are discussed, and suggestions for further work are done.
Primary human chondrocytes respond to compression with plasma membrane receptors and by microtubule activation: a phosphoproteomic study

Chondrocytes are responsible for maintaining the cartilage that helps joints like the knee and hip bear load and move smoothly. These cells typically respond to physiological compression with pathways consistent with matrix synthesis, and chondrocyte mechanotransduction is essential for tissue and joint homeostasis. In osteoarthritis (OA), chondrocyte mechanotransduction appears to be dysregulated, yet many pathways and mechanisms of osteoarthritic chondrocyte mechanotransduction remain poorly understood. The objective of this study is to document the phosphoproteomic responses of primary osteoarthritic chondrocytes to physiological sinusoidal compression. Here we show that OA chondrocytes respond to physiological compression by first activating proteins consistent with cytoskeletal remodeling and decreased transcription, and then later activating proteins for transcription. These results show that several microtubule-related proteins respond to compression, as well as proteins related to calcium signaling, which has previously been extensively shown in chondrocytes. Our results demonstrate that compression is a relevant physiological stimulus for osteoarthritic chondrocytes. We anticipate these data to be a starting point for more sophisticated analysis of both normal and osteoarthritic chondrocyte mechanotransduction. For example, finding differences in compression-induced phosphoproteins between normal and OA cells may lead to druggable targets to restore homeostasis to diseased joints.
Congruency effects can compensate for deficits of healthy older adults in crossmodal integration

One of the pivotal challenges of aging is to maintain independence in the activities of daily life. In order to adapt to changes in the environment, it is crucial to continuously process and accurately combine simultaneous input from different sensory systems, i.e., crossmodal integration. With aging, performance decreases in multiple cognitive domains. The processing of sensory stimuli constitutes one of the key features of this deterioration. Age-related sensory impairments affect all modalities, substantiated by decreased acuity in visual, auditory or tactile detection tasks. However, whether this decline of sensory processing leads to impairments in crossmodal integration remains an unresolved question. While some researchers propose that crossmodal integration degrades with age, others suggest that it is conserved or even gains compensatory importance. To address this question, we compared behavioral performance of older and young participants in a well-established crossmodal matching task, requiring the evaluation of congruency in simultaneously presented visual and tactile patterns. Older participants performed significantly worse than young controls in the crossmodal task when being stimulated at their individual unimodal visual and tactile perception thresholds. Performance increased with adjustment of stimulus intensities. This improvement was driven by better detection of congruent stimulus pairs (p<0.01), while detection of incongruent pairs was not significantly enhanced (p=0.12). These results indicate that age-related impairments lead to poor performance in complex crossmodal scenarios and demanding cognitive tasks. Performance is enhanced when inputs to the visual and tactile systems are congruent. Congruency effects might therefore be used to develop strategies for cognitive training and neurological rehabilitation.
CRISPR-assisted targeted enrichment-sequencing (CATE-seq)

The current targeted sequencing of genome is mainly dependent on various hybridization-based methods. However, the hybridization-based methods are still limited by the intrinsic shortcomings of nucleic acid hybridization. This study developed a new CRISPR-based targeted sequencing technique, CRISPR-assisted targeted enrichment-sequencing (CATE-seq). In this technique, the input genomic DNA (gDNA) was firstly bound by a complex of dCas9 and capture sgRNA (csgRNA). The DNA-dCas9-csgRNA complex was then captured on magnetic beads through an easy room-temperature annealing between a short universal capture sequence (24 bp) at the 3′ end of csgRNA and capture oligonucleotide coupled on magnetic beads. The enriched DNAs were finally analyzed by next generation sequencing. Using this technique, three different scales of targeted enrichments were successfully performed, including enriching 35 target exons of 6 genes from 6 gDNA samples with 54 csgRNAs, 339 target exons of 186 genes from 9 gDNA samples with 367 csgRNAs, and 2031 target exons of 451 genes from 2 gDNA samples with 2302 csgRNAs. This technique has several significant advantages over the current hybridization-based methods, including high simplicity, specificity, sensitivity, throughput, and scalability.
Learning with edutainment: a multi-platform approach

This paper describes a multi platform investigation, that evaluated three "edutainment" environments using three different platforms in order to explore usability aspects of edutainment in e-learning. These three platforms were virtual classroom, game-based and storytelling. Speech, earcons, avatars with graphics and game activity was combined in these three different platforms. A dependent group was used to measure users' performance in terms of user achievement and satisfaction. The empirical results collected indicated that the game-based approach was the best in terms of users' achievement as well as satisfaction with the interface and overall learning experience.
A REVIEW ON OBJECT RECOGNITION TECHNIQUES FOR PRACTICAL APPLICATION

Object recognition is an important part of computer vision because it is closely related to the success of many computer vision applications. A number of object recognition algorithms and systems have been proposed for a long time in order to address this problem. Yet, there still lacks a general and comprehensive solution. Recently, model-based object recognition approach, feature based object recognition approach and appearance-based object recognition approach have demonstrated good performance on a variety of object recognition problems. In this paper, the most representative papers of each approach are first reviewed. After that, some possible extensions to the recently proposed view-based approach and feature-based approach and model-based approach are proposed and discussed in the paper.
The mouse lung early cellular innate immune response is not sufficient to control fungal infection with Cryptococcus neoformans

Cryptococcus neoformans causes life-threatening infection in the immunocompromised. This and other opportunistic pathogens are an increasing threat as immunosuppression increases globally. To counter antibiotic resistance, there is precedent for developing immune enhancing therapy. However, our understanding of how immunocompetent patients resolve these infections is poor as opportunistic infections typically resolve subclinically. Because this has led to a lack of clinical data, we rely on animal models. Current in vivo infection models either lack mammalian immunity or are not compatible with long term high content imaging required to model the complexities of human host-pathogen interactions. Therefore, we have developed an ex vivo murine precision cut lung slice (PCLS) model to understand innate immunity in cryptococcosis. C57BL/6 mice were sacrificed 0 or 24 hours post infection with KN99α cryptococci. Lungs were inflated with 37°C agarose, 300μm thick PCLS were prepared on a vibratome and imaged by confocal or wide-field fluorescence microscopy. Using PCLS and immunofluorescence, we demonstrate cryptococcal replication and clearance rates are balanced over the first 24 hours of infection. Cell-mediated immunity is alveolar macrophage centric, although alveolar macrophages demonstrate limited phagocytosis of cryptococci and enable intracellular cryptococcal replication. Cryptococcus neoformans responded to the lung environment by forming enlarged cells, although these were not large enough to be titan cells. To further understand cryptococcal proliferation in vivo, we also infected animals with plb1 mutant Cryptococcus neoformans that has been shown to exhibit proliferation defects in vivo. We found no difference in fungal burden with plb1 infected animals 24 hours post infection, but observed significantly larger fungal cells and no incidences of phagocytosis. Thus, the PCLS model can be used to assess the lung immune response early in cryptococcal infection, demonstrating that resident lung macrophages cannot control cryptococcal infection and offer an intracellular niche for Cryptococcus neoformans growth.
Effect of Water Temperature to Survival and Development of Larvae of Two Local Aedes Aegypti Strains

Global warming has been reported in last decades. Chang-es in average Earth’s temperature may affect the physiology of many insect species, especially the ones which act as a human disease vec-tor, like Aedes aegypti. In this study, the effect of increasing water temperature on physiological components related to development period, sex ratio, and body size of two distinctively strains, VCRU (Vector Control Research Unit) and Pangandaran. Thirty larvae of each strain kept inside distilled water with the temperature of 25°C, 27°C, 30°C, 33°C, 35°C, 40°C which replicated three times. Observa-tions were conducted until all larvae metamorphed into adults or all larvae dead. Development rate and time were analyzed by frequency dependent mean. The result showed that the optimum temperature for larvae development of VCRU strain was 27-30°C with a survival rate of 84% while it was 30°C for Pangandaran strain, with the surviv-al rate of 83%. Larvae of both strains showed 100% mortality rate when kept inside a container with water temperature exceed 33°C. Both strains showed the highest and the lowest male:female ratio at similar water temperature which were 33°C and 30°C, respec-tivelly. Highest and lowest ratio of VCRU was 1.25 and 0.6, respec-tively, while it was 1.4 and 0.6 for Pangandaran. In general, larvae lived in increasing water temperature showed reducing wing width.
University of Birmingham Theta phase coordinated memory reactivation reoccurs in a slow-oscillatory rhythm during NREM sleep

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