Miracle-dz/UniFAR-FTUs huggingface dataset:
OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes

Purifying (negative) natural selection is a hallmark of functional biological sequences, and can be detected in protein-coding genes using the ratio of nonsynonymous to synonymous substitutions per site (dN/dS). However, when two genes overlap the same nucleotide sites in different frames, synonymous changes in one gene may be nonsynonymous in the other, perturbing dN/dS. Thus, scalable methods are needed to estimate functional constraint specifically for overlapping genes (OLGs). We propose OLGenie, which implements a modification of the Wei-Zhang method. Assessment with simulations and controls from viral genomes (58 OLGs and 176 non-OLGs) demonstrates low false positive rates and good discriminatory ability in differentiating true OLGs from non-OLGs. We also apply OLGenie to the unresolved case of HIV-1’s putative antisense protein gene, showing significant purifying selection. OLGenie can be used to study known OLGs and to predict new OLGs in genome annotation. Software and example data are freely available at https://github.com/chasewnelson/OLGenie.
Towards Conditional Stimulation of the Overactive Bladder : Electrophysiology and Neuromodulation in a Rat Model

The overactive bladder (OAB) is a syndrome based urinary dysfunction characterized by “urgency, with or without urge incontinence, usually with frequency and nocturia”. Earlier we developed a mathematical model of bladder nerve activity during voiding in anaesthetized rats and found that the nerve activity in the relaxation phase of voiding contractions was all afferent. In the present study, we applied this mathematical model to an acetic acid (AA) rat model of bladder overactivity to study the sensitivity of afferent fibers in intact nerves to bladder pressure and volume changes. The afferent activity in the filling phase and the slope i.e. the sensitivity of the afferent fibers to pressure changes in the post void relaxation phase, were found to be significantly higher in AA than in saline measurements, while the offset (nerve activity at pressure ~0) and maximum pressure were comparable. We have thus shown, for the first time, that the sensitivity of afferent fibers in the OAB can be studied without cutting nerves or preparation of single fibers. We conclude that bladder overactivity induced by AA in rats is neurogenic in origin and is caused by increased sensitivity of afferent sensors in the bladder wall.
A High-Linearity Vernier Time-to-Digital Converter on FPGAs With Improved Resolution Using Bidirectional-Operating Vernier Delay Lines

Time-to-digital converters (TDCs) act as a core component in many timing-critical systems. Tapped delay line is the most widely used style for the field-programmable gate-array (FPGA)-based TDCs, but it suffers from several intractable problems such as poor nonlinearity and long delay-line occupation. Recently, a new ring-oscillator-based Vernier TDC circuit using carry chains was demonstrated to have much smaller nonlinearity with a much shorter delay line. Since the used delay line is not compensated, the timing jitter increases (or the precision degrades) remarkably when the oscillation number is large. This would incur undesirable lower resolution selection to maintain acceptable precision. In this article, a novel bidirectional-operating Vernier delay line structure is proposed to reduce the required oscillation number during the fine time measurement. Traditionally, for the Vernier delay line, the fast signal propagates along the slow delay line, while the slow signal propagates along the fast delay line, to which we call the normal Vernier delay line. The new structure proposes two parallelized Vernier delay line, consisting of one normal Vernier delay line and another abnormal Vernier delay line. The term “abnormal” refers to that the fast and slow signals are unusually fed to the fast and slow delay lines, respectively. A prototype TDC circuit based on this new method was implemented on a Stratix III FPGA. Test results demonstrate that by adopting the proposed novel circuit architecture, both the resolution and the root-mean-square error can be improved from the 30–40-ps level to the 20–30-ps level.
The Ukraine and EU trade balance: prediction via various models of time series

This article is the first to study, simulate and forecast the monthly dynamics of the trade balance between Ukraine and the European Union for the period from 2005 to 2019. In the presented work, three types of models were used for modeling and forecasting: Automated Neural Networks, additive models ARIMA *ARIMAS (Autoregressive integrated moving average with season component) and Holts model with a damped trend. When modeling using the Automated Neural Networks module, various ensembles of networks and neuron activation functions in hidden layers were used. It turned out that Automated Neural Networks have poor prognostic ability (as in the case considered by us, when modeling insufficiently long series of dynamics). Therefore, when modeling and forecasting the dynamics of the Ukraine-EU trade balance, classical (so-called Box-Jenkins) time series models were used. In this case, the time series is divided into several components (in our case, terms): the main trend is the trend, the seasonal component and the random component (the so-called white noise). By smoothing the initial series, a trend was found, and an analysis of the autocorrelation functions revealed a one-year seasonality. Eliminating the trend and the seasonal component, we obtained a random component, which has a Gaussian distribution. This made it possible to apply first the ARIMA* ARIMAS additive model, and then the Holt model of exponential smoothing with a damped trend. Adequate models of Ukraine-EU trade balance dynamics have been obtained, according to which the forecast has been made. A comparative analysis of the models used. The best model was chosen for forecasting, which allowed to get a good forecast (in comparison with actual data).
Impact of imbalanced data on the performance of software defect prediction classifiers

Software defect prediction plays an important role in analysing software quality and balancing software cost. However, it lacks suggestions for project managers and software engineers in selecting classifiers. Firstly, a method for building imbalanced distribution data is proposed. Then, Matthews correlation coefficient is used to measure the performance of different classifiers, and the coefficient of variation is utilised to evaluate the stability of classifiers on imbalanced distribution data. Finally, an experiment is conducted on 8 common classifiers and 12 publicly available and widely used data sets. Results show that NaiveBayes behaves steadily when the imbalance rate of data sets changes significantly. The experimental results provide a basis for project managers and software engineers to select classifiers.
Ultrahigh dimensional feature screening for additive model with multivariate response

ABSTRACT We consider feature screening for ultrahigh dimensional additive model with multivariate response in this paper. A new method named generalized correlation based projection screening is proposed by using generalized correlation between each predictor and multivariate response. The sure screening and ranking consistency properties are established under some regularized conditions for the proposed procedure. In addition, we construct an iterative version of the proposed screening procedure to enhance the finite sample screening performance. Both simulation studies and the real data analysis demonstrate that the proposed method works effectively.
Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map

Do machine learning methods improve standard deconvolution techniques for gene expression data? This paper uses a unique new dataset combined with an open innovation competition to evaluate a wide range of gene-expression deconvolution approaches developed by 294 competitors from 20 countries. The objective of the competition was to separate the expression of individual genes from composite measures of gene pairs. Outcomes were evaluated using direct measurements of single genes from the same samples. Results indicate that the winning algorithm based on random forest regression outperformed the other methods in terms of accuracy and reproducibility. More traditional gaussian-mixture methods performed well and tended to be faster. The best deep learning approach yielded outcomes slightly inferior to the above methods. We anticipate researchers in the field will find the dataset and algorithms developed in this study to be a powerful research tool for benchmarking their deconvolution methods and a useful resource for multiple applications.
Validity of Dynamic Capabilities in the Operation Based on New Sustainability Narratives on Nature Tourism SMEs and Clusters

This study aims to validate the relationships between the dynamic capabilities in the operation of small and medium enterprises (SMEs) that constitute the Nature Tourism Cluster (also known as “ecotourism”) in Colombia, through the application of surveys to managers and owners of hotels and lodgings of rural tourism, travel agencies, tour guides and operators, bars, restaurants and tourist transport centers, whose data obtained, support our hypothesis that the dynamic capacities of absorption, adaptation and innovation influence the functioning of SMEs, while at the cluster level, there is an positive relationship in the interaction of absorption and innovation capabilities. The greatest contribution of our research consists in the development of an empirical study that is based on the main contributions of the dynamic capabilities promoted by Teece (absorption, adaptation and innovation), and that allowed to determine the degree of influence that managers have to take decisions and undertake sustainable ecotourism actions, both at the SME level and at the cluster level. For this reason, our research provides a better understanding of how dynamic capabilities operate at the individual commercial level, as well as at the cluster level, in the combination of absorption, adaptation and innovation capabilities to foster new sustainability narratives and maintain sustainable ecotourism. Our results also point out the limitations and challenges for the sustainable tourism sector in Colombia.
Fog-Removing Method for the Monitoring Traffic Image along with Mathematical Analysis of Retinex Algorithm

: In this paper, we have a tendency to propose an improved fog-removing technique along with mathematical analysis of retinex algorithm so as to form the pictures changing into more clear and less difficult to recognize. The projected technique combines the retinex algorithmic rule and wavelet transform algorithmic rule. The projected technique firstly uses Retinex algorithmic rule to reinforce the image, then the wavelet transform algorithmic rule is employed to reinforce the details of the image, finally, a clear image that is removed fog will be obtained once reduce the non-necessary coefficients. Through analyzing the PSNR (Peak S/N Ratio) of the image contrast, the pictures that are processed by our proposed technique have the PSNR values above the standard Retinex algorithms. In this, we intend to build up a novel picture defogging calculation by specifically anticipating the haze thickness of improved pictures as opposed to receiving earlier suppositions or requirements. The proposed method reduces the halo artifacts by adaptively limiting the boundary of an arbitrary haze image. A new multi-scale image fusion method for single image dehazing has also been proposed to produce a more natural visual recovery effect. The results show that this method outperforms state-of-the-art haze removal methods in terms of both efficiency and the dehazing visual effect.
The Link between Relational Models, Lifestyle and Life Satisfaction

The purpose of this article is to have a better understanding of the relationships between relational models, life style and life satisfaction of professionals in the Turkish business context. The relational models theory, which was proposed by A. Fiske, covers four major ways of forming social relationships; communal sharing, market pricing, authority ranking, and equality matching. The concept of life style has been also a hot topic that requires more explanation both in people’s work lives and social lives. Life satisfaction implies the feeling of happiness that is known as subjective wellbeing (SWL) in academic world. The survey covers 403 respondents who are all working mainly in large-scale organizations and three different Likert type questionnaires were used to collect data both through personal administration and Internet based applications. Reliability and factor analysis all of which resulted in highly satisfactory results and different sets of data analyses methods and techniques were performed. Research findings clearly indicated that communal sharing is the most preferred relational model followed by equality matching by Turkish employees. The most interesting finding of the study is the fact that healthy life-style is the most important one despite to the respondents’ desire to have luxurious life style. Furthermore, higher their social class will be resulted in more life satisfaction than the others. It would be emphasized that the association between leisure time activities and SWL has a critical importance regarding their satisfaction of life.
Regional oceanographic features and hydrothermal activity influence protist diversity and biogeography in the Okinawa Trough

Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but factors shaping protist diversity, such as dispersal barriers and environmental selection, remain difficult to parse. Deep-sea water masses, which form geographic barriers, and hydrothermal vents, which represent isolated productivity hotspots, are ideal opportunities for studying the effects of dispersal barriers and environmental selection on protist communities. The Okinawa Trough, a deep, back-arc spreading basin, contains distinct water masses in the bottom waters of northern and southern regions and at least twenty-five active hydrothermal vents. In this study, we used metabarcoding to characterize protist communities from fourteen stations spanning the length of the Okinawa Trough, including three hydrothermal vent sites. Significant differences in community structure reflecting regional oceanography and water mass composition were present, indicating the importance of geographic factors in shaping protist communities. Protist communities in bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.
A Qualitative Study of Improvement and Knowledge Transfer in Norwegian Public Hospitals

The Norwegian health care system is in rapid transformation. Changes in demography and lifestyle impose new challenges, and advances in technology and research have made more diagnoses and conditions treatable. Simultaneously the population continue to demand even higher quality and faster treatment from the public health care service. This study is a contribution to the understanding of knowledge transfer in Norwegian public hospitals. The problem definition answered by the study is how process-related knowledge is transferred successfully or unsuccessfully between surgical departments in Norwegian public hospitals. To answer the problem definition, a qualitative study was performed. 45 health care professionals with different backgrounds and educations from several Norwegian public hospitals were interviewed. These had both managerial and nonmanagerial responsibilities at various hierarchical levels in the organisations. This study has two main contributions to theory. The first contribution of the study is the deduction of the Knowledge transfer model. The second contribution is the understanding of how the specific properties of the model influence the eventual outcome of the knowledge transfer process.
Direct organogenesis in vitro propagation of local balinese banana with thidiazuron

Bali’s community needs for bananas are very high, but cannot be fulfilled from the production of bananas in Bali. The main problem for banana cultivation in Bali is the difficulty of getting seeds. Direct organogenesis is offered to overcome this problem. The objective of the research was to study direct organogenesis on in vitro propagation of local Balinese banana with Thidiazuron. The research was carried out at Tissue Culture Laboratory, Faculty of Agriculture, Udayana University, Denpasar, Bali. The experiment was laid out in a completely randomized design with five treatments of thidiazuron concentration, i.e. 0; 0.5; 1.0; 1.5, and 2.0 ppm. Each treatment was replicated 5 times. The Murashige & Skoog medium added with coconut water and extract of bamboo shoots was used as a basic medium. The local Balinese bananas named Saba and Susu were used as source of planting materials. Explants were taken from shoot tips of suckers of newly growing plants. The results showed that the best treatment for both Saba and Susu, was 1 ppm of thidiazuron, as indicated by the highest number of plantlets produced, the number of shoots and plant height.
Networked Gatekeeping and Networked Framing on Twitter Protests in Mexico about the Ayotzinapa Case

This research focuses on a Twitter protest about the disappearance of 43 students in Mexico in 2014 known as the Ayotzinapa case which used the hashtag #PaseDeLista1al43. Social network analysis, interviews and thematic analyses of 3,616 tweets were conducted to investigate how networked gatekeeping and networked framing processes occurred within this networked public. Results show that on this digital protest, elite and non-elite Twitter users were in charge of gatekeeping activities, collaborating to maintain the discussion of the topic of the missing students. The analysis of frames revealed that the protest sought to: humanize the case emphasizing the life of the students; assign responsibility; and portray itself as a way to take an active role and coping emotionally with the disappearance. This works contributes to the literature on networked publics, combining network analysis with interviews to look beyond the digital footprint of the protest to listen to the perspectives of protesters, providing an insight into the dynamics of gatekeeping and framing within a network. Given the porosity, openness, and permanence of Twitter, results from such collaborative relationship of elite and non-elite voices to protest about an issue are now harder to ignore in the public sphere.
Evidentiality in adverbs of manner of perceivability

Abstract This paper presents an analysis of the expression of evidentiality by the English adverbs manifestly, noticeably, patently and visibly (MNPV the results show that MNP&V are evidential by implication in most cases, and also uncover individual differences in features such as position and domain of evidence and in the extent to which each adverb can be considered as an evidential expression.
Characterization and Genome Analysis of a Novel Escherichia coli Bacteriophage vB_EcoS_W011D

Received: Revised: Accepted: Published online: August 11, 2019 September 25, 2019 October 16, 2019 November 06, 2019 The application of phages against the increased reported drug resistant Escherichia coli is one of the promising alternative therapeutic options. The total number of phages on the earth are more than 10, but the phages that have been isolated and studied are limited. Hence, discovering of new phage and uncovering its characteristics will provide materials for extensive use of phage therapy in the future. In this study, a novel E. coli phage named vB_EcoS_W011D was isolated and the characteristics and genome were explored. The typical morphology of vB_EcoS_W011D is comprised of an icosahedral head and a constricted flexible rolled up tail, revealing that it is the genus TLS virus of Tunavirinae subfamily. One-step growth curve showing the eclipse and latent period of vB_EcoS_W011D was 5 min and 10 min, respectively, with the burst size of 115 PFU/cell. The genome of vB_EcoS_W011D is double-stranded consisting of 49,847 bp with 46.24% of G+C contents and shows ≤77% similarities (with 38% query coverage) to other reported phages. A total 85 putative ORFs were identified. Of which, 43 predicted ORFs had significant homology with other phage proteins of known functions. A putative Zonula occludes toxin was found in its genome. In addition, a clear difference was revealed on the phylogenetic analysis of it terminates large subunit and capsid protein. In conclusion, our study clearly indicates that vB_EcoS_W011D is a newly discovered E. coli phage that could be further investigated to elucidate phage variety and evolutionary relationship between bacteria and phages. ©2019 PVJ. All rights reserved
Four Pedagogical Dimensions for Understanding Flipped Classroom Practices in Higher Education: A Systematic Review

Despite being widely adopted in higher education to support student-centred learning, the pedagogical design of flipped classrooms has been criticised as lacking in theoretical framing. This study proposes that the pedagogical dimensions of personalisation, higher-order thinking, self-direction, and collaboration can be used as theoretical lenses to deconstruct how flipped classroom practices support student-centred learning. Through a systematic review of 56 cases from 51 studies of flipped learning implementation published in peer-reviewed articles, this study found that flipped classrooms personalise learning through resource and teacher access, develops higher-order thinking through problemsolving, and engages students in collaborative learning through both peer groups and design groups. Trends of positive student learning outcomes are more consistent among cases that support collaborative learning and student selfdirection of learning performance review by repeated application and remediation. Nevertheless, majority of the cases reflect students having limited personalisation of learning choice and structured collaborative processes are seldom used apart from the few cases implementing team-based learning. The theoretical applications of the four pedagogical dimensions as well as the implications for the future research and practice of flipped classrooms are discussed.