Miracle-dz/UniFAR-FTUs huggingface dataset:
Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes

MOTIVATION Exome sequencing studies have facilitated the detection of causal genetic variants in yet-unsolved Mendelian diseases. However, the identification of disease causal genes among a list of candidates in an exome sequencing study is still not fully settled, and it is often difficult to prioritize candidate genes for follow-up studies. The inheritance mode provides crucial information for understanding Mendelian diseases, but none of the existing gene prioritization tools fully utilize this information. RESULTS We examined the characteristics of Mendelian disease genes under different inheritance modes. The results suggest that Mendelian disease genes with autosomal dominant (AD) inheritance mode are more haploinsufficiency and de novo mutation sensitive, whereas those autosomal recessive (AR) genes have significantly more non-synonymous variants and regulatory transcript isoforms. In addition, the X-linked (XL) Mendelian disease genes have fewer non-synonymous and synonymous variants. As a result, we derived a new scoring system for prioritizing candidate genes for Mendelian diseases according to the inheritance mode. Our scoring system assigned to each annotated protein-coding gene (N = 18 859) three pathogenic scores according to the inheritance mode (AD, AR and XL). This inheritance mode-specific framework achieved higher accuracy (area under curve = 0.84) in XL mode. CONCLUSION The inheritance-mode specific pathogenicity prioritization (ISPP) outperformed other well-known methods including Haploinsufficiency, Recessive, Network centrality, Genic Intolerance, Gene Damage Index and Gene Constraint scores. This systematic study suggests that genes manifesting disease inheritance modes tend to have unique characteristics. AVAILABILITY AND IMPLEMENTATION ISPP is included in KGGSeq v1.0 (http://grass.cgs.hku.hk/limx/kggseq/), and source code is available from (https://github.com/jacobhsu35/ISPP.git). CONTACT mxli@hku.hkSupplementary information: Supplementary data are available at Bioinformatics online.
Towards Analysis Tools for a Multilingual Blogsphere

Many approaches to Weblog analysis draw on words found in the postings and comments, and the meaning of those words is inherently bound to a language. Moving beyond single-language analysis will require tools that leverage translation resources in ways that are well matched to the task. In this paper, we describe how state of the art techniques developed originally for machine translation and cross-language information retrieval could provide a foundation for extending existing blog analysis tools to learn from many languages things would be harder to see in just one.
Analyzing the role of Facebook-based e-portfolio on motivation and performance in English as a second language learning

This study investigates the role of Facebook posts as online triggers for English as a Second Language (ESL) learner’ motivation and performance. The study explores the motivational dynamics of how Facebook language influences learning in the community by exploring the interconnectedness of emotional linguistic strategies. A mixed-methods approach was adopted to collect Facebook posts and open coding and thematic coding techniques were employed to analyze the data. The participants were administered pre- and post-tests to collect their performance outcomes for t-tests. The findings reveal that Facebook posts about learning English as a second language (L2) provide primary motivation for learners and promote their performance. These posts are triggers for their L2 understanding and enhance their language learning motivation and performance. Their affirmation and agreement, sharing of personal experiences and testimonials, reflection, seeking advice and guidance work as projectors in the motivational strategies of ESL learners. Furthermore, motivation is facilitated by the use of attractive Facebook posts. Additionally, practical implications highlight the importance of creating supportive and engaging language learning environments. Further research is recommended to explore motivational dynamics in different digital contexts and platforms.
Sources of Discrimination and Their Associations With Health in Sexual Minority Adults

ABSTRACT Health disparities exist between sexual minorities and heterosexuals. These health disparities may be due to stressful social situations and environments that are created by discrimination. The current study recruited 277 sexual minorities to complete an online survey to examine the effects of discrimination on health. Discrimination from family and friends, compared to non-family and friends, was found to be more strongly associated with poorer health. This effect was partially statistically mediated by perceived stress reactivity. Findings from this study highlight the importance of distinguishing between different sources of discrimination when examining the effect of discrimination on health in sexual minority adults.
Daytime longitudinal structures of electron density and temperature in the topside ionosphere observed by the Hinotori and DEMETER satellites

[1] Daytime longitudinal structures of the electron density (Ne) and temperature (Te) in the topside ionosphere observed by Hinotori and DEMETER are examined under various conditions of solar flux, local time, and seasons. Results from both satellites show a similar longitudinal Ne structure in the morning from July to October, although the value of Ne observed by Hinotori is higher than that of DEMETER owing to higher solar flux. This result implies that the longitudinal structure of Ne may appear in any solar cycle. Further, a negative correlation between Ne and Te in the longitudinal structures appears in the morning when Ne is low, while a positive correlation appears around the magnetic equator when Ne is sufficiently enhanced during noontime in the high solar flux. A spectrum analysis performed on the DEMETER data reveals that wave numbers 1–2 for Ne and Te are dominant and nondominant. The observed wave numbers 3–4 for Ne are dominant during November–May and June–October, while they are dominant for Te during October–June and July–September. Both Ne and Te show the largest power of wave number 3 in December and wave number 4 in September. Further, observed annual variations of wave numbers 3–4 for Ne and Te also differ from wave numbers 3–4 generated by waves in the lower thermosphere. It can be interpreted as discrepancies between the longitudinal distributions of Ne and Te caused by difference in the condition of zonal winds driving E region dynamo and meridional winds modulating the ionospheric plasma structures.
Development of an evidence evaluation and synthesis system for drug-drug interactions, and its application to a systematic review of HIV and malaria co-infection

Background In all settings, there are challenges associated with safely treating patients with multimorbidity and polypharmacy. The need to characterise, understand and limit harms resulting from medication use is therefore increasingly important. Drug-drug interactions (DDIs) are prevalent in patients taking antiretrovirals (ARVs) and if unmanaged, may pose considerable risk to treatment outcome. One of the biggest challenges in preventing DDIs is the substantial gap between theory and clinical practice. There are no robust methods published for formally assessing quality of evidence relating to DDIs, despite the diverse sources of information. We defined a transparent, structured process for developing evidence quality summaries in order to guide therapeutic decision making. This was applied to a systematic review of DDI data with considerable public health significance: HIV and malaria. Methods and findings This was a systematic review of DDI data between antiretrovirals and drugs used in prophylaxis and treatment of malaria. The data comprised all original research in humans that evaluated pharmacokinetic data and/or related adverse events when antiretroviral agents were combined with antimalarial agents, including healthy volunteers, patients with HIV and/or malaria, observational studies, and case reports. The data synthesis included 36 articles and conference presentations published via PubMed and conference websites/abstract books between 1987-August 2016. There is significant risk of DDIs between HIV protease inhibitors, or NNRTIs and artemesinin-containing antimalarial regimens. For many antiretrovirals, DDI studies with antimalarials were lacking, and the majority were of moderate to very low quality. Quality of evidence and strength of recommendation categories were defined and developed specifically for recommendations concerning DDIs. Conclusions There is significant potential for DDIs between antiretrovirals and antimalarials. The application of quality of evidence and strength of recommendation criteria to DDI data is feasible, and allows the assessment of DDIs to be robust, consistent, transparent and evidence-based.
Constructing a Family of 4‐Critical Planar Graphs with High Edge Density

A graph G=(V,E) is a k‐critical graph if G is not (k−1) ‐colorable but every proper subgraph of G is (k−1) ‐colorable. In this article, we construct a family of 4‐critical planar graphs with n vertices and 7n−133 edges. As a consequence, this improves the bound for the maximum edge density attained by Abbott and Zhou. We conjecture that this is the largest edge density for a 4‐critical planar graph.
Modelling and synthesising F0 contours with the discrete cosine transform

The discrete cosine transform is proposed as a basis for representing fundamental frequency (F0) contours of speech. The advantages over existing representations include deterministic algorithms for both analysis and synthesis and a simple distance measure in the parameter space. A two-tier model using the DCT is shown to be able to model F0 contours to around 10 Hz RMS error. A proof-of-concept system for synthesising DCT parameters is evaluated, showing that the benefits do not come at the expense of speech synthesis applications.
An Axiomatization of Difference-Form Contest Success Functions

This paper presents an axiomatic characterization of difference-form group contests, that is, contests fought among groups and where their probability of victory depends on the difference of their effective efforts. This axiomatization rests on the property of Absolute Consistency, stating that the difference in winning probabilities between two contenders in the grand contest must be the same as when they engage in smaller contests. This property overcomes some of the drawbacks of the widely-used ratio-form contest success functions. Our characterization shows that the criticisms commonly-held against difference-form contests success functions, such as lack of scale invariance, are unfounded. Finally, we extend our axiomatization to relative-difference contests where winning probabilities depend on the difference of contenders effective efforts relative to total aggregate effort.
Topic-weak-correlated Latent Dirichlet allocation

Latent Dirichlet allocation (LDA) has been widely used for analyzing large text corpora. In this paper we propose the topic-weak-correlated LDA (TWC-LDA) for topic modeling, which constrains different topics to be weak-correlated. This is technically achieved by placing a special prior over the topic-word distributions. Reducing the overlapping between the topic-word distributions makes the learned topics more interpretable in the sense that each topic word-distribution can be clearly associated to a distinctive semantic meaning. Experimental results on both synthetic and real-world corpus show the superiority of the TWC-LDA over the basic LDA for semantically meaningful topic discovery and document classification.
Diversity and Composition of Methanotrophs in Chinese Paddy Soil as Affected by Different Long–term Fertilizer Managements

Methane–oxidizing bacteria (methanotrophs) biologically consume and consequently affect the concentration of atmospheric methane (CH 4 ), the second most prominent greenhouse gas, and therefore play critical roles in the mitigation of global warming effect. Long–term fertilization often affects the methanotrophs community and CH 4 oxidation in various soils. The objective of this study was to characterize for a Chinese paddy soil the changes in CH 4 emissions and the diversity and composition of methanotrophs, that resulted from mineral fertilizer, crop residue, and manure applications. In this long-term ( 28 years) field study, use was made of static chambers and gas chromatography, and Illumina high-throughput sequencing of the 165rRNA gene, to analyse the CH 4 emissions from a paddy field soil, and the soil methanotroph abundance and community diversity under five fertilizer treatments. These treatments were: mineral fertilizer alone (MF), rice residue plus mineral fertilizer (RF), low manure rate plus mineral fertilizer (LOM), and high manure rate plus mineral fertilizer (HOM), compared to without fertilizer input (CK). The results indicated that CH 4 from fertilization treatments displayed different emission patterns during the barley growing season. The HOM plot had the highest CH 4 emissions (5.074 g m -2 ) and global warming potentials (GWPs) (1614.77 kg CO 2 –eq ha -1 ), during the barley growing season. It was clear that some methanotrophs species ( Methylosinus , Methylomicrobium , Methylomonas and Methylosarcina ) were identified in the main growth stages of barley. Long–term fertilization managements can both affect the abundance and the composition of the soil methanotrophs. Methanotroph abundance was inhibited by the MF treatment, but enhanced by the RF, LOM and HOM treatments. The mineral fertilizers, crop residues, and manure could be important factors controlling the abundance and community composition of the methanotrophs in the paddy soil. We concluded that the application of organic (chicken manure), and the crop residues enhance the abundance and community composition of methanotrophs in double–cropping paddy fields in southern China through a long–term fertilizer experiment.
UAV vision-based localization techniques using high-altitude images and barometric altimeter

Position information of unmanned aerial vehicles (UAVs) and objects is important for inspections conducted with UAVs. The accuracy with which changes in object to be inspected are detected depends on the accuracy of the past object data being compared; therefore, accurate position recording is important. A global positioning system (GPS) is commonly used as a tool for estimating position, but its accuracy is sometimes insufficient. Therefore, other methods have been proposed, such as visual simultaneous localization and mapping (visual SLAM), which uses monocular camera data to reconstruct a 3D model of a scene and simultaneously estimates the trajectories of the camera using only photos or videos. In visual SLAM, UAV position is estimated on the basis of stereo vision (localization), and 3D points are mapped on the basis of the estimated UAV position (mapping). Processing is implemented sequentially between localization and mapping. Finally, all the UAV positions are estimated and an integrated 3D map is created. For any given iteration in the sequential processing, there will be estimation error, but in the next iteration, the previous estimated position will be used as a base position regardless of this error. As a result, error accumulates until the UAV returns to a location it passed before. Our research aims to mitigate this problem. We propose two new methods. (1) Accumulated error caused by local matching with sequential low-altitude images (i.e. close-up photos) is corrected with global-matching between low- and high-altitude images. To perform global-matching that is robust against error, we implemented a method wherein the expected matching areas are narrowed down on the basis of UAV position and barometric altimeter measurements. (2) Under the assumption that absolute coordinates include axis-rotation error, we proposed an error-reduction method that minimizes the difference in the UAVs’ altitude between the visual SLAM and sensor (bolometer and thermometer) results. The proposed methods reduced accumulated error by using high-altitude images and sensors. Our methods improve the accuracy of UAV- and object-position estimation.
Refinement of a viral transmission risk model for blood donations in seroconversion window phase screened by nucleic acid testing in different pool sizes and repeat test algorithms

BACKGROUND: In minipool nucleic acid test (MP‐NAT) screening protocols, the donations implicated in reactive test pools are released for transfusion when they are nonreactive in a repeat test on the individual samples, but in individual‐donation (ID)‐NAT screening algorithms the release of nonrepeatable reactive (NRR) donations is under discussion.
A design of butterworth low pass filter's layout basideal filter approximation on the ideal filter approximation

This paper presents the study and analysis on Butterworth Low Pass filter, to discover the filter's order effect on the ideal filter approximation. Theoretically, as the numbers of order increased, the filter will approximate ideal filter characteristics. The challenges are; by increasing the filter's order, it will increase the circuit complexity and the cost. In order to reduce the circuit complexity, the Sallen-Key topology has been selected since the topology requires fewer components. This paper also presents the techniques and issues that should be considered while designing the schematic and layout of the filter.
Estimation of Future Probable Maximum Precipitation in Korea Using Multiple Regional Climate Models

In this study, future probable maximum precipitations (PMPs) based on future meteorological variables produced from three regional climate models (RCMs) of 50-km spatial resolution provided by Coordinated Regional Climate Downscaling Experiment (CORDEX) are projected. In order to estimate future PMPs, the hydro-meteorological method is applied. The key future meteorological variable used to analyze the rate of change of future PMPs is the dew-point temperature. Future 12-h persistence 100-year return period extreme dew-point temperatures obtained from future daily dew-point temperature time series by using the scale-invariance method are applied to estimate future PMPs. As a result of estimating future PMPs using several RCMs and representative concentration pathways (RCPs) scenarios, the spatial distribution of future PMPs is expected to be similar to that of the present, but PMPs tend to increase in the future. In addition, it can be seen that the difference in PMPs estimated from various RCMs and RCP scenarios is getting bigger in the future. Especially after 2070, the difference has increased even more. In the short term, it is proposed to establish climate change adaptation policies with an 18% increase in PMPs, which is the ensemble average in the future year 2050.
Thermal environment in growing and finishing pig facilities of different building typologies

The objective of this study was to evaluate the thermal comfort of growing and finishing pigs affected by the different constructive typologies of the installations regarding the floor and lateral partitions. Were evaluated the following pen types: pen with water pit, pen with partially slotted floor on the sides, and pen with partially slotted floor on the sides and in the center of the facilities. The following thermal variables were measured: dry bulb temperature, black globe temperature, relative humidity, and air velocity. Based on these data, the temperature and humidity index, the temperature index of the globe and humidity, and the specific enthalpy were calculated. The pen with a water pit showed higher average relative air humidity and lower black globe temperature compared to the other pens. In the hottest period of the day, the temperature index of the globe and humidity presented mean values above that recommended for adult pigs, although there were no differences between pens. This indicates that animals, irrespective of the type of pen used, have suffered from thermal stress, which most likely affected their performance.
An integrated system for managing the Andalusian Parliament's digital library

Purpose – The purpose of this paper is to present an overview of the reorganisation of the Andalusian Parliament's digital library to improve the electronic representation and access of its official corpus by taking advantage of a document's internal organisation. Video recordings of the parliamentary sessions have also been integrated with their corresponding textual transcriptions.Design/methodology/approach – After analysing the state of the Andalusian Parliament's digital library and determining the aspects that could be improved both in the repository and access mechanisms, this paper describes each component of the developed integrated information system.Findings – A methodology has been developed to tackle the problem and this could be applied to other similar institutions and organisations. Exploiting the internal structure of the parliament's official documents has also proved to be extremely interesting for users as they are directed towards the most relevant parts of the documents.Originality/v.
On the Combination of Accuracy and Diversity Measures for Genetic Selection of Bagging Fuzzy Rule-Based Multiclassification Systems

A preliminary study combining two diversity measures with an accuracy measure in two bicriteria fitness functions to genetically select fuzzy rule-based multiclassification systems is conducted in this paper. The fuzzy rule-based classification system ensembles are generated by means of bagging and mutual information-based feature selection. Several experiments were developed using four popular UCI datasets with different dimensionality in order to analyze the accuracy-complexity trade-off obtained by a genetic algorithm considering the two fitness functions. Comparison are made with the initial fuzzy ensemble and a single fuzzy classifier.
Blind Source Parameters for Performance Evaluation of Despeckling Filters

The speckle noise is inherent to transthoracic echocardiographic images. A standard noise-free reference echocardiographic image does not exist. The evaluation of filters based on the traditional parameters such as peak signal-to-noise ratio, mean square error, and structural similarity index may not reflect the true filter performance on echocardiographic images. Therefore, the performance of despeckling can be evaluated using blind assessment metrics like the speckle suppression index, speckle suppression and mean preservation index (SMPI), and beta metric. The need for noise-free reference image is overcome using these three parameters. This paper presents a comprehensive analysis and evaluation of eleven types of despeckling filters for echocardiographic images in terms of blind and traditional performance parameters along with clinical validation. The noise is effectively suppressed using the logarithmic neighborhood shrinkage (NeighShrink) embedded with Stein's unbiased risk estimation (SURE). The SMPI is three times more effective compared to the wavelet based generalized likelihood estimation approach. The quantitative evaluation and clinical validation reveal that the filters such as the nonlocal mean, posterior sampling based Bayesian estimation, hybrid median, and probabilistic patch based filters are acceptable whereas median, anisotropic diffusion, fuzzy, and Ripplet nonlinear approximation filters have limited applications for echocardiographic images.