Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene activation and repression by the glucocorticoid receptor are mediated by sequestering Ep300 and two modes of chromatin binding

The transcription factor glucocorticoid receptor (GR) is a key mediator of stress response and a broad range of physiological processes. How can GR rapidly activate the expression of some genes while repress others, remains an open question due to the challenge to associate GR binding sites (GBSs) to their distant gene targets. Mapping the full 3D scope of GR-responsive promoters using high-resolution 4C-seq unravelled spatial separation between chromatin interaction networks of GR-activated and repressed genes. Analysing GR binding sites and other regulatory loci in their functional 3D context revealed that GR sequesters the co-activator Ep300 from active non-GBS enhancers in both activated and repressed gene compartments. While this is sufficient for rapid gene repression, gene activation is countered by productive recruitment of Ep300 to GBS. Importantly, in GR-activated compartments Klf4 binding at non-GBS regulatory elements cluster in 3D with GBS and antagonizes GR activation. In addition, we revealed ROR and Rev-erb transcription factors as novel co-regulators for GR-mediated gene expression.
On the mismatch in the strength of competition among fossil and modern species of planktonic Foraminifera

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2019 The Authors. Global Ecology and Biogeography published by John Wiley & Sons Ltd 1Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, United Kingdom 2Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany 3Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada 4Instituto de Física Teórica, Universidade Estadual de São Paulo, Sao Paulo, Brazil 5School of Geography, Earth and Environmental Science, University of Birmingham, Birmingham, United Kingdom
Kir2.2 p.Thr140Met: a genetic susceptibility to sporadic periodic paralysis

Introduction Periodic paralyses (PP) are recurrent episodes of flaccid limb muscle weakness. Next to autosomal dominant forms, sporadic PP (SPP) cases are known but their genetics are unclear. Methods In a patient with hypokalemic SPP, we performed exome sequencing to identify a candidate gene. We sequenced this gene in 263 unrelated PP patients without any known causative mutations. Then we performed functional analysis of all variants found and molecular modelling for interpretation. Results Exome sequencing in the proband yielded three heterozygous variants predicted to be linked to disease. These encoded p.Thr140Met in the Kir2.2 potassium channel, p.Asp229Asn in protein kinase C theta, and p.Thr15943Ile in titin. Since all hitherto known causative PP genes code for ion channels, we studied the Kir2.2-encoding gene, KCNJ12, for involvement in PP pathogenesis. KCNJ12 screening in 263 PP patients revealed three further variants, each in a single individual and coding for p.Gly419Ser, p.Cys75Tyr, and p.Ile283Val. All four Kir2.2 variants were functionally expressed. Only p.Thr140Met displayed relevant functional alterations, i.e. homo-tetrameric channels produced almost no current, and hetero-tetrameric channels suppressed co-expressed wildtype Kir2.1 in a dominant-negative manner. Molecular modelling showed Kir2.2 p.Thr140Met to reduce movement of potassium ions towards binding sites in the hetero-tetramer pore compatible with a reduced maximal current. MD simulations revealed loss of hydrogen bonding with the p.Thr140Met substitution. Discussion The electrophysiological findings of p.Thr140Met are similar to those found in thyrotoxic PP caused by Kir2.6 mutations. Also, the homologous Thr140 residue is mutated in Kir2.6. This supports the idea that Kir2.2 p.Thr140Met conveys susceptibility to SPP and should be included in genetic screening.
Mapping Technology in Visual SLAM: A Review

Simultaneous localization and mapping (SLAM) is a major challenge in the field of robotics. Existing literature reviews are classified according to the localization technology or sensors. However, there are no reviews based on the map construction technology in SLAM currently. As another goal of SLAM, map construction is also very important and is the main resource that can provide significant information for applications in upper layers. This paper summarizes fundamentals of map construction technology involved in Visual SLAM (V-SLAM). In addition, this paper reviews state-of-the-art typical visual SLAM systems, with a major focus on the mapping. Various issues and applications based on SLAM are discussed.
Saccade vigor as an implicit measure of subjective economic value

Decisions are made based on the subjective value that the brain assigns to options. However, subjective value is a mathematical construct that cannot be measured directly, but only inferred from choices. Is there another aspect of behavior that directly reflects subjective valuation of an option? Recent results have demonstrated that movement vigor is modulated by reward, raising the possibility that there is a link between how the brain evaluates an option, and how it controls movements toward that option. Alternatively, vigor may reflect salience and not value of the stimulus, growing larger for both stimuli that promise gain as well as stimuli that foretell loss. To dissociate between these possibilities, we asked people to choose among risky options represented by abstract stimuli, some associated with gain, others with loss. From their choices we estimated the subjective value that they assigned to each stimulus. In probe trials, they viewed only one stimulus at a time, and we measured their saccade vigor. We found that vigor was lowest for stimuli that promised loss, highest for stimuli that promised gain. This implied that vigor corresponded to value not salience. Naturally, a given stimulus was valued more by some participants. Remarkably, those who valued a given stimulus more tended to move with greater vigor in response to that stimulus. Thus, subjective value of a stimulus monotonically modulated the vigor with which the eyes moved to acquire a stimulus, suggesting that subjective valuation may be inferred from movement vigor. Significance statement Does vigor of movements in response to an option reflect the subjective value that the brain has assigned to that option? If this were the case, vigor may provide an objective assay of subjective value, obviating the need to infer this variable from measurements of choice. Here, we show that saccade vigor varies monotonically with subjective value: smallest for stimuli that predict economic loss, and highest for stimuli that predict economic gain. Notably, between-subject differences in valuation may be gleaned from the between-subject differences in their patterns of vigor. “A true theory of economy can only be attained by going back to the great springs of human action --- the feelings of pleasure and pain. ” William Jevons (1866)
Data streams anomaly detection algorithm based on self-set threshold

With the rapid development of big data, smart city and artificial intelligence, anomaly detection technology for data streams has been widely used in big data detection, video surveillance, network intrusion detection, intelligent security analysis and so on. Among them, the distance-based data streams anomaly detection algorithm is well received by researchers because it can adapt well to the infinite growth of data streams. However, the existing distance-based detection algorithm needs to manually estimate the specific value of the detection threshold parameter according to the historical data, which seriously affects the detection efficiency and accuracy. Therefore, this paper introduces the extreme value theory and proposes a data streams anomaly detection algorithm based on self-set threshold with extreme value theory (ESOD). The algorithm can not only automatically set the detection threshold, but also update the threshold in real time according to the detection data to adapt to the data streams environment of concept drift. After theoretical analysis and experimental verification, ESOD algorithm has good usability and high efficiency.
Zebrafish duox mutations provide a model for human congenital hypothyroidism

ABSTRACT Thyroid dyshormonogenesis is a leading cause of congenital hypothyroidism, a highly prevalent but treatable condition. Thyroid hormone (TH) synthesis is dependent on the formation of reactive oxygen species (ROS). In humans, the primary sources for ROS production during thyroid hormone synthesis are the NADPH oxidases DUOX1 and DUOX2. Indeed, mutations in DUOX1 and DUOX2 have been linked with congenital hypothyroidism. Unlike humans, zebrafish has a single orthologue for DUOX1 and DUOX2. In this study, we investigated the phenotypes associated with two nonsense mutant alleles, sa9892 and sa13017, of the single duox gene in zebrafish. Both alleles gave rise to readily observable phenotypes reminiscent of congenital hypothyroidism, from the larval stages through to adulthood. By using various methods to examine external and internal phenotypes, we discovered a strong correlation between TH synthesis and duox function, beginning from an early larval stage, when T4 levels are already noticeably absent in the mutants. Loss of T4 production resulted in growth retardation, pigmentation defects, ragged fins, thyroid hyperplasia/external goiter and infertility. Remarkably, all of these defects associated with chronic congenital hypothyroidism could be rescued with T4 treatment, even when initiated when the fish had already reached adulthood. Our work suggests that these zebrafish duox mutants may provide a powerful model to understand the aetiology of untreated and treated congenital hypothyroidism even in advanced stages of development. This article has an associated First Person interview with the first author of the paper. Summary: Zebrafish harbouring two loss-of-function alleles of the single duox gene exhibit various adult phenotypes reminiscent of human congenital hypothyroidism.
Application of superabsorbent and mulch on some traits of African marigold (Tagetes erecta) under irrigation intervals.

Water scarcity is an important obstacle to the development and expansion of the urban landscape in the arid and semi-arid regions of the world. Nowadays, organic and artificial materials can be used to reduce water consumption without impairing the quality and quantity of urban landscape. In order to study the effect of mulch type on reducing irrigation interval for a popular seasonal plant in the Middle East, African marigold, an experiment was carried out in Mashhad, Iran during 2016-2017 in which two treatments were applied including mulch type (typical soil as control, palm fiber mulch, plastic mulch, and superabsorbent) and irrigation intervals (3, 6 and 9 days). Some morphological, biological, physiological and biochemical traits were evaluated. Results indicated that the superabsorbent could significantly increase most recorded traits. The palm fiber mulch also improved plant height, flower number, and dry shoot weight. In most traits, the 3-day irrigation interval indicated a significant increase versus the 6- and 9-day intervals, but plant height, flower number, and photosynthetic rate did not differ significantly between the 3-day and 9-day irrigation intervals. The findings show that superabsorbent and at the next level, palm fiber mulch with 9-day irrigation intervals can be suggested for African marigold in the arid and semi-arid climates.
Finding similar users from GPS data based on assignment problem

The application of location-aware technology has increasingly accumulated a large amount of user spatiotemporal data, which gives us the opportunity to analyze users' interests and behavior patterns. This paper proposes a new method for constructing user's mobility profiles and measuring their similarity. First, a new method of using the categories of points of interest (POI) to represent the semantics of a geographical area (stay region) where a user stays for a long period of time is proposed. Second, the sequential pattern mining technique is applied to extract the user's mobility profiles. Then, the user similarity is computed based on the maximum benefit assignment problem. Finally, a comparison experiment with the existing works on the real dataset verifies the effectiveness of the proposed approach.
Wiener Loss: A Strong Correlative Loss Applied to Conditional GAN for Color Prediction

Colorization is a task to generate plausible color for a given grayscale image, where the target in input always have variable color styles. Due to the ill-posed inverse problem in colorization, the generated color image easily suffers from the phenomenon of color cast, where unexpected particular color affects the generated image. To cope with such problem, this paper proposes a novel loss function, called Wiener Loss, to constrain the training of colorization network. Concretely, we adopt conditional generative network for training. This paper uses the colorized image from generator and ground truth corporately to calculate their relevance defined as Wiener Loss and feeds this loss back into generator network for training. The experiments demonstrate that our method generates better results compared with its counterpart.
Plastidial (p)ppGpp synthesis by the Ca2+-dependent RelA-SpoT homolog regulates the adaptation of chloroplast gene expression to darkness in Arabidopsis

In bacteria, the hyper-phosphorylated nucleotides, guanosine 5’-diphosphate 3’-diphosphate (ppGpp) and guanosine 5’-triphosphate 3’-diphosphate (pppGpp), function as secondary messengers in the regulation of various metabolic processes of the cell, including transcription, translation, and enzymatic activities, especially under nutrient deficiency. The activity carried out by these nucleotide messengers is known as the stringent response. (p)ppGpp levels are controlled by two distinct enzymes, namely, RelA and SpoT, in Escherichia coli. RelA-SpoT homologs (RSHs) are also conserved in plants and algae where they function in the plastids. The model plant Arabidopsis thaliana contains four RSHs: RSH1, RSH2, RSH3, and Ca2+-dependent RSH (CRSH). Genetic characterizations of RSH1, RSH2, and RSH3 were undertaken, which showed that the (p)ppGpp-dependent plastidial stringent response significantly influences plant growth and stress acclimation. However, the physiological significance of CRSH-dependent (p)ppGpp synthesis remains unclear, as no crsh-null mutant has been available. Here to investigate the function of CRSH, a crsh-knockout mutant of Arabidopsis was constructed using a site-specific gene-editing technique, and its phenotype was characterized. A transient increase of ppGpp was observed for 30 min in the wild type (WT) after light-to-dark transition, but this increase was not observed in the crsh mutant. Similar analyzes were performed with the rsh2rsh3 double and rsh1rsh2rsh3 triple mutants of Arabidopsis and showed that the transient increments of ppGpp in the mutants were higher than those in the WT. The increase of (p)ppGpp in the WT and rsh2rsh3 accompanied decrements in the mRNA levels of psbD transcribed by the plastid-encoded plastid RNA polymerase. These results indicated that the transient increase of intracellular ppGpp at night is due to CRSH-dependent ppGpp synthesis and the (p)ppGpp level is maintained by the hydrolytic activities of RSH1, RSH2, and RSH3 to accustom plastidial gene expression to darkness.
Calprotectin and Calgranulin C as Biomarkers of Pancreatic Tumors: Baseline Levels and Level Changes after Surgery

Pancreatic tumors and their surgical resection are associated with significant morbidity and mortality, and the biomarkers currently used for these conditions have limited sensitivity and specificity. Because calprotectin and calgranulin C serum levels have been demonstrated to be potential biomarkers of certain cancers and complications of major surgery, the levels of both proteins were tested in the current study in patients with benign and malignant pancreatic tumors that were surgically removed. The baseline serum levels and kinetics of calprotectin and calgranulin C during the 7-day postoperative period were evaluated with immunoassays in 98 adult patients who underwent pancreatic surgery. The baseline serum levels of calprotectin and calgranulin C in patients with malignant (n = 84) and benign tumors (n = 14) were significantly higher (p < 0.01) when compared to those in the healthy controls (n = 26). The serum levels of both proteins were also significantly (p < 0.05) higher in patients with benign tumors than in those with malignant tumors. After surgery, the serum levels of calprotectin and calgranulin C were significantly (p < 0.01) higher than their baseline values, and this elevation persisted throughout the seven days of the follow-up period. Interestingly, starting on day 1 of the postoperative period, the serum levels of both proteins were significantly (p < 0.05) higher in the 37 patients who developed postoperative pancreatic fistulas (POPFs) than in the patients who had uneventful recoveries (n = 61). Moreover, the serum levels of calprotectin and calgranulin C demonstrated a significant predictive value for the development of POPF; the predictive values of these two proteins were better than those of the serum level of C-reactive protein and the white blood cell count. Taken together, the results of this study suggest that calprotectin and calgranulin C serum levels are potential biomarkers for pancreatic tumors, surgical injury to the pancreatic tissue and the development of POPFs.
Short Term Prediction Framework for Moroccan Stock Market Using Artificial Neural Networks

In this paper we present a short term forecasting framework for stock markets based on Artificial Neural Networks. We are interested in predicting future trends of stock markets (Up, Down and Unchanged) in the very short term (10 to 60 minutes ahead). We present a framework to efficiently implement different ANN architectures namely Multi-Layers Perceptron (MLP) and the Long Short- Term Memory (LSTM). This framework involves the use of intraday prices data (tick-by-tick data) and a selection of technical indicators as input variables and fixes the issues related to the imbalanced target classes and the non-regularly spaced input data.We conduct different experimentations within the proposed framework on data from the Moroccan stock market.
An Ensemble-Based Densely-Connected Deep Learning System for Assessment of Skeletal Maturity

Assessment of skeletal maturity is important for a clinician to make a decision of the most appropriate treatment on various skeletal disorders. This task is very challenging when using machine learning method due to the limited data and large anatomical variations among different subjects. In this article, we propose an ensemble-based deep learning pipeline to automatically assess the distal radius and ulna (DRU) maturity from left-hand radiographs. At the same time, we adapted the concept of densely connected mechanism in the proposed network architecture to reuse features and prevent gradient disappearance. Therefore, the model acquires two convincing advantages: first, our model preserves the maximum information flow and has a much faster convergence rate. Second, our model avoids overfitting even if training with limited data. The experimental dataset contains 1189 left-hand $X$ -ray scans of children and teenagers. The proposed method achieves 85.27% and 91.68% for radius and ulna classification, respectively. Extensive experiments prove that our model performs better than using other network structures.
Modern aspects of wheat grain proteins

The unique baking properties of wheat have contributed to the large variety of food products made of wheat. Wheat products are immensely popular, which is reflected in their ubiquitous consumption. Concerning wheat quality, a main challenge for intense growing strategies is to adapt wheat plants of unaltered yield and baking quality to decreased nitrogen input, which will limit unwanted nitrogen leaching into drinking water and safe resources. A probably more important challenge for wheat adaptation will be caused by global climate change. For a relative small percentage of the human population wheat grain proteins can cause a number of serious diseases including coeliac disease. Susceptible persons often have to completely avoid wheat, as well as rye and barley products. Methods for detection of gluten protein are well advanced, increasing safety for patients. Wheat breeding using traditional breeding and modern genome editing approaches are seen to be necessary to develop new wheat cultivars for adaptation to new environmental conditions caused by climate change, reduced nitrogen input and increased production efficiency, as well as reduction of disease potential. Wheat grain protein analytical methods are important, e.g. for determination of quality parameters and for decision making in breeding programmes. Aspects of protein extraction, proteomic analysis and database coverage of wheat protein sequences are discussed.
Salient features of an effective immersive non-collaborative virtual reality learning environment

The use of immersive virtual reality learning environments (VRLEs) is changing the way students learn and understand things. A VRLE allows its users to get immersed in the simulation, thus giving the sense of being part of the real world that it represents. Virtual Reality (VR) existed in various forms in the past two decades, but its early adoption in education was hampered by its high cost. Emergence of affordable head-mounted displays (HMD) is now making it possible to provide VR experience in classrooms. This paper aims to apply integrative review of relevant studies conducted in evaluating the effectiveness of VRLEs and in doing so reveal the existing research gaps among VRLE studies. This paper identifies salient features of a fully immersive and non-collaborative VRLEs that uses HMD. Salient features were derived from evaluating different instruments used to measure the effectiveness of immersive VRLEs. A framework and example of instruments to evaluate salient features of an effective VR, using Kokoda VR as a case study, are also provided.
Mesh Establishment Method Based on 2D Portrait

This paper proposes a method of mesh construction based on 2D portrait, which realizes the final 3d face model for arbitrary 2D face images by adjusting mesh. First of all need to 2D portrait photo for face detection, based on the photo collection of facial feature points, set up related parameters of the feature points, then according to the name of the feature points and corresponding coordinate parameters, the model of overall adjustment and local mesh vertex, get the final face image more realistic 3D face models.
Migracje personelu medycznego i jej skutki dla funkcjonowania systemu ochrony zdrowia w Polsce

Migration of the medical professionals Migration of the healthcare personnel started long before Poland joined the EU. However, with the accession more and more people, especially doctors, decided to migrate. The main reason for migration was of a financial nature. In recent years the dynamics of this migration slowed down among physicians, but it increased among nurses. Though at the moment migration does not pose a serious problem for the healthcare system in Poland it may be one of the factors which will cause problems in the future. Majority of migrants are relatively young. There is a threat that there will be no replacement for nurses who will retire in the nearest future. State involvement / action is required to sustain the system.