Miracle-dz/UniFAR-FTUs huggingface dataset:
Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types

Background The 3′ untranslated regions (3′UTRs) of mRNAs contain cis elements involved in post-transcriptional regulation of gene expression. Over half of all mammalian genes contain multiple polyadenylation sites that lead to different 3′UTRs for a gene. Studies have shown that the alternative polyadenylation (APA) pattern varies across tissues, and is dynamically regulated in proliferating or differentiating cells. Generation of induced pluripotent stem (iPS) cells, in which differentiated cells are reprogrammed to an embryonic stem (ES) cell-like state, has been intensively studied in recent years. However, it is not known how 3′UTRs are regulated during cell reprogramming. Methods/Main Findings Using a computational method that robustly examines APA across DNA microarray data sets, we analyzed 3′UTR dynamics in generation of iPS cells from different cell types. We found that 3′UTRs shorten during reprogramming of somatic cells, the extent of which depends on the type of source cell. By contrast, reprogramming of spermatogonial cells involves 3′UTR lengthening. The alternative polyadenylation sites that are highly responsive to change of cell state in generation of iPS cells are also highly regulated during embryonic development in opposite directions. Compared with other sites, they are more conserved, can lead to longer alternative 3′UTRs, and are associated with more cis elements for polyadenylation. Consistently, reprogramming of somatic cells and germ cells involves significant upregulation and downregulation, respectively, of mRNAs encoding polyadenylation factors, and RNA processing is one of the most significantly regulated biological processes during cell reprogramming. Furthermore, genes containing target sites of ES cell-specific microRNAs (miRNAs) in different portions of 3′UTR are distinctively regulated during cell reprogramming, suggesting impact of APA on miRNA targeting. Conclusions/Significance Taken together, these findings indicate that reprogramming of 3′UTRs by APA, which result from regulation of both general polyadenylation activity and cell type-specific factors and can reset post-transcriptional gene regulatory programs in the cell, is an integral part of iPS cell generation, and the APA pattern can be a good biomarker for cell type and state, useful for sample classification. The results also suggest that perturbation of the mRNA polyadenylation machinery or RNA processing activity may facilitate generation of iPS cells.
Human Sensibility Evaluation Using Photoplethysmogram (PPG)

This study presents a method for human sensibility evaluation using photoplethysmogram(PPG) signal instead of electrocardiogram(ECG) or electroence-phalogram(EEG) signals. For this objective, PPG signals for two emotional states(positive/negative) are collected. To evoke the test emotions, happy(or joyful) and sad(or irritating) movie files are collected and played in subjects' monitor. From the acquired PPG signal, the heart rate variability(HRV) is calculated. Using the HRV and its FFT spectra, the human sensibility is evaluated. Since the heart is a representative organ which is controlled by the autonomic nervous system(ANS), the ANS may reflect the changes in emotion. Additionally a biofeedback technique to respond the bad(negative) mood is designed. The biofeedback software is developed with motion image player interacting with the results of the sensibility evaluation. It was shown that HRV was changed according to the subject's emotions. Accordingly, the sensibility evaluation test showed feasibility of our method.
An Evaluation of the Impact of Oral Magnesium Lactate on the Corrected QT Interval of Patients Receiving Sotalol or Dofetilide to Prevent Atrial or Ventricular Tachyarrhythmia Recurrence

Background: Intravenous magnesium reduces the QTc interval of patients receiving ibutilide. Whether oral magnesium can reduce the QTc interval associated with oral sotalol and dofetilide is not known. This study was undertaken to evaluate the impact of oral magnesium on the QTc interval and whether an inherent intracellular magnesium deficiency exists among patients with arrhythmias.
An information theoretic approach for analyzing temporal patterns of gene expression

MOTIVATION Arrays allow measurements of the expression levels of thousands of mRNAs to be made simultaneously. The resulting data sets are information rich but require extensive mining to enhance their usefulness. Information theoretic methods are capable of assessing similarities and dissimilarities between data distributions and may be suited to the analysis of gene expression experiments. The purpose of this study was to investigate information theoretic data mining approaches to discover temporal patterns of gene expression from array-derived gene expression data. RESULTS The Kullback-Leibler divergence, an information-theoretic distance that measures the relative dissimilarity between two data distribution profiles, was used in conjunction with an unsupervised self-organizing map algorithm. Two published, array-derived gene expression data sets were analyzed. The patterns obtained with the KL clustering method were found to be superior to those obtained with the hierarchical clustering algorithm using the Pearson correlation distance measure. The biological significance of the results was also examined. AVAILABILITY Software code is available by request from the authors. All programs were written in ANSI C and Matlab (Mathworks Inc., Natick, MA).
Female ROMK null mice manifest more severe Bartter II phenotype on renal function and higher PGE2 production.

ROMK null mice with a high survival rate and varying severity of hydronephrosis provide a good model to study type II Bartter syndrome pathophysiology (26). During the development of such a colony, we found that more male than female null mice survived, 58.7% vs. 33.3%. To investigate the possible mechanism of this difference, we compared the survival rates, renal functions, degree of hydronephrosis, as well as PGE(2) and TXB(2) production between male and female ROMK wild-type and null mice. We observed that female ROMK Bartter's mice exhibited lower GFR (0.37 vs. 0.54 ml.min(-1). 100 g BW(-1), P < 0.05) and higher fractional Na(+) excretion (0.66% vs. 0.48%, P < 0.05) than male Bartter's. No significant differences in acid-base parameters, urinary K(+) excretion, and plasma electrolyte concentrations were observed between sexes. In addition, we assessed the liquid retention rate in the kidney to evaluate the extent of hydronephrosis and observed that 67% of male and 90% of female ROMK null mice were hydronephrotic mice. Urinary PGE(2) excretion was higher in both sexes of ROMK null mice: 1.35 vs. 1.10 ng/24 h in males and 2.90 vs. 0.87 ng/24 h in females. TXB(2) excretion was higher in female mice in both wild-type and ROMK null mice. The increments of urinary PGE(2) and TXB(2) were significantly higher in female null mice than males, 233.33% vs. 22.74% of PGE(2) and 85.67% vs. 20.36% of TXB(2). These data demonstrate a more severe Bartter phenotype in female ROMK null mice, and higher PGE(2) and TXB(2) production may be one of the mechanisms of this manifestation.
Community-Based Adaptation to Climate Change

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Journal of Graph Algorithms and Applications Kernelization for Maximum Leaf Spanning Tree with Positive Vertex Weights

In this paper we consider a natural generalization of the well-known Max Leaf Spanning Tree problem. In the generalized Weighted Max Leaf problem we get as input an undirected connected graph G, a rational number k not smaller than 1 and a weight function w : V → Q ≥1 on the vertices, and are asked whether a spanning tree T for G exists such that the combined weight of the leaves of T is at least k. We show that it is possible to transform an instance G, w, k of Weighted Max Leaf in polynomial time into an equivalent instance G , w , k such that |V (G)| ≤ 5.5k and k ≤ k. In the context of parameterized complexity this means that Weighted Max Leaf admits a kernel with 5.5k vertices. The analysis of the kernel size is based on a new extremal result which shows that every graph G = (V, E) that excludes some simple substructures always contains a spanning tree with at least |V |/5.5 leaves. We also prove that Weighted Max Leaf does not admit a polynomial-time factor O(n 1 2 −ε) or O(opt 1 3 −ε) approximation algorithm for any ε > 0 unless P = NP.
Stabilization of a Riderless Bicycle [Applications of Control]

The bicycle provides transportation for leisure, recreation, and travel between home and work, throughout the world, in big cities as well as in small villages, supporting human mobility for more than a century. Modeling, analysis, and control of bicycle dynamics has been an attractive area of research in the last century as well as in recent years. Bicycle dynamics has attracted the attention of the automatic control research community because of its peculiar features, such as, for example, the fact that it depends strongly on the bicycle speed and that, under certain conditions, it exhibits both open right-half plane poles and zeros, making the design of feedback controllers for either balancing the bicycle in the upright position or moving it along a predefined path a challenging problem. In this article, the LPV nature of the bicycle dynamics is exploited to design a control system that automatically balances a riderless bicycle in the upright position. More precisely, the problem is formulated as the design of an LPV state-feedback controller that guarantees stability of this two-wheeled vehicle when the speed varies within a given range and its derivative is bounded.
Tourists’ attitudes on tourism offer in north-western part of Montenegro

: The paper explores the attitudes of tourists visiting north-western part of Montenegro towards the significance and quality of certain elements within its tourist offer. The survey was conducted on the sample of 200 randomly selected tourists on the territory of all four constituent municipalities (Žabljak, Pljevlja, Plužine and Šavnik) in Montenegro. Comparative analysis of the attitudes was enabled by means of establishing the prevailing attitudes of tourists on significance and quality of tourist offer at the researched destination. The aim of the research was directed towards defining correlations between significance and quality of the selected elements within the tourist offer for north-western part of Montenegro based on the data analysis obtained by the questionnaire. This would mainly answer the question on correlation level between the significance and quality of the observed elements of the tourist offer. Moreover, by providing these answers, the research gains applicative importance since it renders the possibility of advancing the tourist offer of north-western part of Montenegro and highlights the most significant trends within the tourist offer of the researched area.
ALCAM Regulates Mediolateral Retinotopic Mapping in the Superior Colliculus

ALCAM [activated leukocyte cell adhesion molecule (BEN/SC-1/DM-GRASP)] is a transmembrane recognition molecule of the Ig superfamily (IgSF) containing five Ig domains (two V-type, three C2-type). Although broadly expressed in the nervous and immune systems, few of its developmental functions have been elucidated. Because ALCAM has been suggested to interact with the IgSF adhesion molecule L1, a determinant of retinocollicular mapping, we hypothesized that ALCAM might direct topographic targeting to the superior colliculus (SC) by serving as a substrate within the SC for L1 on incoming retinal ganglion cell (RGC) axons. ALCAM was expressed in the SC during RGC axon targeting and on RGC axons as they formed the optic nerve; however, it was downregulated distally on RGC axons as they entered the SC. Axon tracing with DiI revealed pronounced mistargeting of RGC axons from the temporal retina half of ALCAM null mice to abnormally lateral sites in the contralateral SC, in which these axons formed multiple ectopic termination zones. ALCAM null mutant axons were specifically compromised in medial orientation of interstitial branches, which is known to require the ankyrin binding function of L1. As a substrate, ALCAM–Fc protein promoted L1-dependent attachment of acutely dissociated retinal cells and an L1-expressing, ALCAM-negative cell line, consistent with an ALCAM–L1 heterophilic molecular interaction. Together, these results suggest a model in which ALCAM in the SC interacts with L1 on RGC axons to promote medial extension of RGC axon branches important for mediolateral axon targeting in the formation of retinocollicular maps.
Slovaks in Czechia - Czechs in Slovakia

The article gives an overview of the relations of Czechs and Slovaks and their languages under various points of view. The first part concentrates on an external view of the history of both nations, the migration between the two countries and demographic data, and the legal situation. It is shown that for most of history the political and cultural influence of Czech on Slovak was much stronger than the other way around. The types of migration also differed since Czechs went to Slovakia as teachers, clerks, etc., whereas the Slovak immigration to Czechia concentrated on workers. The legal situation of the two languages was asymmetric until 1938; real equality began only in 1968. Since the division of Czechoslovakia there are quite a lot of regulations on language use in Slovakia (though they concern Czech only to some extent) and so far no regulations in the Czech republic. The second part of the paper is concerned with the presence of written and spoken Czech texts in Slovakia and Slovak texts in Czechia. Written Czech texts have always played an important role in Slovakia and continue to do so in a diminished form today; Slovak texts came to Czechia mainly in the short period of equality within one state. Spoken Czech texts are present in Slovakia in the media, in films, etc., and the same is true to a lesser extent for Slovak texts in Czechia. Mixed texts, which were characteristic for the time between 1968 and 1992, have nearly disappeared, with the exception of information on packages, which is often written in both languages for economic reasons. The third part of the paper deals with linguistic issues such as the mutual intelligibility of the two languages and the real influence of Czech on Slovak and vice versa. The mutual intelligibility, which can be explained by the close relationship of the two languages, is nevertheless variable and to a great extent dependent on the experiences of the individual speaker. In everyday life members of each nation use thei
Initial Surgical Management of Ulcerative Colitis in the Biologic Era

BACKGROUND:The initial minimum operation for ulcerative colitis is a total abdominal colectomy. Healthy patients may undergo proctectomy at the same time; however, for ill patients, proctectomy is delayed. Since the introduction of biologic medications in 2005, ulcerative colitis medical management has changed dramatically. OBJECTIVE:We examined how operative management for ulcerative colitis has changed from the prebiologic to biologic eras. DESIGN:We conducted a retrospective review of data on patients with ulcerative colitis who were included in the Nationwide Inpatient Sample database. SETTINGS:This study was conducted at a single university. PATIENTS:A total of 1,547,852 patients with ulcerative colitis who were admitted to a US hospital from 1991 to 2011 were included in the study. MAIN OUTCOME MEASURES:We examined patients whose initial operation consisted of total abdominal colectomy without proctectomy versus a total proctocolectomy with or without a pouch. We also examined which operation was done at the time of the construction of an ileoanal pouch. Patients who underwent colectomy and pouch construction in the same hospitalization were compared with those who received pouch formation at a subsequent hospitalization. RESULTS:Ulcerative colitis–related admissions rose by 170% during the years examined, and the number of patients who required total abdominal colectomy increased by 44%. Total abdominal colectomy increased by 15%, as opposed to total proctocolectomy (p < 0.001). Pouch construction at a subsequent operation increased by 16% (p = 0.002). Since 2008, total abdominal colectomy has surpassed total proctocolectomy as the most common initial surgical intervention for ulcerative colitis. LIMITATIONS:The Nationwide Inpatient Sample is a retrospective database, and we were limited to examining the variables within it. CONCLUSIONS:Total abdominal colectomy is currently the most common initial operation for patients with ulcerative colitis, and an ileoanal pouch is more frequently constructed at a subsequent hospitalization. These trends coincide with the initiation of biologic treatments and may imply that patients are acutely ill at the time of initial operation. Alternately, there may be surgeon-perceived bias of increased surgical risk or a shift in care to specialized surgeons for pouch construction.
Hybrid Feature Selection Algorithm for Intrusion Detection System

Network security is a serious global concern. Usefulness Intrusion Detection Systems (IDS) are increasing incredibly in Information Security research using Soft computing techniques. In the previous researches having irrelevant and redundant features are recognized causes of increasing the processing speed of evaluating the known intrusive patterns. In addition, an efficient feature selection method eliminates dimension of data and reduce redundancy and ambiguity caused by none important attributes. Therefore, feature selection methods are well-known methods to overcome this problem. There are various approaches being utilized in intrusion detections, they are able to perform their method and relatively they are achieved with some improvements. This work is based on the enhancement of the highest Detection Rate (DR) algorithm which is Linear Genetic Programming (LGP) reducing the False Alarm Rate (FAR) incorporates with Bees Algorithm. Finally, Support Vector Machine (SVM) is one of the best candidate solutions to settle IDSs problems. In this study four sample dataset containing 4000 random records are excluded randomly from this dataset for training and testing purposes. Experimental results show that the LGP_BA method improves the accuracy and efficiency compared with the previous related research and the feature subcategory offered by LGP_BA gives a superior representation of data.
Megapixel imaging of (micro)nutrients in mature barley grains

Understanding the accumulation and distribution of essential nutrients in cereals is of primary importance for improving the nutritional quality of this staple food. While recent studies have improved the understanding of micronutrient loading into the barley grain, a detailed characterization of the distribution of micronutrients within the grain is still lacking. High-definition synchrotron X-ray fluorescence was used to investigate the distribution and association of essential elements in barley grain at the micro scale. Micronutrient distribution within the scutellum and the embryo was shown to be highly variable between elements in relation to various morphological features. In the rest of the grain, the distribution of some elements such as Cu and Zn was not limited to the aleurone layer but extended into the endosperm. This pattern of distribution was less marked in the case of Fe and, in particular, Mn. A significant difference in element distribution was also found between the ventral and dorsal part of the grains. The correlation between the elements was not consistent between and within tissues, indicating that the transport and storage of elements is highly regulated. The complexity of the spatial distribution and associations has important implications for improving the nutritional content of cereal crops such as barley.
Design an Intelligent Neural-Fuzzy Controller for Hybrid Motorcycle

The main propose of this article is to design an intelligent neural-fuzzy controller for hybrid motorcycle. A self-tuning PID tracking controller based on RBF neural network with Fuzzy current limiter is proposed to maneuver the motor and save some energy in hybrid mode. The outer motor control loop is designed to track down the speed fluctuations by Neural-PID controller. Besides, one inner loop is designed to limit the armature current whenever the power demand is diminished according to a set of Fuzzy rules. The proposed structure is put into tests by Matlab programming. Simulations confirm this RBF-PID controller with Fuzzy current limiter can save 23.5% energy for a tracking task.
Discriminative Training for Near-Synonym Substitution

Near-synonyms are useful knowledge resources for many natural language applications such as query expansion for information retrieval (IR) and paraphrasing for text generation. However, near-synonyms are not necessarily interchangeable in contexts due to their specific usage and syntactic constraints. Accordingly, it is worth to develop algorithms to verify whether near-synonyms do match the given contexts. In this paper, we consider the near-synonym substitution task as a classification task, where a classifier is trained for each near-synonym set to classify test examples into one of the near-synonyms in the set. We also propose the use of discriminative training to improve classifiers by distinguishing positive and negative features for each near-synonym. Experimental results show that the proposed method achieves higher accuracy than both pointwise mutual information (PMI) and n-gram-based methods that have been used in previous studies.
Host immune system strikes back

Autophagy-mediated major histocompatibility complex (MHC) class I presentation can follow either the conventional MHC class I pathway or a recently described vacuolar pathway. In the vacuolar pathway, protein degradation is effected by lysosomal proteases, peptide exchange takes place with recirculating MHC complexes and the newly formed peptide-MHC complexes reach the cell surface by the endocytic pathway. This pathway is independent of the proteasome and the transporter associated with antigen processing (TAP) complex, but generates the same, or a similar, epitope as that from the conventional MHC class I pathway. Here, we discuss different mechanisms by which autophagy mediates MHC class I-restricted antigen presentation, which is crucial to its role in the control of intracellular pathogens.