Miracle-dz/UniFAR-FTUs huggingface dataset:
Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.
Transforming Growth Factor Beta in the Central Nervous System

By definition, growth factors are polypeptides that modulate the proliferation of mammalian cells by acting on their receptors at low concentration. Based on similarities in their sequences and their receptors, growth factors can be divided into several superfamilies including platelet-derived growth factors, epidermal growth factors, insulin-like growth factors, the transforming growth factor-beta (TGF-β) family, fibroblast growth factors, nerve growth factors (neurotrophins), erythropoietin, and hemopoietic colony stimulating factors. Transforming growth factors were originally named by their capacity to induce oncogenic transformation in rat kidney fibroblasts (Roberts et al., 1981). Transforming growth factor alpha has a structure and action similar to epidermal growth factor (Wells, 1999) and is not a subject of the present chapter. The TGF-β superfamily includes products of over 25 distinct genes. Comparison of the deduced amino acid sequences led to the definition of several groups within the superfamily, such as TGF-βs, bone morphogenetic proteins, multiple isoforms of activins and inhibins, anti-Mullerian hormone, decapentaplegic protein in Drosophila, and Vg1 protein in Xenopus (Burt & Law, 1994). There are five TGF-β sequences including three mammalian isoforms (TGF-β1, β2 and β3), which are encoded by unique genes located on different chromosomes (Lawrence, 1996). Besides the regulation of cell growth and division, TGF-βs can control the proliferation, survival, differentiation, migration, or function of cells depending on the circumstance. The best established activities of TGF-βs are the following: they inhibit proliferation of most cells, but can stimulate the growth of some mesenchymal cells; they enhance the formation of extracellular matrix; and they exert immunosuppressive effects (Roberts, 1998). Based on their effects on cells of the immune system, TGF-βs can also be considered cytokines (Kiefer et al., 1995).
Texture Classification Using Wavelet Frame Representation Based Feature

Texture classification is an important component in image analysis and understanding. The wavelet, a multiresolution signal analysis technique, has been successfully applied to describe the texture. It is noticed that the wavelet transform modulus maximum and minimum can effectively characterize a signal. This paper employs the density of modulus maxima and the density of modulus minima of the wavelet frame representation as features for texture classification. In order to avoid the problem of curse of dimensionality, the feature selection algorithm, sequential forward floating selection (SFFS), is used to select feature subset. The experimental results on two benchmark databases indicate that the new feature is better than existing features based on modulus extrema, zero-crossings and local extrema
The Physics of Atom-Surface Interactions

A tutorial overview is given on interactions between atoms and surfaces that are mediated by the electromagnetic field. The emphasis is on dispersion (or van der Waals) forces and transitions induced by thermal fluctuations in the near field of a surface. Applications with cold atoms held in microscopic traps near surfaces ("atom chips") provide the experimental background for this theory lecture. We do not cover the chemical physics aspects that are relevant at distances comparable to the atomic scale, like adsorption and diffusion on surfaces, growth of nanostructures, or atomic beam diffraction from crystalline surfaces. These are covered by other lecturers.
Engineering of regulated stochastic cell fate determination

Both microbes and multicellular organisms actively regulate their cell fate determination to cope with changing environments or to ensure proper development. Here, we use synthetic biology approaches to engineer bistable gene networks to demonstrate that stochastic and permanent cell fate determination can be achieved through initializing gene regulatory networks (GRNs) at the boundary between dynamic attractors. We realize this experimentally by linking a synthetic GRN to a natural output of galactose metabolism regulation in yeast. Combining mathematical modeling and flow cytometry, we show that our engineered systems are bistable and that inherent gene expression stochasticity does not induce spontaneous state transitioning at steady state. Mathematical analysis predicts that stochastic cell fate determination in this case can only be realized when gene expression fluctuation occurs on or near attractor basin boundaries (the points of instability). Guided by numerical simulations, experiments are designed and performed with quantitatively diverse gene networks to test model predictions, which are verified by both flow cytometry and single-cell microscopy. By interfacing rationally designed synthetic GRNs with background gene regulation mechanisms, this work investigates intricate properties of networks that illuminate possible regulatory mechanisms for cell differentiation and development that can be initiated from points of instability.
A TIGHT UPPER LIMIT ON OSCILLATIONS IN THE AP STARǫ URSAE MAJORIS FROMWIRE PHOTOMETRY

Observations ofǫ UMa obtained with the star tracker on the Wide Field Infrared Explorer (WIRE) satellite during a month in mid-2000 are analyzed. This is one of the mos t precise photometry of an Ap star. The amplitude spectrum is used to set an upper limit of 75 parts per million f or the amplitude of stellar pulsations in this star unless it accidentally oscillates with a single mode at the s at llite orbit, its harmonics or their one day aliases. This is the tightest limit put on the amplitude of oscillations in a Ap star. As the rotation period of ǫ UMa is relatively short (5.1 d), it cannot be argued that the observations were made at a wrong rotational phase. Our results thus support the idea that some Ap stars do not pulsate at all. Subject headings: stars: individuals ( ǫ UMa)—stars: oscillations
The Emergent Structure of the Drosophila Wing - A Dynamic Model Generator

Drosophila melanogaster is a model organism in genetics thanks to the compactness of its genome and its relative simplicity. Recently, certain developmental patterns in Drosophila have been studied by mathematical models, with the aim of gaining deeper and quantitative insight into the morphogenesis of this insect. There is a need for accurate dynamical of the epithelial cell structure and organization within the fly wing, to further the understanding of a phenomenon known as planar cell polarity. The present study tackles the problem of retrieving such a salient structure using classical tools of dynamical system theory embedded with network and graph concepts. On the one hand the goal is to provide a visual detection and representation of the cell packaging that is accurate and fine. Particular care is also put in obtaining a model of this structure, whose main features are the compactness and simplicity.
How to (crowd-)fund and manage the (user-)innovation: the case of Big Buck Bunny

It seems a non-sense for an economist that a producer assembles, manages and pays a temporary team of experts to create a product that will be freely available for customers. It seems a non-sense that professional artists and developers decide to work underpaid. It seems a further non-sense that customers decide to pre-order (or order) and pay for a DVD copy of this movie despite they know that it will be (or it is already) freely available (by download) and freely recordable. To understand why it happens, we conducted a case study focused on the production of the movie called Big Buck Bunny. Than, using Creative Commons and User-Innovation theory we propose a model that explains how a producer can manage Intellectual Propriety Right and community of users to identify needs and absorb innovations.
Witchcraft and supernatural harm: navigating spiritual ethics in political science research

This article addresses a significant ethical oversight I am responsible for in my doctoral research program: the failure to account for and comprehensively prevent the threat of spiritual harm for my research assistants in Ghana and Cameroon. In this work, I discuss spiritual care as a major lacunae of research methodology considerations and ethics procedures in relation to my own work in the field of political science. Through an analysis of my methods and ethics preparations and subsequent fieldwork, I hope to demonstrate how epistemological and structural biases I enacted are also embedded in academic processes and how these helped facilitate this oversight. I argue that a modernist approach to research and ethics can lead researchers, such as myself, to overlook important considerations regarding spiritual care.
Sleep deprivation and obesity in shift workers in southern Brazil

Abstract Objective The objective of our study was to explore the association between sleep deprivation and obesity among shift workers. Design A cross-sectional study was conducted. Obesity was defined as BMI ≥30 kg/m2. Time of sleep was categorized as: >5 h of continuous sleep/d; ≤5 h of continuous sleep/d with some additional rest (sleep deprivation level I); and ≤5 h of continuous sleep/d without any additional rest (sleep deprivation level II). Sociodemographic, parental and behavioural variables were evaluated by means of a standardized pre-tested questionnaire. Potential confounding factors were controlled for in the multivariable model. Setting A poultry-processing plant in southern Brazil. Subjects Nine hundred and five shift workers (63 % female). Results Obesity was more prevalent in the participants who were female, aged 40 years and older, who had less schooling and reported excess weight in both parents. Sleep deprivation levels I and II were associated with increased income, number of meals consumed throughout the day and nightshift work. All of the workers who exhibited a degree of sleep deprivation worked the night shift. After controlling for potential confounding factors, the prevalence ratios of obesity were 1·4 (95 % CI 0·8, 2·2) and 4·4 (95 % CI 2·4, 8·0) in the workers with sleep deprivation levels I and II, respectively, compared with the reference group. Conclusions These results show a strong association between sleep deprivation and obesity in shift workers and that sleep deprivation may be a direct consequence of working at night.
Dual-Arm Robotic Needle Insertion With Active Tissue Deformation for Autonomous Suturing

A major issue for needle insertion into soft tissue during suturing is the induced tissue deformation that hinders the minimization of tip-target positioning error. In this letter, we present a new robot control framework to solve target deviation by integrating active deformation control. We characterize the motion behavior of the desired target under needle-tissue interaction by introducing the needle-induced deformation matrix. Note that the modeling does not require the exact knowledge of tissue or needle insertion properties. The unknown parameters are online updated during the insertion procedure by an adaptive estimator via sensor-based measurement. A closed-loop controller is then proposed for dual-arm robotic execution upon image guidance. The dual-arm control aims to regulate a feature vector concerning the tip-target alignment to ensure target reachability. The feasibility of the proposed algorithm is studied via simulations and experiments on different biological tissues to simulate robotic minimally-invasive suturing using the da Vinci Research Kit as the control platform.
Effect of preoperative multimedia information on perioperative anxiety in patients undergoing procedures under regional anaesthesia.

BACKGROUND Provision of preoperative information can alleviate patients' anxiety. However, the ideal method of delivering this information is unknown. Video information has been shown to reduce patients' anxiety, although little is known regarding the effect of preoperative multimedia information on anxiety in patients undergoing regional anaesthesia. METHODS We randomized 110 patients undergoing upper or lower limb surgery under regional anaesthesia into the study and control groups. The study group watched a short film (created by the authors) depicting the patient's in-hospital journey including either a spinal anaesthetic or a brachial plexus block. Patients' anxiety was assessed before and after the film and 1 h before and within 8 h after their operation, using the Spielberger state trait anxiety inventory and a visual analogue scale. RESULTS There was no difference in state and trait anxiety between the two groups at enrollment. Women had higher baseline state and trait anxiety than men (P=0.02). Patients in the control group experienced an increase in state anxiety immediately before surgery (P<0.001), and patients in the film group were less anxious before operation than those in the control group (P=0.04). After operation, there was a decrease in state anxiety from baseline in both groups, but patients in the film group were less anxious than the control group (P=0.005). CONCLUSIONS Preoperative multimedia information reduces the anxiety of patients undergoing surgery under regional anaesthesia. This type of information is easily delivered and can benefit many patients.
Preparation of ApoA-I – and ApoA-IMilano – Containing Phospholipid Particles

Oxidation of LDL is associated with degradation of phosphatidylcholine into platelet-activating factor (PAF)–like phospholipids and lysophosphatidylcholine (LPC). Exposure of cultured human smooth muscle cells to PAF and LPC in a concentration of 25 mmol/L was found to result in complete cell death, as assessed by the MTT cytotoxicity assay and cell counting. Addition of 50 mg/mL apolipoprotein A-I– and apolipoprotein A-IMilano–containing phospholipid particles completely inhibited this cytotoxicity. Phospholipid complexes alone were almost as effective, whereas free apolipoprotein A-IMilano and albumin were without effect, suggesting that the effect was phospholipid dependent. Experiments using [C]LPC demonstrated that apolipoprotein A-I– and apolipoprotein A-IMilano–containing phospholipid particles effectively bind LPC. The results show that HDL-like phospholipid particles effectively inhibit the toxic effect of phospholipids and other lipid-soluble factors. The ability of HDL to inhibit the proinflammatory and toxic effects of phospholipids generated during oxidation of LDL may be responsible for part of the antiatherogenic properties of HDL. (Arterioscler Thromb Vasc Biol. 1998;18:13-19.)
DECISION TREES DO NOT GENERALIZE TO NEW VARIATIONS

The family of decision tree learning algorithms is among the most widespread and studied. Motivated by the desire to develop learning algorithms that can generalize when learning highly varying functions such as those presumably needed to achieve artificial intelligence, we study some theoretical limitations of decision trees. We demonstrate formally that they can be seriously hurt by the curse of dimensionality in a sense that is a bit different from other nonparametric statistical methods, but most importantly, that they cannot generalize to variations not seen in the training set. This is because a decision tree creates a partition of the input space and needs at least one example in each of the regions associated with a leaf to make a sensible prediction in that region. A better understanding of the fundamental reasons for this limitation suggests that one should use forests or even deeper architectures instead of trees, which provide a form of distributed representation and can generalize to variations not encountered in the training data.
Secretory microRNAs as a versatile communication tool

The physiological role of microRNAs (miRNAs) is widely appreciated as a fine-tuner to post-transcriptionally regulate the expression of multiple genes in the cells of origin. Here, we highlight two significant characteristics of miRNAs: (1) they are secreted from the producing cells, and (2) they can deliver the gene silencing signals between living cells in vitro and in vivo. The circulation of miRNAs in human body fluids can be provided with a logical explanation by our discovery that the release of miRNAs is actively controlled through a ceramide-dependent machinery associated with exosome secretion. This finding can contribute to the development of circulating miRNAs as diagnostic biomarkers for a variety of diseases. We also demonstrated that secretory miR-16 was transferred into prostate cancer PC-3M cells subcutaneously xenografted in nude mice, resulting in the suppression of its target gene. This result suggests that faithfully to their primary role, secretory miRNAs can function as a translational inhibitor in recipient cells as well. In conclusion, miRNAs are liberated from their incipient cells, whereby they can exert their full potentials as a silence master of gene expressions.
The Topology-aware Ant Colony Optimization algorithm based on Forest Growth for IPTV live service

IPTV live service has strict requirements of QoS. IP Multicast is an effective technology, but the limited availability of IP Multicast in the Internet motives researchers to apply application-layer multicast to implement IPTV live service. In application-layer multicast, applications arrange themselves as a logical tree. The application-layer multicast for IPTV live service can be modeled as the minimum diameter, degree-bounded spanning tree (MDDBST) problem. However, application-layer multicast is a Peer-to-Peer (P2P) style. Applications don't have information of the underlying network topology and select distant peers, which generates much unnecessary traffic. Thus in the application-layer multicast for IPTV live service application-layer traffic optimization (ALTO) should be also considered. This paper proposes a Topology-aware Ant Colony Optimization algorithm based on Forest Growth (TACOF) which is mesh-first solution to solve the MDDBST problem considering ALTO. The results of a series of simulations show the effectiveness of the proposed solution.
Impact de la détection de la parole pour différentes tâches de traitement automatique de la parole

Dans cet article, nous proposons de comparer plusieurs systemes de detection de la parole et leurs impacts sur deux tâches du traitement de la parole : la Segmentation et le Regroupement de Locuteurs (SRL) et la Reconnaissance Automatique de la Parole (RAP). Des systemes a base de mixtures de Gaussiennes (GMM), de reseaux de neurones profonds (DNN) et recurrents (RNN) sont compares, ainsi que l'utilisation d'un systeme de RAP pour detecter la frontiere des mots. Les experiences presentees ici ont ete conduites sur les corpus issus des campagnes d'evaluation ESTER1 et 2, ETAPE et REPERE1, constitues d'emissions de radio et de television francaise.
Teaching Thinking and Writing for a New Century

How can we design writing instruction to help students develop the traits needed to function in a competitive high-performance work environment? Students will need to develop critical, independent thinking skills, the ability to work with others, and the capacity to understand multiple perspectives. Johannessen recommends instructional methods to meet these goals—including collaborative workgroups and inquiry—and includes examples that illustrate each principle.
DISCOVERY OF NEW INTERACTING SUPERNOVA REMNANTS IN THE INNER GALAXY

OH(1720 MHz) masers are excellent signposts of interaction between supernova remnants (SNRs) and molecular clouds. Using the Green Bank Telescope and Very Large Array we have surveyed 75 SNRs and six candidates for masers. Four SNRs are detected with OH masers: G5.4-1.2, G5.7-0.0, G8.7-0.1, and G9.7-0.0. Two SNRs, G5.7-0.0 and G8.7-0.1, have TeV γ-ray counterparts which may indicate a local cosmic ray enhancement. It has been noted that maser-emitting (ME) SNRs are preferentially distributed in the molecular ring and nuclear disk. We use the present and existing surveys to demonstrate that masers are strongly confined to within |l| ⩽ 50° at a rate of 15% of the total SNR population. All new detections are within 10° Galactic longitude emphasizing this trend. Additionally, a substantial number of SNR masers have peak fluxes at or below the detection threshold of existing surveys. This calls into question whether maser surveys of Galactic SNRs can be considered complete and how many ME remnants remain to be detected in the Galaxy.
Processing of Signals Recorded Through Smart Devices: Sleep-Quality Assessment

In this paper, we discuss the possibility of performing a sleep evaluation from signals, which are not usually used for this purpose. In particular, we take into consideration the heart rate variability (HRV) and respiratory signals for automatic sleep staging, arousals detection, and apnea recognition. This is particularly useful for wearable or textile devices that could be employed for home monitoring of sleep. The HRV and the respiration were analyzed in the frequency domain, and the statistics on the spectral and cross-spectral parameters put into evidence the possibility of a sleep evaluation on their basis. Comparison with traditional polysomnography (PSG) revealed a classification accuracy of 89.9% in rapid eye movement (REM) non-REM sleep separation and an accuracy of 88% for sleep apnea detection. Additional information can be achieved from the number of microarousals recognized in correspondence of typical modifications in the HRV signal. The obtained results support the idea of automatic sleep evaluation and monitoring through signals that are not traditionally used in clinical PSG, but can be easily recorded at home through wearable devices (for example, a sensorized T-shirt) or systems integrated into the environment (a sensorized bed). This is a first step for the development of systems for sleep screening on large populations that can constitute a complement for the traditional clinical evaluation.