Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Properties of Gene Regulatory Networks: Definitions and Connections

The study of gene regulatory networks is a significant problem in systems biology. Of particular interest is the problem of determining the unknown or hidden higher level regulatory signals by using gene expression data from DNA microarray experiments. Several studies in this area have demonstrated the critical aspect of the network structure in tackling the network modelling problem. Structural analysis of systems has proved useful in a number of contexts, viz., observability, controllability, fault diagnosis, sparse matrix computations etc. In this contribution, we formally define structural properties that are relevant to gene regulatory networks. We explore the structural implications of certain quantitative methods and explain completely the connections between the identifiability conditions and structural criteria of observability and distinguishability. We illustrate these concepts in case studies using representative biologically motivated network examples. The present work bridges the quantitative modelling methods with those based on the structural analysis.
Diversity of the CD8+ T Cell Repertoire Elicited against an Immunodominant Epitope Does Not Depend on the Context of Infection

The diversity of the pathogen-specific T cell repertoire is believed to be important in allowing recognition of different pathogen epitopes and their variants and thereby reducing the opportunities for mutation-driven pathogen escape. However, the extent to which the TCR repertoire can be manipulated by different vaccine strategies so as to obtain broad diversity and optimal protection is incompletely understood. We have investigated the influence of the infectious/inflammatory context on the TCR diversity of the CD8+ T cell response specific for the immunodominant epitope in C57BL/6 mice, derived from glycoprotein B of HSV-1. To that effect, we compared TCR V segment utilization, CDR3 length, and sequence diversity of the response to natural HSV-1 infection with those elicited by either Listeria monocytogenes or vaccinia virus expressing the immunodominant epitope in C57BL/6 mice. We demonstrate that although the type of infection in which the epitope was encountered can influence the magnitude of the CD8+ T cell responses, TCR β-chain repertoires did not significantly differ among the three infections. These results suggest that widely different live vaccine vectors may have little impact upon the diversity of the induced CTL response, which has important implications for the design of live CTL vaccine strategies against acute and chronic infections.
Electrical Stimulation Influences Satellite Cell Proliferation and Apoptosis in Unloading-Induced Muscle Atrophy in Mice

Muscle atrophy caused by disuse is accompanied by adverse physiological and functional consequences. Satellite cells are the primary source of skeletal muscle regeneration. Satellite cell dysfunction, as a result of impaired proliferative potential and/or increased apoptosis, is thought to be one of the causes contributing to the decreased muscle regeneration capacity in atrophy. We have previously shown that electrical stimulation improved satellite cell dysfunction. Here we test whether electrical stimulation can also enhance satellite cell proliferative potential as well as suppress apoptotic cell death in disuse-induced muscle atrophy. Eight-week-old male BALB/c mice were subjected to a 14-day hindlimb unloading procedure. During that period, one limb (HU-ES) received electrical stimulation (frequency: 20 Hz; duration: 3 h, twice daily) while the contralateral limb served as control (HU). Immunohistochemistry and western blotting techniques were used to characterize specific proteins in cell proliferation and apoptosis. The HU-ES soleus muscles showed significant improvement in muscle mass, cross-sectional area, and peak tetanic force relative to the HU limb (p<0.05). The satellite cell proliferative activity as detected within the BrdU+/Pax7+ population was significantly higher (p<0.05). The apoptotic myonuclei (detected by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling) and the apoptotic satellite cells (detected by cleaved Poly [ADP-ribose] polymerase co-labeled with Pax7) were reduced (p<0.05) in the HU-ES limb. Furthermore the apoptosis-inducing factor and cleaved caspase-3 were down-regulated while the anti-apoptotic Bcl-2 protein was up-regulated (p<0.05), in the HU-ES limb. These findings suggest that the electrical stimulation paradigm provides an effective stimulus to rescue the loss of myonuclei and satellite cells in disuse muscle atrophy, thus maintaining a viable satellite cell pool for subsequent muscle regeneration. Optimization of stimulation parameters may enhance the outcome of the intervention.
Splitter Placement Problem on Directed Fiber Trees

Wavelength division multiplexing technique can greatly increase the bandwidth of all-optical networks without the reconstruction of physical infrastructure. Optical power splitters can reduce the number of required wavelengths for multicast requests by dividing the incoming optical signal into multiple outcoming signals with equal optical power. This paper considered the problem of how to reduce the number of splitters on a directed fiber tree and not to decrease the quality of service too much, compared against the case that each node on the tree is equipped with one splitter. The proposed splitter placing strategy showed satisfying performance in the experiments.
Postnatal changes in the mammalian respiratory network as revealed by the transverse brainstem slice of mice.

1. Spontaneous rhythmic activity in hypoglossal (XII) rootlets is generated at all postnatal stages from postnatal day (P) 0 to P22 in the transverse brainstem slice of mice containing the pre‐Bötzinger complex (PBC). The PBC is known to be a region essential for respiratory rhythm generation. It contains neurones generating periodic bursts that occur in synchrony with rhythmic XII activity. This synchrony indicates that the rhythmic PBC activity generated by the transverse slice is the central respiratory rhythm. 2. The strength of coupling between XII bursts and PBC bursts decreased during early postnatal development. In younger mice (P0‐4) each burst in XII rootlets corresponded to one burst in the PBC. In older mice (P5‐18) one burst in XII rootlets occurred only every third to fourth burst in PBC neurones. 3. Cycle length and burst duration of rhythmic XII activity did not change significantly during the first three postnatal weeks. However, the pattern of XII bursts changed from decrementing (P0‐7) to bell shaped (P8‐18) while the rate of rise of XII bursts decreased significantly. 4. The rate of rise of rhythmic depolarizations in neurones of the PBC discharging in phase with XII bursts (‘inspiratory neurones’) decreased with postnatal development. During interburst intervals, membrane potentials of neurones of older mice (P6‐18) were characterized by waves of synaptic input that were not observed in neonatal animals (P0‐5). 5. Blockade of glycine receptors by strychnine increased the frequency of rhythmic XII activity in neonatal and older mice (P0‐22). Although in expiratory PBC neurones glycinergic transmission was blocked at 10 microM strychnine, in inspiratory PBC neurones and XII rootlets even higher concentrations of up to 50 microM strychnine failed to abolish rhythmic activity.
Opened Pins Recommendation System to promote tourism sector in Chiang Rai Thailand

Internet and mobile technologies have significantly influenced the people in this century. This paper investigates on how to promote the local tourism sector that matches with the changing customer behavior of tourists in ICTs generations. The study shows the ICTs system that is designed for sharing and accessing the points of interest or tourist destination for local tourism and business sector, known as the "Opened Pins Recommendation System". The results show that there are positive user's satisfactions of the system design and a prototyping on the tourist users and local tourism sector.
Twitter truths: Authenticating analysis of information credibility

With the growth of internet, life of people have also changed. People share a huge amount of information on social media, thus increasing the amount of information at a very fast rate. This has made Social Data Analytics an important area of research. Analyzing the opinions or sentiments of people on the data shared can serve as a great means for making decisions in various domains. Also, not each and every data present on social media is correct as various people try to spread rumors, mostly just for fun. Due to this, it is required that there exist methods using which people can easily check information credibility of data concerning social media. The research carried out till now have mainly focused on tracking and modeling sentiments of public. This paper proposes a method for assessing the credibility of information by emulating the methods of topic and opinion classifications, primarily focusing on Twitter data. Improved Latent Dirichlet Allocation (LDA) algorithm has been used for classification of topics within the tweets and semi-supervised method (SVM) has been used for sentiment analysis. Finally, majority decision by comparing the number of contrastive opinions about a topic is performed, for credibility analysis. Though, English and Hinglish languages have been used here, however, this method can be adapted easily to other languages since Twitter API allows specifying the language of the retrieved posts.
Feed forward pre-training for recurrent neural network language models

The recurrent neural network language model (RNNLM) has been demonstrated to consistently reduce perplexities and automatic speech recognition (ASR) word error rates across a variety of domains. In this paper we propose a pre-training method for the RNNLM, by sharing the output weights of the feed forward neural network language model (NNLM) with the RNNLM. This is accomplished by first fine-tuning the weights of the NNLM, which are then used to initialise the output weights of an RNNLM with the same number of hidden units. We have carried out text-based experiments on the Penn Treebank Wall Street Journal data, and ASR experiments on the TED talks data used in the International Workshop on Spoken Language Translation (IWSLT) evaluation campaigns. Across the experiments, we observe small improvements in perplexity and ASR word error rate.
The stability of buoyant bubbles in the atmospheres of galaxy clusters

The buoyant rise of hot plasma bubbles inflated by active galactic nuclei outflows in galaxy clusters can heat the cluster gas and thereby compensate radiative energy losses of this material. Numerical simulations of this effect often show the complete disruption of the bubbles followed by the mixing of the bubble material with the surrounding cluster gas due to fluid instabilities on the bubble surface. This prediction is inconsistent with the observations of apparently coherent bubble structures in clusters. We derive a general description in the linear regime of the growth of instabilities on the surface between two fluids under the influence of a gravitational field, viscosity, surface tension provided by a magnetic field and relative motion of the two fluids with respect to each other. We demonstrate that Kelvin–Helmholtz instabilities are always suppressed, if the fluids are viscous. They are also suppressed in the inviscid case for fluids of very different mass densities. We show that the effects of shear viscosity as well as a magnetic field in the cluster gas can prevent the growth of Rayleigh–Taylor instabilities on relevant scalelengths. Rayleigh–Taylor instabilities on parsec scales are suppressed even if the kinematic viscosity of the cluster gas is reduced by two orders of magnitude compared to the value given by Spitzer for a fully ionized, unmagnetized gas. Similarly, magnetic fields exceeding a few ? G result in an effective surface tension preventing the disruption of bubbles. For more massive clusters, instabilities on the bubble surface grow faster. This may explain the absence of thermal gas in the north-west bubble observed in the Perseus cluster compared to the apparently more disrupted bubbles in the Virgo cluster.
Sulindac Enhances the Killing of Cancer Cells Exposed to Oxidative Stress

Background Sulindac is an FDA-approved non-steroidal anti-inflammatory drug (NSAID) that affects prostaglandin production by inhibiting cyclooxygenases (COX) 1 and 2. Sulindac has also been of interest for more than decade as a chemopreventive for adenomatous colorectal polyps and colon cancer. Principal Findings Pretreatment of human colon and lung cancer cells with sulindac enhances killing by an oxidizing agent such as tert-butyl hydroperoxide (TBHP) or hydrogen peroxide. This effect does not involve cyclooxygenase (COX) inhibition. However, under the conditions used, there is a significant increase in reactive oxygen species (ROS) within the cancer cells and a loss of mitochondrial membrane potential, suggesting that cell death is due to apoptosis, which was confirmed by Tunel assay. In contrast, this enhanced killing was not observed with normal lung or colon cells. Significance These results indicate that normal and cancer cells handle oxidative stress in different ways and sulindac can enhance this difference. The combination of sulindac and an oxidizing agent could have therapeutic value.
Fine-Tuning of a Protected Area Effectiveness Evaluation Tool: Implementation on Two Emblematic Spanish National Parks

As global biodiversity trends worsen, protected area (PA) environmental effectiveness needs to be assessed to identify strengths and areas to improve. Through a participatory process including PA managers and scientists, we refined the System for the Integrated Assessment of Protected Areas (SIAPA), in order to increase its legitimacy, credibility and salience to end users in Spain. Then, we tested the optimised version of the SIAPA on two emblematic Spanish national parks (NPs): Ordesa y Monte Perdido NP (Ordesa NP) and Sierra de Guadarrama NP (Guadarrama NP). PA managers and scientists largely coincided in the ratings of SIAPA’s indicators and indices. Collaboration with Ordesa NP’s managers was regular, allowing a nearly complete evaluation of the NP. However, greater collaboration between PA managers and scientists remains a priority in Guadarrama NP. Results show that potential effectiveness is moderate for Ordesa NP and low for Guadarrama NP, according to the indicators that could be evaluated. For Ordesa NP, lack of data on focal habitats and other focal features determined a deficient valuation of its conservation state, although the remaining indicators in that category showed adequate or moderate values. The compilation of those data should be overriding in the NP. In contrast, only climate change posed a serious threat in that NP. The social perception and valuation of both NPs was good, suggesting broad support from local populations and eased management.
Classroom action research using student team achievement division approach case study: business process modelling course on bpmn subtopics

Business Process Modeling is a subject that becomes the basis of student of information systems in designing business processes. The purpose of this course is to provide an overview of the analysis of business processes in a specific case study. The results for the odd semester of last year for the Business Process Modeling course showed the results that students’ understanding was not satisfactory towards this subject with conventional learning methods. This study designs a learning method with Student Team-Achievement Division (STAD) approach that aims to improve students’ understanding of Business Process Modeling Notation (BPMN), both basic and advanced modeling that support Final Assessment and to determine the effect of STAD method on the final grade of Final Assessment in this course. This research stage consists of two cycles. The first cycle activities consist of planning, class action, observation, and analysis and reflection. Activity in cycle two is based on reflection from cycle one divided into redesign, implementation and observation, and reflection. Based on the two cycles that have been done, the positive change is indicated by the increase in the grade of Post Test 2 on Post Test 1. In all study classes there was an increase of 13.12% in class A, 8.01% in class B and 4.82% at class B. This study confirmed that STAD learning method can increase the average grade of class test, increase student participation in learning process such as listening, discussing, asking and expressing opinion. In addition, STAD method is also able to increase the sense of responsibility, cooperation, socialization.
Rapid desensitization converts prolonged glutamate release into a transient EPSC at ribbon synapses between retinal bipolar and amacrine cells

The mechanisms underlying the conversion of prolonged glutamate release from ribbon synapses in bipolar cells to sustained and transient excitatory postsynaptic responses in identified retinal amacrine cells were studied in tiger salamander (Ambystoma tigrinum) retina. A retina slice preparation with whole cell patch recording techniques under voltage‐ and current‐clamp conditions was used to assay the electrical properties of bipolar and amacrine cells. Amacrine cells were categorized into two basic forms: (i) transient amacrine cells that respond to a step of light with a burst of spikes only at the transitions of the step; and (ii) sustained amacrine cells that respond with continuous spiking during the entire light step. The two cell types each had a characteristic morphology: transient amacrine cells possessed wide dendritic fields (χ = 375 μm), while sustained cells had much more narrowly confined dendritic fields (χ = 85 μm). Whole cell voltage‐gated currents of the transient and sustained cell types were not significantly different. Both cell types had spikes that were sensitive to tetradotoxin (TTX, 0.3 μm) with voltage deflections of up to 100 mV. Light‐evoked excitatory synaptic currents relaxed rapidly in transient neurons (τ1/2 = 100 ms) and more slowly in sustained neurons (τ1/2 = 1.2 s). EPSCs in both cells reversed near 0 mV. Rapid application of glutamate or kainate elicited rapidly desensitizing ionic currents (τ1/2 = 85 ms) followed by a slowly desensitizing component. Cyclothiazide, a drug that eliminates rapid desensitization, lengthened the time course of the glutamate gated current from τ1/2 = 85 ms to about 3 s, and the relaxation kinetics of the glutamatergic EPSC from τ1/2 = 85 ms to about 1.0 s. These data suggest that a key determinant in forming transient versus sustained responses in amacrine cells of vertebrate retina is the differences in their excitatory, glutamatergic synaptic inputs, and that rapid desensitization of glutamate receptors plays a role in converting the presynaptic signal associated with sustained glutamate release into a postsynaptic, transient signal at the ribbon synapse.
Working Papers in Economics and Statistics Group polarization in the team dictator game reconsidered

While most papers on team decision-making find that teams behave more selfishly, less trustingly and less altruistically than individuals, Cason and Mui (1997) report that teams are more altruistic than individuals in a dictator game. Using a within-subjects design we re-examine group polarization by letting subjects make individual as well as team decisions in an experimental dictator game. In our experiment teams are more selfish than individuals, and the most selfish team member has the strongest influence on team decisions. Various explanations for the different findings in Cason and Mui (1997) and in our paper are discussed. JEL classification: C72, C91, C92, D70
Genes of the Ecdysone Biosynthesis Pathway Are Regulated by the dATAC Histone Acetyltransferase Complex in Drosophila

ABSTRACT Uncovering mechanisms that regulate ecdysone production is an important step toward understanding the regulation of insect metamorphosis and processes in steroid-related pathologies. We report here the transcriptome analysis of DrosophilamelanogasterdAda2a and dAda3 mutants, in which subunits of the ATAC acetyltransferase complex are affected. In agreement with the fact that these mutations lead to lethality at the start of metamorphosis, both the ecdysone levels and the ecdysone receptor binding to polytene chromosomes are reduced in these flies. The cytochrome genes (spookier, phantom, disembodied, and shadow) involved in steroid conversion in the ring gland are downregulated, while the gene shade, which is involved in converting ecdysone into its active form in the periphery, is upregulated in these dATAC subunit mutants. Moreover, driven expression of dAda3 at the site of ecdysone synthesis partially rescues dAda3 mutants. Mutants of dAda2b, a subunit of the dSAGA histone acetyltransferase complex, do not share phenotype characteristics and RNA profile alterations with dAda2a mutants, indicating that the ecdysone biosynthesis genes are regulated by dATAC, but not by dSAGA. Thus, we provide one of the first examples of the coordinated regulation of a functionally linked set of genes by the metazoan-specific ATAC complex.
Cilostazol, an Inhibitor of Type 3 Phosphodiesterase, Produces Endothelium-Independent Vasodilation in Pressurized Rabbit Cerebral Penetrating Arterioles

We investigated the effects of cilostazol, a potent inhibitor of cGMP-inhibited cAMP phosphodiesterase, on mechanical activity of isolated pressurized rabbit cerebral penetrating arterioles with special reference to the function of the endothelium. Both cilostazol and milrinone, another inhibitor of cAMP phosphodiesterase, produced vasodilation of the cerebral penetrating arterioles in a dose-dependent manner. Pretreatment with selective inhibitors of cyclooxygenase or nitric oxide synthase, or chemical denudation of the endothelial cells caused no significant effect on the cilostazol-mediated vasodilation of the cerebral arterioles. A selective large-conductance calcium-activated potassium channel inhibitor, iberiotoxin, and a selective protein kinase A inhibitor, H-89, caused no significant effect on the cilostazol-mediated vasodilation. In the cerebral arterioles, low concentration (10–6M) of cilostazol or milrinone caused a significant shift of the dose-vasodilatory response curve for adenosine to the left. These findings suggest that cilostazol produces vasodilation independent of the presence of the endothelium or activation of endogenous vasodilative prostaglandins, nitric oxide, calcium-activated potassium channel and protein kinase A. In conclusion, the vasodilator action of cilostazol may, in part, contribute to the beneficial effect of preventing lacunar cerebral infarction in patients with functional damage of the endothelium in cerebral penetrating arterioles.