Miracle-dz/UniFAR-FTUs huggingface dataset:
Retinoic acid regulates endothelial cell proliferation during vasculogenesis

A dietary deficiency of vitamin A is associated with cardiovascular abnormalities in avian and murine systems. Retinoic acid (RA) is the active metabolite of vitamin A and whether it directly regulates mammalian blood vessel formation has not been determined and is investigated herein. We used mice rendered RA-deficient via targeted deletion of retinaldehyde dehydrogenase 2 (Raldh2-/-), the enzyme required to produce active RA in the embryo. Histological examination at E8.0-8.5, prior to cardiac function and systemic blood circulation, revealed that capillary plexi formed in Raldh2-/- yolk sacs and embryos, but were dilated, and not appropriately remodeled or patterned. Raldh2-/- endothelial cells exhibited significantly increased expression of phosphohistone 3 and decreased expression of p21 and p27, suggesting that RA is required to control endothelial cell cycle progression during early vascular development. Uncontrolled endothelial cell growth, in Raldh2-/- mutants, was associated with decreased endothelial cell maturation, disrupted vascular plexus remodeling and lack of later stages of vessel assembly, including mural cell differentiation. Maternally administrated RA restored endothelial cell cycle control and vascular patterning. Thus, these data indicate that RA plays a crucial role in mammalian vascular development; it is required to control endothelial cell proliferation and vascular remodeling during vasculogenesis.
Abnormal Striatal Dopamine Transmission in Schizophrenia

Despite numerous revisions and reformulations, dopamine (DA) hypothesis of schizophrenia remains a pivotal neurochemical hypothesis of this illness. The aim of this review is to expose and discuss findings from positron emission tomography (PET) or single-photon-emission computed tomography (SPECT) studies investigating DA function in the striatum of medicated, drug-naïve or drug-free patients with schizophrenia and in individuals at risk compared with healthy volunteers. DA function was studied at several levels: i) at a presynaptic level where neuroimaging studies investigating DOPA uptake capacity clearly show an increase of DA synthesis in patients with schizophrenia; ii) at a synaptic level where neuroimaging studies investigating dopamine transporter availability (DAT) does not bring any evidence of dysfunction; iii) and finally, neuroimaging studies investigating DA receptor density show a mild increase of D2 receptor density in basic condition and, an hyperreactivity of DA system in dynamic condition. These results are discussed regarding laterality, sub-regions of striatum and implications for the at-risk population. Striatal DA abnormalities are now clearly demonstrated in patients with schizophrenia and at risk population and could constitute an endophenotype of schizophrenia. Subtle sub-clinical striatal DA abnormalities in at risk population could be a biomarker of transition from a vulnerability state to the expression of frank psychosis.
Genetic reinforcement learning for cooperative traffic signal control

Optimization of a group of traffic signals over an area is a large, multi-agent-type real-time planning problem without a precise reference model being given. To do this planning, each signal should learn not only to acquire its control plans individually through reinforcement learning, but also to cooperate with other signals. These two objectives-distributed learning of agents and cooperation among agents-conflict with each other, and a method that blends these two objectives together is required. In the method proposed in this paper, these two objectives correspond to localized reinforcement learning and global combinatorial optimization, respectively, and the method thus achieves cooperation in the long term without bothering with autonomy. The outline of the idea is as follows: each agent performs reinforcement learning and reports its cumulative performance evaluation, and combinatorial optimization is simultaneously carried out to find appropriate parameters for long-term learning that maximize the total profit of the signals (agents). <<ETX>>
Essential dynamics of DNA containing a cis.syn cyclobutane thymine dimer lesion.

Conformational properties of a UV-damaged DNA decamer containing a cis.syn cyclobutane thymine dimer (PD) have been investigated by molecular dynamics (MD) simulations. Results from MD simulations of the damaged decamer DNA show a kink of approximately 21.7 degrees at the PD damaged site and a disruption of H bonding between the 5'-thymine of the PD and its complementary adenine. However, no extra-helical flipping of the 3'-adenine complementary to the PD was observed. Comparison to two undamaged DNA decamers, one with the same sequence and the other with an AT replacing the TT sequence, indicates that these properties are specific to the damaged DNA. Essential dynamics (ED) derived from the MD trajectories of the three DNAs show that the backbone phosphate between the two adenines complementary to the PD of the damaged DNA has considerably larger mobility than the rest of the molecule and occurs only in the damaged DNA. As observed in the crystal structure of T4 endonuclease V in a complex with the damaged DNA, the interaction of the enzyme with the damaged DNA can lead to bending along the flexible joint and to induction of adenine flipping into an extra-helical position. Such motions may play an important role in damage recognition by repair enzymes.
Optimization of video synthesis by means of cost-guided multimodal photometric correction

In this paper, a novel texture synthesis approach with spatio-temporal boundary conditions is presented. The proposed method is non-parametric and patch-based. Blending between overlapping patches is optimized using a graph-cut technique. Furthermore, a set of photometric correction algorithms, namely Poisson [1] and covariant [2] cloning, is used simultaneously to fit continuation patches into a given neighborhood of the synthetic texture, which minimizes the visibility of patch transitions. The selection of the optimal correction mode is steered by a perceptual cost function. The Poisson and covariant cloning approaches are modified to fit the video synthesis framework proposed in this paper. Our experiments show that the synthesis quality of complex textures can be improved by up to 82% by using an online cost-guided selection of the optimal photometric correction method compared to graph-cut-only approach.
Mesenchymal-stem-cell-based experimental and clinical trials: current status and open questions

Introduction: Mesenchymal stem cells (MSCs) possess remarkable self-renewal ability and are able to differentiate into various cell lineages. MSCs can also enhance tissue repair and angiogenesis through a paracrine mechanism. It has been recognized that these cells hold great promise for tissue regeneration and treatment of immune-related diseases. Areas covered: This review aims at discussing the mechanisms of MSC-mediated immunomodulation and tissue repair and the related clinical trials, with special emphasis on factors that influence the efficiency of MSC-based therapy, including the source of MSCs, cell passage, cell dose, timing and route of administration. Expert opinion: MSCs may facilitate tissue repair through cell replacement and/or improving the microenvironment by releasing growth factors. Some of these factors also mediate the immunomodulatory effects of MSCs. It is important to establish global guidelines, protocols and standards for production and clinical trials of MSCs, so that MSCs can become a therapeutic agent with a reliable efficacy and good safety.
Remote object detection in cluster-based java

Our work combines Java compilation to native code with a run-time library that executes Java threads in a distributed-memory environment with true parallelism. This approach is implemented within the Hyperion system for the distributed execution of compiled Java programs on clusters of PCs. To provide the illusion of a shared memory to Java threads, Hyperion has been built on top of DSM-PM2, a portable implementation platform for multithreaded distributed-shared-memory protocols. We have designed, implemented and experimented with two alternative consistency protocols compliant with the Java Memory Model. The protocols have different mechanisms for access detection: the first one uses explicit locality checks, whereas the second one is based on page faults. We illustrate the effects of the two access-detection techniques with five applications run on two clusters with different interconnection networks: BIP/Myrinet and SISCI/SCI.
Brain-Computer Interface (BCI) Based Musical Composition

In this paper we present, for the first time in Brain-Computer Interface (BCI) research, a novel application for music composition. We developed, based on the I$^2$R NeuroComm BCI platform, a novel Graphical User Interface (GUI) to allow composition of short melodies by selecting individual musical notes. The user can select any individual musical key (quarter note with Do, R\'{e}, Mi, Fa, Sol, La, Si, Do, etc.), insert a silence (quarter rest), delete (Del) the last note to correct the composition, or listen (Play) to the final melody, shown in text form and as a musical partition. Our BCI system for music composition has been successfully demonstrated and shown to be, with very short training time, effective and easy to use. This work is the first step towards a more intelligent BCI system that will extend current BCI-based Virtual Reality (VR) navigation for e.g. exploring a Virtual Synthesizer Museum/shop, in which the user would first move around within the virtual museum/shop and at the point of interest would try the synthesizer by composing music. More advanced modes (e.g. musical puzzle) with various levels of difficulty will be added in future developments as well as using the Open Vibe environment and mobile platforms such as the Apple's iPAD.
Etingof Trace, Path Hypergeometric Functions and Integrable Systems

Under a certain condition, we find the explicit formulas for the trace functions of certain intertwining operators among gl(n)-modules, introduced by Etingof in connection with the solutions of the Calogero-Sutherland model. If n=2, the master function of the trace function is exactly the classical Gauss hypergeometric function. When n>2, the master functions of the trace functions are a new family of multiple hypergeometric functions, whose differential property and integral representation are dominated certain polynomials of integral paths connecting pairs of positive integers. Moreover, we define and explicitly find similar trace functions for sp(2n), which give rise to solutions of the Olshanesky-Perelomov model of type C. The master functions of the trace functions for sp(2n) are similar new multiple path hypergeometric functions. Analogous multiple path hypergeometric functions for orthogonal Lie algebras are defined and studied.
Global Ischemia-Induced Increases in the Gap Junctional Proteins Connexin 32 (Cx32) and Cx36 in Hippocampus and Enhanced Vulnerability of Cx32 Knock-Out Mice

Gap junctions are conductive channels that connect the interiors of coupled cells. In the hippocampus, GABA-containing hippocampal interneurons are interconnected by gap junctions, which mediate electrical coupling and synchronous firing and thereby promote inhibitory transmission. The present study was undertaken to examine the hypothesis that the gap junctional proteins connexin 32 (Cx32; expressed by oligodendrocytes, interneurons, or both), Cx36 (expressed by interneurons), and Cx43 (expressed by astrocytes) play a role in defining cell-specific patterns of neuronal death in hippocampus after global ischemia in mice. Global ischemia did not significantly alter Cx32 and Cx36 mRNA expression and slightly increased Cx43 mRNA expression in the vulnerable CA1, as assessed by Northern blot analysis and in situ hybridization. Global ischemia induced a selective increase in Cx32 and Cx36 but not Cx43 protein abundance in CA1 before onset of neuronal death, as assessed by Western blot analysis. The increase in Cx32 and Cx36 expression was intense and specific to parvalbumin-positive inhibitory interneurons of CA1, as assessed by double immunofluorescence. Protein abundance was unchanged in CA3 and dentate gyrus. The finding of increase in connexin protein without increase in mRNA suggests regulation of Cx32 and Cx36 expression at the translational or post-translational level. Cx32(Y/−) null mice exhibited enhanced vulnerability to brief ischemic insults, consistent with a role for Cx32 gap junctions in neuronal survival. These findings suggest that Cx32 and Cx36 gap junctions may contribute to the survival and resistance of GABAergic interneurons, thereby defining cell-specific patterns of global ischemia-induced neuronal death.
Membrane Recruitment of Scaffold Proteins Drives Specific Signaling

Cells must give the right response to each stimulus they receive. Scaffolding, a signaling process mediated by scaffold proteins, participates in the decoding of the cues by specifically directing signal transduction. The aim of this paper is to describe the molecular mechanisms of scaffolding, i.e. the principles by which scaffold proteins drive a specific response of the cell. Since similar scaffold proteins are found in many species, they evolved according to the purpose of each organism. This means they require adaptability. In the usual description of the mechanisms of scaffolding, scaffold proteins are considered as reactors where molecules involved in a cascade of reactions are simultaneously bound with the right orientation to meet and interact. This description is not realistic: (i) it is not verified by experiments and (ii) timing and orientation constraints make it complex which seems to contradict the required adaptability. A scaffold protein, Ste5, is used in the MAPK pathway of Saccharomyces Cerevisiae for the cell to provide a specific response to stimuli. The massive amount of data available for this pathway makes it ideal to investigate the actual mechanisms of scaffolding. Here, a complete treatment of the chemical reactions allows the computation of the distributions of all the proteins involved in the MAPK pathway when the cell receives various cues. These distributions are compared to several experimental results. It turns out that the molecular mechanisms of scaffolding are much simpler and more adaptable than previously thought in the reactor model. Scaffold proteins bind only one molecule at a time. Then, their membrane recruitment automatically drives specific, amplified and localized signal transductions. The mechanisms presented here, which explain how the membrane recruitment of a protein can produce a drastic change in the activity of cells, are generic and may be commonly used in many biological processes.
MAIGO2 Is Involved in Exit of Seed Storage Proteins from the Endoplasmic Reticulum in Arabidopsis thaliana[W][OA]

Seed storage proteins are synthesized on the endoplasmic reticulum (ER) as precursors and then transported to protein storage vacuoles, where they are processed into mature forms. Here, we isolated an Arabidopsis thaliana mutant, maigo2 (mag2), that accumulated the precursors of two major storage proteins, 2S albumin and 12S globulin, in dry seeds. mag2 seed cells contained many novel structures, with an electron-dense core that was composed of the precursor forms of 2S albumin. 12S globulins were segregated from 2S albumin and were localized in the matrix region of the structures together with the ER chaperones lumenal binding protein and protein disulfide isomerase, which were more abundant in mag2 seeds. The MAG2 gene was identified as At3g47700, and the MAG2 protein had a RINT-1/TIP20 domain in the C-terminal region. We found that some MAG2 molecules were peripherally associated with the ER membrane. MAG2 had an ability to bind to two ER-localized t-SNAREs (for target-soluble NSF [N-ethylmaleimide–sensitive fusion protein] attachment protein receptor; At Sec20 and At Ufe1). Our findings suggest that MAG2 functions in the transport of storage protein precursors between the ER and Golgi complex in plants.
HIV stigma and social interaction : examining strategies to influence perceivers' emotional and behavioral reactions in initial encounters

• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
On Probabilistic Diagnosis for Free-Choice Petri Nets

We describe an on-line probabilistic diagnosis algorithm for free choice Petri nets. The plant observation is given by a subset of transitions whose occurrence is reported while the rest of transitions including faults are unobservable silent. We propose two notions for the probabilistic diagnosis, the likelihood that a fault must have happened prior to the last observed event, and the likelihood that a fault may have happened given the available observations.
Students’ engagement with learning technologies

This paper seeks to add to the discussion surrounding young adults’ relationship and engagement with learning technologies, exploring whether they naturally engage with these technologies when the use of them is either compulsory or optional.We discuss our findings in relation to whether young people are truly engaging with technologies or whether they are simply passive consumers of some technology, and unenthusiastic innovators in others. Participants in the UK (N=6, Mean Age 20.66, undergraduate psychology students) provided their responses to a short series of face–to–face interviews using open–ended questions designed to elicit a critical exploration of their learning experience with particular emphasis on learning technologies. Participants in the US (N=26, Mean Age=22.38, pre–service teachers) responded to a series of short open–ended questions submitted online using asynchronous video journals uploaded to a private classroom space on YouTube.We found that young people are generally unenthusiastic users of learning technologies, which has significant implications for the educational sector in the UK and the US, as many of our participants are pre-service teachers. At a time when great emphasis is being placed on increasing student access to technologies in the classroom to enrich the learning experience, and to offer greater opportunity for understanding and discovery of information, trainee educators seem reluctant to engage with many types of educational technologies.
Glutamine Acts as a Neuroprotectant against DNA Damage, Beta-Amyloid and H2O2-Induced Stress

Glutamine is the most abundant free amino acid in the human blood stream and is ‘conditionally essential’ to cells. Its intracellular levels are regulated both by the uptake of extracellular glutamine via specific transport systems and by its intracellular synthesis by glutamine synthetase (GS). Adding to the regulatory complexity, when extracellular glutamine is reduced GS protein levels rise. Unfortunately, this excess GS can be maladaptive. GS overexpression is neurotoxic especially if the cells are in a low-glutamine medium. Similarly, in low glutamine, the levels of multiple stress response proteins are reduced rendering cells hypersensitive to H2O2, zinc salts and DNA damage. These altered responses may have particular relevance to neurodegenerative diseases of aging. GS activity and glutamine levels are lower in the Alzheimer's disease (AD) brain, and a fraction of AD hippocampal neurons have dramatically increased GS levels compared with control subjects. We validated the importance of these observations by showing that raising glutamine levels in the medium protects cultured neuronal cells against the amyloid peptide, Aβ. Further, a 10-day course of dietary glutamine supplementation reduced inflammation-induced neuronal cell cycle activation, tau phosphorylation and ATM-activation in two different mouse models of familial AD while raising the levels of two synaptic proteins, VAMP2 and synaptophysin. Together, our observations suggest that healthy neuronal cells require both intracellular and extracellular glutamine, and that the neuroprotective effects of glutamine supplementation may prove beneficial in the treatment of AD.
Galaxy Morphology without Classification: Self-organizing Maps

We examine a general framework for visualizing data sets of high (greater than 2) dimensionality and demonstrate the framework by taking the morphology of galaxies at moderate redshifts as an example. The distributions of various populations of such galaxies are examined in a space spanned by four purely morphological parameters. Galaxy images are taken from the Hubble Space Telescope Wide Field Planetary Camera 2 in the I band (using the F814W filter). Since we have little prior knowledge on how galaxies are distributed in morphology space, we use an unsupervised learning method (a variant of Kohonen's self-organizing maps, or SOMs). This method allows the data to organize themselves onto a two-dimensional space while conserving most of the topology of the original space. It thus enables us to visualize the distribution of galaxies and study it more easily. The process is fully automated, does not rely on any kind of “eyeball” classification and is readily applicable to large numbers of images. We apply it to a sample of 2934 galaxies and find that the morphology correlates well with the apparent magnitude distribution and, to a lesser extent, with color and bulge dominance. The resulting map traces a morphological sequence similar to the Hubble sequence, albeit two-dimensional. We use the SOM as a diagnostic tool and rediscover a population of bulge-dominated galaxies with morphologies characteristic of peculiar galaxies. This result is achieved without recourse to classification by eye. We also examine the effect of noise on the resulting SOM, and conclude that our results are reliable down to an I magnitude of 24. We propose using this method as a framework into which more physical data can be incorporated as they become available. We hope that this method will lead to a deeper understanding of galaxy evolution.