Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of depolarization in the survival and differentiation of cerebellar granule cells in culture

Cultures greatly enriched in granule cells from early postnatal cerebellum (P8) were grown in a medium containing fetal calf serum. Under the conditions used, nerve cells died, usually within a week, unless the K+ concentration in the medium was greater than or equal to 20 mM. The requirement for elevated [K+]e was manifested by about 3 d in vitro, and after this time continuous exposure to high [K+]e was essential for the survival of the granule cells. The initial morphological and biochemical maturation of the granule cells was similar in the presence and the absence of elevated [K+]e, suggesting that the dependence on depolarizing conditions develops in parallel with the expression of the differentiated characteristics of the cells. The positive effect of elevated [K+]e on granule cell survival was not influenced by preventing bioelectric activity in the cultures with TTX and xylocaine. On the other hand, depolarization-induced transmembrane Ca2+ flux was essential in securing the maintenance of the granule cells. Depolarized nerve cells were compromised when Ca2+ entry was blocked by elevated Mg2+, EGTA, or organic Ca2+ antagonists, while dihydropyridine Ca2+ agonists [BAY K 8644, (+)-(S)-202 79 1 and CGP 28392] were potent agents preventing nerve cell loss in the presence of 15 mM [K+]e, which was ineffective on its own. Calmodulin inhibitors (1 microM trifluoperazine or calmidazolium) blocked the beneficial effect of K+-induced depolarization on granule cells. The comparison of the timing of the differentiation and innervation of the postmitotic granule cells in vivo with the development of the K+ dependence in vitro would indicate that depolarization of the granule neurons in culture mimics the influence of the physiological stimulation in vivo through excitatory amino acid receptors, including N-methyl-D-aspartate receptors, involving Ca2+ entry and the activation of a Ca2+/calmodulin- dependent protein kinase.
Anticancer and Antitumor Potential of Fucoidan and Fucoxanthin, Two Main Metabolites Isolated from Brown Algae

Seaweed is one of the largest producers of biomass in marine environment and is a rich arsenal of active metabolites and functional ingredients with valuable beneficial health effects. Being a staple part of Asian cuisine, investigations on the crude extracts of Phaeophyceae or brown algae revealed marked antitumor activity, eliciting a variety of research to determine the active ingredients involved in this potential. The sulfated polysaccharide of fucoidan and carotenoid of fucoxanthin were found to be the most important active metabolites of brown algae as potential chemotherapeutic or chemopreventive agents. This review strives to provide detailed account of all current knowledge on the anticancer and antitumor activity of fucoidan and fucoxanthin as the two major metabolites isolated from brown algae.
The pugilistDominant Mutation of Drosophila melanogaster: A Simple-Sequence Repeat Disorder Reveals Localized Transport in the Eye

The pugilist-Dominant mutation results from fusion of a portion of the gene encoding the tri-functional Methylene Tetrahydrofolate Dehydrogenase (E.C.1.5.1.5, E.C.3.5.4.9, E.C.6.3.4.3) to approximately one kb of a heterochromatic satellite repeat. Expression of this fusion gene results in an unusual ring pattern of pigmentation around the eye. We carried out experiments to determine the mechanism for this pattern. By using FLP-mediated DNA mobilization to place different pugD transgenes at pre-selected sites we found that variation in repeat length makes a strong contribution to variability of the pug phenotype. This variation is manifest primarily as differences in the thickness of the pigmented ring. We show that similar phenotypic variation can also be achieved by changing gene copy number. We found that the pugD pattern is not controlled by wingless, which is normally expressed in a similar ring pattern. Finally, we found that physical injury to a pugD eye can lead to pigment deposition in parts of the eye that would not have been pigmented in the absence of injury. Our results are consistent with a model in which a metabolite vital for pigment formation is imported from the periphery of the eye, and pugD limits the extent of its transport towards the center of the eye, thus revealing the existence of a hitherto unknown mechanism of localized transport in the eye.
Influence of Exposure and Toxicokinetics on Measures of Aquatic Toxicity for Organic Contaminants: A Case Study Review

This theoretical and case study review of dynamic exposures of aquatic organisms to organic contaminants examines variables important for interpreting exposure and therefore toxicity. The timing and magnitude of the absorbed dose change when the dynamics of exposure change. Thus, the dose metric for interpreting toxic responses observed during such exposure conditions is generally limited to the specific experiment and cannot be extrapolated to either other experiments with different exposure dynamics or to field exposures where exposure dynamics usually are different. This is particularly true for mixture exposures, for which the concentration and composition and, therefore, the timing and magnitude of exposure to individual components of different potency and potentially different mechanisms of action can vary. Aquatic toxicology needs studies that develop temporal thresholds for absorbed toxicant doses to allow for better extrapolation between conditions of dynamic exposure. Improved experimental designs are required that include high‐quality temporal measures of both the exposure and the absorbed dose to allow better interpretation of data. For the short term, initial water concentration can be considered a conservative measure of exposure, although the extent to which this is true cannot be estimated specifically unless the dynamics of exposure as well as the toxicokinetics of the chemicals in the exposure scenario for the organism of interest are known. A better, but still limited, metric for interpreting the exposure and, therefore, toxicity is the peak absorbed dose, although this neglects toxicodynamics, requires appropriate temporal measures of accumulated dose to determine the peak concentration, and requires temporal thresholds for critical body residue for each component of the mixture. Integr Environ Assess Manag 2013; 9: 196–210. © 2012 SETAC
Optimal transport theory for power-efficient deployment of unmanned aerial vehicles

In this paper, the optimal deployment of multiple unmanned aerial vehicles (UAVs) acting as flying base stations is investigated. Considering the downlink scenario, the goal is to minimize the total required transmit power of UAVs while satisfying the users' rate requirements. To this end, the optimal locations of UAVs as well as the cell boundaries of their coverage areas are determined. To find those optimal parameters, the problem is divided into two sub-problems that are solved iteratively. In the first sub-problem, given the cell boundaries corresponding to each UAV, the optimal locations of the UAVs are derived using the facility location framework. In the second sub-problem, the locations of UAVs are assumed to be fixed, and the optimal cell boundaries are obtained using tools from optimal transport theory. The analytical results show that the total required transmit power is significantly reduced by determining the optimal coverage areas for UAVs. These results also show that, moving the UAVs based on users' distribution, and adjusting their altitudes can lead to a minimum power consumption. Finally, it is shown that the proposed deployment approach, can improve the system's power efficiency by a factor of 20 χ compared to the classical Voronoi cell association technique with fixed UAVs locations.
Human-humanoid collaborative object transportation

Les robots humanoides sont les plus appropries pour travailler en cooperation avec l'homme. En effet, puisque les humains sont naturellement habitues a collaborer entre eux, un robot avec des capacites sensorielles et de locomotion semblables aux leurs, sera le plus adapte. Cette these vise a rendre les robot humanoides capables d'aider l'homme, afin de concevoir des 'humanoides collaboratifs'. On considere ici la tâche de transport collaboratif d'objets. D'abord, on montre comment l'utilisation simultanee de vision et de donnees haptiques peut ameliorer la collaboration. Une strategie combinant asservissement visuel et commande en admittance est proposee, puis validee dans un scenario de transport collaboratif homme/humanoide.Ensuite, on presente un algorithme de generation de marche, prenant intrinsequement en compte la collaboration physique. Cet algorithme peut etre specifie suivant que le robot guide (leader) ou soit guide (follower) lors de la tâche. Enfin, on montre comment le transport collaboratif d'objets peut etre realise dans le cadre d'un schema de commande optimale pour le corps complet.
Collagen can modulate cell interactions with fibronectin

We have examined the effects of soluble collagen on the function of fibronectin in baby hamster kidney (BHK) cells. Collagen and its purified alpha1(l) chain noncompetitively inhibited cell spreading on substrates precoated with fibronectin or a 75,000-D cell-binding fragment of fibronectin. Neither preincubation of cells with collagen followed by washing nor the addition of collagen to previously spread cells had any inhibitory effect on cell spreading, which indicates a requirement for the concurrent presence of collagen during the process of spreading. Treatment of collagen or alpha1(l) chain with collagenase abolished the inhibitory effect on fibronectin-mediated cell spreading. However, direct attachment of BHK cells to fibronectin-coated or 75,000- D fragment-coated substrates was not inhibited by collagen or by the alpha1(l) chain. Moreover, the binding of [3H]fibronectin or the 3'- 75,000-D fragment to cell surfaces was not inhibited by the presence of soluble collagen, whereas soluble fibronectin inhibited binding. Although the binding of [3H]fibronectin-coated beads to BHK cell surfaces was also not inhibited by collagen, the phagocytosis of such beads was inhibited by the presence of collagen. On the other hand, soluble fibronectin partially inhibited the binding of fibronectin- coated beads but did not inhibit phagocytosis of the beads that did bind. The mechanism of the inhibition of fibronectin function by collagen and the possible interactions of two different kinds of receptors on the cell surface are discussed.
Prognostic value of stromal cell-derived factor 1 expression in patients with gastric cancer after surgical resection

Aberrant chemokine stromal cell‐derived factor 1 (SDF‐1) expression has been shown to be involved in the development and progression of various malignancies. Our present study aims to investigate the clinical and prognostic value of SDF‐1 expression and improve risk stratification in patients with gastric cancer. Peritumoral and intratumoral SDF‐1 levels were assessed in 220 retrospectively enrolled gastric cancer patients, and their relations with clinicopathological features and clinical outcomes were evaluated. A predictive nomogram was created to refine risk stratification for overall survival of gastric cancer patients. Compared with peritumor tissues, tumor tissues showed decreased SDF‐1 expression levels according to TNM stage progression in gastric cancer specimens. Peritumoral SDF‐1 expression correlated positively with tumor invasion depth and lymph node metastasis, whereas intratumoral SDF‐1 expression associated negatively with tumor size, tumor differentiation, tumor invasion depth, lymph node metastasis, and clinical TNM stage. Moreover, both low peritumoral SDF‐1 expression and high intratumoral SDF‐1 expression indicated favorable overall survival, and SDF‐1 risk derived from the peritumoral/intratumoral SDF‐1 expression signature could stratify prognosis of patients with gastric cancer. After backward elimination, SDF‐1 risk was identified as an independent prognostic factor for survival. Finally, a predictive nomogram was generated with identified independent prognosticators to assess patient survival at 3 and 5 years following surgery. Conclusively, SDF‐1 risk, an identified independent prognostic factor, could be developed into a nomogram with tumor invasion depth, lymph node involvement, and distant metastasis to refine predictive accuracy for survival in patients with gastric cancer after surgical resection.
2 Chapter 1 Identification and localization of the NR 1 sub-unit homologue of the NMDA glutamate receptor in the honeybee brain

2.1: Abstract The NR1 subunit homologue of the NMDA glutamate receptor was characterized in the honeybee. Sequence analysis suggests that the honeybee NMDA receptor may be act as a coincidence detector molecule similar to its counterpart in the mammalian nervous system. The localization of the expression sites at the mRNA and the protein levels indicates that the receptor is expressed throughout the brain, in neurons and in glial cells.
Brownian Dynamics of Active Sphere Suspensions Confined Near a No-Slip Boundary

We develop numerical methods for performing efficient Brownian dynamics of colloidal suspensions confined to remain in the vicinity of a no-slip wall by gravity or active flows. We present a stochastic Adams-Bashforth integrator for the Brownian dynamic equations, which is second-order accurate deterministically and uses a random finite difference to capture the stochastic drift proportional to the divergence of the mobility matrix. We generate the Brownian increments using a Krylov method, and show that for this geometry the number of iterations is independent of the number of particles. This allows us to develop an implementation on Graphical Processing Units (GPUs) that can efficiently simulate many thousands of particles over relevant timescales. We demonstrate the utility of our methods by simulating a recently-observed fingering instability in an active suspension of colloidal rollers. Our numerical experiments show that the thermal fluctuations are critical to set the characteristic height of the colloids above the wall, which in turn controls the growth rate of the fingering instability.
Ontogenomic study of the relationship between number of gene splice variants and GO categorization

MOTIVATION Splice variation plays important roles in evolution and cancer. Different splice variants of a gene may be characteristic of particular cellular processes, subcellular locations or organs. Although several genomic projects have identified splice variants, there have been no large-scale computational studies of the relationship between number of splice variants and biological function. The Gene Ontology (GO) and tools for leveraging GO, such as GoMiner, now make such a study feasible. RESULTS We partitioned genes into two groups: those with numbers of splice variants <or=b and >b (b=1,., 10). Then we used GoMiner to determine whether any GO categories are enriched in genes with particular numbers of splice variants. Since there was no a priori 'appropriate' partition boundary, we studied those 'robust' categories whose enrichment did not depend on the selection of a particular partition boundary. Furthermore, because the distribution of splice variant number was a snapshot taken at a particular point in time, we confirmed that those observations were stable across successive builds of GenBank. A small number of categories were found for genes in the lower partitions. A larger number of categories were found for genes in the higher partitions. Those categories were largely associated with cell death and signal transduction. Apoptotic genes tended to have a large repertoire of splice variants, and genes with splice variants exhibited a distinctive 'apoptotic island' in clustered image maps (CIMs). AVAILABILITY Supplementary tables and figures are available at URL http://discover.nci. nih.gov/OG/supplementaryMaterials.html. The Safari browser appears to perform better than Firefox for these particular items.
Effects of Testosterone and Evoked Resistance Exercise after Spinal Cord Injury (TEREX-SCI): study protocol for a randomised controlled trial

Introduction Individuals with spinal cord injury (SCI) are at a lifelong risk of obesity and chronic metabolic disorders including insulin resistance and dyslipidemia. Within a few weeks of injury, there is a significant decline in whole body fat-free mass, particularly lower extremity skeletal muscle mass, and subsequent increase in fat mass (FM). This is accompanied by a decrease in anabolic hormones including testosterone. Testosterone replacement therapy (TRT) has been shown to increase skeletal muscle mass and improve metabolic profile. Additionally, resistance training (RT) has been shown to increase lean mass and reduce metabolic disturbances in SCI and other clinical populations. Methods and analysis 26 individuals with chronic, motor complete SCI between 18 and 50 years old were randomly assigned to a RT+TRT group (n=13) or a TRT group (n=13). 22 participants completed the initial 16-week training phase of the study and 4 participants withdrew. 12 participants of the 22 completed 16 weeks of detraining. The TRT was provided via transdermal testosterone patches (4–6 mg/day). The RT+TRT group had 16 weeks of supervised unilateral progressive RT using surface neuromuscular electrical stimulation with ankle weights. This study will investigate the effects of evoked RT+TRT or TRT alone on body composition (muscle cross-sectional area, visceral adipose tissue, %FM) and metabolic profile (glucose and lipid metabolism) in individuals with motor complete SCI. Findings from this study may help in designing exercise therapies to alleviate the deterioration in body composition after SCI and decrease the incidence of metabolic disorders in this clinical population. Ethics and dissemination The study is currently approved by the McGuire VA Medical Center and Virginia Commonwealth University. All participants read and signed approved consent forms. Results will be submitted to peer-reviewed journals and presented at national and international conferences. Trial registration number Pre-result, NCT01652040.
Re: File Number S7-02010, " Concept Release on Equity Market Structure "

We are a group of scientists and business people who share a common interest in the application to financial systems of a scientific methodology called agent-based modeling (ABM). We believe this methodology represents a scientifically validated and powerful tool to facilitate the Commission's regulation of equity markets. We believe that its use would enable the Commission to make scientifically informed responses to questions posed in the Release and to anticipate both the intended and unintended consequences of proposed regulations. We also note that a number of other agencies of government now successfully employ this type of science. The Commission's facilitation of the establishment of a national market system as directed by Congress in 1934 has been significantly affected by the emergence of new computing and communications technologies. These have affected the architectural structure of the system itself as well as how it functions. This is now reflected in a shift from manual trading to automated trading over increasingly faster time scales in increasingly more complex networks. The pace of this change has increased dramatically in only the last decade. As the Release notes, this now poses a number of important new regulatory issues for the Commission. ABM could help address these issues, as subsequently described in this letter. ABMs are computational scientific test beds. While they trace their scientific origins to the 1940's, in the 1990's they began to find growing and widespread application in a variety of fields. Their growth has been enhanced by the same rapidly increasing computing and communication capabilities that have also dramatically affected the structure and functioning of our national equity markets resulting in the need for new regulations. ABMs are a class of computational model used to analyze the emergent behaviors of complex systems. They simulate the interactions of autonomous agents to assess their effects on both a system as a whole and on the individual agents and classes of agents which comprise it. These models are based on the
MODELLING THE SEDS OF SPIRAL GALAXIES

Modelling the UV/optical - infrared/submm SEDs of spiral galaxies observed with Herschel will be an essential tool to quanti- tatively interpret these observations in terms of the present and past star-formation activity of these systems. In this lecture we describe the SED modelling technique we have developed, its applications and tests of its predictions. We show that both the panchromatic SED modelling of individual galaxies and the B-band attenuation-inclination relation of large statistical samples suggest that spiral galaxies in the nearby Universe behave as optically thick systems in their global properties and large-scale distribution of light (central face-on B-band opacity of � f B � 4). However disk galaxies are very inhomogeneous systems, hav- ing both optically thick components (e.g. spiral arms), and optically thin components (e.g. the interarm regions), the latter making galaxies transparent to background galaxies.
Orthogonal frequency division multiplexing with index modulation in the presence of high mobility

In this paper, a novel orthogonal frequency division multiplexing (OFDM) scheme, which is called OFDM with index modulation (OFDM-IM), is proposed for frequency-selective fading channels in the presence of high mobility. In this scheme, inspiring from the recently introduced spatial modulation concept for multiple-input multiple-output (MIMO) channels, the information is conveyed not only by M-ary signal constellations as in classical OFDM, but also by the indices of the subcarriers, which are activated according to the incoming bit stream. Different low complexity transceiver structures based on maximum likelihood (ML) detection or log-likelihood ratio (LLR) calculation are proposed. It is shown via computer simulations that the proposed scheme achieves significantly better error performance than classical OFDM.
Modeling the Number of Active Software Users

More and more software applications are developed within a software ecosystem (SECO), such as the Face book ecosystem and the iPhone AppStore. A core asset of a software ecosystem is its users, and the behavior of the users strongly affects the decisions of software vendors. The number of active users reflects user satisfaction and quality of the applications in a SECO. However, we can hardly find any literature about the number of active software users. Because software users are one of the most important assets of a software business, this information is very sensitive. In this paper, we analyzed the traces of software application users within a large scale software ecosystem with millions of active users. We identified useful patterns of user behavior, and proposed models that help to understand the number of active application users. The model we proposed better predicts the number of active users than just looking at the traditional retention rate. It also provides a fast way to monitor user satisfaction of online software applications. We have therefore provided an alternative way for SECO platform vendors to identify rising or falling applications, and for third party application vendors to identify risks and opportunity of their products.