Miracle-dz/UniFAR-FTUs huggingface dataset:
Adenosine signalling at immature parallel fibre–Purkinje cell synapses in rat cerebellum

The purine adenosine is an extracellular signalling molecule involved in a large number of physiological and pathological conditions throughout the mammalian brain. However little is known about how adenosine release and its subsequent clearance change during brain development. We have combined electrophysiology and microelectrode biosensor measurements to investigate the properties of adenosine signalling at early stages of cerebellar development, when parallel fibre–Purkinje cell synapses have recently been formed (postnatal days 9–12). At this stage of development, we could detect little or no inhibitory A1 receptor tone in basal conditions and during trains of stimuli. Addition of pharmacological agents, to inhibit adenosine clearance, had only minor effects on synaptic transmission suggesting that under basal conditions, the concentration of adenosine moving in and out of the extracellular space is small. Active adenosine release was stimulated with hypoxia and trains of electrical stimuli. Although hypoxia released significant concentrations of adenosine, the release was delayed and slow. No adenosine release could be detected following electrical stimulation in the molecular layer. In conclusion, at this stage of development, although adenosine receptors and the mechanisms of adenosine clearance are present there is very little adenosine release.
The RAD52 ortholog of Yarrowia lipolytica is essential for nuclear integrity and DNA repair.

Yarrowia lipolytica (Yl) is a dimorphic fungus that has become a well-established model for a number of biological processes, including secretion of heterologous and chimerical proteins. However, little is known on the recombination machinery responsible for the integration in the genome of the exogenous DNA encoding for those proteins. We have carried out a phenotypic analysis of rad52 deletants of Y. lipolytica. YlRad52 exhibited 20-30% identity with Rad52 homologues of other eukaryotes, including Saccharomyces cerevisiae and Candida albicans. Ylrad52-Δ strains formed colonies on YPD-agar plates which were spinier and smaller than those from wild type, whereas in YPD liquid cultures they exhibited a decreased grow rate and contained cells with aberrant morphology and fragmented chromatin, supporting a role for homologous recombination (HR) in genome stability under nondamaging conditions. In addition, Ylrad52 mutants showed moderate to high sensitivity to UV light, oxidizing agents and compounds that cause single- (SSB) and double-strand breaks (DSB), indicating an important role for Rad52 in DNA repair. These findings extend to Yl previous observations indicating that RAD52 is a crucial gene for DNA repair in other fungi, including S. cerevisiae, C. albicans and Schizosaccharomyces pombe.
Sülüklü Göl (Bolu-Adapazarı / Türkiye) çevresinin florası

Bu calisma, Suluklu Gol cevresinin florasinin belirlenmesi amaciyla yapilmistir. Calisma alanindan 2009-2010 yillarinda 579 damarli bitki ornegi toplanmistir. 79 familyaya [ Pteridophyta (4), Pinophytina (3), Magnoliophytina (72)] ve 230 cinse [ Pteridophyta (4), Pinophytina (4), Magnoliophytina (222)] ait 406 takson tespit edilmistir. Toplam 38 takson endemiktir ve endemizim orani %9,36’dir. Taksonlarin fitocografik bolgelere gore dagilimi soyledir; %26,6’si Avrupa-Sibirya (108 takson), %8,37’si Akdeniz (34 takson), %4,93’u Iran-Turan (20 takson) ve %60,1’i cok bolgeli ve bilinmeyen (244 takson) dir.
Sharing the magic circle with spatially inclusive games

Four types of interactive environments explored ways to extend gaming beyond the limitations of the personal computer's conventional desktop interface. These projects aimed to challenge John Huizinga's notion of a "magic circle", the imaginary boundaries of the fantasy world that players of a game occupy. By expanding and diffusing the "magic circle", we believe we can more richly and thematically immerse the player, and more directly involve the audience. The projects were: surround projection environments (using a spherical mirror and warping code); surround projection in custom-built surround spaces with thematically designed tangible interfaces; arcade-style games; and bodily aware-games (using indirect and subconscious biofeedback that changes the music, "boss" monsters, and shaders). The working prototypes were considered successful by the students' peers and by visitors, but were also successful in engaging the students with the interface possibilities and interaction issues of unconventional game design. We also intend to further develop and provide some of these tools to the wider academic community.
Vacuolar transporter Avt4 is involved in excretion of basic amino acids from the vacuoles of Saccharomyces cerevisiae

Basic amino acids (lysine, histidine and arginine) accumulated in Saccharomyces cerevisiae vacuoles should be mobilized to cytosolic nitrogen metabolism under starvation. We found that the decrease of vacuolar basic amino acids in response to nitrogen starvation was impaired by the deletion of AVT4 gene encoding a vacuolar transporter. In addition, overexpression of AVT4 reduced the accumulation of basic amino acids in vacuoles under nutrient-rich condition. In contrast to AVT4, the deletion and overexpression of AVT3, which encodes the closest homologue of Avt4p, did not affect the contents of vacuolar basic amino acids. Consistent with these, arginine uptake into vacuolar membrane vesicles was decreased by Avt4p-, but not by Avt3p-overproduction, whereas various neutral amino acids were excreted from vacuolar membrane vesicles in a manner dependent on either Avt4p or Avt3p. These results suggest that Avt4p is a vacuolar amino acid exporter involving in the recycling of basic amino acids. Graphical Abstract In the budding yeast Saccharomyces cerevisiae, basic amino acids that are highly accumulated in vacuoles are extruded by vacuolar amino acid transporter Avt4.
Improved Higher Order Differential Attack and Its Application to Nyberg-Knudsen's Designed Block Cipher

Since the proposal of differential cryptanalysis and linear cryptanalysis in 1991 and 1993, respectively, the resistance to these cryptanalysis has been studied. In FSE2, Knudsen proposed a method of attacking block ciphers that used the higher order differential, and in FSE4, Jakobsen and Knudsen applied it to a cipher proposed by Nyberg and Knudsen. Their approach, however, requires large complexity of running time. In this paper, we improve this attack and show that our improved algorithm requires much fewer chosen texts and much less complexity than those of previous works. key words: block cipher, higher order differential attack, KN cipher, algebraic equation
Density Functions subject to a Co-Matroid Constraint

In this paper we consider the problem of finding the densest subset subject to co-matroid constraints. We are given a monotone supermodular set function f defined over a universe U, and the density of a subset S is defined to be f(S)/|S|. This generalizes the concept of graph density. Co-matroid constraints are the following: given matroid M a set S is feasible, iff the complement of S is independent in the matroid. Under such constraints, the problem becomes NP-hard. The specific case of graph density has been considered in literature under specific co-matroid constraints, for example, the cardinality matroid and the partition matroid. We show a 2-approximation for finding the densest subset subject to co-matroid constraints. Thereby we improve the approximation guarantees for the result for partition matroids in the literature.
A survival analysis method for stock market prediction

Stock market prediction focus on developing approaches to determine the future price of a stock or other financial product. The key task of stock market prediction is to determine the timing for the buying or selling of stock, undoubtedly, it is very difficult due to the high volatility and nonlinear relationships driven by short-term fluctuations in investment demand. In this work, we address this problem by adopting the Cox's hazard model to predict a stock's future rising or dropping probabilities. Specifically, we define the problem of Buy-and-Sell-Point Prediction from the survival analysis perspective. The Cox's hazard model is proposed as the model of choice for this prediction problem due to several reasons including the ability to model the dynamics in the stock movement, and to easily incorporate different types of technical indexes as covariates. In the experiment, we apply the trained model for the stock market forecasting on six stocks in Shanghai Stock Exchange. The results show that the proposed model is superior to several baseline models in terms of accuracy, and the stock return evaluations have revealed that the profits produced by the proposed model are higher.
A study into the usability of e-encyclopaedias

This paper describes a usability study performed on three different e-encyclopaedias, all of which were available on the web, contained similar content and targeted similar audiences, but differed in their styles of presentation. The purpose of the study was to discover the effectiveness of each design in terms of overall usability and subjective satisfaction, to extract general guidelines for the successful design of e-encyclopaedias, and to examine the requirements of different user groups.
BioJS: an open source standard for biological visualisation – its status in 2014

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi. ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.
Documents de Travail du Centre d ’ Economie de la Sorbonne Social preferences in the online laboratory : A randomized experiment

Internet is a very attractive technology for experiments implementation, both in order to reach more diverse and larger samples and as a field of economic research in its own right. This paper reports on an experiment performed both online and in the laboratory, designed so as to strengthen the internal validity of decisions elicited over the Internet. We use the same subject pool, the same monetary stakes and the same decision interface, and randomly assign two groups of subjects between the Internet and a traditional University laboratory to compare behavior in a set of social preferences games. This comparison concludes in favor of the reliability of behaviors elicited through the Internet. Our behavioral results contradict the predictions of social distance theory, as we find that subjects allocated to the Internet treatment behave as if they were more altruistic, more trusting, more trustworthy and less risk averse than laboratory subjects. Those findings have practical importance for the growing community of researchers interested in using the Internet as a vehicle for social experiments and bear interesting methodological lessons for social scientists interested in using experiments to research the Internet as a field. JEL classification: C90, C93, C70
Motion blur free HDR image acquisition using multiple exposures

The high dynamic range image (HDRI) acquisition method based on Markov random field model is proposed. By combining multiple exposure images shot with different shutter speed, we estimate the irradiance value for each pixel. Our method estimates displacements, occlusion and saturated regions, and by using them construct the motion blur free HDRI with higher quality than other existing methods.
Some New Results on the Multiple-AccessWiretap Channel

In this paper, some new results on the multiple-access wiretap channel (MAC-WT) are provided. Specifically, first, we investigate the degraded MAC-WT, where two users transmit their corresponding confidential messages (no common message) to a legitimate receiver via a multiple-access channel (MAC), while a wiretapper wishes to obtain the messages via a physically degraded wiretap channel. The secrecy capacity region of this model is determined for both the discrete memoryless and Gaussian cases. For the Gaussian case, we find that this secrecy capacity region is exactly the same as the achievable secrecy rate region provided by Tekin and Yener, i.e., Tekin–Yener’s achievable region is exactly the secrecy capacity region of the degraded Gaussian MAC-WT. Second, we study a special Gaussian MAC-WT, and find the power control for two kinds of optimal points (max-min point and single user point) on the secrecy rate region of this special Gaussian model.
A Hierarchical EMS for Aggregated BESSs in Energy and Performance-Based Regulation Markets

The battery energy storage systems (BESSs) have been increasingly installed in the power system, especially with the growing penetration rate of the renewable energy sources. However, it is difficult for BESSs to be profitable due to high capital costs. In order to boost the economic value of BESSs, this paper proposes a hierarchical energy management system (HiEMS) to aggregate multiple BESSs, and to achieve multimarket business operations. The proposed HiEMS optimizes the multimarket bids considering a realistic BESS performance model, and coordinates the BESSs and manages their state of charge values, according to their price penalties based on dynamically generated annualized cost. By taking part in the energy market and regulation market at the same time, the cost-performance index (CPI) of the BESS aggregation is greatly improved. The impact of photovoltaic generation on system performance and CPI is also studied.
Multipath TCP: Analysis, Design, and Implementation

Multipath TCP (MP-TCP) has the potential to greatly improve application performance by using multiple paths transparently. We propose a fluid model for a large class of MP-TCP algorithms and identify design criteria that guarantee the existence, uniqueness, and stability of system equilibrium. We clarify how algorithm parameters impact TCP-friendliness, responsiveness, and window oscillation and demonstrate an inevitable tradeoff among these properties. We discuss the implications of these properties on the behavior of existing algorithms and motivate our algorithm Balia (balanced linked adaptation), which generalizes existing algorithms and strikes a good balance among TCP-friendliness, responsiveness, and window oscillation. We have implemented Balia in the Linux kernel. We use our prototype to compare the new algorithm to existing MP-TCP algorithms.
Seminal plasma metabolomics approach for the diagnosis of unexplained male infertility

We used a gas chromatography-mass spectrometry (GC-MS) based metabolomics approach to obtain the metabolic profiling of unexplained male infertility (UMI), and identified seminal plasma biomarkers associated with UMI by a two-stage population study. A robust OPLS-DA model based on these identified metabolites was able to distinguish 82% of the UMI patients from health controls with a specificity of 92%. In this model, 44 metabolites were found differentially expressed in UMI subjects compared with health controls. By pathway enrichment analysis, we identified several major changed metabolic pathways related to UMI. Our findings provide new perspective for the diagnosis of UMI.
Analytical Performance Prediction for Evaluation and Tuning of GPGPU Applications

In this paper we present an analytical model to predict the performance of general purpose applications on a GPU architecture. Themodel is designed to provide performance information to an auto-tuning compiler and assist it narrow the search to the more promising implementations. This work is based on the NVIDIAGPUs using CUDA (ComputeUnified Device Architecture). We analyze each CUDA kernel and generate the corresponding string model which is a concise representation of the operations of a kernel. String model for a kernel summarizes how the kernel exercises major GPU microarchitecture features. Based on the string model we estimate the average execution time of a warp, which is the SIMD work granularity for CUDA. We validated the performance model using a few data parallel benchmarks that exploit different microarchitecture features of GPU architecture. The model captures full system complexity and shows high accuracy in predicting the performance trend of different optimized implementations. We also describe our approach to extract the performance model automatically.
Robustness and Vulnerability of Scale-Free Random Graphs

Recently many new "scale-free" random graph models have been introduced, motivated by the power-law degree sequences observed in many large-scale, real-world networks. Perhaps the best known, the Barabási-Albert model, has been extensively studied from heuristic and experimental points of view. Here we consider mathematically two basic characteristics of a precise version of this model, the LCD model, namely robustness to random damage, and vulnerability to malicious attack. We show that the LCD graph is much more robust than classical random graphs with the same number of edges, but also more vulnerable to attack. In particular, if vertices of the n-vertex LCD graph are deleted at random, then as long as any positive proportion remains, the graph induced on the remaining vertices has a component of order n. In contrast, if the deleted vertices are chosen maliciously, a constant fraction less then 1 can be deleted to destroy all large components. For the Barabási-Albert model, these questions have been studied experimentally and heuristically by several groups.
Tobacco smoking and excess mortality in multiple sclerosis: a cohort study

Objective As patients with multiple sclerosis (MS) have more than 2.5-fold increased mortality risk, we sought to investigate the impact of tobacco smoking on the risk of premature death and its contribution to the excess mortality in MS patients. Methods We studied 1032 patients during the period 1994–2013 in a UK-based register. Cox regression model was used to investigate the impact of smoking on the risk of premature death, controlling for confounders. Smoking-specific mortality rates were compared with the UK general population. Results Of 923 patients with clinically definite MS, 80 (46 males and 34 females) had died by December 2012. HRs for death in current smokers and ex-smokers relative to never smokers were 2.70 (95% CI 1.59 to 4.58, p<0.001) and 1.30 (95% CI 0.72 to 2.32; p = 0.37). The standardised mortality ratio, compared with the UK general population, when stratified by smoking status was 3.83 (95% CI 2.71 to 5.42) in current smokers, 1.96 (95% CI 1.27 to 3.0) in ex-smokers and 1.27 (95% CI 0.87 to 1.86) in non-smokers. Never smokers and ex-smokers with MS had similar mortality rates compared with never smokers and ex-smokers without MS in the male British doctors cohort (1.12 (95% CI 0.63 to 1.97) and 0.54 (95% CI 0.26 to 1.14), respectively), while current smokers with MS had 84% higher rate of death compared with current smokers without MS (95% CI 1.24 to 2.72). Conclusions Tobacco smoking can account for some of the excess mortality associated with MS and is a risk determinant for all-cause and MS-related death.
BioLit: integrating biological literature with databases

BioLit is a web server which provides metadata describing the semantic content of all open access, peer-reviewed articles which describe research from the major life sciences literature archive, PubMed Central. Specifically, these metadata include database identifiers and ontology terms found within the full text of the article. BioLit delivers these metadata in the form of XML-based article files and as a custom web-based article viewer that provides context-specific functionality to the metadata. This resource aims to integrate the traditional scientific publication directly into existing biological databases, thus obviating the need for a user to search in multiple locations for information relating to a specific item of interest, for example published experimental results associated with a particular biological database entry. As an example of a possible use of BioLit, we also present an instance of the Protein Data Bank fully integrated with BioLit data. We expect that the community of life scientists in general will be the primary end-users of the web-based viewer, while biocurators will make use of the metadata-containing XML files and the BioLit database of article data. BioLit is available at http://biolit.ucsd. edu.
Neurotrophin-3 regulates ribbon synapse density in the cochlea and induces synapse regeneration after acoustic trauma

Neurotrophin-3 (Ntf3) and brain derived neurotrophic factor (Bdnf) are critical for sensory neuron survival and establishment of neuronal projections to sensory epithelia in the embryonic inner ear, but their postnatal functions remain poorly understood. Using cell-specific inducible gene recombination in mice we found that, in the postnatal inner ear, Bbnf and Ntf3 are required for the formation and maintenance of hair cell ribbon synapses in the vestibular and cochlear epithelia, respectively. We also show that supporting cells in these epithelia are the key endogenous source of the neurotrophins. Using a new hair cell CreERT line with mosaic expression, we also found that Ntf3's effect on cochlear synaptogenesis is highly localized. Moreover, supporting cell-derived Ntf3, but not Bbnf, promoted recovery of cochlear function and ribbon synapse regeneration after acoustic trauma. These results indicate that glial-derived neurotrophins play critical roles in inner ear synapse density and synaptic regeneration after injury. DOI: http://dx.doi. org/10.7554/eLife.03564. 001
Design to Minimize Diameter on Building-Block Network

This paper proposes a simple algorithm for the graph design of small-diameter networks. For given nodes n and degree d, this algorithm can be used to construct a directed graph with diameter ⌈logd n⌉, which is at most one larger than the lower bound ⌈logd (n(d − 1) + 1)⌉ − 1. Its average distance is also close to the lower bound. The algorithm can be used to construct a directed graph with smaller diameter, compared with any other conventional methods, when n is larger.