Miracle-dz/UniFAR-FTUs huggingface dataset:
Paternal Allele Influences High Fat Diet-Induced Obesity

C57BL/6J (B6) mice are susceptible to high-fat diet (HFD)-induced obesity and have been used in metabolism research for many decades. However, the genetic component of HFD-induced obesity has not yet been elucidated. This study reports evidence for a paternal transmission of HFD-induced obesity and a correlated expression of Igf2 and Peg3 (paternal expressed gene 3) imprinted genes. We found that PWK mice are resistant to HFD-induced obesity compared to C57BL/6J mice. Therefore, we generated and analyzed reciprocal crosses between these mice, namely; (PWK×B6) F1 progeny with B6 father and (B6×PWK) F1 progeny with PWK father. The (PWK×B6) F1 mice were more sensitive to diet-induced obesity compared to (B6×PWK) F1 mice, suggesting a paternal transmission of diet-induced obesity. Expression analysis of imprinted genes in adipocytes revealed that HFD influences the expression of some of the imprinted genes in adipose tissue in B6 and PWK mice. Interestingly, Igf2 and Peg3, which are paternally expressed imprinted genes involved in the regulation of body fat accumulation, were down-regulated in B6 and (PWK×B6) F1 mice, which are susceptible to HFD-induced obesity, but not in PWK and (B6×PWK) F1 mice, which are resistant. Furthermore, in vitro analysis showed that Igf2, but not Peg3, had an anti-inflammatory effect on TNF-α induced MCP-1 expression in adipocytes. Taken together, our findings suggest that the down-regulation of Igf2 and Peg3 imprinted genes in adipocytes may be involved in the paternal transmission of HFD-induced obesity.
A linear time exact hidden surface algorithm

This paper presents a new hidden surface algorithm. Its output is the set of the visible pieces of edges and faces, and is as accurate as the arithmetic precision of the computer. Thus calculating the hidden surfaces for a higher resolution device takes no more time. If the faces are independently and identically distributed, then the execution time is linear in the number of faces. In particular, the execution time does not increase with the depth complexity. This algorithm overlays a grid on the screen whose fineness depends on the number and size of the faces. Edges and faces are sorted into grid cells. Only objects in the same cell can intersect or hide each other. Also, if a face completely covers a cell then nothing behind it in the cell is relevant. Three programs have tested this algorithm. The first verified the variable grid concept on 50,000 intersecting edges. The second verified the linear time, fast speed, and irrelevance of depth complexity for hidden lines on 10,000 spheres. This also tested depth complexities up to 30, and showed that perspective scenes with the farther objects smaller are even faster to calculate. The third verified this for hidden surfaces on 3000 squares.
Recent Developments in the Role of High-Mobility Group Box 1 in Systemic Lupus Erythematosus

High-mobility group box 1 (HMGB1) is an important molecule for several nuclear processes. Recently, HMGB1 has gained much attention as a damage-associated molecular pattern (DAMP) and has been implicated in the pathogenesis of several (auto)-immune diseases, in particular, systemic lupus erythematosus (SLE). A main pathogenic feature in SLE is the accumulation of apoptotic cells. Since HMGB1 is released from apoptotic cells it has been hypothesized that HMGB1 might fuel the inflammatory processes, as seen in this disease, and play a fundamental role in the pathogenesis. In this review, we discuss evidence in support of the theory that HMGB1 is an important mediator in SLE and may be considered a new autoantigen.
KeJia: The Intelligent Domestic Robot for RoboCup@Home 2015

This paper aims at reporting the recent progress of search on our intelligent robot KeJia, whose long-term goal is to develop and integrate intelligence into a domestic robot. It covers issues ranging from hardware design, perception and high-level cognitive functions. All these techniques have been tested in former RoboCup@Home tests and other open demostrations.
A Major Role for Mitotic cdc2 Kinase Inactivation in the Establishment of the Mitotic DNA Damage Checkpoint

Cdc2 kinase is inactivated when DNA damage occurs during the spindle assembly checkpoint. Here, we show that the level of mitotic Bloom syndrome protein phosphorylation reflects the level of cdc2 activity. A complete inactivation of cdc2 by either introduction of DNA double-strand breaks or roscovitine treatment prevents exit from mitosis. Thus, mitotic cdc2 inactivation plays a major role in the establishment of the mitotic DNA damage checkpoint. In response to mitotic cdc2 inactivation, the M/G1 transition is delayed after releasing the drug block in nonmalignant cells, whereas tumor cells exit mitosis without dividing and rereplicate their DNA, which results in mitotic catastrophe. This opens the way for new chemotherapeutic strategies.
Fuzzy logic controller for large, grid-integrated wind farm under variable wind speeds

Wind turbines have attracted considerable attention as a renewable energy source due to the environmental concerns and fossil fuel depletion. When connected to existing power systems, wind turbines can cause a number of issues related to the system stability and power quality. Dynamic performance of an electric power grid with wind turbines under variable wind speeds is considered and investigated in this paper. A four-machine-two-area benchmark system has been adopted from the IEEE, and combined with the wind turbines. Wind power generation system with variable-speed provides an opportunity to extract more wind power compared to fixed speed systems. However, the use of variable-speed generators leads to variable output power, frequency and voltage, all due to the wind speed fluctuations. The performance of the output power can be improved if adequate control mechanism is implemented in the system. To maintain the output power, voltage and frequency of system at desired values, a fuzzy logic system is designed as a damping controller for the power output and frequency fluctuations of a variable-speed wind power generation system. Control is implemented by changing the blade pitch angle of the wind turbine. Dynamic modeling, control and simulation study of the two area-wind power generation system is performed using MATLAB/Simulink. The simulation results show that the controlled variables reach required operation values in a very short time, and improve the dynamic response and the transient stability of the power system.
Zero-Error Source&#8211;Channel Coding With Side Information

This correspondence presents a novel application of the theta function defined by Lovasz. The problem of coding for transmission of a source through a channel without error when the receiver has side information about the source is analyzed. Using properties of the Lovasz theta function, it is shown that separate source and channel coding is asymptotically suboptimal in general. By contrast, in the case of vanishingly small probability of error, separate source and channel coding is known to be asymptotically optimal. For the zero-error case, it is further shown that the joint coding gain can in fact be unbounded. Since separate coding simplifies code design and use, conditions on sources and channels for the optimality of separate coding are also derived
On inferring TCP behavior

Most of the traffic in today's Internet is controlled by the Transmission Control Protocol (TCP). Hence, the performance of TCP has a significant impact on the performance of the overall Internet. TCP is a complex protocol with many user-configurable parameters and a range of different implementations. In addition, research continues to produce new developments in congestion control mechanisms and TCP options, and it is useful to trace the deployment of these new mechanisms in the Internet. As a final concern, the stability and fairness of the current Internet relies on the voluntary use of congestion control mechanisms by end hosts. Therefore it is important to test TCP implementations for conformant end-to-end congestion control. Since web traffic forms the majority of the TCP traffic, TCP implementations in today's web servers are of particular interest. We have developed a tool called TCP Behavior Inference Tool (TBIT) to characterize the TCP behavior of a remote web server. In this paper, we describe TBIT, and present results about the TCP behaviors of major web servers, obtained using this tool. We also describe the use of TBIT to detect bugs and non-compliance in TCP implementations deployed in public web servers.
Infrastructure-assisted routing in vehicular networks

Deploying roadside access points (APs) or an infrastructure can improve data delivery. Our empirical results from real trace driven simulations show that deploying APs produces up to 5× performance gain in delivery ratio and reduces delivery delay by as much as 35% with simple routing. However, we also find that buffer resources at the APs become a critical factor and poor buffer allocation leads to marginal performance gain for inter-vehicle routing. Motivated by this important observation, we investigate the optimal infrastructure-assisted routing for inter-vehicle data delivery. It remains a challenging issue for two major reasons. First, the addition of APs dramatically changes delivery opportunities between vehicles, which has not been well understood by existing work. Second, packet forwarding and buffer allocation are inter-dependent and should be addressed together. To tackle the challenges, we first characterize packet delivery probability as a function of predicted vehicle trajectories and AP locations. Then, we formulate the coexisting problem of packet forwarding and buffer allocation as an optimization problem and show that it is a knapsack problem. We design a global algorithm to solve this optimization problem. For more realistic settings, we propose a distributed algorithm for packet forwarding and buffer allocation in which each vehicle and the APs make decisions locally. Through trace-driven simulations, we demonstrate that the distributed algorithm steadily outperforms other alternative approaches under a wide range of network configurations.
Large-scale Virtualization in the Emulab Network Testbed

Network emulation is valuable largely because of its ability to study applications running on real hosts and "somewhat real" networks. However, conservatively allocating a physical host or network link for each corresponding virtual entity is costly and limits scale. We present a system that can faithfully emulate, on low-end PCs, virtual topologies over an order of magnitude larger than the physical hardware, when running typical classes of distributed applications that have modest resource requirements. This version of Emulab virtualizes hosts, routers, and networks, while retaining near-total application transparency, good performance fidelity, responsiveness suitable for interactive use, high system throughput, and efficient use of resources. Our key design techniques are to use the minimum degree of virtualization that provides transparency to applications, to exploit the hierarchy found in real computer networks, to perform optimistic automated resource allocation, and to use feed-back to adaptively allocate resources. The entire system is highly automated, making it easy to use even when scaling to more than a thousand virtual nodes. This paper identifies the many problems posed in building a practical system, and describes the system's motivation, design, and preliminary evaluation.
Assessment of Reactive Motor Performance with Event-Related Brain Potentials: Attention Processes in Elite Table Tennis Players

Motor readiness, visual attention, and reaction time (RT) were assessed in 15 elite table tennis players (TTP) and 15 controls (C) during Posner’s cued attention task. Lateralized readiness potentials (LRP) were derived from contingent negative variation (CNV) at Sites C3 and C4, elicited between presentation of directional cueing (S1) and the appearance of the imperative stimulus (S2), to assess preparation for hand movement while P1 and N1 component amplitudes were derived from occipital event-related potentials (ERPs) in response to S2 to assess visual attention. Both groups had faster RT to validly cued stimuli and slower RT to invalidly cued stimuli relative to the RT to neutral stimuli that were not preceded by directional cueing, but the groups did not differ in attention benefit or cost. However, TTP did have faster RT to all imperative stimuli; they maintained superior reactivity to S2 whether preceded by valid, invalid, or neutral warning cues. Although both groups generated LRP in response to t.
Biological Characterization and Pluripotent Identification of Sheep Dermis-Derived Mesenchymal Stem/Progenitor Cells

Dermis-derived mesenchymal stem/progenitor cells (DMS/PCs) were a multipotential stem cell population, which has potential applications in the tissue damage repair and skin transplant. Although a large number of studies deal with the human DMS/PCs self-renewal and regulation, however, the study of livestock-derived DMS/PCs has rarely been reported. Here, sheep DMS/PCs were isolated from one-month-old sheep embryos and studied at the cellular and molecular level. And then the DMS/PCs biological characteristics were analysed by RT-PCR and immunofluorescence. Experimental results showed that DMS/PCs could be expanded for 48 passages and the cells viability and hereditary character were steady. In addition, the DMS/PCs maker β-integrin, CD71, CD44, and CD73 were expressed positively through RT-PCR and immunofluorescence. Passage 3 DMS/PCs were successfully induced to differentiate into adipocytes, osteoblasts, chondrocytes, and neurocytes, respectively. The above results suggest that DMS/PCs not only have strong self-renewal capacity but also have the potential to differentiate into adipocytes, osteoblasts, chondrocytes, and neurocytes. The study provides theoretical basis and experimental evidence for potential clinical application.
All The World's A Botfighter Stage: Notes on Location-based Multi-User Gaming

This paper investigates some aspects of how location-based game concepts are challenging the traditions of gaming. The initial hypothesis is that location-based gaming that utilizes city space as a game board seem to be in confl ict with the classical defi nitions of ‘play’ and ‘game’. The nature of pervasive gaming is investigated in relation to different levels of mobile use and the social construction of urban space. The routines attached to mobile phones are mainly connected to interpersonal communication but also include certain ‘play with location’. Therefore a mobile phone, regardless of its interface limitations, suits quite well the location-based multi-user approach. I also argue that playing in familiar real world locations brings new nuances and meanings to these places. On the other hand some elements of real life can take part in shaping the entire gaming experience.
Removal of a frameshift between the hsdM and hsdS genes of the EcoKI Type IA DNA restriction and modification system produces a new type of system and links the different families of Type I systems

The EcoKI DNA methyltransferase is a trimeric protein comprised of two modification subunits (M) and one sequence specificity subunit (S). This enzyme forms the core of the EcoKI restriction/modification (RM) enzyme. The 3′ end of the gene encoding the M subunit overlaps by 1 nt the start of the gene for the S subunit. Translation from the two different open reading frames is translationally coupled. Mutagenesis to remove the frameshift and fuse the two subunits together produces a functional RM enzyme in vivo with the same properties as the natural EcoKI system. The fusion protein can be purified and forms an active restriction enzyme upon addition of restriction subunits and of additional M subunit. The Type I RM systems are grouped into families, IA to IE, defined by complementation, hybridization and sequence similarity. The fusion protein forms an evolutionary intermediate form lying between the Type IA family of RM enzymes and the Type IB family of RM enzymes which have the frameshift located at a different part of the gene sequence.
Comparison of food recommendations varying in sustainability: Impact on dietary intake and motivation to follow recommendations

Food recommendations increasingly focus on sustainability in addition to nutritional value. By providing participants with standard versus sustainable (plant-based) dietary recommendations for 3 weeks, the present research tested the impact of recommendations on dietary compliance. Furthermore, predictors of food intake were tested across food categories. Participants in the sustainable diet condition complied less with recommendations as compared to those in the standard diet condition and were less motivated to continue complying after the intervention. Taste was the main predictor of intake across food categories. Together, this stresses the importance of considering factors stimulating consumers’ compliance when formulating food recommendations.
The periodic variations of a white-light flare observed with ULTRACAM

High time resolution observations of a white-light flare on the active star EQ PegB show evidence of intensity variations with a period of ≈10 s. The period drifts to longer values during the decay phase of the flare. If the oscillation is interpreted as an impulsively-excited, standing-acoustic wave in a flare loop, the period implies a loop length of ≈3.4 Mm and ≈6.8 Mm for the case of the fundamental mode and the second harmonic, respectively. However, the small loop lengths imply a very high modulation depth making the acoustic interpretation unlikely. A more realistic interpretation may be that of a fast-MHD wave, with the modulation of the emission being due to the magnetic field. Alternatively, the variations could be due to a series of reconnection events. The periodic signature may then arise as a result of the lateral separation of individual flare loops or current sheets with oscillatory dynamics (i.e., periodic reconnection).
Physical Characterization and Effect of Effective Surface Area on the Sensing Properties of Tin Dioxide Thin Solid Films in a Propane Atmosphere

The physical properties and the effect of effective surface area (ESA) on the sensing properties of tin dioxide [SnO2] thin films in air and propane [C3H8] atmosphere as a function of operating temperature and gas concentration have been studied in this paper. SnO2 thin films with different estimated thicknesses (50, 100 and 200 nm) were deposited on glass substrates by the chemical spray technique. Besides, they were prepared at two different deposition temperatures (400 and 475 °C). Tin chloride [SnCl4 · 5H2O] with 0.2 M concentration value and ethanol [C2H6O] were used as tin precursor and solvent, respectively. The morphological, and structural properties of the as-prepared films were analyzed by AFM and XRD, respectively. Gas sensing characteristics of SnO2 thin solid films were measured at operating temperatures of 22, 100, 200, and 300 °C, and at propane concentration levels (0, 5, 50, 100, 200, 300, 400, and 500 ppm). ESA values were calculated for each sample. It was found that the ESA increased with the increasing thickness of the films. The results demonstrated the importance of the achieving of a large effective surface area for improving gas sensing performance. SnO2 thin films deposited by spray chemical were chosen to study the ESA effect on gas sensing properties because their very rough surfaces were appropriate for this application.
Inhibition of glutathione S-transferase zeta and tyrosine metabolism by dichloroacetate: a potential unifying mechanism for its altered biotransformation and toxicity.

Dichloroacetate (DCA) inhibits its own metabolism and is converted to glyoxylate by glutathione S-transferase zeta (GSTz). GSTz is identical to maleylacetoacetate isomerase, an enzyme of tyrosine catabolism that converts maleylacetoacetate (MAA) to fumarylacetoacetate and maleylacetone (MA) to fumarylacetone. MAA and MA are alkylating agents. Rats treated with DCA for up to five days had markedly decreased hepatic GSTz activity and increased urinary excretion of MA. When dialyzed cytosol obtained from human liver was incubated with DCA, GSTz activity was unaffected. In contrast, DCA incubation inhibited enzyme activity in dialyzed hepatic cytosol from rats. Incubation of either rat or human hepatic cytosol with MA led to a dose dependent inhibition of GSTz. These data indicate that humans or rodents exposed to DCA may accumulate MA and/or MAA which inhibit(s) GSTz and, consequently, DCA biotransformation. Moreover, DCA-induced inhibition of tyrosine catabolism may account for the toxicity of this xenobiotic in humans and other species.
Analysis of the Protein Phosphotome of Entamoeba histolytica Reveals an Intricate Phosphorylation Network

Phosphorylation is the most common mechanism for the propagation of intracellular signals. Protein phosphatases and protein kinases play a dynamic antagonistic role in protein phosphorylation. Protein phosphatases make up a significant fraction of eukaryotic proteome. In this article, we report the identification and analysis of protein phosphatases in the intracellular parasite Entamoeba histolytica. Based on an in silico analysis, we classified 250 non-redundant protein phosphatases in E. histolytica. The phosphotome of E. histolytica is 3.1% of its proteome and 1.3 times of the human phosphotome. In this extensive study, we identified 42 new putative phosphatases (39 hypothetical proteins and 3 pseudophosphatases). The presence of pseudophosphatases may have an important role in virulence of E. histolytica. A comprehensive phosphotome analysis of E. histolytica shows spectacular low similarity to human phosphatases, making them potent candidates for drug target.
Translational incorporation of L‐3,4‐dihydroxyphenylalanine into proteins

An Escherichia coli cell‐free transcription/translation system was used to explore the high‐level incorporation of l‐3,4‐dihydroxyphenylalanine (DOPA) into proteins by replacing tyrosine with DOPA in the reaction mixtures. ESI‐MS showed specific incorporation of DOPA in place of tyrosine. More than 90% DOPA incorporation at each tyrosine site was achieved, allowing the recording of clean 15N‐HSQC NMR spectra. A redox‐staining method specific for DOPA was shown to provide a sensitive and generally applicable method for assessing the cell‐free production of proteins. Of four proteins produced in soluble form in the presence of tyrosine, two resulted in insoluble aggregates in the presence of high levels of DOPA. DOPA has been found in human proteins, often in association with various disease states that implicate protein aggregation and/or misfolding. Our results suggest that misfolded and aggregated proteins may result, in principle, from ribosome‐mediated misincorporation of intracellular DOPA accumulated due to oxidative stress. High‐yield cell‐free protein expression systems are uniquely suited to obtain rapid information on solubility and aggregation of nascent polypeptide chains.