Miracle-dz/UniFAR-FTUs huggingface dataset:
Helicobacter pylori and toll-like receptor agonists induce syndecan-4 expression in an NF-κB-dependent manner

The syndecans are a family of transmembrane heparan sulfate proteoglycans (HSPG) that have been implicated in a wide variety of biological functions including the regulation of growth factor signaling, adhesion, tumorigenesis, and inflammation. In the current studies, we examined the regulation of syndecan-4 gene expression in gastric epithelial cells and macrophages in response to infection with live Helicobacter pylori and purified toll-like receptor (TLR) agonists. H. pylori, PAM₃CSK₄ (a TLR2 agonist), and Escherichia coli flagellin (a TLR5 agonist) all induced the rapid expression of syndecan-4 mRNA in MKN45 gastric epithelial cells. Similarly, lipopolysaccharide (LPS) (a TLR4 agonist) also induced the expression of syndecan-4 in macrophages. The H. pylori- and TLR-induced increase in syndecan-4 mRNA was blocked by the proteosome inhibitor MG-132 suggesting a role for nuclear factor [kappa]B (NF-[kappa]B) in the regulation of syndecan-4 gene expression. An 895-bp fragment of the human syndecan-4 promoter was cloned upstream of the luciferase reporter. When transfected into MKN45 cells, the activity of this promoter was inducible by H. pylori and TLR agonists. Inducible activity of the syndecan-4 promoter was blocked by cotransfection with a dominant negative I[kappa]B[alpha] expression plasmid. Electrophoretic mobility shift assays (EMSA) demonstrated the presence of a highly conserved NF-[kappa]B-binding site. Mutation of this site within the context of the full-length syndecan-4 promoter resulted in a complete loss of responsiveness to H. pylori and TLR agonists. These results thus demonstrate that the response of the syndecan-4 gene to infectious agents, or their products, is a direct result of NF-[kappa]B binding to the promoter and induction of de novo transcription.
Consistent, small effects of treefall disturbances on the composition and diversity of four Amazonian forests

Understanding the resilience of moist tropical forests to treefall disturbance events is important for understanding the mechanisms that underlie species coexistence and for predicting the future composition of these ecosystems. Here, we test whether variation in the functional composition of Amazonian forests determines their resilience to disturbance. We studied the legacy of natural treefall disturbance events in four forests across Amazonia that differ substantially in functional composition. We compared the composition and diversity of all free‐standing woody stems 2–10 cm diameter in previously disturbed and undisturbed 20 × 20 m subplots within 55, one‐hectare, long‐term forest inventory plots. Overall, stem number increased following disturbance, and species and functional composition shifted to favour light‐wooded, small‐seeded taxa. Alpha‐diversity increased, but beta‐diversity was unaffected by disturbance, in all four forests. Changes in response to disturbance in both functional composition and alpha‐diversity were, however, small (2 – 4% depending on the parameter) and similar among forests. Synthesis. This study demonstrates that variation in the functional composition of Amazonian forests does not lead to large differences in the response of these forests to treefall disturbances, and overall, these events have a minor role in maintaining the diversity of these ecosystems.
An Equivariant Fast Fourier Transform Algorithm

This paper presents a generalization of the Cooley-Tukey fast Fourier transform algorithm that respects group symmetries. The algorithm, when applied to a function invariant under a group of symmetries, fully exploits these symmetries to reduce both the number of arithmetic operations and the amount of memory used. The symmetries accommodated by the algorithm include all of the crystallographic groups. These groups arise in crystallographic structure analysis, which was the motivating application for the algorithm presented in this paper.
Interval Routing Schemes for Circular-Arc Graphs

Interval routing is a space efficient method to realize a distributed routing function. In this paper we show that every circular-arc graph allows a shortest path strict 2-interval routing scheme, i.e., by introducing a global order on the vertices and assigning at most two (strict) intervals in this order to the ends of every edge allows to depict a routing function that implies exclusively shortest paths. Since circular-arc graphs do not allow shortest path 1-interval routing schemes in general, the result implies that the class of circular-arc graphs has strict compactness 2, which was a hitherto open question. Additionally, we show that the constructed 2-interval routing scheme is a 1-interval routing scheme with at most one additional interval assigned at each vertex and we an outline algorithm to calculate the routing scheme for circular-arc graphs in O(n^2) time, where n is the number of vertices.
Threshold broadcast encryption with reduced complexity

Threshold broadcast encryption (TBE) is a promising extension of threshold cryptography with its advantages over traditional threshold cryptosystems, such as eliminating the need of a trusted party, the ability of setting up the system by individual users independently and the ability of choosing the threshold parameter and the group of privileged receivers at the time of encryption. An ElGamal-based solution for TBE was proposed by Ghodosi et al. In this paper, we propose an improved ElGamal-based TBE scheme with reduced transmission cost.
The Geographic Reach of Market and Non – Market Channels of University Research Commercialization

This paper compares the geographic “reach” of knowledge flows from university inventions through two important channels: market contracts (licenses) and non–market “spillovers” exemplified by patent citations. We find that knowledge flows through market transactions to be more geographically localized than those operating through non–market spillovers. Moreover, the differential effects of distance on licenses and citations are most pronounced for exclusively licensed university patents. We interpret these findings as reflecting the incomplete nature of licensing contracts and the need for licensees to maintain access to inventor know– how for many university inventions. Such access appears to be less important for inventions that are non–exclusively licensed (e.g. “research tools”). JEL Classifications: O31, O32, R12
Berberine Inhibited Radioresistant Effects and Enhanced Anti-Tumor Effects in the Irradiated-Human Prostate Cancer Cells

The purpose of this study was to elucidate the mechanism underlying enhanced radiosensitivity to ^60Co γ-irradiation in human prostate PC-3 cells pretreated with berberine. The cytotoxic effect of the combination of berberine and irradiation was superior to that of berberine or irradiation alone. Cell death and Apoptosis increased significantly with the combination of berberine and irradiation. Additionally, ROS generation was elevated by berberine with or without irradiation. The antioxidant NAC inhibited berberine and radiation-induced cell death. Bax, caspase-3, p53, p38, and JNK activation increased, but activation of Bcl-2, ERK, and HO-1 decreased with berberine treatment with or without irradiation. Berberine inhibited the anti-apoptotic signal pathway involving the activation of the HO-1/NF-κB-mediated survival pathway, which prevents radiation-induced cell death. Our data demonstrate that berberine inhibited the radioresistant effects and enhanced the radiosensitivity effects in human prostate cancer cells via the MAPK/ caspase-3 and ROS pathways.
A Meiotic Chromosomal Core Consisting of Cohesin Complex Proteins Recruits DNA Recombination Proteins and Promotes Synapsis in the Absence of an Axial Element in Mammalian Meiotic Cells

ABSTRACT The behavior of meiotic chromosomes differs in several respects from that of their mitotic counterparts, resulting in the generation of genetically distinct haploid cells. This has been attributed in part to a meiosis-specific chromatin-associated protein structure, the synaptonemal complex. This complex consist of two parallel axial elements, each one associated with a pair of sister chromatids, and a transverse filament located between the synapsed homologous chromosomes. Recently, a different protein structure, the cohesin complex, was shown to be associated with meiotic chromosomes and to be required for chromosome segregation. To explore the functions of the two different protein structures, the synaptonemal complex and the cohesin complex, in mammalian male meiotic cells, we have analyzed how absence of the axial element affects early meiotic chromosome behavior. We find that the synaptonemal complex protein 3 (SCP3) is a main determinant of axial-element assembly and is required for attachment of this structure to meiotic chromosomes, whereas SCP2 helps shape the in vivo structure of the axial element. We also show that formation of a cohesin-containing chromosomal core in meiotic nuclei does not require SCP3 or SCP2. Our results also suggest that the cohesin core recruits recombination proteins and promotes synapsis between homologous chromosomes in the absence of an axial element. A model for early meiotic chromosome pairing and synapsis is proposed.
Life Satisfaction Over Time Among Rural Low-Income Mothers

The satisfaction with life (SWL) among rural low-income mothers was assessed using a sample of 163 mothers who participated in a multi-state, three-year longitudinal study. Dependent variables included those that represented various forms of capital (health, human, personal and social) as well as the mothers’ levels of life satisfaction from prior years. Nearly two-thirds of the rural mothers were satisfied with their life in all three years. Their level of satisfaction appeared to be constant, however, such persistence had a time frame of only one year. In all three years, their depression score and the adequacy of their income had a significant effect on SWL. Their confidence as a parent and home ownership affected their life satisfaction during two years. Finally, their satisfaction with social relationships, age of the youngest child, and total number of children had an impact on their life satisfaction for one year.
Low-Cost Fiber-Tip Fabry-Perot Interferometer and its Application for Transverse Load Sensing

A Fabry-Perot interferometer sensor based on a fiber-tip bubble-structure micro-cavity is proposed, fabricated, and demonstrated for transverse load sensing. The micro-cavity is fabricated by using arc discharge at the end of a multimode fiber which has been processed with chemical etching. A transverse load sensitivity of 3.64 nm/N and a relative low temperature sensitivity of about 2 pm/ ◦ C are experimentally demonstrated for the proposed fiber-tip bubble-structure micro-cavity sensor. The sensor has the advantages of low-cost, ease of fabrication and compact size, which make it a promising candidate for transverse load sensing in harsh environments.
The Jeans mass and the origin of the knee in the IMF

We use numerical simulations of the fragmentation of a 1000 M ⊙ molecular cloud and the formation of a stellar cluster to study how the initial conditions for star formation affect the resulting initial mass function (IMF). In particular, we are interested in the relation between the thermal Jeans mass in a cloud and the knee of the IMF, i.e. the mass separating the region with a flat IMF slope from that typified by a steeper, Salpeter-like, slope. In three isothermal simulations with M Jeans = 1,2 and 5 M ⊙ , the number of stars formed, at comparable dynamical times, scales roughly with the number of initial Jeans masses in the cloud. The mean stellar mass also increases (though less than linearly) with the initial Jeans mass in the cloud. It is found that the IMF in each case displays a prominent knee, located roughly at the mass scale of the initial Jeans mass. Thus clouds with higher initial Jeans masses produce IMFs which are shallow to higher masses. This implies that a universal IMF requires a physical mechanism that sets the Jeans mass to be near 1 M ⊙ . Simulations including a barotropic equation of state as suggested by Larson, with cooling at low densities followed by gentle heating at higher densities, are able to produce realistic IMFs with the knee located at ≈1 M ⊙ , even with an initial M Jeans = 5 M ⊙ . We therefore suggest that the observed universality of the IMF in the local Universe does not require any fine tuning of the initial conditions in star forming clouds but is instead imprinted by details of the cooling physics of the collapsing gas.
Molecular Evolution of the TET Gene Family in Mammals

Ten-eleven translocation (TET) proteins, a family of Fe2+- and 2-oxoglutarate-dependent dioxygenases, are involved in DNA demethylation. They also help regulate various cellular functions. Three TET paralogs have been identified (TET1, TET2, and TET3) in humans. This study focuses on the evolution of mammalian TET genes. Distinct patterns in TET1 and TET2 vs. TET3 were revealed by codon-based tests of positive selection. Results indicate that TET1 and TET2 genes have experienced positive selection more frequently than TET3 gene, and that the majority of codon sites evolved under strong negative selection. These findings imply that the selective pressure on TET3 may have been relaxed in several lineages during the course of evolution. Our analysis of convergent amino acid substitutions also supports the different evolutionary dynamics among TET gene subfamily members. All of the five amino acid sites that are inferred to have evolved under positive selection in the catalytic domain of TET2 are localized at the protein’s outer surface. The adaptive changes of these positively selected amino acid sites could be associated with dynamic interactions between other TET-interacting proteins, and positive selection thus appears to shift the regulatory scheme of TET enzyme function.
Video Segmentation and Camera Motion CharacterizationUsing Compressed

We address the problem of automatically extracting visual indexes from videos, in order to provide sophisticated access methods to the contents of a video server. We focus on two tasks, namely the decomposition of a video clip into uniform segments (shots), and the characterization of each shot by camera motion parameters. For the rst task we use a Bayesian classiication approach to detecting scene cuts by analyzing motion vectors. For the second task a least-squares tting procedure determines the pan/tilt/zoom camera parameters. In order to guarantee the highest processing speed, all techniques process and analyze directly MPEG-1 motion vectors, without need for video decompression. Experimental results are reported for a database of news video clips.
An Efficient Scalable Spatial Data Search for Location-Aware Mobile Services

Various studies related to spatial indices are currently being conducted. Most of these studies focus on lowering the costs for indexed searches in on-demand environments during spatial query processing. However, on-demand environments often have issues with service delays when there is a congestion of the query on the server when dealing with information about complicated moving objects. Therefore, a study on spatial indices that considers broadcast environment is required. Studies on information transfer in broadcast environments should consider the characteristics of one-dimensional sequential flow. However, studies thus far on indexing methods that consider such characteristic are insufficient. In particular, there has been no study that considers both the data transfer sequence and an index structure capable of managing a moving object within a broadcast environment. In this paper, we propose a data transfer method that considers the location/distribution of objects and the air index structure for the location management of moving objects within a broadcast environment. The results from theoretical analyses and experiments show the proposed algorithms that use the GSI method are scalable and energy efficient for range queries and k-nearest neighbor queries.
A Distributed Demand Response Control Strategy Using Lyapunov Optimization

Motivated by the potential ability of heating ventilation and air-conditioning (HVAC) systems in demand response (DR), we propose a distributed DR control strategy to dispatch the HVAC loads considering the current aggregated power supply (including the intermittent renewable power supply). The control objective is to reduce the variation of nonrenewable power demand without affecting the user-perceived quality of experience. To solve the problem, first, a queueing model is built for the thermal dynamics of the HVAC unit based on the equivalent thermal parameters (ETP) model. Second, optimization problems are formulated. Based on an extended Lyapunov optimization approach, a control algorithm is proposed to approximately solve the problems. Third, a DR control strategy with a low communication requirement is proposed to implement the control algorithm in a distributed way. Finally, practical data sets are used to evaluate and demonstrate the effectiveness and efficiency of the proposed control algorithm.
Trust overlay networks for global reputation aggregation in P2P grid computing

This paper presents a new approach to trusted grid computing in a peer-to-peer (P2P) setting. Trust and security are essential to establish lasting working relationships among the peers. A P2P reputation system collects peer trust scores and aggregates them to yield a global reputation. We use a new trust overlay network (TON) to model the trust relationships among the peers. After analyzing the eBay transaction trace data, we discover a power-law distribution in user feedbacks. We develop a new reputation system, PowerTrust, to leverage power-law feedback characteristics. The PowerTrust system is built with locality-preserving hash functions and a lookahead random walk strategy. Dynamic system reconfiguration is enabled by the use of power nodes with well-established reputations. Through P2P simulation experiments on distributed file sharing and grid parameter-sweeping applications (PSA), we demonstrate the PowerTrust advantages in fast reputation convergence and accurate ranking of peer reputations. We report performance results with enhanced P2P query success rate, shortened job makespan, and increased job success rate in scalable P2P grid applications
The connection between submillimeter continuum flux and binary separation in young binaries: evidence of interaction between stars and disks

We present 800 micron continuum photometry of pre-main-sequence binary stars with projected separations a_p < 150 AU in the Sco-Oph star-forming region. Combining our observations with published 1300 micron photometry, we find that binaries in Sco-Oph with 1 < a_p < 50--100 AU have lower submillimeter fluxes than wider binaries or single stars, as previously found for Taurus- Auriga binaries. The wide binaries and single stars have indistinguishable submillimeter flux distributions. Thus, binary companions with separations less than 50--100 AU significantly influence the nature of associated disks. We have explored the hypothesis that the reduction in submillimeter flux is the result of gaps cleared in disks by companions. Gap clearing produces the qualitative dependence of submillimeter flux on binary separation, and a simple model suggests that large gaps in disks with surface densities typical of wide-binary or single-star disks can reduce submillimeter fluxes to levels consistent with the observed limits. This model shows that the present submillimeter flux upper limits do not necessarily imply a large reduction in disk surface densities. Two-thirds of the young binaries were detected by IRAS, showing that most binaries have circumstellar disks. These fluxes place lower limits of 10^{-5} M_sun on circumstellar disk masses. The submillimeter fluxes place upper limits of 0.005 M_sun on circumbinary disk masses. Thus massive circumbinary disks are rare among binaries with separations between a few AU and 100 AU. Circumbinary disks are found around some close binaries.
Telomere length measurement by a novel monochrome multiplex quantitative PCR method

The current quantitative polymerase chain reaction (QPCR) assay of telomere length measures telomere (T) signals in experimental DNA samples in one set of reaction wells, and single copy gene (S) signals in separate wells, in comparison to a reference DNA, to yield relative T/S ratios that are proportional to average telomere length. Multiplexing this assay is desirable, because variation in the amount of DNA pipetted would no longer contribute to variation in T/S, since T and S would be collected within each reaction, from the same input DNA. Multiplexing also increases throughput and lowers costs, since half as many reactions are needed. Here, we present the first multiplexed QPCR method for telomere length measurement. Remarkably, a single fluorescent DNA-intercalating dye is sufficient in this system, because T signals can be collected in early cycles, before S signals rise above baseline, and S signals can be collected at a temperature that fully melts the telomere product, sending its signal to baseline. The correlation of T/S ratios with Terminal Restriction Fragment (TRF) lengths measured by Southern blot was stronger with this monochrome multiplex QPCR method (R2 = 0.844) than with our original singleplex method (R2 = 0.677). Multiplex T/S results from independent runs on different days were highly reproducible (R2 = 0.91).
Modern Portal Tools And Solutions with Vine Toolkit for Science Gateways

Motivation: Science Gateways are web portal environments targeted for given community and dedicated to the specific scientific domain. End users require different set of tools, applications, data integration patterns to be able to satisfy special demands of different kind of scientific research approach. To let users benefit from computational resources and storage, a portal framework should support access to the grid and storage services. To accomplish this, PSNC [1] developed Vine Toolkit framework (in short Vine) integrated with Adobe Flex/BlazeDs technologies, offering unified abstract API for different grid middleware infrastructures. Additionally it automates integration process with portal frameworks like Liferay [2] or GridSphere [3], allowing to set up a portal solution in relatively short time. The Vine project also introduces so called subprojects, which can extend core API or define new business components at low level or web applications at high level. This way Science Gateway prototyping process is definitely shortened. The architecture of the solution allows programmers to prepare building blocks which can be reused in a simple manner and applied for different gateways. This article presents different tools and solutions prepared by means of Vine framework as an illustration of success stories.