Miracle-dz/UniFAR-FTUs huggingface dataset:
Adenovirus-mediated down-regulation of X-linked inhibitor of apoptosis protein inhibits colon cancer

Our previous studies and those of others have indicated that X-linked inhibitor of apoptosis protein (XIAP) holds promise as a target gene in colon cancer gene therapy. In this study, we constructed an adenoviral vector to deliver small hairpin RNA (shRNA) against XIAP (XIAP-shRNA) into colon cancer cells and tested its therapeutic efficacy in vitro and in vivo. We first confirmed an overexpression of XIAP in colon cancer cells and human cancer tissues. We then designed XIAP-small interfering RNA (siRNA) and confirmed the knockdown effect of these siRNAs in colon cancer cells. The sequences of the effective siRNAs were converted into shRNA and then packed into replication-deficient adenoviral vectors using BLOCK-iT Adenoviral RNAi Expression System to generate Adv-XIAP-shRNA. Infection of HT29 and HCT116 cells with Adv-XIAP-shRNA led to enhanced caspase-3 activity, which was associated with increased apoptosis and reduced cell proliferation. The therapeutic effect of Adv-XIAP-shRNA was then tested in xenograft tumors in nude mice. We showed that treatment of the xenograft tumors derived from HCT116 cells with Adv-XIAP-shRNA resulted in a retardation of tumor growth, which was associated with enhanced apoptosis, increased caspase-3 activity, and reduced expression of proliferating cell nuclear antigen in the tumor tissues. Treatment of xenograft tumors with Adv-XIAP-shRNA did not affect the expressions of inflammatory cytokines in tumor-bearing mice. Thus, Adv-XIAP-shRNA–mediated down-regulation of XIAP exerts a therapeutic effect in colon cancer by promoting apoptosis and inhibiting proliferation of colon cancer cells, and the antitumor effect of Adv-XIAP-shRNA was unlikely to be related to virus-induced immune response. [Mol Cancer Ther 2009;8(9):2762–70]
An Evaluation Technique for Binarization Algorithms

Document binarization is an active research area for many years. The choice of the most appropriate binarization algorithm for each case proved to be a very difficult procedure itself. In this paper, we propose a new technique for the validation of document binarization algorithms. Our method is simple in its implementation and can be performed on any binarization algorithm since it doesn't require anything more than the binarization stage. As a demonstration of the proposed technique, we use the case of degraded historical documents. Then we apply the proposed technique to 30 binarization algorithms. Experimental results and conclusions are presented.
Structural Operational Semantics Sos '04

This article proposes a new mathematical definition of the execution of pure Prolog, in the form of axioms in a structural operational semantics. The main advantage of the model is its ease in representing backtracking, due to the functionality of the transition relation and its converse. Thus, forward and backward derivation steps are possible. A novel concept of stages is introduced, as a refinement of final states, which captures the evolution of a backtracking computation. An advantage over the traditional stack-of-stacks approaches is a modularity property. Finally, the model combines the intuition of the traditional ‘Byrd box’ metaphor with a compact representation of execution state, making it feasible to formulate and prove theorems about the model. In this paper we introduce the model and state some useful properties.
Role of calcium-phosphate product and bone-associated proteins on vascular calcification in renal failure.

Cardiovascular events are the most frequent cause of death in patients with chronic renal failure ([1][1],[2][2]). Heterotopic calcification of blood vessel walls occurs frequently with advanced age, atherosclerosis, and diabetes mellitus ([3][3]). In chronic renal failure, autopsy ([4][4],[5][5])
Winter 12-1-2013 An Algorithm for Triangulating 3 D Polygons

OF THE THESIS AN ALGORITHM FOR TRIANGULATING 3D POLYGONS by Ming Zou Master of Science in Computer Science Washington University in St. Louis, December 2013 Research Advisor: Professor Tao Ju In this thesis, we present an algorithm for obtaining a triangulation of multiple, non-planar 3D polygons. The output minimizes additive weights, such as the total triangle areas or the total dihedral angles between adjacent triangles. Our algorithm generalizes a classical method for optimally triangulating a single polygon. The key novelty is a mechanism for avoiding non-manifold outputs for two and more input polygons without compromising optimality. For better performance on real-world data, we also propose an approximate solution by feeding the algorithm with a reduced set of triangles. In particular, we demonstrate experimentally that the triangles in the Delaunay tetrahedralization of the polygon vertices offer a reasonable trade off between performance and optimality.
MODUS: model-based user interfaces prototyping

Model-based methodologies, supported by automatic generation, have been proposed as a solution to reduce software development costs. In the case of interactive computing systems specific challenges arise. On the one hand, a high level of automation requires the use of detailed models, which is contrary to the iterative development process, based on the progressive refinement of user interface mockups, typical of user centered development processes. On the other hand, layered software architectures imply a distinction between the models used in the business logic and in the user interface, raising consistency problems between the models at each level. This article proposes a tool supported approach to user interface generation directly from the architectural models of the business logic. In many situations, user interfaces provide similar features inside a specific domain. The identification of the application domain is thus a key factor in supporting the automation of the generation process.
A Replicative Self-Renewal Model for Long-Lived Plasma Cells: Questioning Irreversible Cell Cycle Exit

Plasma cells are heterogenous in terms of their origins, secretory products, and lifespan. A current paradigm is that cell cycle exit in plasma cell differentiation is irreversible, following a pattern familiar in short-lived effector populations in other hemopoietic lineages. This paradigm no doubt holds true for many plasma cells whose lifespan can be measured in days following the completion of differentiation. Whether this holds true for long-lived bone marrow plasma cells that are potentially maintained for the lifespan of the organism is less apparent. Added to this the mechanisms that establish and maintain cell cycle quiescence in plasma cells are incompletely defined. Gene expression profiling indicates that in the transition of human plasmablasts to long-lived plasma cells a range of cell cycle regulators are induced in a pattern that suggests a quiescence program with potential for cell cycle re-entry. Here a model of relative quiescence with the potential for replicative self-renewal amongst long-lived plasma cells is explored. The implications of such a mechanism would be diverse, and the argument is made here that current evidence is not sufficiently strong that the possibility should be disregarded.
Introducing agile methods: three years of experience

The work summarizes three years of experience of introducing agile practices in academic environments. The perceptions of students from four different academic programs (Diploma, Applied Bachelor's, Bachelor's and Master's) from two institutions are analyzed. Specifically, pair programming, test-driven development and project planning using the planning game were studied in detail. Overwhelmingly, students' experiences are positive and their opinions indicate the preference to continue to use agile practices if allowed. No major problems with agile techniques appeared in the evaluation contexts and benefits in these contexts have been seen.
Methylesters of plant oils as diesel fuels, either straight or in blends

Engine and vehicle tests were carried out with three alternative Diesel fuels: straight methylester of soybean oil (MESO), 75 to 25 gasoil-MESO blend, and 68-23-9 gasoil-MESO-ethanol (anhydrous) blend. Fuel-relevant characteristics of the three Diesel alternatives are given, together with the phase diagram of the ternary blend. Power, torque and volumetric brake specific fuel consumption in an unmodified IDI Diesel engine reflect mainly the net volumetric heating values. Smoke decreases with the presence of oxygenate compounds as does the emission of CO, as measured on the chassis dynamometer. A rigorous durability bench test on straight MESO shows results entirely within VW specifications. Analyses have indicated that, for IDI engines, no lube-oil problems are anticipated. Investigation of compatibility of MESO with fuel system material reveals considerable similarity to gasoil, but some items may require adaptation or even substitution. 3 figures, 9 tables.
Nonspherical perturbations of critical collapse and cosmic censorship

Choptuik has demonstrated that naked singularities can arise in gravitational collapse from smooth, asymptotically flat initial data, and that such data have codimension one in spherical symmetry. Here we show, for perfect fluid matter with an equation of state p=? /3, by perturbing around spherical symmetry, that such data have in fact codimension one in the full phase space, at least in a neighborhood of spherically symmetric data.
AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants

Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250 000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL:http://probes.pw. usda.gov/AIM
Action Spectrum for Melatonin Regulation in Humans: Evidence for a Novel Circadian Photoreceptor

The photopigment in the human eye that transduces light for circadian and neuroendocrine regulation, is unknown. The aim of this study was to establish an action spectrum for light-induced melatonin suppression that could help elucidate the ocular photoreceptor system for regulating the human pineal gland. Subjects (37 females, 35 males, mean age of 24.5 ± 0.3 years) were healthy and had normal color vision. Full-field, monochromatic light exposures took place between 2:00 and 3:30 A.M. while subjects' pupils were dilated. Blood samples collected before and after light exposures were quantified for melatonin. Each subject was tested with at least seven different irradiances of one wavelength with a minimum of 1 week between each nighttime exposure. Nighttime melatonin suppression tests (n = 627) were completed with wavelengths from 420 to 600 nm. The data were fit to eight univariant, sigmoidal fluence–response curves (R2 = 0.81–0.95). The action spectrum constructed from these data fit an opsin template (R2 = 0.91), which identifies 446–477 nm as the most potent wavelength region providing circadian input for regulating melatonin secretion. The results suggest that, in humans, a single photopigment may be primarily responsible for melatonin suppression, and its peak absorbance appears to be distinct from that of rod and cone cell photopigments for vision. The data also suggest that this new photopigment is retinaldehyde based. These findings suggest that there is a novel opsin photopigment in the human eye that mediates circadian photoreception.
Hybridizing evolutionary algorithms with opportunistic local search

There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt raised the question if there are problems where VDS performs badly. We answer this question in the affirmative in the following way. We analyze MAs with VDS, which is also known as Kernighan-Lin for the TSP, on an artificial problem and show that MAs with a simple first-improvement local search outperform VDS. Moreover, we show that the performance gap is exponential. We analyze the features leading to a failure of VDS and derive a new local search operator, coined Opportunistic Local Search, that can easily overcome regions of the search space where local optima are clustered. The power of this new operator is demonstrated on the Rastrigin function encoded for binary hypercubes. Our results provide further insight into the problem of how to prevent local search algorithms to get stuck in local optima from a theoretical perspective. The methods stem from discrete probability theory and combinatorics.
Scalable Temporal Latent Space Inference for Link Prediction in Dynamic Social Networks (Extended Abstract)

Understanding and characterizing the processes driving social interactions is one of the fundamental problems in social network research. A particular instance of this problem, known as link prediction, has recently attracted considerable attention in various research communities. Link prediction has many important commercial applications, e.g., recommending friends in an online social network such as Facebook and suggesting interesting pins in a collection sharing network such as Pinterest. This work is focused on the temporal link prediction problem: Given a sequence of graph snapshots G1, · ··, Gt from time 1 to t, how do we predict links in future time t + 1? To perform link prediction in a network, one needs to construct models for link probabilities between pairs of nodes. A temporal latent space model is proposed that is built upon latent homophily assumption and temporal smoothness assumption. First, the proposed modeling allows to naturally incorporate the well-known homophily effect (birds of a feather flock together). Namely, each dimension of the latent space characterizes an unobservable homogeneous attribute, and shared attributes tend to create a link in a network.
Forecasting potential global environmental costs of livestock production 2000–2050

Food systems—in particular, livestock production—are key drivers of environmental change. Here, we compare the contributions of the global livestock sector in 2000 with estimated contributions of this sector in 2050 to three important environmental concerns: climate change, reactive nitrogen mobilization, and appropriation of plant biomass at planetary scales. Because environmental sustainability ultimately requires that human activities as a whole respect critical thresholds in each of these domains, we quantify the extent to which current and future livestock production contributes to published estimates of sustainability thresholds at projected production levels and under several alternative endpoint scenarios intended to illustrate the potential range of impacts associated with dietary choice. We suggest that, by 2050, the livestock sector alone may either occupy the majority of, or significantly overshoot, recently published estimates of humanity’s “safe operating space” in each of these domains. In light of the magnitude of estimated impacts relative to these proposed (albeit uncertain) sustainability boundary conditions, we suggest that reining in growth of this sector should be prioritized in environmental governance.
Overview of Intercalibration of Satellite Instruments

Intercalibration of satellite instruments is critical for detection and quantification of changes in the Earth's environment, weather forecasting, understanding climate processes, and monitoring climate and land cover change. These applications use data from many satellites; for the data to be interoperable, the instruments must be cross-calibrated. To meet the stringent needs of such applications, instruments must provide reliable, accurate, and consistent measurements over time. Robust techniques are required to ensure that observations from different instruments can be normalized to a common scale that the community agrees on. The long-term reliability of this process needs to be sustained in accordance with established reference standards and best practices. Furthermore, establishing physical meaning to the information through robust Système International d'unités traceable calibration and validation (Cal/Val) is essential to fully understand the parameters under observation. The processes of calibration, correction, stability monitoring, and quality assurance need to be underpinned and evidenced by comparison with “peer instruments” and, ideally, highly calibrated in-orbit reference instruments. Intercalibration between instruments is a central pillar of the Cal/Val strategies of many national and international satellite remote sensing organizations. Intercalibration techniques as outlined in this paper not only provide a practical means of identifying and correcting relative biases in radiometric calibration between instruments but also enable potential data gaps between measurement records in a critical time series to be bridged. Use of a robust set of internationally agreed upon and coordinated intercalibration techniques will lead to significant improvement in the consistency between satellite instruments and facilitate accurate monitoring of the Earth's climate at uncertainty levels needed to detect and attribute the mechanisms of change. This paper summarizes the state-of-the-art of postlaunch radiometric calibration of remote sensing satellite instruments through intercalibration.
Combining universal beauty and cultural context in a unifying model of visual aesthetic experience

In this work, I propose a model of visual aesthetic experience that combines formalist and contextual aspects of aesthetics. The model distinguishes between two modes of processing. First, perceptual processing is based on the intrinsic form of an artwork, which may or may not be beautiful. If it is beautiful, a beauty-responsive mechanism is activated in the brain. This bottom–up mechanism is universal amongst humans; it is widespread in the visual brain and responsive across visual modalities. Second, cognitive processing is based on contextual information, such as the depicted content, the intentions of the artist or the circumstances of the presentation of the artwork. Cognitive processing is partially top–down and varies between individuals according to their cultural experience. Processing in the two channels is parallel and largely independent. In the general case, an aesthetic experience is induced if processing in both channels is favorable, i.e., if there is resonance in the perceptual processing channel (“aesthetics of perception”), and successful mastering in the cognitive processing channel (“aesthetics of cognition”). I speculate that this combinatorial mechanism has evolved to mediate social bonding between members of a (cultural) group of people. Primary emotions can be elicited via both channels and modulate the degree of the aesthetic experience. Two special cases are discussed. First, in a subset of (post-)modern art, beauty no longer plays a prominent role. Second, in some forms of abstract art, beautiful form can be enjoyed with minimal cognitive processing. The model is applied to examples of Western art. Finally, implications of the model are discussed. In summary, the proposed model resolves the seeming contradiction between formalist perceptual approaches to aesthetic experience, which are based on the intrinsic beauty of artworks, and contextual approaches, which account for highly individual and culturally dependent aspects of aesthetics.
Palaeofire activity in western Tasmania: climate drivers and land-cover changes

Southern Annular Mode (SAM) is the primary mode of atmospheric variability in the Southern Hemisphere. While it is well established that the current anthropogenic-driven trend in SAM is responsible for decreased rainfall in southern Australia, its role in driving fire regimes in this region has not been explored. We examined the connection between fire activity and SAM in southwest Tasmania, which lies in the latitudinal band of strongest correlation between SAM and rainfall in the Southern Hemisphere. We reveal that fire activity during a fire season is significantly correlated with the phase of SAM in the preceding year using superposed epoch analysis. We then synthesized new 14 charcoal records from southwest Tasmania spanning the last 1000 years, revealing a tight coupling between fire activity and SAM at centennial timescales, observing a multi-century increase in fire activity over the last 500 years and a spike in fire activity in the 21st century in response to natural and anthropogenic SAM trends.
Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

We describe a general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and integrates a residue neighboring network approach. Our process achieves stable and high accuracies on both DNA- and RNA-binding proteins and illustrates how the main driving forces for nucleic acid binding are common. Because of the effective integration of the synergetic effects of the network of neighboring residues and the fact that the prediction yields a hierarchical scoring on the protein surface, energy funnels for nucleic acid binding appear on protein surfaces, pointing to the dynamic process occurring in the binding of nucleic acids to proteins.
Bandwidth Adapted Hierarchical Multicast Overlay

As the infrastructure-centric model of peer-to-peer streaming, recent overlay construction schemes compose a hierarchical topology of peers by grouping them into clusters. There is a server in each cluster that receives data from the source and relays it to its cluster members. In this paper, we propose an alternative infrastructure-centric peer-to-peer framework called BAHMO that constructs a hierarchical multicast tree. BAHMO does not utilize server bandwidth and rely only on peer bandwidth for data transfers. It achieves both the stability of the infrastructure-centric model and the bandwidth efficiency of the fully-distributed model. Bandwidth assignment for inter-cluster data transfers affects the performance of BAHMO. We propose a bandwidth transfer scheme that results in bandwidth adaptation along the global overlay of BAHMO that removes the requirement for change in the global overlay due to peer dynamics. We evaluate BAHMO in a number of network topologies in terms of bandwidth requirements.