Miracle-dz/UniFAR-FTUs huggingface dataset:
NetAligner—a network alignment server to compare complexes, pathways and whole interactomes

The many ongoing genome sequencing initiatives are delivering comprehensive lists of the individual molecular components present in an organism, but these reveal little about how they work together. Follow-up initiatives are revealing thousands of interrelationships between gene products that need to be analyzed with novel bioinformatics approaches able to capture their complex emerging properties. Recently, we developed NetAligner, a novel network alignment tool that allows the identification of conserved protein complexes and pathways across organisms, providing valuable hints as to how those interaction networks evolved. NetAligner includes the prediction of likely conserved interactions, based on evolutionary distances, to counter the high number of missing interactions in current interactome networks, and a fast assessment of the statistical significance of individual alignment solutions, which increases its performance with respect to existing tools. The web server implementation of the NetAligner algorithm presented here features complex, pathway and interactome to interactome alignments for seven model organisms, namely Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. The user can query complexes and pathways of arbitrary topology against a target species interactome, or directly compare two complete interactomes to identify conserved complexes and subnetworks. Alignment solutions can be downloaded or directly visualized in the browser. The NetAligner web server is publicly available at http://netaligner.irbbarcelona. org/.
SET8 methyltransferase activity during the DNA double-strand break response is required for recruitment of 53BP1

DNA double‐strand breaks (DSBs) activate a signaling pathway known as the DNA damage response (DDR) which via protein–protein interactions and post‐translational modifications recruit signaling proteins, such as 53BP1, to chromatin flanking the lesion. Depletion of the SET8 methyltransferase prevents accumulation of 53BP1 at DSBs; however, this phenotype has been attributed to the role of SET8 in generating H4K20 methylation across the genome, which is required for 53BP1 binding to chromatin, prior to DNA damage. Here, we report that SET8 acts directly at DSBs during the DNA damage response (DDR). SET8 accumulates at DSBs and is enzymatically active at DSBs. Depletion of SET8 just prior to the induction of DNA damage abrogates 53BP1's accumulation at DSBs, suggesting that SET8 acts during DDR. SET8's occupancy at DSBs is regulated by histone deacetylases (HDACs). Finally, SET8 is functionally required for efficient repair of DSBs specifically via the non‐homologous end‐joining pathway (NHEJ). Our findings reveal that SET8's active role during DDR at DSBs is required for 53BP1's accumulation.
Learning to Answer Questions from Wikipedia Infoboxes

A natural language interface to answers on the Web can help us access information more ef-ﬁciently. We start with an interesting source of information—infoboxes in Wikipedia that summarize factoid knowledge—and develop a comprehensive approach to answering questions with high precision. We ﬁrst build a system to access data in infoboxes in a structured manner. We use our system to construct a crowdsourced dataset of over 15,000 high-quality, diverse questions. With these questions, we train a convolutional neural network model that outperforms models that achieve top results in similar answer selection tasks.
Resource Bounded Unprovability of Computational Lower Bounds

This paper introduces new notions of asymptotic proofs, PT(polynomial-time)-extensions, PTM(polynomial-time Turing machine)-omega-consistency, etc. on formal theories of arithmetic including PA (Peano Arithmetic). This paper shows that P not= NP (more generally, any super-polynomial-time lower bound in PSPACE) is unprovable in a PTM-omega-consistent theory T, where T is a consistent PT-extension of PA. This result gives a unified view to the existing two major negative results on proving P not= NP, Natural Proofs and relativizable proofs, through the two manners of characterization of PTM-omega-consistency. We also show that the PTM-omega-consistency of T cannot be proven in any PTM-omega-consistent theory S, where S is a consistent PT-extension of T.
The Role Object Pattern

An object-oriented system is typically based on a set of key abstractions. Each key abstraction is modeled by a corresponding class in terms of abstract state and behavior. This usually works fine for the design of smaller applications. However, once we want to scale up the system into an integrated suite of applications, we have to deal with different clients that need context-specific views on our key abstractions.
Elevated percentage of perforin positive cells in active pulmonary tuberculosis.

BACKGROUND & OBJECTIVES Perforin is one of the major effector molecules of cytotoxic cells associated with killing of cells harbouring intracellular bacterial infection. The precise role of perforin positive cells in tuberculosis still remains controversial. The present study was done to determine the number of circulating CD4(+) and CD8(+) perforin positive cells to assess the level of cytotoxic response against Mycobacterium tuberculosis in patients with pulmonary tuberculosis. METHODS Intracellular perforin and surface CD4 and CD8 staining of peripheral blood lymphocytes was done using specific monoclonal antibodies and enumerated using flowcytometry. RESULTS A significantly decreased total lymphocytes (P<0.01), CD4 (P<0.001) and CD8 (P<0.01) lymphocyte counts in PTB patients was observed compared to normal healthy individuals (NHS). Intracellular perforin staining showed significantly elevated percentages of total (P<0.05) and CD8 (P<0.01) perforin positive cells in PTB patients compared to NHS. However, the absolute counts of total, CD4 and CD8 cells positive for perforin were similar in patients and NHS. INTERPRETATION & CONCLUSION Our results suggest that during active stage of pulmonary tuberculosis there was an increased percentage of CD8 cells positive for perforin, irrespective of their absolute counts. Further, CD8(+) perforin positive cells may have increased cytolytic activity against M. tuberculosis in active pulmonary tuberculosis.
An Experimental Investigation of Steady and Unsteady Combustion Phenomena in the HyShot II Combustor

A series of experiments has been carried out in the HEG facility (High Enthalpy Shock Tunnel, Gottingen) to obtain detailed measurements on the HyShotII scramjet configuration under both steady and unsteady combustion conditions. Standard pressure measurements are performed, but a main focus of this campaign is the use of optical and visualization techniques: high-speed visualizations of OH* chemiluminescence together with pulsed-diode laser Schlieren imaging are employed to gain information about the approximate flame location as well as the interaction between the flow features and combustion characteristics. In particular, this allows an unprecedented level of insight into the transient combustioninduced phenomena present in the combustion chamber at high equivalence ratios. Measurements are compared with computational data obtained from the DLR TAU code. I. Introduction
Communicating citizenship in China’s digital society

ABSTRACT This research explores the (inter-) cultural dimension of communicating citizenship in China’s new media environment. It adopts speech codes theory as a theoretical and methodological framework to examine the historically situated and socially constructed meanings of citizenship and the normative communicative conduct for practicing “good citizenship” in China. Through a systematic analysis of Chinese online discourse surrounding two social events, this study captures one speech code pertaining to communicating citizenship that is premised on a paradox – citizenship is interpreted by the Chinese as a legal entitlement that they deserve, but it is simultaneously treated as an aspirational and unattainable ideal. Additionally, speaking sensibly and morally with a communal orientation is heavily emphasized in this speech code as it is considered a valuable communicative practice for performing “good citizenship. ” Finally, participating in online collective actions such as “topping posts” is rendered an acceptable and effective way to communicate and enact citizen rights in China.
On the statistical performance of music for distributed sources

This paper addresses the statistical behaviour of the MUSIC method for DoA estimation, in a scenario where each source signal direct path is disturbed by a clutter spreading in an angular neighborhood around the source DoA. In this scenario, it is well-known that subspace methods performance suffers from an additional clutter subspace, which breaks the orthogonality between the source steering vectors and noise subspace. To perform a statistical analysis of the MUSIC DoA estimates, we consider an asymptotic regime in which both the number of sensors and the sample size tend to infinity at the same rate, and rely on classical random matrix theory results. We establish the consistency of the MUSIC estimates and provide numerical results illustrating their performance in this non standard scenario.
The Role of Platelets in the Pathogenesis of Viral Hemorrhagic Fevers

Viral hemorrhagic fevers (VHF) are acute zoonotic diseases that, early on, seem to cause platelet destruction or dysfunction. Here we present the four major ways viruses affect platelet development and function and new evidence of molecular factors that are preferentially induced by the more pathogenic members of the families Flaviviridae, Bunyaviridae, Arenaviridae, and Filoviridae. A systematic search was performed through the main medical electronic databases using as parameters all current findings concerning platelets in VHF. Additionally, the review contains information from conference proceedings.
Financial Statement Quality and Debt Contracting: Evidence from a Survey of Commercial Lenders

We survey commercial bank lenders to better understand how they evaluate and react to variation in financial statement quality and how they view recent changes in accounting standards. A unique aspect of this study is that our respondents focus on medium-size loans to private companies. In fact, more than 90 percent of the survey respondents primarily make credit decisions on loans between $250 thousand and $50 million. This is in contrast to prior archival research, which focuses primarily on very large loans to public firms or very small loans to private firms. We find that lenders in our sample distinguish among financial statements in terms of quality, including conservatism, primarily on the basis of accrual patterns and restatements. While this general result holds throughout our sample, financial statement quality is substantially more important for lenders making larger loans (over $10 million) as compared to very small loans (under $1 million). In addition, bank lenders are much more likely to respond to low quality reporting with collateral and guarantee requirements than with an increase in the interest rate charged. This finding is consistent for lenders making both larger and smaller loans. Finally, despite concerns in the academic literature, bank lenders in our sample actually hold a neutral-to-positive view of recent changes in accounting standards. In addition, most do not support current efforts to exempt private companies from some accounting standards.
The Genetic Architecture of Neuroticism in 3301 Dutch Adolescent Twins as a Function of Age and Sex: A Study From the Dutch Twin Register

Abstract The objective of this study was to estimate the magnitude of genetic and environmental influences to variation in adolescent neuroticism as a function of age and sex. Neuroticism was assessed using the Amsterdamse Biografische Vragenlijst (ABV): a self-report personality instrument similar in content to the Eysenck Personality Questionnaire. Genetic modeling procedures, including age as modifier, were fitted to the total sample of 3301 Dutch adolescent twins aged 12 to 17 years (mean age 15.5). Significant influences of additive genetic factors (.59, 95% confidence intervals [CI] .54–.63) and unshared environmental factors (.41, 95% CI .37–.45) were found. Our data did not support a role of shared environment. Results showed that different genes may influence variation in neuroticism between girls and boys. No interaction was found between the variance components and age. Results generally support prior findings in adults and young children that neuroticism is influenced principally by additive genetic and unique environmental factors. The magnitude of the genetic component appears higher in the present sample of adolescents than in most studies of adults. The present study suggests that, in adolescence, different genes are expressed in boys and girls.
Topology, decoherence, and semiclassical gravity.

We address the issue of recovering the time-dependent Schr\"odinger equation from quantum gravity in a natural way. To reach this aim it is necessary to understand the nonoccurrence of certain superpositions in quantum gravity. We explore various possible explanations and their relation. These are the delocalization of interference terms through interaction with irrelevant degrees of freedom (decoherence), gravitational anomalies, and the possibility of \ensuremath{\theta} states. The discussion is carried out in both the geometrodynamical and connection representations of canonical quantum gravity.
Future Inequality in CO 2 Emissions and the Projected Impact of Abatement Proposals

The authors wish to thank Thomas Selden for helping develop the emissions projections model referenced in this paper and his encouragement to examine its distribution implications. Gratitude is also due Robin Hahnel and Robert Lerman. The views expressed here are those of the authors and should not be attributed to the U.S. government nor to the World Bank.
Extending naïve Bayes classifiers using long itemsets

Itemsets provide local descriptions of the data. This work proposes to use itemsets as basic means for classification purposes too. To enable this, the concept of class support SUpi of an itemset is introduced, i.e., how many times an itemset occurs when a specific class Ci is present. Class supports of frequent itemsets are computed in the training phase. Upon arrival of a new case to be classified, some of the generated itemsets are selected and their class supports SUpi are used to compute the probability that the case belongs to class cc The result is the class ci with highest such probability. We show that selecting and combining many and long itemsets providing new evidence (interesting) is an effective strategy for computing the class probabilities. The proposed classification technique is called Large Bayes as it happens to reduce to Naive Bayes classifier when all itemsets selected are of size one only. Experimental results on a large number of benchmark data sets show that Large Bayes consistently outperforms the widely used Ndive Bayes classifier. In many cases, Large Bayes is also superior to other state of the art classification methods such as C4.5, CBA (a recently proposed rule classifier built from association rules), and TAN (a Bayesian network extension of Ndive Bayes).
Intellectual Property Rights and Economic Growth

Interest in links between protection of intellectual property and growth has been revived by developments in new growth theory and by the WTO's TRIPS Agreement. The relationship between the strength of a country's intellectual property rights (IPRs) regime and rate of growth is ambiguous from a theoretical standpoint, reflecting the variety of channels through which technology can be acquired and their differing importance at different stages of development. We investigate the impact of IPR protection on economic growth in a panel of 79 countries using threshold regression analysis. We show that whilst the effect of IPR protection on growth depends upon the level of development, it is positively and significantly related to growth for low- and high-income countries, but not for middle-income countries. This suggests that, although IPR protection encourages innovation in high-income countries, and technology flows to low-income countries, middle-income countries may have offsetting losses from reduced scope for imitation. Copyright © 2006 The Authors; Journal compilation © 2006 Blackwell Publishing Ltd.
Aerosol and Cloud Microphysical Characteristics of Rifts and Gradients in Maritime Stratocumulus Clouds

A cloud rift is characterized as a large-scale, persistent area of broken, low-reflectivity stratocumulus clouds usually surrounded by a solid deck of stratocumulus. A rift observed off the coast of California was investigated using an instrumented aircraft to compare the aerosol, cloud microphysical, and thermodynamic properties in the rift with those of the surrounding solid stratocumulus deck. The microphysical characteristics in the solid stratocumulus deck differ substantially from those of a broken, cellular rift where cloud droplet concentrations are a factor of 2 lower than those in the solid cloud. Furthermore, cloud condensation nuclei (CCN) concentrations were found to be about 3 times greater in the solid-cloud area compared with those in the rift. Although drizzle was observed near cloud top in parts of the solid stratocumulus cloud, the largest drizzle rates were associated with the broken clouds within the rift area and with extremely large effective droplet sizes retrieved from satellite data. Minimal thermodynamic differences between the rift and solid cloud deck were observed. In addition to marked differences in particle concentrations, evidence of a mesoscale circulation near the solid cloud–rift boundary is presented. This mesoscale circulation may provide a mechanism for maintaining a rift, but further study is required to understand the initiation of a rift and the conditions that may cause it to fill. A review of results from previous studies indicates similar microphysical characteristics in rift features sampled serendipitously. These observations indicate that cloud rifts are depleted of aerosols through the cleansing associated with drizzle and are a manifestation of natural processes occurring in marine stratocumulus.
Evaluating Risk Measures and Capital Allocations Based on Multi-Losses Driven by a Heavy-Tailed Background Risk: The Multivariate Pareto-II Model

Evaluating risk measures, premiums, and capital allocation based on dependent multi-losses is a notoriously difficult task. In this paper, we demonstrate how this can be successfully accomplished when losses follow the multivariate Pareto distribution of the second kind, which is an attractive model for multi-losses whose dependence and tail heaviness are influenced by a heavy-tailed background risk. A particular attention is given to the distortion and weighted risk measures and allocations, as well as their special cases such as the conditional layer expectation, tail value at risk, and the truncated tail value at risk. We derive formulas that are either of closed form or follow well-defined recursive procedures. In either case, their computational use is straightforward.
The 18-kDa Translocator Protein (TSPO) Disrupts Mammary Epithelial Morphogenesis and Promotes Breast Cancer Cell Migration

Mitochondria play important roles in cancer progression and have emerged as viable targets for cancer therapy. Increasing levels of the outer mitochondrial membrane protein, 18-kDa translocator protein (TSPO), are associated with advancing breast cancer stage. In particular, higher TSPO levels are found in estrogen receptor (ER)-negative breast tumors, compared with ER-positive tumors. In this study, we sought to define the roles of TSPO in the acquisition of breast cancer malignancy. Using a three-dimensional Matrigel culture system, we determined the impact of elevated TSPO levels on mammary epithelial morphogenesis. Our studies demonstrate that stable overexpression of TSPO in mammary epithelial MCF10A acini drives proliferation and provides partial resistance to luminal apoptosis, resulting in enlarged acinar structures with partially filled lumen that resemble early stage breast lesions leading to breast cancer. In breast cancer cell lines, TSPO silencing or TSPO overexpression significantly altered the migratory activity. In addition, we found that combination treatment with the TSPO ligands (PK 11195 or Ro5-4864) and lonidamine, a clinical phase II drug targeting mitochondria, decreased viability of ER-negative breast cancer cell lines. Taken together, these data demonstrate that increases in TSPO levels at different stages of breast cancer progression results in the acquisition of distinct properties associated with malignancy. Furthermore, targeting TSPO, particularly in combination with other mitochondria-targeting agents, may prove useful for the treatment of ER-negative breast cancer.
Performance Analysis of Computational Imaging Systems and its Practical Implications

Over the last decade, a number of Computational Imaging (CI) systems have been proposed for tasks such as motion deblurring, defocus deblurring and multispectral imaging. These techniques increase the amount of light reaching the sensor via multiplexing and then undo the deleterious effects of multiplexing by appropriate reconstruction algorithms. Given the widespread appeal and the considerable enthusiasm generated by these techniques, a detailed performance analysis of the benefits conferred by this approach is important. Unfortunately, a detailed analysis of CI has proven to be a challenging problem because performance depends equally on three components: (1) the optical multiplexing, (2) the noise characteristics of the sensor, and (3) the reconstruction algorithm which typically uses signal priors. A few recent papers [10], [9], [42] have performed analysis taking multiplexing and noise characteristics into account. However, analysis of CI systems under state-of-the-art reconstruction algorithms, most of which exploit signal prior models, has proven to be unwieldy. In this paper, we present a comprehensive analysis framework incorporating all three components. In order to perform this analysis, we model the signal priors using a Gaussian Mixture Model (GMM). A GMM prior confers two unique characteristics. Firstly, GMM satisfies the universal approximation property which says that any prior density function can be approximated to any fidelity using a GMM with appropriate number of mixtures. Secondly, a GMM prior lends itself to analytical tractability allowing us to derive simple expressions for the ‘minimum mean square error’ (MMSE) which we use as a metric to characterize the performance of CI systems. We use our framework to analyze several previously proposed CI techniques (focal sweep, flutter shutter, parabolic exposure, etc.), giving conclusive answer to the question: ‘How much performance gain is due to use of a signal prior and how much is due to multiplexing? Our analysis also clearly shows that multiplexing provides significant performance gains above and beyond the gains obtained due to use of signal priors.