Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential Binary Gene Ratio Tests Define a Novel Molecular Diagnostic Strategy for Malignant Pleural Mesothelioma

Purpose: To develop a standardized approach for molecular diagnostics, we used the gene expression ratio bioinformatic technique to design a molecular signature to diagnose malignant pleural mesothelioma (MPM) from among other potentially confounding diagnoses and differentiate the epithelioid from the sarcomatoid histologic subtype of MPM. In addition, we searched for pathways relevant in MPM in comparison with other related cancers to identify unique molecular features in MPM. Experimental Design: We conducted microarray analysis on 113 specimens including MPMs and a spectrum of tumors and benign tissues comprising the differential diagnosis of MPM. We generated a sequential combination of binary gene expression ratio tests able to discriminate MPM from other thoracic malignancies. We compared this method with other bioinformatic tools and validated this signature in an independent set of 170 samples. Functional enrichment analysis was conducted to identify differentially expressed probes. Results: A sequential combination of gene expression ratio tests was the best molecular approach to distinguish MPM from all the other samples. Bioinformatic and molecular validations showed that the sequential gene ratio tests were able to identify the MPM samples with high sensitivity and specificity. In addition, the gene ratio technique was able to differentiate the epithelioid from the sarcomatoid type of MPM. Novel genes and pathways specifically activated in MPM were identified. Conclusions: New clinically relevant molecular tests have been generated using a small number of genes to accurately distinguish MPMs from other thoracic samples, supporting our hypothesis that the gene expression ratio approach could be a useful tool in the differential diagnosis of cancers. Clin Cancer Res; 19(9); 2493–502. ©2013 AACR.
Basins of Attraction, Long-Run Stochastic Stability, and the Speed of Step-by-Step Evolution

The paper examines the behaviour of "evolutionary" models with ɛ-noise like those which have been used recently to discuss the evolution of social conventions. The paper is built around two main observations: that the "long run stochastic stability" of a convention is related to the speed with which evolution toward and away from the convention occurs, and that evolution is more rapid (and hence more powerful) when it may proceed via a series of small steps between intermediate steady states. The formal analysis uses two new measures, the radius and modified coradius, to characterize the long run stochastically stable set of an evolutionary model and to bound the speed with which evolutionary change occurs. Though not universally powerful, the result can be used to make many previous analyses more transparent and extends them by providing results on waiting times. A number of applications are also discussed. The selection of the risk dominant equilibrium in 2 × 2 games is generalized to the selection of ½-dominant equilibria in arbitrary games. Other applications involve two-dimensional local interaction and cycles as long run stochastically stable sets.
Online estimation of RF interference

Increased AP density in enterprise WLANs leads to increasing RF interference and decreasing performance. An important step towards mitigating this problem is to construct precise RF maps in the form of a conflict graph. Prior work on conflict graph construction, mostly using bandwidth tests [17], suffers from two problems: a) It is limited to static settings and cannot support mobility, and b) It incurs significant measurement overhead and must be performed offline (e.g. overnight). An alternative to bandwidth tests is "micro-probing" [4] that operates on millisecond-level time scales. Micro-probing rapidly constructs the conflict graph even while the network is in use (i.e. online). While interesting in principle, micro-probing has only been evaluated in simulation. In this work, we empirically study micro-probing on a 40-node wireless testbed. In doing so, we not only show that micro-probing is in fact practically realizable, but also present key insights that drive the design choices for our implementation. We benchmark micro-probing against bandwidth tests and find that micro-probing is just as accurate but with up to a 400 times reduction in overhead. Finally, we argue that a successful implementation of micro-probing opens up the space for further innovations in real-time WLAN adaptation and optimization.
LEAP: Looking beyond pixels with continuous-space EstimAtion of Point sources

Context. Two main classes of imaging algorithms have emerged in radio interferometry: the CLEAN algorithm and its multiple variants, and compressed-sensing inspired methods. They are both discrete in nature, and estimate source locations and intensities on a regular grid. For the traditional CLEAN-based imaging pipeline, the resolution power of the tool is limited by the width of the synthesized beam, which is inversely proportional to the largest baseline. The finite rate of innovation (FRI) framework is a robust method to find the locations of point-sources in a continuum without grid imposition. The continuous formulation makes the FRI recovery performance only dependent on the number of measurements and the number of sources in the sky. FRI can theoretically find sources below the perceived tool resolution. To date, FRI had never been tested in the extreme conditions inherent to radio astronomy: weak signal / high noise, huge data sets, large numbers of sources. Aims. The aims were (i) to adapt FRI to radio astronomy, (ii) verify it can recover sources in radio astronomy conditions with more accurate positioning than CLEAN, and possibly resolve some sources that would otherwise be missed, (iii) show that sources can be found using less data than would otherwise be required to find them, and (v) show that FRI does not lead to an augmented rate of false positives. Methods. We implemented a continuous domain sparse reconstruction algorithm in Python. The angular resolution performance of the new algorithm was assessed under simulation, and with visibility measurements from the LOFAR telescope. Existing catalogs were used to confirm the existence of sources. Results. We adapted the FRI framework to radio interferometry, and showed that it is possible to determine accurate off-grid point source locations and their corresponding intensities. In addition, FRI-based sparse reconstruction required less integration time and smaller baselines to reach a comparable reconstruction quality compared to a conventional method. The achieved angular resolution is higher than the perceived instrument resolution, and very close sources can be reliably distinguished. The proposed approach has cubic complexity in the total number (typically around a few thousand) of uniform Fourier data of the sky image estimated from the reconstruction. It is also demonstrated that the method is robust to the presence of extended-sources, and that false-positives can be addressed by choosing an adequate model order to match the noise level.
Multilingual dependency parsing: A pipeline approach

This paper develops a general framework for machine learning based dependency parsing based on a pipeline approach, where a task is decomposed into several sequential stages. To overcome the error accumulation problem of pipeline models, we propose two natural principles for pipeline frameworks: (i) make local decisions as reliable as possible, and (ii) reduce the number of sequential decisions made. We develop an algorithm that provably satises these principles and show that the proposed principles support several algorithmic choices that improve the dependency parsing accuracy signicantly. We present state of the art experimental results for English and several other languages. 1
Measuring Information Acquisition from Sensory Input Using Automated Scoring of Natural-Language Descriptions

Information acquisition, the gathering and interpretation of sensory information, is a basic function of mobile organisms. We describe a new method for measuring this ability in humans, using free-recall responses to sensory stimuli which are scored objectively using a “wisdom of crowds” approach. As an example, we demonstrate this metric using perception of video stimuli. Immediately after viewing a 30 s video clip, subjects responded to a prompt to give a short description of the clip in natural language. These responses were scored automatically by comparison to a dataset of responses to the same clip by normally-sighted viewers (the crowd). In this case, the normative dataset consisted of responses to 200 clips by 60 subjects who were stratified by age (range 22 to 85y) and viewed the clips in the lab, for 2,400 responses, and by 99 crowdsourced participants (age range 20 to 66y) who viewed clips in their Web browser, for 4,000 responses. We compared different algorithms for computing these similarities and found that a simple count of the words in common had the best performance. It correctly matched 75% of the lab-sourced and 95% of crowdsourced responses to their corresponding clips. We validated the measure by showing that when the amount of information in the clip was degraded using defocus lenses, the shared word score decreased across the five predetermined visual-acuity levels, demonstrating a dose-response effect (N = 15). This approach, of scoring open-ended immediate free recall of the stimulus, is applicable not only to video, but also to other situations where a measure of the information that is successfully acquired is desirable. Information acquired will be affected by stimulus quality, sensory ability, and cognitive processes, so our metric can be used to assess each of these components when the others are controlled.
A probabilistic linear genetic programming with stochastic context-free grammar for solving symbolic regression problems

Traditional Linear Genetic Programming algorithms are based only on the selection mechanism to guide the search. Genetic operators combine or mutate random portions of the individuals, without knowing if the result will lead to a fitter individual. Probabilistic Model Building Genetic Programming was proposed to overcome this issue through a probability model that captures the structure of the fit individuals and use it to sample new individuals. This work proposes the use of LGP with a Stochastic Context-Free Grammar, that has a probability distribution that is updated according to selected individuals. We proposed a method for adapting the grammar into the linear representation of LGP. Tests performed with the proposed probabilistic method, and with two hybrid approaches, on several symbolic regression benchmark problems show that the results are statistically better than the obtained by the traditional LGP.
Validation of SOAR VIIRS Over‐Water Aerosol Retrievals and Context Within the Global Satellite Aerosol Data Record

This study validates aerosol properties retrieved using a Satellite Ocean Aerosol Retrieval (SOAR) algorithm applied to Visible Infrared Imaging Radiometer Suite (VIIRS) measurements, from Version 1 of the VIIRS Deep Blue data set. SOAR is the over‐water complement to the over‐land Deep Blue algorithm and has two processing paths: globally, 95% of pixels are processed with the full retrieval algorithm, while the 5% of pixels in shallow or turbid (mostly coastal) waters are processed with a backup algorithm. Aerosol Robotic Network (AERONET) data are used to validate and compare the midvisible (550 nm) aerosol optical depth (AOD), Ångström exponent (AE), and fine mode fraction of AOD at 550 nm (FMF). AOD uncertainty is shown to be approximately ±(0.03 + 10%) for the full and ±(0.03 + 15%) for the backup algorithms, with a small positive median bias around 0.02. When AOD is below about 0.2, the AE and FMF have small negative offsets from AERONET around −0.15 and −0.04, respectively. For higher AOD, AE is less offset and the magnitudes of differences versus AERONET are about ±0.2 and ±0.14, respectively. Aerosol‐type classifications provided by SOAR are found to be reasonable, matching optical‐based classifications from AERONET over 80% of the time. Spatial and temporal patterns of AOD and AE are also compared with those of other contemporary over‐water satellite aerosol data sets; dependent on region, the satellite data sets show varying levels of consistency, with SOAR broadly in‐family, and the largest discrepancies in regions with persistent heavy cloud cover.
Vulnerability to assault injury: an emergency department perspective

Objective: To evaluate risk and protective factors for violence-related injuries from an emergency department (ED) perspective. Method: Three study groups were recruited: (1) patients attending a major ED who had suffered an assault (n = 148), (2) patients attending a major ED who had not suffered an assault (n = 151) and (3) non-patients from public places in Cardiff (n = 171). Participants completed one of two proforma questionnaires: questions related to sociodemographic factors including their alcohol consumption and, for those in the assault group, the circumstances of the assault injury. Results: The non-assault groups consumed more alcohol units per annum but fewer alcohol units per drinking session than the assault group. The assault group visited entertainment venues more frequently than the non-assault groups. The relationship between alcohol units consumed per drinking session and the risk of assault injury was non-linear. The risk of assault injury increased for both genders with alcohol consumption (up to 5 units for women and 11 units for men), but at a slower rate for women. The model predicted that, at zero alcohol consumption, the risk of assault injury in men and women was similar. Conclusions: In the context of the number of alcohol units consumed in a drinking session, the risk of sustaining injury in assault for men and women is different. The risk of injury in assault for men and women is the same when no alcohol is consumed. Alcohol consumption may lead to different risk-taking behaviour in men and women.
MEF/ELF4 transactivation by E2F1 is inhibited by p53

Myeloid elf-1-like factor (MEF) or Elf4 is an E-twenty-six (ETS)-related transcription factor with strong transcriptional activity that influences cellular senescence by affecting tumor suppressor p53. MEF downregulates p53 expression and inhibits p53-mediated cellular senescence by transcriptionally activating MDM2. However, whether p53 reciprocally opposes MEF remains unex-plored. Here, we show that MEF is modulated by p53 in human cells and mice tissues. MEF expression and promoter activity were suppressed by p53. While we found that MEF promoter does not contain p53 response elements, intriguingly, it contains E2F consensus sites. Subsequently, we determined that E2F1 specifically binds to MEF promoter and transactivates MEF. Nevertheless, E2F1 DNA binding and transactivation of MEF promoter was inhibited by p53 through the association between p53 and E2F1. Furthermore, we showed that activation of p53 in doxorubicin-induced senescent cells increased E2F1 and p53 interaction, diminished E2F1 recruitment to MEF promoter and reduced MEF expression. These observations suggest that p53 downregulates MEF by associating with and inhibiting the binding activity of E2F1, a novel transcriptional activator of MEF. Together with previous findings, our present results indicate that a negative regulatory mechanism exists between p53 and MEF.
An RFID Distance Bounding Protocol

Radio-frequency identification tokens, such as contactless smartcards, are vulnerable to relay attacks if they are used for proximity authentication. Attackers can circumvent the limited range of the radio channel using transponders that forward exchanged signals over larger distances. Cryptographic distance-bounding protocols that measure accurately the round-trip delay of the radio signal provide a possible countermeasure. They infer an upper bound for the distance between the reader and the token from the fact that no information can propagate faster than at the speed of light. We propose a new distance-bounding protocol based on ultra-wideband pulse communication. Aimed at being implementable using only simple, asynchronous, low-power hardware in the token, it is particularly well suited for use in passive low-cost tokens, noisy environments and high-speed applications.
Collateral Constraints and Macroeconomic Asymmetries

Using Bayesian methods, we estimate a nonlinear general equilibrium model where occasionally binding collateral constraints on housing wealth drive an asymmetry in the link between housing prices and economic activity. The estimated model shows that, as collateral constraints became slack during the housing boom of 2001-2006, expanding housing wealth made a small contribution to consumption growth. By contrast, the housing collapse that followed tightened the constraints and sharply exacerbated the recession of 2007-2009. The empirical relevance of this asymmetry is corroborated by evidence from state- and MSA-level data.
Perfluorooctane sulfonate affects proliferation and differentiation of pluripotent human teratocarcinoma cells

Perfluorinated compounds have raised concern due to their potential association with detrimental postnatal outcomes in animals and humans. We tested the effects of perfluorooctane sulfonate (PFOS) on a human pluripotent teratocarcinoma (known as NCCIT) cells as an in vitro prototype for developmental toxicity in mammals. NCCIT contains stem-cells able to differentiate into endoderm, mesoderm and ectoderm. We tested our cell model using a teratogenic compound, retinoic acid (RA), a cytotoxin, nocodazole (ND), and PFOS. We assayed cells proliferation, morphology and expression of stem cell and germ layer marker genes. PFOS reduced NCCIT cell proliferation in a concentration-dependent manner and induced morphological changes in cell cultures that resembled ectodermal phenotypes. A tendency towards a differentiated state in NCCIT was confirmed by real-time gene expression. PFOS triggered up-regulation of the gene nestin, indicative of ectodermal lineage differentiation, and interfered with the expression of the pluripotency stem-cell marker TERT. PFOS produced effects on both cells proliferation and differentiation, although not as severe as those observed for RA and ND, at levels that fall within the range of concentrations found in animal and human plasma. We discuss our findings in the context of possible interference of PFOS with the processes governing the early development of mammalian tissues.
Subspace based linear programming support vector machines

In subspace methods, the subspace associated with a class is represented by a small number of vectors called dictionaries and using the dictionaries the similarity measure is defined and an input is classified into the class with the highest similarity. Usually, each dictionary is given an equal weight. But if subspaces of different classes overlap, the similarity measures for the overlapping regions will not give useful information for classification. In this paper, we propose optimizing the weights for the dictionaries using the idea of support vector machines (SVMs). Namely, first we map the input space into the empirical feature space, perform kernel principal component analysis (KPCA) for each class, and define a similarity measure. Then considering that the similarity measure corresponds to the hyperplane, we formulate the optimization problem as maximizing the margin between the class associated with the dictionaries and the remaining classes. The optimization problem results in all-at-once formulation of linear SVMs. We demonstrate the effectiveness of the proposed method with that of the conventional methods for two-class problems.
Learning Effective Search Heuristics

SAGE.2 is a production system that improves its search strategies with practice. The program incorporates four different heuristics for assigning credit and blame, and employs a discrimination process to direct its search through the space of move-proposing rules. The system has shown its generality by learning search heuristics in five different task domains. In addition to improving its search behavior on practice problems, SAGE.2 was able to transfer its expertise to scaled-up versions of a task, and in one case transferred its acquired search strategy to problems with different initial and goal states.
Three Reverse Engineering Patterns

Whereas a design pattern describes and discusses a solution to a design problem, a reverse engineering pattern describes how to understand aspects of an object-oriented design and how to identify problems in that design. In the context of a project developing a methodology for reengineering object-oriented legacy systems into frameworks, weare working on a pattern language for reengineering. This paper presents three samples of that pattern language, all dealing with reverse engineering.
Hyphal Growth in Human Fungal Pathogens and Its Role in Virulence

Most of the fungal species that infect humans can grow in more than one morphological form but only a subset of pathogens produce filamentous hyphae during the infection process. This subset is phylogenetically unrelated and includes the commonly carried yeasts, Candida albicans, C. dubliniensis, and Malassezia spp. , and the acquired pathogens, Aspergillus fumigatus and dermatophytes such as Trichophyton rubrum and T. mentagrophytes. The primary function of hypha formation in these opportunistic pathogens is to invade the substrate they are adhered to, whether biotic or abiotic, but other functions include the directional translocation between host environments, consolidation of the colony, nutrient acquisition and the formation of 3-dimensional matrices. To support these functions, polarised hyphal growth is co-regulated with other factors that are essential for normal hypha function in vivo.
Measuring mechanical motion with a single spin

We study theoretically the measurement of a mechanical oscillator using a single two-level system as a detector. In a recent experiment, we used a single electronic spin associated with a nitrogen–vacancy center in diamond to probe the thermal motion of a magnetized cantilever at room temperature (Kolkowitz et al 2012 Science 335 1603). Here, we present a detailed analysis of the sensitivity limits of this technique, as well as the possibility to measure the zero-point motion of the oscillator. Further, we discuss the issue of measurement backaction in sequential measurements and find that although backaction heating can occur, it does not prohibit the detection of zero-point motion. Throughout the paper, we focus on the experimental implementation of a nitrogen–vacancy center coupled to a magnetic cantilever; however, our results are applicable to a wide class of spin–oscillator systems. The implications for the preparation of nonclassical states of a mechanical oscillator are also discussed.