nils-herrmann/clean_scirepeval huggingface dataset:
RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates

Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in the inferred expression levels can result. In this study, we use simulated reads generated from real transcriptomes to determine the accuracy of read mapping, and measure the error resulting from using an incomplete transcriptome. We show that the two primary sources of count- ing error are 1) alternative splice variants that share reads and 2) missing transcripts from the reference. Alternative splice variants increase the false positive rate of mapping while incomplete reference tran- scriptomes decrease the true positive rate, leading to inaccurate transcript expression levels. Grouping transcripts by gene or read sharing (similar to mapping to a reference genome) significantly decreases false positives, but only by improving the reference transcriptome itself can the missing transcript problem be addressed. We also demonstrate that employing different mapping software does not yield substantial increases in accuracy on simulated data. Finally, we show that read lengths or insert sizes must increase past 1kb to resolve mapping ambiguity.
RECONNAISSANCE OF THE HR 8799 EXOSOLAR SYSTEM. I. NEAR-INFRARED SPECTROSCOPY

We obtained spectra in the wavelength range λ = 995–1769 nm of all four known planets orbiting the star HR 8799. Using the suite of instrumentation known as Project 1640 on the Palomar 5 m Hale Telescope, we acquired data at two epochs. This allowed for multiple imaging detections of the companions and multiple extractions of low-resolution (R ∼ 35) spectra. Data reduction employed two different methods of speckle suppression and spectrum extraction, both yielding results that agree. The spectra do not directly correspond to those of any known objects, although similarities with L and T dwarfs are present, as well as some characteristics similar to planets such as Saturn. We tentatively identify the presence of CH4 along with NH3 and/or C2H2, and possibly CO2 or HCN in varying amounts in each component of the system. Other studies suggested red colors for these faint companions, and our data confirm those observations. Cloudy models, based on previous photometric observations, may provide the best explanation for the new data presented here. Notable in our data is that these presumably co-eval objects of similar luminosity have significantly different spectra; the diversity of planets may be greater than previously thought. The techniques and methods employed in this paper represent a new capability to observe and rapidly characterize exoplanetary systems in a routine manner over a broad range of planet masses and separations. These are the first simultaneous spectroscopic observations of multiple planets in a planetary system other than our own.
A new method for the extraction of mid-infrared gamma-ray emitting candidate blazars

We present a new method for identifying blazar candidates by examining the locus, i.e. the region occupied by the Fermi gamma-ray blazars in the three-dimensional color space defined by the WISE infrared colors. This method is a refinement of our previous approach that made used of the two-dimensional projection of the the distribution of WISE gamma-ray emitting blazars (the Strip) in the three WISE color-color planes. In this paper, we define the three-dimensional locus by means of a Principal Component analysis of the the colors distribution of a large sample of blazars composed by all the ROMA-BZCAT sources with counterparts in the WISE All-Sky Catalog and associated to a gamma-ray source in the second Fermi LAT catalog (2FGL) (the WISE Fermi Blazars sample, WFB). Our new procedure, as reported in [D'Abrusco et al. 2013], yields a total completeness of c=81% and total efficiency of e=97%.
Higgs Boson -- on Your Own

One of the highlights of 2012 in physics is related to two papers, published by the ATLAS and the CMS Collaborations, that announced the discovery of at least one new particle in pp collisions at CERN LHC. At least one of the properties of this new particle is found to be similar to that of the Higgs boson, the last and most difficult to find building block from the Standard Model of particle physics. Physics teachers are frequently approached by their media-educated students, who inquire about the properties of the Higgs boson, but physics teachers are rarely trained to teach this elusive aspect of particle physics in elementary, middle or junior high schools. In this paper I describe a card-game, that can be considered as a hands-on and easily accessible tool that allows interested teachers, students and also motivated lay-persons to play with the properties of the newly found Higgs-like particle. This new particle was detected through its decays to directly observable, final state particles. Many of these final state particles are represented in a deck of cards, that represent elementary particles, originally invented to popularize the physics of quark matter in the so-called Quark Matter Card Games. The Higgs decay properties can be utilized, playfully, in a Higgs boson search card game. The rules of this game illustrate also the need for some luck, to complement knowledge and memory, useful skills that this game also helps to develop. The paper is organized as a handout or booklet, that directly describes how to play the Higgs boson on Your Own card game.
Optogenetic manipulation of neural activity in C. elegans: From synapse to circuits and behaviour

The emerging field of optogenetics allows for optical activation or inhibition of excitable cells. In 2005, optogenetic proteins were expressed in the nematode Caenorhabditis elegans for the first time. Since then, C. elegans has served as a powerful platform upon which to conduct optogenetic investigations of synaptic function, circuit dynamics and the neuronal basis of behaviour. The C. elegans nervous system, consisting of 302 neurons, whose connectivity and morphology has been mapped completely, drives a rich repertoire of behaviours that are quantifiable by video microscopy. This model organism's compact nervous system, quantifiable behaviour, genetic tractability and optical accessibility make it especially amenable to optogenetic interrogation. Channelrhodopsin‐2 (ChR2), halorhodopsin (NpHR/Halo) and other common optogenetic proteins have all been expressed in C. elegans. Moreover, recent advances leveraging molecular genetics and patterned light illumination have now made it possible to target photoactivation and inhibition to single cells and to do so in worms as they behave freely. Here, we describe techniques and methods for optogenetic manipulation in C. elegans. We review recent work using optogenetics and C. elegans for neuroscience investigations at the level of synapses, circuits and behaviour.
Data Retrieval over DNS in SQL Injection Attacks

This paper describes an advanced SQL injection technique where DNS resolution process is exploited for retrieval of malicious SQL query results. Resulting DNS requests are intercepted by attackers themselves at the controlled remote name server extracting valuable data. Open source SQL injection tool sqlmap has been adjusted to automate this task. With modifications done, attackers are able to use this technique for fast and low profile data retrieval, especially in cases where other standard ones fail.
Dynamical Trading Mechanisms in Limit Order Markets

This work's main purpose is to understand the price dynamics in a generic limit order market, and illustrate a dynamical trading mechanism that can be applied to explore its market microstructure. First and foremost, we capture the iterative nature of the limit order market, and quantitatively identify its capacities as a means to develop switching schemes for the appearances of different sorts of traders. After formally introducing a dynamical trading system to replace the complex limit order market, we then study trading processes in that trading system from both deterministic and stochastic perspectives, in the purpose of recognizing conditions of general instability and stochastic stability in the trading system. In the final part of this work, the dynamics of the spread and mid-price in a controlled trading system will be investigated, which fairly serves to verify the robustness of stochastic stability appearing in an uncontrolled trading system.
A Greedy Approximation of Bayesian Reinforcement Learning with Probably Optimistic Transition Model

Bayesian Reinforcement Learning (RL) is capable of not only incorporating domain knowledge, but also solving the exploration-exploitation dilemma in a natural way. As Bayesian RL is intractable except for special cases, previous work has proposed several approximation methods. However, these methods are usually too sensitive to parameter values, and finding an acceptable parameter setting is practically impossible in many applications. In this paper, we propose a new algorithm that greedily approximates Bayesian RL to achieve robustness in parameter space. We show that for a desired learning behavior, our proposed algorithm has a polynomial sample complexity that is lower than those of existing algorithms. We also demonstrate that the proposed algorithm naturally outperforms other existing algorithms when the prior distributions are not significantly misleading. On the other hand, the proposed algorithm cannot handle greatly misspecified priors as well as the other algorithms can. This is a natural consequence of the fact that the proposed algorithm is greedier than the other algorithms. Accordingly, we discuss a way to select an appropriate algorithm for different tasks based on the algorithms' greediness. We also introduce a new way of simplifying Bayesian planning, based on which future work would be able to derive new algorithms.
Flow Motifs Reveal Limitations of the Static Framework to Represent Human interactions

Networks are commonly used to define underlying interaction structures where infections, information, or other quantities may spread. Although the standard approach has been to aggregate all links into a static structure, some studies have shown that the time order in which the links are established may alter the dynamics of spreading. In this paper, we study the impact of the time ordering in the limits of flow on various empirical temporal networks. By using a random walk dynamics, we estimate the flow on links and convert the original undirected network (temporal and static) into a directed flow network. We then introduce the concept of flow motifs and quantify the divergence in the representativity of motifs when using the temporal and static frameworks. We find that the regularity of contacts and persistence of vertices (common in email communication and face-to-face interactions) result on little differences in the limits of flow for both frameworks. On the other hand, in the case of communication within a dating site and of a sexual network, the flow between vertices changes significantly in the temporal framework such that the static approximation poorly represents the structure of contacts. We have also observed that cliques with 3 and 4 vertices containing only low-flow links are more represented than the same cliques with all high-flow links. The representativity of these low-flow cliques is higher in the temporal framework. Our results suggest that the flow between vertices connected in cliques depend on the topological context in which they are placed and in the time sequence in which the links are established. The structure of the clique alone does not completely characterize the potential of flow between the vertices.
UNVEILING THE NATURE OF THE UNIDENTIFIED GAMMA-RAY SOURCES. V. ANALYSIS OF THE RADIO CANDIDATES WITH THE KERNEL DENSITY ESTIMATION

Nearly one-third of the γ-ray sources detected by Fermi are still unidentified, despite significant recent progress in this area. However, all of the γ-ray extragalactic sources associated in the second Fermi-LAT catalog have a radio counterpart. Motivated by this observational evidence, we investigate all the radio sources of the major radio surveys that lie within the positional uncertainty region of the unidentified γ-ray sources (UGSs) at a 95% level of confidence. First, we search for their infrared counterparts in the all-sky survey performed by the Wide-field Infrared Survey Explorer (WISE) and then we analyze their IR colors in comparison with those of the known γ-ray blazars. We propose a new approach, on the basis of a two-dimensional kernel density estimation technique in the single [3.4] − [4.6] −  μm WISE color–color plot, replacing the constraint imposed in our previous investigations on the detection at 22 μm of each potential IR counterpart of the UGSs with associated radio emission. The main goal of this analysis is to find distant γ-ray blazar candidates that, being too faint at 22 μm, are not detected by WISE and thus are not selected by our purely IR-based methods. We find 55 UGSs that likely correspond to radio sources with blazar-like IR signatures. An additional 11 UGSs that have blazar-like IR colors have been found within the sample of sources found with deep recent Australia Telescope Compact Array observations.
The New Milky Way: a wide-field survey of optical transients near the Galactic plane

Currently, it may take days for a bright nova outburst to be detected. With the few exceptions, little is known about novae behaviour prior to maximum light. A theoretically-predicted population of ultra-fast novae with t2<1d is evading observational discovery because it is not possible to routinely organize fast follow-up observations of nova candidates. With the aim of brining the detection time of novae and other bright (V<13.5) optical transients from days down to hours or less, we develop an automated wide-field (8x6 deg.) system capable of surveying the whole Milky Way area visible from the observing site in one night. The system is built using low-cost mass-produced components and the transient detection pipeline is based on the open source VaST software. We describe the instrument design and report results of the first observations conducted in October-November 2011 and January-April 2012. The results include the discovery of Nova Sagittarii 2012 No. 1 as well as two X-ray emitting cataclysmic variables 1RXS J063214.8+25362 and XMMSL1 J014956.7+533504. The rapid detection of Nova Sagittarii 2012 No. 1 enabled us to conduct its X-ray and UV observations with Swift 22 hours after discovery (~31 hour after the outburst onset). All images obtained during the transient search survey are available online.
Optical thickness determination of hexagonal boron nitride flakes

Optical reflectivity contrast provides a simple, fast, and noninvasive method for characterization of few monolayer samples of two-dimensional materials. Here, we apply this technique to measure the thickness of thin flakes of hexagonal Boron Nitride (hBN), which is a material of increasing interest in nanodevice fabrication. The optical contrast shows a strong negative peak at short wavelengths and zero contrast at a thickness dependent wavelength. The optical contrast varies linearly for 1-80 layers of hBN, which permits easy calibration of thickness. We demonstrate the applicability of this quick characterization method by comparing atomic force microscopy and optical contrast results.
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database

The biological significance of genomic features is often context dependent. Annotating a particular dataset with existing external data can provide insight into function.



We present CruzDB, a fast and intuitive programmatic interface to the University of California, Santa Cruz (UCSC) genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using microRNA binding sites as examples, and further demonstrate its utility with three biological discoveries. First, DNA replication timing is stratified in gene regions-exons tend to replicate early and introns late during S phase. Second, several non-coding variants associated with cognitive functions map to lincRNA transcripts of relevant function, suggesting potential function of these regulatory RNAs in neuronal diseases. Third, lamina-associated genomic regions are highly enriched in olfaction-related genes, indicating a role of nuclear organization in their regulation.
US Corporate Bond Yield Spread: A default risk debate

According to theoretical models of valuing risky corporate securities, risk of default is primary component in overall yield spread. However, sizable empirical literature considers it otherwise by giving more importance to non-default risk factors. Current study empirically attempts to provide relative solution to this conundrum by presuming that problem lies in the subjective empirical treatment of default risk. By using post-hoc estimator approach of Lubotsky & Wittenberg (2006), we construct an efficient indicator for risk of default, by using sample of 252 US non-financial corporate data (2000-2010). On average, our results validate that almost 48% of change in yield spread is explained by default risk especially in recent financial crisis period (2007-2009). Hence, our results relatively suggest that potential problem lies in the ad-hoc measurement methods used in existing empirical literature
Cosmology with Ricci dark energy

We assume the cosmological dark sector to consist of pressureless matter and holographic dark energy with a cutoff length proportional to the Ricci scale. The requirement of separate energymomentum conservation of the components is shown to establish a relation between the matter fraction and the (necessarily time-dependent) equation-of-state parameter of the dark energy. Focusing on intrinsically adiabatic pressure perturbations of the dark-energy component, the matter perturbations are found as linear combinations of the total energy-density perturbations of the cosmic medium and the relative (nonadiabatic) perturbations of the components. The resulting background dynamics is consistent with observations from supernovae of type Ia, baryonic acoustic oscillations and the differential age of old objects. The perturbation dynamics, on the other hand, is plagued by instabilities which excludes any phantom-type equation of state. The only stable configuration is singled out by a fixed relation between the present matter fraction m0 and the present value !0 of the equation-of-state parameter of the dark energy. However, this instabilityavoiding configuration is only marginally consistent with the observationally preferred background values of the mentioned parameters.
The Evolutionary Vaccination Dilemma in Complex Networks

In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so that individuals take or do not take the vaccine upon their previous experience. Our framework thus puts in competition two well-known dynamical properties of scale-free networks: the fast propagation of diseases and the promotion of cooperative behaviors. Our results show that when vaccine is perfect, scale-free networks enhance the vaccination behavior with respect to random graphs with homogeneous connectivity patterns. However, when imperfection appears we find a crossover effect so that the number of infected (vaccinated) individuals increases (decreases) with respect to homogeneous networks, thus showing the competition between the aforementioned properties of scale-free graphs.
Study of some steller iron group fusion materials for (n,p) reactions

The excitation functions for (n,p) reactions from reaction threshold to 24 MeV on some important iron (Fe) group target elements for astrophysical (n, p) reactions such as Si, Ca, Sc, Ti, Cr, Fe, Co and Ni were calculated using TALYS-1.0 nuclear model code. The new calculations on the excitation functions Of 28Si(n,p)28Al, 29Si(n, p)29Al, 42Ca(n, p)42K, 45Sc(n, p)45Ca, 46Ti(n,p)46Sc, 52Cr(n, p)52V, 53Cr(n, p)53V, 54Fe(n,p)54Mn, 57Fe(n,p)57Mn, 59Co(n, p)59Fe, 58Ni(n, p)58Co and 60Ni(n, p)60Co reactions have been carried out up to 24 MeV incident neutron energy. In these calculations, the pre-equilibrium and equilibrium effects have been investigated. Statistical model calculations, based on the Hauser-Feshbach formalism, have been carried out using the TALYS-1.0 and were compared with existing experimental data as well as with evaluated data files (Experimental Nuclear Reaction Data (EXFOR).According to these calculations, we assume that these model calculations can be applied to some heavy elements, ejected into interstellar medium by dramatic supernova events.
Ghost propagator and ghost-gluon vertex from Schwinger-Dyson equations

The research of J. P. is supported by the Spanish MEYC under Grant No. FPA2011-23596. The work of A. C. A is supported by the National Council for Scientific and Technological Development-CNPq under the Grant No. 306537/2012-5 and Project No. 473260/2012-3 and by Sao Paulo Research Foundation-FAPESP through Project No. 2012/15643-1.
Angular momentum blockade in nanoscale high-Tc superconducting grains

We discuss the angular momentum blockade in small d-wave superconducting grains in an external field. We find that abrupt changes in the angular momentum state of the condensate, angular momentum blockade, occur as a result of changes in the angular momentum of the condensate in an external magnetic field. The effect represents a direct analogy with the Coulomb blockade. We use the Ginzburg–Landau formalism to illustrate how a magnetic field induces a deviation from the d-wave symmetry which is described by a (dx2−y2 + idxy)-order parameter. We derive the behavior of the volume magnetic susceptibility as a function of the magnetic field, and corresponding magnetization jumps at critical values of the field that should be experimentally observable in superconducting grains.
A biologically-motivated system is poised at a critical state

We explore the critical behaviors in the dynamics of information transfer of a biologically-inspired system by an individual-based model. "Quorum response", a type of social interaction which has been recognized taxonomically in animal groups, is applied as the sole interaction rule among particles. We assume a truncated Gaussian distribution to quantitatively depict the distribution of the particles' vigilance level and find that by fine-tuning the parameters of the mean and the standard deviation of the Gaussian distribution, the system is poised at a critical state in the dynamics of information transfer. We present the phase diagrams to exhibit that the phase line divides the parameter space into a super-critical and a sub-critical zone, in which the dynamics of information transfer varies largely.
Topic Discovery through Data Dependent and Random Projections

We present algorithms for topic modeling based on the geometry of cross-document word-frequency patterns. This perspective gains significance under the so called separability condition. This is a condition on existence of novel-words that are unique to each topic. We present a suite of highly efficient algorithms with provable guarantees based on data-dependent and random projections to identify novel words and associated topics. Our key insight here is that the maximum and minimum values of cross-document frequency patterns projected along any direction are associated with novel words. While our sample complexity bounds for topic recovery are similar to the state-of-art, the computational complexity of our random projection scheme scales linearly with the number of documents and the number of words per document. We present several experiments on synthetic and real-world datasets to demonstrate qualitative and quantitative merits of our scheme.