Miracle-dz/UniFAR-FTUs huggingface dataset:
The periodicity of the η Carinae events

Extensive spectral observations of η Carinae over the last cycle, and particularly around the 2003.5 low-excitation event, have been obtained. The variability of both narrow and broad lines, when combined with data taken from two earlier cycles, reveal a common and well-defined period. We have combined the cycle lengths derived from the many lines in the optical spectrum with those from broad-band X-rays, optical and near-infrared observations, and obtained a period length of P pres = 2022.7 ± 1.3 d. Spectroscopic data collected during the last 60 yr yield an average period of P avg = 2020 ± 4 d, consistent with the present-day period. The period cannot have changed by more than AP/P = 0.0007 since 1948. This confirms the previous claims of a true, stable periodicity, and gives strong support to the binary scenario. We have used the disappearance of the narrow component of He I 6678 to define the epoch of the Cycle 11 minimum, To = JD 245 2819.8. The next event is predicted to occur on 2009 January 11 (±2 d). The dates for the start of the minimum in other spectral features and broad-bands are very close to this date, and have well-determined time-delays from the He I epoch.
Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions

MOTIVATION Analyzing short time-courses is a frequent and relevant problem in molecular biology, as, for example, 90% of gene expression time-course experiments span at most nine time-points. The biological or clinical questions addressed are elucidating gene regulation by identification of co-expressed genes, predicting response to treatment in clinical, trial-like settings or classifying novel toxic compounds based on similarity of gene expression time-courses to those of known toxic compounds. The latter problem is characterized by irregular and infrequent sample times and a total lack of prior assumptions about the incoming query, which comes in stark contrast to clinical settings and requires to implicitly perform a local, gapped alignment of time series. The current state-of-the-art method (SCOW) uses a variant of dynamic time warping and models time series as higher order polynomials (splines). RESULTS We suggest to model time-courses monitoring response to toxins by piecewise constant functions, which are modeled as left-right Hidden Markov Models. A Bayesian approach to parameter estimation and inference helps to cope with the short, but highly multivariate time-courses. We improve prediction accuracy by 7% and 4%, respectively, when classifying toxicology and stress response data. We also reduce running times by at least a factor of 140; note that reasonable running times are crucial when classifying response to toxins. In conclusion, we have demonstrated that appropriate reduction of model complexity can result in substantial improvements both in classification performance and running time. AVAILABILITY A Python package implementing the methods described is freely available under the GPL from http://bioinformatics.rutgers. edu/Software/MVQueries/.
Intracellular ATP Assay of Live Cells Using PTD-Conjugated Luciferase

Luciferase is a sensitive, reliable biological sensor used for measuring ATP. However, its widespread application in drug discovery and toxicology studies has been limited due to unavoidable cell extraction processes, which cause inaccurate measurements of intracellular ATP and obstruct the application of homogenous high-throughput screening. Recently, we developed a protein transduction domain-conjugated luciferase (PTD-Luc) for measuring cellular uptake efficacy. In this study, we evaluated the applicability of PTD-Luc to an intracellular ATP assay of live cells. The predominant fluorescence of Alexa 647-PTD-Luc was in the cytosol, whereas the fluorescence of Alexa 647-Luc was visualized surrounding the cell membrane, as confirmed by Western blot analysis. In vitro, PTD-Luc could detect less than 10–9 M ATP, and the correlation between the luciferase activity of PTD-Luc and the ATP content was strong (R = 0.999, p < 0.001). In vivo, luminescence signals of PTD-Luc detected intracellular ATP in as few as 50 HeLa cells, with a strong correlation between luminescence and cell number, suggesting high sensitivity and reliability. Furthermore, two blockers of the glycolytic pathway (2-deoxyglucose and iodoacetic acid) inhibited the signal in a dose-dependent manner, whereas potassium cyanide, an inhibitor of oxidative phosphorylation, had no effect on intracellular ATP in vivo, as seen with the PTD-Luc sensor. These data show that PTD-Luc can directly measure the intracellular ATP content in live cells, allowing real-time kinetic studies, suggesting that it is a promising tool for high-throughput drug screening and cytotoxicity assays.
Blind Low Complexity Time-Of-Arrival Estimation Algorithm for UWB Signals

This letter presents a novel time-of-arrival (TOA) blind estimation technique for ultra wideband energy detection receivers with reduced complexity. The proposed method is blind in the sense that it does not exploit any information about channel or noise power. This new approach is based on a set of approximations of the exact likelihood function (ELF) of the observed energy. Even though these approximations achieve an important reduction of complexity, the shape of the new approximated function is accurate enough compared to the ELF. Application of a threshold to the differential of the approximated log-likelihood function completes the procedure. Simulations show that the performance of the proposed method in terms of the cumulative distribution function of the estimation error approaches that of a method based on the ELF and a genie-aided algorithm with perfect knowledge of the optimal threshold.
SemEval-2007 Task 04: Classification of Semantic Relations between Nominals

The NLP community has shown a renewed interest in deeper semantic analyses, among them automatic recognition of relations between pairs of words in a text. We present an evaluation task designed to provide a framework for comparing different approaches to classifying semantic relations between nominals in a sentence. This is part of SemEval, the 4th edition of the semantic evaluation event previously known as SensEval. We define the task, describe the training/test data and their creation, list the participating systems and discuss their results. There were 14 teams who submitted 15 systems.
EVALUATING THE EFFECTS OF UNCERTAINTY IN FUEL PRICE ON TRANSMISSION NETWORK EXPANSION PLANNING USING IADPSO APPROACH

Transmission network expansion planning (TNEP) is a basic part of power system planning that determines where, when and how many new transmission lines should be added to the network so that the load is adequately supplied. There are several factors affecting TNEP, which sometimes make the problem results inaccurate and impractical because of their complicacy. Therefore, it should be tried to possibly introduce them in TNEP problem by using appropriate scientific tools. One of these parameters which is significantly effective in TNEP result, is the uncertainty of different parameters such as load growth, location of power plants in horizon year, and especially fuel price which indirectly affects the transmission lines loading and consequently the optimality of transmission plans via changing of loss and unsupplied load which are dependent on the power generation of power plants. Thus, in this paper, by considering the uncertainty of fuel price, in different scenarios, its determining role in TNEP result has been evaluated using IADPSO algorithm. To study the proposed approach, the 17-bus real network of Azerbaijan Regional Electrical Company is considered.
Chromatic Signatures in the Microlensing of GRB Afterglows

We calculate the radial surface brightness profile of the image of a GammaRay-Burst (GRB) afterglow. The afterglow spectrum consists of several power-law segments separated by breaks. The image profile changes considerably across each of the spectral breaks. It also depends on the density profile of the ambient medium into which the GRB fireball propagates. Gravitational microlensing by an intervening star can resolve the afterglow image. We calculate the predicted magnification history of GRB afterglows as a function of observed frequency and ambient medium properties. We find that intensive monitoring of a microlensed afterglow lightcurve can be used to reconstruct the parameters of the fireball and its environment, and provide constraints on particle acceleration and magnetic field amplification in relativistic blast waves. Subject headings: gamma rays: bursts—gravitational lensing
A comparative study of stereo-matching algorithms for road-modeling in the presence of windscreen wipers

In this study we examine three road-modeling methods, which we evaluate on seven stereo matching algorithms. The road-modeling methods we consider are a B-spline modeling technique based on region-growing and two versions of the popular v-disparity approach. The used stereo algorithms are variations or different parameterizations of belief propagation, graph cut and semi-global matching.
A Novel Cellular Protein, VPEF, Facilitates Vaccinia Virus Penetration into HeLa Cells through Fluid Phase Endocytosis

ABSTRACT Vaccinia virus is a large DNA virus that infects many cell cultures in vitro and animal species in vivo. Although it has been used widely as a vaccine, its cell entry pathway remains unclear. In this study, we showed that vaccinia virus intracellular mature virions bound to the filopodia of HeLa cells and moved toward the cell body and entered the cell through an endocytic route that required a dynamin-mediated pathway but not a clathrin- or caveola-mediated pathway. Moreover, virus penetration required a novel cellular protein, vaccinia virus penetration factor (VPEF). VPEF was detected on cell surface lipid rafts and on vesicle-like structures in the cytoplasm. Both vaccinia virus and dextran transiently colocalized with VPEF, and, importantly, knockdown of VPEF expression blocked vaccinia virus penetration as well as intracellular transport of dextran, suggesting that VPEF mediates vaccinia virus entry through a fluid uptake endocytosis process in HeLa cells. Intracellular VPEF-containing vesicles did not colocalize with Rab5a or caveolin but partially colocalized with Rab11, supporting the idea that VPEF plays a role in vesicle trafficking and recycling in HeLa cells. In summary, this study characterized the mechanism by which vaccinia virus enters HeLa cells and identified a cellular factor, VPEF, that is exploited by vaccinia virus for cell entry through fluid phase endocytosis.
New AdS(3) x G/H compactifications of chiral IIB supergravity

We present a new class of solutions of D=10, N=2 chiral supergravity. A nonvanishing background for the field strength G_{MNR} of the complex two-form triggers AdS_3 x M_7 compactifications, where M_7 is a 7-dimensional compact manifold. When M_7 is a nonsymmetric coset space G/H, we can always find a set of constants G_{MNR} covariantly conserved and thus satisfying the field equations. For example the structure constants of G with indices in the G/H directions are a covariantly conserved tensor. In some symmetric G/H, where these structure constants vanish, there may still exist conserved 3-forms, yielding AdS_3 x G/H solutions. The conditions for supersymmetry of the AdS_3 x M_7 compactifications are derived, and tested for the supersymmetric solutions AdS_3 x S^3 x T^4 and AdS_3 x S^3 x S^3 x S^1. Finally, we show that the AdS_3 x S^3 x T^4 supersymmetric background can be seen as the sigma = 0 limit in a one-parameter class of solutions of the form AdS_3 x S^3 x CP^2, the parameter sigma being the inverse "radius" of CP^2. For sigma different from 0 all supersymmetries are broken.
The Dual Faces of Misery

THE DUAL FACES OF MISERY By Arden Moscati, M. A. (Oxon) A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2017 Dissertation Advisor: Kenneth S. Kendler, MD Rachel Brown Banks Distinguished Professor of Psychiatry Director of The Virginia Institute for Psychiatric and Behavioral Genetics
The Evolutionary Biology and Population Genetics Underlying Fungal Strain Typing

SUMMARY Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested.
Tug of War between Survival and Death: Exploring ATM Function in Cancer

Ataxia-telangiectasia mutated (ATM) kinase is a one of the main guardian of genome stability and plays a central role in the DNA damage response (DDR). The deregulation of these pathways is strongly linked to cancer initiation and progression as well as to the development of therapeutic approaches. These observations, along with reports that identify ATM loss of function as an event that may promote tumor initiation and progression, point to ATM as a bona fide tumor suppressor. The identification of ATM as a positive modulator of several signalling networks that sustain tumorigenesis, including oxidative stress, hypoxia, receptor tyrosine kinase and AKT serine-threonine kinase activation, raise the question of whether ATM function in cancer may be more complex. This review aims to give a complete overview on the work of several labs that links ATM to the control of the balance between cell survival, proliferation and death in cancer.
Contour Independent Real-Time Improved Level Set Method for Segmentation

The recent development of parallel processing, is a fast alternative approach for solving partial differential equations and has attracted recent research work and is applied in the level set method for image segmentation. In this paper we propose an independent of selection of initial contour based approach with high efficiency algorithm. The proposed algorithm is validated on the standard database which consists of standard, astronomical and medical images.
SGD: Saccharomyces Genome Database

The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the literature supporting these data. The amount of information and the number of features provided by SGD have increased greatly following the release of the S.cerevisiae genomic sequence, which is currently the only complete sequence of a eukaryotic genome. SGD aids researchers by providing not only basic information, but also tools such as sequence similarity searching that lead to detailed information about features of the genome and relationships between genes. SGD presents information using a variety of user-friendly, dynamically created graphical displays illustrating physical, genetic and sequence feature maps. SGD can be accessed via the World Wide Web at http://genome-www.stanford. edu/Saccharomyces/
Reduced Autobiographical Memory Specificity Predicts Depression and Posttraumatic Stress Disorder After Recent Trauma

In this prospective longitudinal study, the authors examined the relationship between reduced specificity in autobiographical memory retrieval and the development of depression, posttraumatic stress disorder (PTSD), and specific phobia after injury in an assault. Assault survivors (N = 203) completed the Autobiographical Memory Test (J. M. G. Williams & K. Broadbent, 1986) at 2 weeks after the trauma as well as structured clinical interviews at 2 weeks and 6 months. Participants with acute stress disorder or major depression at 2 weeks, but not those with phobia, retrieved fewer specific autobiographical memories than those without the respective disorder. Reduced memory specificity at 2 weeks also predicted subsequent PTSD and major depression at 6 months over and above what could be predicted from initial diagnoses and symptom severity. Moderator analyses showed that low memory specificity predicted later depression in participants with prior episodes of major depression but not in those without prior depression. Mediation analyses suggested that rumination partly mediated and perceived permanent change fully mediated the effects of low memory specificity on posttrauma psychopathology at follow-up.
Can Styles Improve Architectural Pattern Reuse ?

Software patterns are generic solutions to recurring problems. They are represented as a triplet (problem, context, solution). Several kinds of software patterns were identified, examples of which are analysis, architecture, design or implementation patterns. The current practice is to represent patterns as documents that communicate best practices. Their reuse is limited by several factors among which the lack of formalization. In the context of architecture centered software development, architectural styles are means to represent families of software systems. Several architecture description languages offer support for representing architectural styles. We believe that the use of architectural styles in the representation of architectural pattern solutions can improve the pattern reuse level. The paper details how this improvement can be achieved.
Solution generating technique for noncommutative orbifolds

We propose the relationships between the noncommutative solitons and the (fractional) D-branes on the C 2 /Z N orbifold and extend the solution generating technique for the orbifold. As applications, we determine how tachyon condensations occur in various D-D systems on the orbifolds. The calculations give results consistent with BSFT. The extended solution generating technique enables us to calculate more general decay modes of D-D systems.
Reconstruction of facial features from the skull: an evaluation of its usefulness in forensic anthropology.

Although facial reconstructions from the skull have been widely used in forensic anthropology, their effectiveness has not been objectively assessed. Photographs of two reconstructions produced in this laboratory were shown to FAA employees and local policemen who were asked to select the subject's in vivo photograph when included with those of six other randomly-selected individuals of the same sex, race, and general age. While in both tests the reconstruction subject was chosen with significantly greater frequency than the controls, the results ranged from 26% correct (N = 104) on the first subject, a 67-year-old female, to 67% correct (N = 200) on the second, a 36-year-old male. In both tests policemen and civilian females performed better than civilian males.
Performance of back propagation networks for associative database retrieval

Back-propagation networks have been successfully used to perform a variety of input-output mapping tasks for recognition, generalization, and classification. In spite of this method's popularity, virtually nothing is known about its saturation/capacity and, in more general terms, about its performance as an associative memory. The authors address these issues using associative database retrieval as an original application domain. Experimental results show that the quality of recall and the network capacity are very significantly affected by the network topology (the number of hidden units), data representation (encoding), and the choice of learning parameters. On the basis of their results and the fact that back-propagation learning is not recursive, the authors conclude that back-propagation networks can be used mainly as read-only associative memories and represent a poor choice for read-and-write associative memories. <<ETX>>
A Trade-Off Between Depth and Impurity for Pruning Decision Trees

Most pruningmethodsfor decisiontreesminimize a classification error rate. In uncertaindomains,somesub-treeswhich do not lessen theerrorratecanberelevant to point out somepopulationsof specific interestor to givea representationof a largedatafile. Weproposehere a new pruningmethod(called pruning)which takes into account the complexity of sub-treesandwhich is able to keepsub-treeswith leavesyielding to determinaterelevantdecisionrules,evenwhenkeeping theseonesdoesnot increasetheclassificationefficiency.
I-Grabber: expanding physical reach in a large-display tabletop environment through the use of a virtual grabber

While working on large tabletop interfaces, reaching and manipulating objects beyond the physical reach of a user can be considerably vexing. In order to reach such an object, a user may have to physically move to the object's location. Alternatively, a user could attempt to reach for the object from his/her current location, but the territory of other users may become obstructed as a result. We propose a multi-touch interaction technique which enables users to easily select and manipulate objects that are beyond their physical reach. Our technique provides direct visual feedback to users, which allows them to be aware of their current active location. Using a controllable "interactive grabber" (I-Grabber) as a virtual hand extension, users can reach and manipulate any object from their current location.
The Optical Gravitational Lensing Experiment . Red Clump Stars as a Distance Indicator

We present calibration of the mean I-band brightness of red clump stars on metallic-ity. Red clump stars were proposed to be a very attractive standard candle for distance determination. The calibration is based on 218 nearby red giant stars whose high quality spectra allowed to determine accurate individual metal abundances. High quality par-allaxes (σπ/π < 10%) and photometry of these very bright stars come from Hipparcos measurements. Metallicity of the sample covers a large range: −0.6<[Fe/H] <+0.2 dex. We find only a weak dependence of the mean I-band magnitude on metallicity (0.15 mag/dex) in good agreement with previous empirical and theoretical work. What is more important, the range of metallicity of the Hipparcos sample overlaps with the metallicity of field stars in the LMC, thus making it possible to determine the distance to the LMC by direct comparison of brightness of the local Hipparcos red clump giants with that of LMC stars. Photometry of field red clump giants in four low extinction regions of the LMC halo collected during the OGLE-II microlensing survey compared with the Hipparcos red clump stars data yields the final (free from population effects) " red-clump method " distance modulus to the LMC: (m − M) = 18.23 ± 0.05 mag. So far, this is the most robust and accurate distance determination to the LMC. We also present empirical relations between the color indices U − B, B − V and V − I and metallicity of nearby red clump stars.