Miracle-dz/UniFAR-FTUs huggingface dataset:
TimeTubes: Visualization of polarization variations in blazars

Optical polarization provides important clues to the magnetic field in blazar jets. It is easy to find noteworthy patterns in the time-series data of the polarization degree (PD) and position angle (PA). On the other hand, we need to see the trajectory of the object in the Stokes Q U plane when the object has multiple polarized components. In this case, ironically, the more data we have, the more difficult it is to gain any knowledge from it. Here, we introduce TimeTubes, a new visualization scheme to explore the time-series data of polarization observed in blazars. In TimeTubes, the data is represented by tubes in 3D (Q, U, and time) space. The measurement errors of Q and U, color, and total flux of objects are expressed as the size, color, and brightness of the tubes. As a result, TimeTubes allows us to see the behavior of six variables in one view. We used TimeTubes for our data taken by the Kanata telescope between 2008 and 2014. We found that this tool facilitates the recognition of the patterns in blazar variations; for example, favored PA of flares and PA rotations associated with a series of flares.
Federal Reserve Bank of New York Staff Reports The Effect of Employee Stock Options on Bank Investment Choice , Borrowing , and Capital Hamid Mehran

In this paper, we assess the effects of CEO stock options on three key corporate policies for banks: investment choice, amount of borrowing, and level of capital. Using a sample of 549 bank-years for publicly traded banks from 1992 to 2002, we find that stock option grants lead CEOs to undertake riskier investments. In particular, higher levels of option grants are associated with higher levels of equity and asset volatility. Consistent with the role of options as a nondebt tax shield, we also show that option grants reduce the banks’ incentive to borrow as evidenced by lower levels of interest expense and federal funds borrowing. Furthermore, we demonstrate that increases in CEO and employee stock option grants result in increased bank capital levels, perhaps because option grants create a contingent liability for the firm that needs to be funded in advance.
Some comments on gravitational entropy and the inverse mean curvature flow

The Geroch-Wald-Jang-Huisken-Ilmanen approach to the positive energy problem may be extended to give a negative lower bound for the mass of asymptotically anti-de Sitter spacetimes containing horizons with exotic topologies having ends or infinities of the form g × , in terms of the cosmological constant. We also show how the method gives a lower bound for the mass of time-symmetric initial data sets for black holes with vectors and scalars in terms of the mass, |Z(Q,P)| of the double-extreme black hole with the same charges. I also give a lower bound for the area of an apparent horizon, and hence a lower bound for the entropy in terms of the same function |Z(Q,P)|. This shows that the so-called attractor behaviour extends beyond the static spherically symmetric case. and underscores the general importance of the function |Z(Q,P)|. There are hints that higher-dimensional generalizations may involve the Yamabe conjectures.
Evidence for Novel pH-Dependent Regulation of Candida albicans Rim101, a Direct Transcriptional Repressor of the Cell Wall β-Glycosidase Phr2

ABSTRACT Candida albicans is a commensal fungus of mucosal surfaces that can cause disease in susceptible hosts. One aspect of the success of C. albicans as both a commensal and a pathogen is its ability to adapt to diverse environmental conditions, including dramatic variations in environmental pH. The response to a neutral-to-alkaline pH change is controlled by the Rim101 signal transduction pathway. In neutral-to-alkaline environments, the zinc finger transcription factor Rim101 is activated by the proteolytic removal of an inhibitory C-terminal domain. Upon activation, Rim101 acts to induce alkaline response gene expression and repress acidic response gene expression. Previously, recombinant Rim101 was shown to directly bind to the alkaline-pH-induced gene PHR1. Here, we demonstrate that endogenous Rim101 also directly binds to the alkaline-pH-repressed gene PHR2. Furthermore, we find that of the three putative binding sites, only the −124 site and, to a lesser extent, the −51 site play a role in vivo. In C. albicans, the predicted Rim101 binding site was thought to be CCAAGAA, divergent from the GCCAAG site defined in Aspergillus nidulans and Saccharomyces cerevisiae. Our results suggest that the Rim101 binding site in C. albicans is GCCAAGAA, but slight variations are tolerated in a context-dependent fashion. Finally, our data suggest that Rim101 activity is governed not only by proteolytic processing but also by an additional mechanism not previously described.
Boundary Effects in Integrable Field Theory on a Half Line

Boundary effects caused by boundary interactions in various integrable field theories on a half line are discussed at the classical as well as quantum level. Only so-called "integrable" boundary interactions are discussed. They are obtained by the requirement that certain combinations of the lower members of the infinite set of conserved quantities should be preserved. Contrary to the naive expectations, some "integrable" boundary interactions can drastically change the character of the theory. In some cases, for example, the sinh-Gordon theory, the theory becomes ill-defined due to the instability introduced by "integrable" boundary interactions for a certain range of a parameter.
Structural Aspects of the Association of FcεRI with Detergent-resistant Membranes*

We recently showed that aggregation of the high affinity IgE receptor on mast cells, FcεRI, causes this immunoreceptor to associate rapidly with specialized regions of the plasma membrane, where it is phosphorylated by the tyrosine kinase Lyn. In this study, we further characterize the detergent sensitivity of this association on rat basophilic leukemia-2H3 mast cells, and we compare the capacity of structural variants of FcεRI and other receptors to undergo this association. We show that this interaction is not mediated by the β subunit of the receptor or the cytoplasmic tail of the γ subunit, both of which are involved in signaling. Using chimeric receptor constructs, we found that the extracellular segment of the FcεRI α subunit was not sufficient to mediate this association, implicating FcεRI α and/or γ transmembrane segments. To determine the specificity of this interaction, we compared the association of several other receptors. Interleukin-1 type I receptors on Chinese hamster ovary cells and α4 integrins on rat basophilic leukemia cells showed little or no association with isolated membrane domains, both before and after aggregation on the cells. In contrast, interleukin-2 receptor α (Tac) on Chinese hamster ovary cells exhibited aggregation-dependent membrane domain association similar to FcεRI. These results provide insights into the structural basis and selectivity of lipid-mediated interactions between certain transmembrane receptors and detergent-resistant membranes.
Blister-inducing antibodies target multiple epitopes on collagen VII in mice

Epidermolysis bullosa acquisita (EBA) is an autoimmune subepidermal blistering disease of mucous membranes and the skin caused by autoantibodies against collagen VII. In silico and wet laboratory epitope mapping studies revealed numerous distinct epitopes recognized by EBA patients' autoantibodies within the non‐collagenous (NC)1 and NC2 domains of collagen VII. However, the distribution of pathogenic epitopes on collagen VII has not yet been described. In this study, we therefore performed an in vivo functional epitope mapping of pathogenic autoantibodies in experimental EBA. Animals (n = 10/group) immunized against fragments of the NC1 and NC2 domains of collagen VII or injected with antibodies generated against the same fragments developed to different extent experimental EBA. Our results demonstrate that antibodies targeting multiple, distinct epitopes distributed over the entire NC1, but not NC2 domain of collagen VII induce blistering skin disease in vivo. Our present findings have crucial implications for the development of antigen‐specific B‐ and T cell‐targeted therapies in EBA.
Computing Minimal Sets on Propositional Formulae I: Problems & Reductions

Boolean Satisfiability (SAT) is arguably the archetypical NP-complete decision problem. Progress in SAT solving algorithms has motivated an ever increasing number of practical applications in recent years. However, many practical uses of SAT involve solving function as opposed to decision problems. Concrete examples include computing minimal unsatisfiable subsets, minimal correction subsets, prime implicates and implicants, minimal models, backbone literals, and autarkies, among several others. In most cases, solving a function problem requires a number of adaptive or non-adaptive calls to a SAT solver. Given the computational complexity of SAT, it is therefore important to develop algorithms that either require the smallest possible number of calls to the SAT solver, or that involve simpler instances. This paper addresses a number of representative function problems defined on Boolean formulas, and shows that all these function problems can be reduced to a generic problem of computing a minimal set subject to a monotone predicate. This problem is referred to as the Minimal Set over Monotone Predicate (MSMP) problem. This exercise provides new ways for solving well-known function problems, including prime implicates, minimal correction subsets, backbone literals, independent variables and autarkies, among several others. Moreover, this exercise motivates the development of more efficient algorithms for the MSMP problem. Finally the paper outlines a number of areas of future research related with extensions of the MSMP problem.
Cosmetic Mergers: The Effect of Style Investing on the Market for Corporate Control

We study the impact of "style investing" on the market for corporate control. We argue that the choice of the bidder is influenced by the fact that the merge with a firm that belongs to an investment style more popular with the market may boost the bidder's value. By using data on the flows in mutual funds, we construct a measure of popularity, which relies directly on the identification of sentiment-induced investor demand, rather than being a direct transformation of stock market data. We show that differences in popularity between bidder and target help to explain their pairing. The merger with a more popular target generates a halo effect from the target to the bidder that induces the market to evaluate the assets of the less popular bidder at the (inflated) market value of the more popular target. Both bidder and target premiums are positively related to the difference in popularity between the target and the bidder. However, the target's ability to appropriate the gain is reduced by the fact that its bargaining position is weaker when the bidder's potential for asset appreciation is higher. We document a better short- and medium-term performance of less popular firms taking over more popular firms. The bidder managers engaging in these cosmetic mergers take advantage of the window of opportunity induced by the deal to reduce their stake in the firm under convenient conditions.
Fully integrated low phase-noise VCOs with on-chip MEMS inductors

We present fully integrated high-performance voltage-controlled oscillators (VCOs) with on-chip microelectromechanical system (MEMS) inductors for the first time. MEMS inductors have been realized from the unique CMOS-compatible MEMS process that we have developed to provide suspended thick metal structures for high-quality (Q) factors. Fully integrated CMOS VCOs have been fabricated by monolithically integrating these MEMS inductors on the top of the CMOS active circuits realized by the TSMC 0.18-/spl mu/m mixed-mode CMOS process. Low phase noise has been achieved as -124 and -117 dBc/Hz at 300-kHz offset from carrier frequencies of 1 and 2.6 GHz, respectively, in the fabricated single-chip VCOs.
Open Access Research Article Population-level Transcriptome Sequencing of Nonmodel Organisms Erynnis Propertius and Papilio Zelicaon

Background: Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task. Results: Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae) and the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments. Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6× on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (Bombyx mori) protein-this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. Conclusions: Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene). Background Although the costs of genome sequencing have declined dramatically, full genome sequencing efforts are still impractical for many nonmodel species. In such cases, transcriptome sequencing provides a greatly informative and cost effective alternative [1,2]. Expressed Sequence Tag (EST) sequencing has been used in a variety of spe
Cellular Correlates of Enhanced Anxiety Caused by Acute Treatment with the Selective Serotonin Reuptake Inhibitor Fluoxetine in Rats

Selective serotonin reuptake inhibitors (SSRIs) are used extensively in the treatment of depression and anxiety disorders. The therapeutic benefits of SSRIs typically require several weeks of continuous treatment. Intriguingly, according to clinical reports, symptoms of anxiety may actually increase during the early stages of treatment although more prolonged treatment alleviates affective symptoms. Consistent with earlier studies that have used animal models to capture this paradoxical effect of SSRIs, we find that rats exhibit enhanced anxiety-like behavior on the elevated plus-maze 1 h after a single injection of the SSRI fluoxetine. Next we investigated the potential neural substrates underlying the acute anxiogenic effects by analyzing the morphological and physiological impact of acute fluoxetine treatment on principal neurons of the basolateral amygdala (BLA), a brain area that plays a pivotal role in fear and anxiety. Although earlier studies have shown that behavioral or genetic perturbations that are anxiogenic for rodents also increase dendritic spine density in the BLA, we find that a single injection of fluoxetine does not cause spinogenesis on proximal apical dendritic segments on BLA principal neurons an hour later. However, at the same time point when a single dose of fluoxetine caused enhanced anxiety, it also enhanced action potential firing in BLA neurons in ex vivo slices. Consistent with this finding, in vitro bath application of fluoxetine caused higher spiking frequency and this increase in excitability was correlated with an increase in the input resistance of these neurons. Our results suggest that enhanced excitability of amygdala neurons may contribute to the increase in anxiety-like behavior observed following acute fluoxetine treatment.
The Gap Detection Test: Can It Be Used to Diagnose Tinnitus?

Objectives: Animals with induced tinnitus showed difficulties in detecting silent gaps in sounds, suggesting that the tinnitus percept may be filling the gap. The main purpose of this study was to evaluate the applicability of this approach to detect tinnitus in human patients. The authors first hypothesized that gap detection would be impaired in patients with tinnitus, and second, that gap detection would be more impaired at frequencies close to the tinnitus frequency of the patient. Design: Twenty-two adults with bilateral tinnitus, 20 age-matched and hearing loss–matched subjects without tinnitus, and 10 young normal-hearing subjects participated in the study. To determine the characteristics of the tinnitus, subjects matched an external sound to their perceived tinnitus in pitch and loudness. To determine the minimum detectable gap, the gap threshold, an adaptive psychoacoustic test was performed three times by each subject. In this gap detection test, four different stimuli, with various frequencies and bandwidths, were presented at three intensity levels each. Results: Similar to previous reports of gap detection, increasing sensation level yielded shorter gap thresholds for all stimuli in all groups. Interestingly, the tinnitus group did not display elevated gap thresholds in any of the four stimuli. Moreover, visual inspection of the data revealed no relation between gap detection performance and perceived tinnitus pitch. Conclusions: These findings show that tinnitus in humans has no effect on the ability to detect gaps in auditory stimuli. Thus, the testing procedure in its present form is not suitable for clinical detection of tinnitus in humans.
A Molecular Screening Approach to Identify and Characterize Inhibitors of Glioblastoma Stem Cells

Glioblastoma (GBM) is among the most lethal of all cancers. GBM consist of a heterogeneous population of tumor cells among which a tumor-initiating and treatment-resistant subpopulation, here termed GBM stem cells, have been identified as primary therapeutic targets. Here, we describe a high-throughput small molecule screening approach that enables the identification and characterization of chemical compounds that are effective against GBM stem cells. The paradigm uses a tissue culture model to enrich for GBM stem cells derived from human GBM resections and combines a phenotype-based screen with gene target-specific screens for compound identification. We used 31,624 small molecules from 7 chemical libraries that we characterized and ranked based on their effect on a panel of GBM stem cell-enriched cultures and their effect on the expression of a module of genes whose expression negatively correlates with clinical outcome: MELK, ASPM, TOP2A, and FOXM1b. Of the 11 compounds meeting criteria for exerting differential effects across cell types used, 4 compounds showed selectivity by inhibiting multiple GBM stem cells-enriched cultures compared with nonenriched cultures: emetine, n-arachidonoyl dopamine, n-oleoyldopamine (OLDA), and n-palmitoyl dopamine. ChemBridge compounds #5560509 and #5256360 inhibited the expression of the 4 mitotic module genes. OLDA, emetine, and compounds #5560509 and #5256360 were chosen for more detailed study and inhibited GBM stem cells in self-renewal assays in vitro and in a xenograft model in vivo. These studies show that our screening strategy provides potential candidates and a blueprint for lead compound identification in larger scale screens or screens involving other cancer types. Mol Cancer Ther; 10(10); 1818–28. ©2011 AACR.
Proactive Caching for Mobile Video Streaming in Millimeter Wave 5G Networks

Mobile video streaming is fundamental to advanced applications in the fifth generation (5G) networks. Millimeter wave (mmWave) communication represents a leading 5G technology, which provides rich bandwidth and, therefore, great potentials for high-quality mobile video streaming. However, mobile video streaming in mmWave 5G networks faces fundamental challenges due to mmWave antenna directivity and high user mobility. As such, users typically have short connection durations and frequent handoffs, making video streaming suffer from long handoff delays and connection latency. In this paper, we tackle the issues by developing a caching-based mmWave framework, which precaches video contents at the base station for handoff users and thus significantly reduces the connection and retrieval delays. As a result, high-mobility users with frequent handoffs can enjoy continuous high-quality video streaming. Specifically, we model the proposed system as a cache management problem and attain optimal video streaming quality by using Markov decision process to dynamically allocate proper cache memory space of each base station to mobile users. A cell-by-cell decomposition method is proposed to solve the dynamic programming problem with significantly reduced computational complexity. Using extensive simulations, we demonstrate that the proposed solution can effectively maintain high-quality mobile video streaming for high-mobility 5G users moving among mmWave small cells with directional antenna.
Identification of natural inhibitors of Entamoeba histolytica cysteine synthase from microbial secondary metabolites

Amebiasis is a common worldwide diarrheal disease, caused by the protozoan parasite, Entamoeba histolytica. Metronidazole has been a drug of choice against amebiasis for decades despite its known side effects and low efficacy against asymptomatic cyst carriers. E. histolytica is also capable of surviving sub-therapeutic levels of metronidazole in vitro. Novel drugs with different mode of action are therefore urgently needed. The sulfur assimilatory de novo L-cysteine biosynthetic pathway is essential for various cellular activities, including the proliferation and anti-oxidative defense of E. histolytica. Since the pathway, consisting of two reactions catalyzed by serine acetyltransferase (SAT) and cysteine synthase (CS, O-acetylserine sulfhydrylase), does not exist in humans, it is a rational drug target against amebiasis. To discover inhibitors against the CS of E. histolytica (EhCS), the compounds of Kitasato Natural Products Library were screened against two recombinant CS isozymes: EhCS1 and EhCS3. Nine compounds inhibited EhCS1 and EhCS3 with IC50 values of 0.31–490 μM. Of those, seven compounds share a naphthoquinone moiety, indicating the structural importance of the moiety for binding to the active site of EhCS1 and EhCS3. We further screened >9,000 microbial broths for CS inhibition and purified two compounds, xanthofulvin and exophillic acid from fungal broths. Xanthofulvin inhibited EhCS1 and EhCS3. Exophillic acid showed high selectivity against EhCS1, but exhibited no inhibition against EhCS3. In vitro anti-amebic activity of the 11 EhCS inhibitors was also examined. Deacetylkinamycin C and nanaomycin A showed more potent amebicidal activity with IC50 values of 18 and 0.8 μM, respectively, in the cysteine deprived conditions. The differential sensitivity of trophozoites against deacetylkinamycin C in the presence or absence of L-cysteine in the medium and the IC50 values against EhCS suggest the amebicidal effect of deacetylkinamycin C is due to CS inhibition.