Miracle-dz/UniFAR-FTUs huggingface dataset:
Sonic-hedgehog-mediated proliferation requires the localization of PKA to the cilium base

Cerebellar granular neuronal precursors (CGNPs) proliferate in response to the mitogenic activity of Sonic hedgehog (Shh), and this proliferation is negatively regulated by activation of cAMP-dependent protein kinase (PKA). In the basal state, the PKA catalytic subunits (C-PKA) are inactive because of their association with the regulatory subunits (R-PKA). As the level of cAMP increases, it binds to R-PKA, displacing and thereby activating the C-PKA. Here we report that, in the presence of Shh, inactive C-PKA accumulates at the cilium base of proliferative CGNPs whereas removal of Shh triggers the activation of PKA at this particular location. Furthermore, we demonstrate that the anchoring of the PKA holoenzyme to the cilium base is mediated by the specific binding of the type II PKA regulatory subunit (RII-PKA) to the A-kinase anchoring proteins (AKAPs). Disruption of the interaction between RII-PKA and AKAPs inhibits Shh activity and, therefore, blocks proliferation of CGNP cultures. Collectively, these results demonstrate that the pool of PKA localized to the cilium base of CGNP plays an essential role in the integration of Shh signal transduction.
An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System

Summary: Bisulfite sequencing allows cytosine methylation, an important epigenetic marker, to be detected via nucleotide substitutions. Since the Applied Biosystems SOLiD System uses a unique di-base encoding that increases confidence in the detection of nucleotide substitutions, it is a potentially advantageous platform for this application. However, the di-base encoding also makes reads with many nucleotide substitutions difficult to align to a reference sequence with existing tools, preventing the platform's potential utility for bisulfite sequencing from being realized. Here, we present SOCS-B, a reference-based, un-gapped alignment algorithm for the SOLiD System that is tolerant of both bisulfite-induced nucleotide substitutions and a parametric number of sequencing errors, facilitating bisulfite sequencing on this platform. An implementation of the algorithm has been integrated with the previously reported SOCS alignment tool, and was used to align CpG methylation-enriched Arabidopsis thaliana bisulfite sequence data, exhibiting a 2-fold increase in sensitivity compared to existing methods for aligning SOLiD bisulfite data. Availability: Executables, source code, and sample data are available at http://solidsoftwaretools.com/gf/project/socs/ Contact: bergmann@nbacc.net Supplementary information: Supplementary data are available at Bioinformatics online.
Dark Matter Halos around Elliptical Galaxies: How Reliable Is the Stellar Kinematical Evidence?

Hierarchical models of galaxy formation and various observational evidence suggest that elliptical galaxies are, like disk galaxies, embedded in massive dark matter halos. Stellar kinematics are considered the most important tracer for this dark halo at a few effective radii. Using detailed modeling techniques, several authors have recently presented stellar kinematical evidence of a dark halo for a number of elliptical galaxies. In these modeling techniques, dust attenuation (absorption and scattering of starlight by dust grains) has not been taken into account. Nevertheless, elliptical galaxies contain a significant amount of interstellar dust, which affects all observable quantities, including the observed kinematics. We constructed a set of dynamical models for elliptical galaxies, in which dust attenuation is included through a Monte Carlo technique. We find that a dust component, shallower than the stellar distribution and with an optical depth of order unity, affects the observed kinematics significantly, in the way that it mimics the presence of a dark halo. If such dust distributions are realistic in elliptical galaxies, we are faced with a new mass-dust degeneracy. Taking dust attenuation into account in dynamical modeling procedures will hence reduce or may even eliminate the need for a dark matter halo at a few effective radii.
Applications of protein microarrays for biomarker discovery

The search for new biomarkers for diagnosis, prognosis, and therapeutic monitoring of diseases continues in earnest despite dwindling success at finding novel reliable markers. Some of the current markers in clinical use do not provide optimal sensitivity and specificity, with the prostate cancer antigen (PSA) being one of many such examples. The emergence of proteomic techniques and systems approaches to study disease pathophysiology has rekindled the quest for new biomarkers. In particular the use of protein microarrays has surged as a powerful tool for large‐scale testing of biological samples. Approximately half the reports on protein microarrays have been published in the last two years especially in the area of biomarker discovery. In this review, we will discuss the application of protein microarray technologies that offer unique opportunities to find novel biomarkers.
Adaptive combination of tag and link-based user similarity in flickr

Finding similar users is one of the probable applications in social media. The similarity between users can be measured in two different approaches: the semantic similarity and the similarity in terms of social relations. These two approaches can be combined with different weight factors. However, the conventional combination scheme has a critical drawback that the weight factors are fixed for every user and thus it is not optimized at those users that are using rare terms or do not have sufficient relations with other users. To address this problem, in this paper, we propose an adaptive combination scheme of tag-based similarity and link-based similarity in which the weight factors are dynamically determined for each user by evaluating each user's characteristics such as tag commonness and link strength. The experimental results with a Flickr data set show that the proposed scheme consistently outperforms the previous work by about 20%.
Clinical treatment options for patients with homonymous visual field defects

The objective of this review is to evaluate treatments for homonymous visual field defects (HVFDs). We distinguish between three treatments: visual restoration training (VRT), optical aids, and compensatory training. VRT is both the most ambitious and controversial approach, aiming to restore portions of the lost visual field. While early studies suggested that VRT can reduce the visual field defect, recent studies using more reliable means of monitoring the patients’ fixation could not confirm this effect. Studies utilizing modern optical aids have reported some promising results, but the extent to which these aids can reliably reduce the patients’ visual disability has yet to be confirmed. Compensatory approaches, which teach patients more effective ways of using their eyes, are currently the only form of treatment for which behavioral improvements have been demonstrated. However, with the exception of one study using a reading training, placebo-controlled clinical evaluation studies are lacking. It is also not yet clear whether the training benefits found in laboratory tasks lead to reliable improvements in activities of daily living and which of the various forms of compensatory training is the most promising. It is therefore too early to recommend any of the currently available treatment approaches.
A Typology and Discourse Semantics for Motion Verbs and Spatial PPs in French

Les As. proposent une etude semantique et une classification des verbes de mouvement et des verbes de mouvement complexes. Sur la base des proprietes semantiques des verbes et de leurs arguments, ils definissent les proprietes semantiques spatiotemporelles des verbes de mouvement complexes. Ils montrent comment combiner l'information lexicale avec l'information du discours pour determiner la structure spatiotemporelle des textes et favoriser la desambiguisation lexicale
Differential cytokine induction by doses of lipopolysaccharide and monophosphoryl lipid A that result in equivalent early endotoxin tolerance

The phenomenon of early endotoxin tolerance, which is induced by sublethal injection of lipopolysaccharide (LPS), results in a protracted period of hyporesponsiveness that is most profound at 3 to 4 days after injection and is marked by reduced cytokine production after a challenge injection of LPS. Early endotoxin tolerance is also induced by the nontoxic LPS derivative monophosphoryl lipid A (MPL), although much more of the monophosphoryl derivative is required to produce a state of tolerance equivalent to that evoked by LPS. In this study, equivalent tolerance-inducing doses of LPS and MPL were tested, and the levels of cytokines induced by LPS and MPL were compared. Although induced levels of colony-stimulating factor were comparable following doses of LPS and MPL that elicited an equivalent state of early endotoxin tolerance, levels of tumor necrosis factor, interleukin-6, and interferon were significantly lower in MPL-injected animals. These results suggest that the lowered toxicity of MPL may be related to its elicitation of significantly lower levels of potentially toxic intermediaries such as tumor necrosis factor, interferon, and interleukin-6.
Prices, Debt and Market Structure in an Agent-Based Model of the Financial Market

We develop an agent-based model in which heterogeneous and boundedly rational agents interact by trading a risky asset at an endogenously set price. Agents are endowed with balance sheets comprising the risky asset as well as cash on the asset side and equity capital as well as debt on the liabilities side. A number of findings emerge when simulating the model: we find that the empirically observable log-normal distribution of bank balance sheet size naturally emerges and that higher levels of leverage lead to a greater inequality among agents. Furthermore, greater leverage increases the frequency of bankruptcies and systemic events. Credit frictions, which we define as the stickiness of debt adjustments, are able to explain a key difference in the relation between leverage and assets observed for different bank types. Lowering credit frictions leads to an increasingly procyclical behavior of leverage, which is typical for investment banks. Nevertheless, the impact of credit frictions on the fragility of the model financial system is complex. Lower frictions do increase the stability of the system most of the time, while systemic events become more probable. In particular, we observe an increasing frequency of severe liquidity crises that can lead to the collapse of the entire model financial system.
A Special Class of Fractional QCQP and Its Applications on Cognitive Collaborative Beamforming

In this paper, we investigate a special class of the fractional quadratically constrained quadratic problem (QCQP) with more than two quadratic constraints. We propose to effectively solve this special fractional QCQP by one or two convex semidefinite programmings (SDPs). For the two SDPs, one is equivalent to the original fractional QCQP with rank-one relaxation from the Charnes-Cooper transformation and the other, exploiting the optimal value of the former SDP, always has rank-one solution, which is optimal to the former SDP. Theoretical analysis shows that our proposed non-iterative SDP-based algorithm achieves the global optimal solution to the special fractional QCQP. In specific scenarios, our proposed non-iterative SDP-based algorithm has lower computational complexity compared to the second-order cone programming (SOCP)-based and constrained concave convex procedure (CCCP)-based iterative algorithms. We apply the proposed non-iterative SDP-based algorithm on two collaborative beamforming problems in cognitive relay networks, specifically, one is the achievable rate region for two-way non-regenerative cognitive relay networks and the other is the achievable secrecy rate for one-way regenerative cognitive relay networks. Simulation results have shown that our proposed non-iterative SDP-based algorithm achieves the same performance as the SOCP-based iterative algorithm. Our proposed algorithm achieves the better performance than the CCCP-based iterative algorithm.
Combined Co- and Cross-Polarized SAR Measurements Under Extreme Wind Conditions

During summer 2016, the European Space Agency (ESA) set up the Satellite Hurricane Observations Campaign, a campaign dedicated to hurricane observations with Sentinel-1 synthetic aperture radar (SAR) in both vertical-vertical (VV) and vertical-horizontal (VH) polarizations acquired in wide swath modes. Among the 70 Sentinel-1 passes scheduled by the ESA mission planning team, more than 20 observations over hurricane eyes were acquired and tropical cyclones were captured at different development stages. This enables us to detail the sensitivity difference of VH and VV normalized radar cross section (NRCS) to the response of intense ocean surface winds. As found, the sensitivity of the VH-NRCS computed at 3-km resolution is reported to be more than 3.5 times larger than in VV. Taking opportunity of SAR high resolution, we also show that the decrease in resolution (up to 25 km) does not dramatically change the sensitivity difference between VV and VH polarizations. For wind speeds larger than 25 m/s, a new geophysical model function (MS1A) to interpret cross-polarized signal is proposed. Both channels are then combined to get ocean surface wind vectors. SAR winds are further compared at 40-km resolution against L-band soil moisture active and passive mission (SMAP) radiometer winds with co-locations less than 30 min. Overall excellent consistency is found between SMAP and this new SAR winds. This paper opens perspectives for MetOp-SG SCA, the next-generation C-band scatterometer with co- and cross-polarization capability.
Partnering relations : justification and success factors from facilities management services perspective

There is an ongoing transition towards more collaborative approaches (i.e., usage of partnering relations) in the procurement of facilities management (FM) services. However, sometimes partnering is used also in cases in which it is not the most appropriate choice. This may happen due to the fact that most organizations do not have adequate knowledge of the advantages and disadvantages of different relationship approaches. In addition, confusion prevails about the nature of partnering relations as relationships and the manner in which they should be managed. This study looks at issues surrounding the selection of relationship type and the management of partnering relations between a client and FM service providers, and integrates five scientifically reviewed research papers. The objectives of the study are to find out in which situations partnering approach is chosen and to identify the factors rendering a partnering relation a success. Furthermore, reasons for the dissolution of earlier relationships are identified. The empirical part of the study consists of two phases. The first phase is qualitative one, and the data are collected by semi-structured and focus group interviews. It aims towards deeper understanding of the selection criteria of relationship type, the differences between alternative relationship types in FM services, and partnering success factors. Although the focus is on the client's perspective, the representatives of service providers are also interviewed in order to achieve greater wealth of information. In order to confirm the findings of the first phase and, furthermore, to recognize the procurement trends of FM services, a survey is carried out as a second part of the empirical study. The data are collected using an internet-based questionnaire provided by client companies. The results provide understanding of partnering phenomenon in the FM services context and suggest new insights on when to choose partnering approach and how to manage partnering relations successfully. The results indicate that companies should adopt a more strategic approach towards sourcing decisions in relation to FM services. Furthermore, in order to ensure the partnering success, precise goal setting with organized forms of cooperation and interaction is needed.
Context-aware adaptation for mobile devices

This paper discusses the problem of content adaptation for mobile devices. The adaptation considers the context of the client and also the environment where the client request is received. A device independent model is defined and used in order to achieve automatic adaptation of the content based on its semantic and the capabilities of the target device. Our system includes a context description model and a client repository and offers device contexts management and querying functions. The proposed system uses the XQuery language to query the profiles and delivers the results in the form of SOAP services.
A Culturally Enhanced Smoking Cessation Study among Chinese and Korean Smokers.

English: This study assessed the feasibility of and presents preliminary findings on a culturally enhanced, theory-driven smoking cessation intervention for adult Chinese and Korean smokers. A one-group pre-post test design was used. The intervention consisted of behavioral and nicotine replacement strategies. Participants (N=43) were recruited through Asian community networks, Asian Community Cancer Coalition, health clinics and newspaper advertisements. Demographic characteristics, psychosocial factors, mediating variables including self-efficacy and risk perception, smoking cessation and reduction rates, stages of change, tobacco use history, smoking behavior, and program satisfaction were evaluated. At baseline, no participants were in the action stage, whereas 57.7% were in the action stage at 1-week and 61.5% at 3-months follow-up. At 3-months post-intervention follow-up, quit rate was 59%. The psychosocial profile of smokers showed that they were more likely to be receptive about cues, more likely to perceive smoking risks, and less likely to avoid health messages that are inconsistent with their own behavior. Participants reported low levels of distress and moderate levels of self-efficacy in quitting. Overall, the cons of smoking exceeded the pros. A culturally appropriate smoking cessation program for Asian smokers can effectively move smokers between stages of change. Spanish: Este estudio determinado la viabilidad de y presenta preliminar resultados en una intervencion cultural realzada, teori'a-conducida de la cesacion que fuma para fumadores chinos y coreanos del adulto.Un diseno de la prueba del pre-poste del uno-grupo era utilizado.El reemplazo del comportamiento y de la nicotina consistido en intervencion estrategias.Reclutaron a los participantes (N=43) a traves de comunidad asiatica redes, coalicion asiatica del cancer de la comunidad, clinicas de la salud y periodico anuncios.Dcaracteristicas emographic, factores sicosociales, variables el mediar incluyendo uno mismo-eficacia y riesgo opinion, cesacion que fuma y tarifas de la reduccion, etapas del cambio, tabaco utilice la historia, comportamiento que fuma, y la satisfaccion del programa fue evaluada. En la linea de fondo, no hay participantes en la etapa de la accion, mientras que 57.los 7% estaban en accion etapa en de una semana y 61.el 5% en la carta recordativa 3-months.En la poste-intervencio'n 3-months la carta recordativa, paro tarifa era el 59%. El perfil sicosocial de fumadores demostrado que eran mas probables ser receptivos alrededor senales, mas probables percibir riesgos que fuman, y menos para evitar probablemente los mensajes de la salud que son contrarios con su propio comportamiento. Participantes divulgados niveles bajos de la senal de socorro y niveles moderados de uno mismo-eficacia en parar.Total, el contra de fumar excedio los pros.A el programa cultural apropiado de la cesacion que fuma para los fumadores asiaticos puede mueva con eficacia a fumadores entre las etapas del cambio.
Use of Differentiating Adult Stem Cells (Marrow Stromal Cells) to Identify New Downstream Target Genes for Transcription Factors

We developed a strategy for use of microarray data to rapidly identify new downstream targets of transcription factors known to drive differentiation by following the time courses of gene expression as a relatively homogeneous population of stem/progenitor cells are differentiated to multiple phenotypes. Microarray assays were used to follow the differentiation of human marrow stromal cells (MSCs) into chondrocytes or adipocytes in three different experimental conditions. The steps of the analysis were the following: (a) hierarchical clustering was used to define groups of similarly behaving genes in each experiment, (b) candidates for new downstream targets of transcription factors that drive differentiation were then identified as genes that were consistently co‐expressed with known downstream target genes of the transcription factors, and (c) the list of candidate new target genes was refined by identifying genes whose signal intensities showed a highly significant linear regression with the signal intensities of the known targets in all the data sets. Analysis of the data identified multiple new candidates for downstream targets for SOX9, SOX5, CCAAT/enhancer binding protein (C/EBP)‐α, and peroxisome proliferator‐activated receptor (PPAR)‐γ. To validate the analysis, we demonstrated that PPAR‐γ protein specifically bound to the promoters of four new targets identified in the analyses. The same multistep analysis can be used to identify new downstream targets of transcription factors in other systems. Also, the same analysis should make it possible to use MSCs from bone marrow to define new mutations that alter chondogenesis or adipogenesis in patients with a variety of syndromes.
Mathematics of Control , Signals , and Systems The Complementary-Slackness Class of Hybrid Systems *

Abstract. In this paper we understand a "hybrid system" to be one that combines features of continuous dynamical systems with characteristics of finite automata. We study a special class of such systems which we call the complementaryslackness class. We study existence and uniqueness of solutions in the special 'cases of linear and Hamiltonian complementary-slackness systems. For the latter class we also prove an energy inequality.
SnapNet-R: Consistent 3D Multi-view Semantic Labeling for Robotics

In this paper we present a new approach for semantic recognition in the context of robotics. When a robot evolves in its environment, it gets 3D information given either by its sensors or by its own motion through 3D reconstruction. Our approach uses (i) 3D-coherent synthesis of scene observations and (ii) mix them in a multi-view framework for 3D labeling. (iii) This is efficient locally (for 2D semantic segmentation) and globally (for 3D structure labeling). This allows to add semantics to the observed scene that goes beyond simple image classification, as shown on challenging datasets such as SUNRGBD or the 3DRMS Reconstruction Challenge.
A set of independent admittance bases for decoupled analysis of unbalanced three-phase systems

The d-q transformation is widely used in the three-phase system analysis, targeting for symmetrical and balanced systems where the time-varying line-frequency sinusoidal terms of the system state variables can be fully canceled out. With the introduction of the distributed generations, more and more unbalanced infrastructures can be connected to the grid, creating unbalanced systems. It will be desirable to have effective analytical methods and modeling techniques for unbalanced systems. This paper proposes a new approach to analyzing unbalanced systems by demonstrating a decoupled analytical technique for resolving the unbalanced system into the balanced positive-, negative- and zero-sequence system components in the circuit level. The proposed method decomposes the unbalanced admittance of the system into independent admittance bases (IAB) each of which belongs to one of the positive-, negative-or zero-sequence system component to ease subsequent analyses.