Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Cationic Amphiphiles Induce a Niemann-Pick C Phenotype and Inhibit Ebola Virus Entry and Infection

Ebola virus (EBOV) is an enveloped RNA virus that causes hemorrhagic fever in humans and non-human primates. Infection requires internalization from the cell surface and trafficking to a late endocytic compartment, where viral fusion occurs, providing a conduit for the viral genome to enter the cytoplasm and initiate replication. In a concurrent study, we identified clomiphene as a potent inhibitor of EBOV entry. Here, we screened eleven inhibitors that target the same biosynthetic pathway as clomiphene. From this screen we identified six compounds, including U18666A, that block EBOV infection (IC50 1.6 to 8.0 µM) at a late stage of entry. Intriguingly, all six are cationic amphiphiles that share additional chemical features. U18666A induces phenotypes, including cholesterol accumulation in endosomes, associated with defects in Niemann–Pick C1 protein (NPC1), a late endosomal and lysosomal protein required for EBOV entry. We tested and found that all six EBOV entry inhibitors from our screen induced cholesterol accumulation. We further showed that higher concentrations of cationic amphiphiles are required to inhibit EBOV entry into cells that overexpress NPC1 than parental cells, supporting the contention that they inhibit EBOV entry in an NPC1-dependent manner. A previously reported inhibitor, compound 3.47, inhibits EBOV entry by blocking binding of the EBOV glycoprotein to NPC1. None of the cationic amphiphiles tested had this effect. Hence, multiple cationic amphiphiles (including several FDA approved agents) inhibit EBOV entry in an NPC1-dependent fashion, but by a mechanism distinct from that of compound 3.47. Our findings suggest that there are minimally two ways of perturbing NPC1-dependent pathways that can block EBOV entry, increasing the attractiveness of NPC1 as an anti-filoviral therapeutic target.
Strategies for accelerating on-line learning of hotkeys

Hotkeys are extremely useful in leveraging expert performance, but learning them is a slow process. This paper investigates alternative menu designs that can motivate and help users remember associations between menu commands and hotkeys. Building upon previous work on paired-associate learning, we suggest that the transition to expert use can be accelerated by manipulating feedback and cost associated with menu selection. We evaluate five designs in a pilot study and then two of the most promising ones in a formal experiment, showing that the speed of hotkey learning can indeed be significantly increased with little modifications to the standard menu/hotkey paradigm.
Learning a Propagable Graph for Semisupervised Learning: Classification and Regression

In this paper, we present a novel framework, called learning by propagability, for two essential data mining tasks, i.e., classification and regression. The whole learning process is driven by the philosophy that the data labels and the optimal feature representation jointly constitute a harmonic system, where the data labels are invariant with respect to the propagation on the similarity graph constructed based on the optimal feature representation. Based on this philosophy, a unified framework of learning by propagability is proposed for the purposes of both classification and regression. Specifically, this framework has three characteristics: 1) the formulation unifies the label propagation and optimal feature representation pursuing, and thus the label propagation process is enhanced by benefiting from the refined similarity graph constructed with the derived optimal feature representation instead of the original representation; 2) it unifies the formulations for supervised and semisupervised learning in both classification and regression tasks; and 3) it can directly deal with the multiclass classification problems. Extensive experiments for the classification task on UCI toy data sets, handwritten digit recognition, face recognition, and microarray recognition as well as for the regression task of human age estimation on the FG-NET aging database, all validate the effectiveness of our proposed learning framework, compared with the state-of-the-art counterparts.
Income Inequality and Macroeconomic Volatility: An Empirical Investigation

We explore the impact of macroeconomic volatility on the distribution of income. Using a cross-section of developed and developing countries, we find that greater output volatility, defined as the standard deviation of the rate of output growth, is associated with a higher Gini coefficient and income share of the top quintile. The coefficients suggest that a strong effect on inequality resulting from a reduction in volatility: the Gini coefficient of a country like Chile would fall by 6 points if it were to reduce its volatility to the same level as Sweden or Norway. Our results seem not to be driven by the high-inequality/high-volatility Latin American countries.
Journal of Sustainable Water in the Built Environment

The Journal of Sustainable Water in the Built Environment presents activity and research developments in water issues, challenges, and opportunities throughout the developed landscape. The scope covers sustainable stormwater management and broader water systems interactions. Subjects include urban stormwater quantity, quality, hydrology, characterization, treatability, and impacts; water harvesting; urban water ecosystem services; sustainable urban watershed management; urban streams; combined sewer overflow/stormwater interactions; urban energy/water interactions; lifecycle analysis; and related policy, implementation, and economics. All papers are encouraged to have design or regulatory implications that are applicable to moving the profession forward.
Discovery of WASP-65b and WASP-75b: Two hot Jupiters without highly inflated radii

We report the discovery of two transiting hot Jupiters, WASP-65b (Mpl = 1.55 ± 0.16 MJ; Rpl = 1.11 ± 0.06 RJ), and WASP-75b (Mpl = 1.07 ± 0.05 MJ; Rpl = 1.27 ± 0.05 RJ). They orbit their host star every ∼2.311, and ∼2.484 days, respectively. The planet host WASP-65 is a G6 star (Teff = 5600 K, [Fe/H] = −0.07 ± 0.07, age 8 Gyr); WASP-75 is an F9 star (Teff = 6100 K, [Fe/H] = 0.07 ± 0.09, age ∼ 3 Gyr). WASP-65b is one of the densest known exoplanets in the mass range 0.1 and 2.0 MJ (ρpl = 1.13 ± 0.08 ρJ), a mass range where a large fraction of planets are found to be inflated with respect to theoretical planet models. WASP-65b is one of only a handful of planets with masses of ∼1.5 MJ, a mass regime surprisingly underrepresented among the currently known hot Jupiters. The radius of WASP-75b is slightly inflated (10%) as compared to theoretical planet models with no core, and has a density similar to that of Saturn (ρpl = 0.52 ± 0.06 ρJ).
A novel way of computing dissimilarities between nodes of a graph

This work presents a new perspective on characterizing the similarity between elements of a database or, more generally, nodes of a weighted, undirected, graph. It is based on a Markov-chain model of random walk through the database. More precisely, we compute quantities (the average commute time, the pseudoinverse of the Laplacian matrix of the graph, etc) that provide similarities between any pair of nodes, having the nice property of increasing when the number of paths connecting those elements increases and when the “length” of paths decreases. It turns out that the square root of the average commute time is a Euclidean distance and that the pseudoinverse of the Laplacian matrix is a kernel (it contains inner-products closely related to commute times). A procedure for computing the subspace projection of the node vectors of the graph that preserves as much variance as possible in terms of the commute-time distance – a principal components analysis (PCA) of the graph – is also introduced. This graph PCA provides a nice interpretation to the “Fiedler vector”, widely used for graph partitioning. The model is evaluated on a collaborative-recommendation task where suggestions are made about which movies people should watch based upon what they watched in the past. Experimental results on the MovieLens database show that the Laplacian-based similarities perform well in comparison with other methods. The model, which nicely fits into the so-called “statistical relational learning” framework, could also be used to compute document or word similarities, and, more generally, could be applied to machine-learning and pattern-recognition tasks involving a database. François Fouss, Alain Pirotte and Marco Saerens are with the Information Systems Research Unit (ISYS), IAG, Université catholique de Louvain, Place des Doyens 1, B-1348 Louvain-la-Neuve, Belgium. Email: {saerens, pirotte, fouss}@isys.ucl. ac.be. Jean-Michel Renders is with the Xerox Research Center Europe, Chemin de Maupertuis 6, 38240 Meylan (Grenoble), France. Email: jean-michel.renders@xrce.xerox. com.
On a generalization of a theorem by Vosper.

Let S, T be subsets of Z/pZ with min{|S|, |T |} > 1. The Cauchy–Davenport theorem states that |S + T | ≥ min{p, |S| + |T | − 1}. A theorem by Vosper characterizes the critical pair in the above inequality. We prove the following generalization of Vosper’s theorem. If |S + T | ≤ min{p− 2, |S|+ |T |+m}, 2 ≤ |S|, |T |, and |S| ≤ p− ( m+4 2 ) , then S is a union of at most m+ 2 arithmetic progressions with the same difference. The term ( m+4 2 ) is best possible, i.e. cannot be replaced by a smaller number.
Contributing factors to colorectal cancer and hepatitis B screening among Vietnamese Americans.

PURPOSE/OBJECTIVES To identify factors associated with screening for colorectal cancer (CRC) and hepatitis B, because hepatitis B can increase the risk of liver cancer. DATA SOURCES MEDLINE®, CINAHL®, and PsycINFO databases from January 1998 to April 2012. DATA SYNTHESIS The 23 reviewed studies included 15 descriptive, 2 intervention, 3 qualitative, 2 chart or medical record review, and 1 mixed method. Most studies used an investigator-developed instrument with no reported reliability. Inconsistent operational definitions for contributing factors to screening made it challenging to make comparisons. CONCLUSIONS CRC and hepatitis B screening are consistently low among Vietnamese Americans. Contributing factors included sociodemographics, knowledge, cultural beliefs, and external factors. External factors such as having a regular place of care and a healthcare provider were crucial because they influenced adherence to screening recommendations. Use of a public media education plus healthcare provider model and a culturally tailored intervention using Vietnamese lay advisors appeared to be promising for improving CRC screening. Additional intervention studies are needed to increase screening. IMPLICATIONS FOR NURSING Vietnamese is a fast-growing subgroup within the Asian American Pacific Islander (AAPI) group that may require targeted approaches to screening for disease. Future studies should focus on immigrants or those who were born in the United States (men and women) as disaggregated subgroups. Such research can inform culturally sensitive and appropriate interventions that may improve cancer screening rates. KNOWLEDGE TRANSLATION Although Vietnamese is the fourth largest racial-ethnic subgroup within the AAPI group, the literature about contributing factors to CRC and hepatitis B screening is limited among this subgroup. CRC and hepatitis B screening are consistently low among Vietnamese Americans. Use of public media education plus a healthcare provider model and a culturally tailored intervention using Vietnamese lay advisors appears promising for improving CRC screening.
Orientation of gravels and soft-sediment clasts in subaqueous debrites – implications for palaeodirection reconstruction: case study from Puck Bay, northern Poland

Subaqueous debrites on a fan were recognized at Rzucewo (N Poland). Analysis of debrite fabric enabled debris-flow palaeodirections to be traced on the fan. The long axis azimuth and dip direction of lithic clasts (gravels) as well as soft-sediment clasts (SSC) were measured in the debrites. The results obtained indicate a palaeotransport direction to NNW, similar to the palaeocurrents interpreted from the asymmetrical ripples. However, detailed measurements of both gravels and SSC orientation show variability of palaeoflow directions between NW and NE sectors. In the proximal part of the fan, gravels indicate variable dip directions and dip angles, and a mostly scattered distribution of a-axis orientation. In the medial and distal parts of the fan, clasts are better ordered and usually their a-axes are oriented upslope or transverse to the palaeoslope inclination direction. Probably during the decelerating and halting of debris flows, the compression processes induced clast rotation and a change of inclination. In the distal part of the fan, debrites reveal a distinct variability of palaeoflow directions caused by flattened topography in which debris-flow lobes split and spread freely in different directions. Finally, we conclude that the individual sets of clast fabric usually indicate only local debris-flow directions.
Identification and Evaluation of Discriminative Lexical Features of Malware URL for Real-Time Classification

This study identifies and evaluates discriminative lexical features of malware URLs for building a real-time malware URL classification. The lexical features of malware URL are first identified from existing blacklisted malware URLs through manual examination. Feature identification is followed by studying the prevalence of these features on newly collected malware URLs through empirical analysis. Our empirical analysis revealed that attackers follow the same pattern in crafting malware URL. To evaluate the performance and effectiveness of these features, we applied a Support Vector Machine (SVM) classification algorithm on a dataset comprising of benign and malware URLs. By applying the WEKA data mining tool on our trained dataset, a 96.95 % accuracy was achieved with a low False Negative Rate (FNR) of 0.018 and a moderate False Positive Rate (FPR) of 0.046.
Material for : A Systems Approach to Mapping DNA Damage Response Pathways

Supporting Online Material for: A Systems Approach to Mapping DNA Damage Response Pathways Christopher T. Workman, H. Craig Mak, Scott McCuine, Jean-Bosco Tagne, Maya Agarwal, Owen Ozier, Thomas J. Begley, Leona D. Samson, and Trey Ideker 1 University of California San Diego, La Jolla, CA 92093 2 Whitehead Institute for Biomedical Research, Cambridge, MA 02139 3 University of Albany-State University of New York, Rensselaer, NY 12144 4 Massachusetts Institute of Technology, Cambridge, MA 02139 * These authors contributed equally to the manuscript.  To whom correspondence should be addressed. E-mail: trey@bioeng.ucsd. edu
A Differential Role for CD248 (Endosialin) in PDGF-Mediated Skeletal Muscle Angiogenesis

CD248 (Endosialin) is a type 1 membrane protein involved in developmental and pathological angiogenesis through its expression on pericytes and regulation of PDGFRβ signalling. Here we explore the function of CD248 in skeletal muscle angiogenesis. Two distinct forms of capillary growth (splitting and sprouting) can be induced separately by increasing microcirculatory shear stress (chronic vasodilator treatment) or by inducing functional overload (extirpation of a synergistic muscle). We show that CD248 is present on pericytes in muscle and that CD248-/- mice have a specific defect in capillary sprouting. In contrast, splitting angiogenesis is independent of CD248 expression. Endothelial cells respond to pro-sprouting angiogenic stimulus by up-regulating gene expression for HIF1α, angiopoietin 2 and its receptor TEK, PDGF-B and its receptor PDGFRβ; this response did not occur following a pro-splitting angiogenic stimulus. In wildtype mice, defective sprouting angiogenesis could be mimicked by blocking PDGFRβ signalling using the tyrosine kinase inhibitor Imatinib mesylate. We conclude that CD248 is required for PDGFRβ-dependant capillary sprouting but not splitting angiogenesis, and identify a new role for CD248 expressed on pericytes in the early stages of physiological angiogenesis during muscle remodelling.
Morphology and cell type heterogeneities of the inner ear epithelia in adult and juvenile zebrafish (Danio rerio)

Although the zebrafish has become an important model for genetic analysis of the vertebrate auditory system, a comprehensive description of the zebrafish ear has been provided for embryonic and larval development only (Haddon and Lewis [ 1996 ] J. Comp. Neurol. 365:113). Here we describe the development of sensory maculae in juvenile fish and the morphology of the adult zebrafish ear. This description was obtained via three‐dimensional reconstruction of serial sections and confocal microscopy of immunolabeled preparations and includes the Weberian ossicles and fluid spaces. Phalloidin staining, which labels actin filaments of stereocilia, was used to delineate the sensory epithelia, to visualize the distribution of hair cells, to estimate their density in different areas of the maculae, and to perform hair cell counts. Morphology of ciliary bundles in different regions of the lagena, saccule, utricle, macula neglecta, and cristae was characterized with an anti‐acetylated tubulin antibody and by phalloidin staining. We have identified two antibodies characterized by region‐specific staining patterns in the inner ear epithelia. Zn‐1 antibody staining largely correlates with the presence of short‐bundle hair cells in the peripheral regions of sensory epithelia. Zn‐4 antibody, on the other hand, labels a zone of epithelial cells surrounding the sensory maculae. These analyses extend previous observations of cell‐type heterogeneity in both sensory and nonsensory epithelia of the fish ear. J. Comp. Neurol. 438:173–190, 2001. © 2001 Wiley‐Liss, Inc.
Modelling and interpreting the dependence of clustering on the spectral energy distributions of galaxies

We extend our previous physically based halo occupation distribution models to include the dependence of clustering on the spectral energy distributions of galaxies. The high-resolution Millennium Simulation is used to specify the positions and the velocities of the model galaxies. The stellar mass of a galaxy is assumed to depend only on M infall , the halo mass when the galaxy was last the central dominant object of its halo. Star formation histories are parametrized using two additional quantities that are measured from the simulation for each galaxy: its formation time (t from ), and the time when it first becomes a satellite (t infall ). Central galaxies begin forming stars at time t form with an exponential time-scale τ c· If the galaxy becomes a satellite, its star formation declines thereafter with a new time-scale T s· We compute 4000-A break strengths for our model galaxies using stellar population synthesis models. By fitting these models to the observed abundances and projected correlations of galaxies as a function of break strength in the Sloan Digital Sky Survey, we constrain τ c and τ s as functions of galaxy stellar mass. We find that central galaxies with large stellar masses have ceased forming stars. At low stellar masses, central galaxies display a wide range of different star formation histories, with a significant fraction experiencing recent starbursts. Satellite galaxies of all masses have declining star formation rates, with similar e-folding times, τ s ∼ 2.5 Gyr. One consequence of this long e-folding time is that the colour-density relation is predicted to flatten at redshifts > 1.5, because star formation in the majority of satellites has not yet declined by a significant factor. This is consistent with recent observational results from the DEEP and VVDS surveys.
Parametric Rainfall Retrieval Algorithms for Passive Microwave Radiometers

Abstract A methodology is described to construct fully parametric rainfall retrieval algorithms for a variety of passive microwave sensors that exist today and are planned for the future. The Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) is used to retrieve nonraining geophysical parameters. The method then blends these background geophysical parameters with three-dimensional precipitation fields obtained by matching the TRMM precipitation radar (PR) reflectivity profiles with cloud-resolving model simulations to produce a consistent three-dimensional atmospheric description. Based upon this common description, radiative transfer simulations corresponding to specific microwave sensors are then employed to compute radiances from clear and rainy scenes, as might be seen by any specified microwave radiometer. Last, a Bayesian retrieval methodology is used in conjunction with this database to derive the most likely surface rainfall as well as its vertical structure. By avoiding any depende.
A Lustrum of Malware Network Communication: Evolution and Insights

Both the operational and academic security communities have used dynamic analysis sandboxes to execute malware samples for roughly a decade. Network information derived from dynamic analysis is frequently used for threat detection, network policy, and incident response. Despite these common and important use cases, the efficacy of the network detection signal derived from such analysis has yet to be studied in depth. This paper seeks to address this gap by analyzing the network communications of 26.8 million samples that were collected over a period of five years. Using several malware and network datasets, our large scale study makes three core contributions. (1) We show that dynamic analysis traces should be carefully curated and provide a rigorous methodology that analysts can use to remove potential noise from such traces. (2) We show that Internet miscreants are increasingly using potentially unwanted programs (PUPs) that rely on a surprisingly stable DNS and IP infrastructure. This indicates that the security community is in need of better protections against such threats, and network policies may provide a solid foundation for such protections. (3) Finally, we see that, for the vast majority of malware samples, network traffic provides the earliest indicator of infection—several weeks and often months before the malware sample is discovered. Therefore, network defenders should rely on automated malware analysis to extract indicators of compromise and not to build early detection systems.
Localization of Wireless Sensor Nodes Using Proximity Information

This paper proposes a simple yet efficient localization algorithm for GPS-free sensor nodes in wireless sensor networks (WSN). Our approach is hybrid in the sense that it utilizes a combination of GPS-enabled and localized GPS-free nodes. It relaxes the need to equip a large number of nodes with GPS interfaces, to have high radio ranges for all nodes, and to have a uniform deployment of GPS-enabled nodes. The proposed strategy performs well, extends the lifetime of WSN (GPS and high radio ranges drain energy faster), and reduces cost (GPS devices increase the cost of sensors considerably).
Digital Signal Reconstruction in the ATLAS Hadronic Tile Calorimeter

We present an Optimal Filtering (OF) algorithm to reconstruct the energy, time and pedestal of a photomultiplier signal from its digital samples. The OF algorithm was first developed for liquid ionization calorimeters, its implementation in scintillator calorimeters, specifically in the ATLAS hadronic Tile calorimeter (TileCal), is the aim of this study. The objective is to implement the algorithm on the DSPs of the Read Out Driver cards in order to reconstruct online the energy of the calorimeter and provide it to the second level trigger. The algorithm is tested and compared with a plain filtering algorithm using both calibration and real data from the TileCal detector. The results are promising specially in the regions where the electronic noise contributes significantly to the resolution