A Faster Implementation of Online Run-Length Burrows-Wheeler Transform

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in $O(n\lg r)$ time and $O(r\lg n)$ bits of space, where $n$ is the length of input string $S$ received so far and $r$ is the number of runs in the BWT of the reversed $S$. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201

Knife-edge based measurement of the 4D transverse phase space of electron beams with picometer-scale emittance

Precise manipulation of high brightness electron beams requires detailed knowledge of the particle phase space shape and evolution. As ultrafast electron pulses become brighter, new operational regimes become accessible with emittance values in the picometer range, with enormous impact on potential scientific applications. Here we present a new characterization method for such beams and demonstrate experimentally its ability to reconstruct the 4D transverse beam matrix of strongly correlated electron beams with sub-nanometer emittance and sub-micrometer spot size, produced with the HiRES beamline at LBNL. Our work extends the reach of ultrafast electron accelerator diagnostics into picometer-range emittance values, opening the way to complex nanometer-scale electron beam manipulation techniques

Soc-based in-cycle load identification of induction heating appliances

The equivalent load of an induction hob is strongly dependent on many parameters such as the switching frequency, the excitation level and the size, type, and material of the vessel. However, real-time methods with the ability to capture the variation of the load with the excitation level have not been proposed in the literature. This is an essential issue as most of the commercial induction hobs are based on an ac-bus voltage arrangement. This article proposes a method based on a phase-sensitive detector that offers an online tracking of the equivalent impedance for this type of arrangements. This algorithm enables advanced control functionalities such as clustering of vessels, material recognition, and premature detection of ferromagnetic saturation, among others. After simulation and experimental validation, the method is implemented into a prototype with a system-on-chip to verify its real-time behavior. The proposed approach is applied to different real-life situations that prove its great performance and applicability

Flat Central Density Profile and Constant DM Surface Density in Galaxies from Scalar Field Dark Matter

The scalar field dark matter (SFDM) model proposes that galaxies form by condensation of a scalar field (SF) very early in the universe forming Bose-Einstein Condensates (BEC) drops, i.e., in this model haloes of galaxies are gigantic drops of SF. Here big structures form like in the LCDM model, by hierarchy, thus all the predictions of the LCDM model at big scales are reproduced by SFDM. This model predicts that all galaxies must be very similar and exist for bigger redshifts than in the LCDM model. In this work we show that BEC dark matter haloes fit high-resolution rotation curves of a sample of thirteen low surface brightness galaxies. We compare our fits to those obtained using a Navarro-Frenk-White and Pseudo-Isothermal (PI) profiles and found a better agreement with the SFDM and PI profiles. The mean value of the logarithmic inner density slopes is -0.27 +/- 0.18. As a second result we find a natural way to define the core radius with the advantage of being model-independent. Using this new definition in the BEC density profile we find that the recent observation of the constant dark matter central surface density can be reproduced. We conclude that in light of the difficulties that the standard model is currently facing the SFDM model can be a worthy alternative to keep exploring further.Comment: Submitted to MNRAS, 9 pages, 32 Figures, 2 Tables.The paper with better resolution figures can be downloaded at "http://estudiantes.fis.cinvestav.mx/vrobles/SFDMfile.pd

Ultrafast Relativistic Electron Nanoprobes

One of the frontiers in electron scattering is to couple ultrafast temporal resolution with highly localized probes to investigate the role of microstructure on material properties. Here, taking advantage of the unprecedented average brightness of the APEX electron gun providing relativistic electron pulses at high repetition rates, we demonstrate for the first time the generation of ultrafast relativistic electron beams with picometer-scale emittance and their ability to probe nanoscale features on materials with complex microstructures. At the sample plane, the APEX beam is tightly focused by a custom in-vacuum lens system based on permanent magnet quadrupoles, and its evolution around the waist is tracked by a knife-edge technique, allowing accurate reconstruction of the beam shape and local density. We then use the focused beam to characterize a Ti-6 wt\% Al polycrystalline sample by correlating the diffraction and imaging modality, showcasing the capability to locate grain boundaries and map adjacent crystallographic domains with sub-micron precision. This work provides a new paradigm for ultrafast electron instrumentation, demonstrating the ability to generate relativistic beams with ultrasmall transverse phase space volumes enabling novel characterization techniques such as relativistic ultrafast electron nano-diffraction and ultrafast scanning transmission electron microscopy

Efficient and Compact Representations of Some Non-canonical Prefix-Free Codes

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-46049-9_5[Abstract] For many kinds of prefix-free codes there are efficient and compact alternatives to the traditional tree-based representation. Since these put the codes into canonical form, however, they can only be used when we can choose the order in which codewords are assigned to characters. In this paper we first show how, given a probability distribution over an alphabet of σσ characters, we can store a nearly optimal alphabetic prefix-free code in o(σ)o(σ) bits such that we can encode and decode any character in constant time. We then consider a kind of code introduced recently to reduce the space usage of wavelet matrices (Claude, Navarro, and Ordóñez, Information Systems, 2015). They showed how to build an optimal prefix-free code such that the codewords’ lengths are non-decreasing when they are arranged such that their reverses are in lexicographic order. We show how to store such a code in O(σlogL+2ϵL)O(σlog⁡L+2ϵL) bits, where L is the maximum codeword length and ϵϵ is any positive constant, such that we can encode and decode any character in constant time under reasonable assumptions. Otherwise, we can always encode and decode a codeword of ℓℓ bits in time O(ℓ)O(ℓ) using O(σlogL)O(σlog⁡L) bits of space.Ministerio de Economía, Industria y Competitividad; TIN2013-47090-C3-3-PMinisterio de Economía, Industria y Competitividad; TIN2015-69951-RMinisterio de Economía, Industria y Competitividad; ITC-20151305Ministerio de Economía, Industria y Competitividad; ITC-20151247Xunta de Galicia; GRC2013/053Chile. Núcleo Milenio Información y Coordinación en Redes; ICM/FIC.P10-024FCOST. IC1302Academy of Finland; 268324Academy of Finland; 25034

Numerical simulation code for self-gravitating Bose-Einstein condensates

We completed the development of simulation code that is designed to study the behavior of a conjectured dark matter galactic halo that is in the form of a Bose-Einstein Condensate (BEC). The BEC is described by the Gross-Pitaevskii equation, which can be solved numerically using the Crank-Nicholson method. The gravitational potential, in turn, is described by Poisson's equation, that can be solved using the relaxation method. Our code combines these two methods to study the time evolution of a self-gravitating BEC. The inefficiency of the relaxation method is balanced by the fact that in subsequent time iterations, previously computed values of the gravitational field serve as very good initial estimates. The code is robust (as evidenced by its stability on coarse grids) and efficient enough to simulate the evolution of a system over the course of 1E9 years using a finer (100x100x100) spatial grid, in less than a day of processor time on a contemporary desktop computer.Comment: 13 pages, 1 figure; updated to reflect changes in the published versio

Fundamental, Quantitative Traits of the “Sociotype”

In whatever domain of life, from cells to organisms to societies, communicative exchanges underlie the formation and maintenance, and decay, of the emerging collective structures. It can be clearly seen in the human social world. The different classes of social bonds in a complex society revolve around, and are intimately related with, the communicative relationships that every individual entertains—essentially via face-to-face conversation. In the present work we have investigated the fundamental metrics of both social bonds and communicative exchanges along the development of the “sociotype” construct. It is a new approach developed by the authors within the genotype-phenotype-sociotype conceptual triad. The sociotype means the relative constancy, or better the similar fabric, of the social world in which each individual life is developed. In order to ascertain the metrics of the fundamental quantitative traits inherent in the sociotype, a fieldwork involving a total of 1475 individuals (68.59% female, and 49.79 mean age, SD = 21.47) was carried out. The four relational realms of family, friends, work/study, and acquaintances were investigated. The overall results about conversation time (an average of 220 min/day), and about the number of social bonds (an average of 98), differ from previous assumptions, such as Dunbar's number or Killworth's number. Other results about gender, age, and use of social media and Internet contribute to highlight significant differences among the different social segments, and particularly the diminished “sociotype” of the elderly. Finally, it is curious that a non-Gaussian distribution has been obtained for the specific population allotment of these metrics, and intriguingly the Planckian distribution equation (PDE) appears to be a most cogent fit

A Phase II Trial of Prexasertib (LY2606368) in Patients With Extensive-Stage Small-Cell Lung Cancer

Checkpoint kinase 1 inhibitor; Pharmacokinetics; Small cell lung cancerInhibidor de quinasa de punto de control 1; Farmacocinética; Cáncer de pulmón de células pequeñasInhibidor de la quinasa del punt de control 1; Farmacocinètica; Càncer de pulmó de cèl·lules petitesBackground This study assessed the checkpoint kinase 1 inhibitor prexasertib in patients with extensive-stage small-cell lung cancer (ED-SCLC). Patients and Methods This was a parallel-cohort phase II study of 105 mg/m2 prexasertib once every 14 days for patients who progressed after no more than two prior therapies and had platinum-sensitive (Cohort 1) or platinum-resistant/platinum-refractory (Cohort 2) disease. The primary endpoint was objective response rate (ORR). Secondary endpoints included disease control rate (DCR), progression-free survival (PFS), overall survival (OS), safety, and pharmacokinetics. Exploratory endpoints included biomarker identification and assessment of an alternative regimen (Cohort 3: 40 mg/m2 days 1-3, 14-day cycle). Results In Cohort 1 (n = 58), ORR was 5.2%; DCR, 31%; median PFS, 1.41 months (95% confidence interval [CI], 1.31-1.64); and median OS, 5.42 months (95% CI, 3.75-8.51). In Cohort 2 (n = 60), ORR was 0%; DCR, 20%; median PFS, 1.36 months (95% CI, 1.25-1.45); and median OS, 3.15 months (95% CI, 2.27-5.52). The most frequent all-grade, related, treatment-emergent adverse events were decreased neutrophil count (Cohort 1, 69.6%; Cohort 2, 73.3%), decreased platelet count (Cohort 1, 51.8%; Cohort 2, 50.0%), decreased white blood cell count (Cohort 1, 28.6%; Cohort 2, 40.0%), and anemia (Cohort 1, 39.3%; Cohort 2, 28.3%). Eleven patients (19.6%) in Cohort 1 and one patient (1.7%) in Cohort 2 experienced grade ≥3 febrile neutropenia. Prexasertib pharmacokinetics were consistent with prior studies. Cohort 3 outcomes were similar to those of Cohorts 1 and 2. No actionable biomarkers were identified. Conclusion Prexasertib did not demonstrate activity to warrant future development as monotherapy in ED-SCLC.This research was funded by Eli Lilly and Company

Controlled Release of Therapeutics from Thermoresponsive Nanogels: A Thermal Magnetic Resonance Feasibility Study

Thermal magnetic resonance (ThermalMR) accommodates radio frequency (RF)-induced temperature modulation, thermometry, anatomic and functional imaging, and (nano)molecular probing in an integrated RF applicator. This study examines the feasibility of ThermalMR for the controlled release of a model therapeutics from thermoresponsive nanogels using a 7.0-tesla whole-body MR scanner en route to local drug-delivery-based anticancer treatments. The capacity of ThermalMR is demonstrated in a model system involving the release of fluorescein-labeled bovine serum albumin (BSA-FITC, a model therapeutic) from nanometer-scale polymeric networks. These networks contain thermoresponsive polymers that bestow environmental responsiveness to physiologically relevant changes in temperature. The release profile obtained for the reference data derived from a water bath setup used for temperature stimulation is in accordance with the release kinetics deduced from the ThermalMR setup. In conclusion, ThermalMR adds a thermal intervention dimension to an MRI device and provides an ideal testbed for the study of the temperature-induced release of drugs, magnetic resonance (MR) probes, and other agents from thermoresponsive carriers. Integrating diagnostic imaging, temperature intervention, and temperature response control, ThermalMR is conceptually appealing for the study of the role of temperature in biology and disease and for the pursuit of personalized therapeutic drug delivery approaches for better patient care