Muppet: MapReduce-Style Processing of Fast Data

MapReduce has emerged as a popular method to process big data. In the past few years, however, not just big data, but fast data has also exploded in volume and availability. Examples of such data include sensor data streams, the Twitter Firehose, and Facebook updates. Numerous applications must process fast data. Can we provide a MapReduce-style framework so that developers can quickly write such applications and execute them over a cluster of machines, to achieve low latency and high scalability? In this paper we report on our investigation of this question, as carried out at Kosmix and WalmartLabs. We describe MapUpdate, a framework like MapReduce, but specifically developed for fast data. We describe Muppet, our implementation of MapUpdate. Throughout the description we highlight the key challenges, argue why MapReduce is not well suited to address them, and briefly describe our current solutions. Finally, we describe our experience and lessons learned with Muppet, which has been used extensively at Kosmix and WalmartLabs to power a broad range of applications in social media and e-commerce.Comment: VLDB201

A Systems Approach to Housing Market Analysis: The Role of Search and Migration in Market Dynamics in Greater Manchester

Housing markets are complex and dynamic entities. They are fragmented across space and their structure and functionality alters over time. This complexity makes monitoring and steering markets difficult and is one of the reasons that planning for housing is analytically and technically challenging. To analyse housing effectively, it is widely held that we should conceptualise the market as a part of a system of linked but spatially coherent Housing Markets Areas, comprising internally of inter-linked submarkets that are over time subject to changes in configuration and function. In response, this thesis adopts a systems approach to frame the analysis of housing market dynamics (O’Sullivan et al, 2004). Within this framework, the study aims to understand the spatial and temporal dynamics of the Greater Manchester housing system in recent years. The analysis seeks to demonstrate the usefulness of a market systems approach that employs visual data analytical methods to provide insights into market processes. Specifically the thesis analyses housing search, migration and house price and offers a case study that explores the interactions between HMAs, and submarket connections within an HMA. The major contribution is to highlight the importance of considering a housing market as a system of linked HMAs and submarkets, to illustrate the useful insights that might be generated using visual data methods and to provide a novel analysis that combines role of housing search, migration and house price data in gaining a better understanding of how a local housing market works. In doing so, the study is at the forefront of the emerging literature that uses new micro-datasets to analyse search information

New record for Asia-Pacific of Protoperidinium anomaloplaxum (Peridiniales, Dinophyceae) from Vietnamese waters

Minusculum (Lebour) Balech is one of four subgenera of the genus Protoperidinium Bergh 1881. Only five species of this subgenus have been discovered worldwide, most of which are distributed in cold waters. In this study, Protoperidinium anomaloplaxum (Balech) Balech is reported from Vietnam and thus for the first time from Asia-Pacific waters. This species is illustrated with line drawing, light and scanning electron microscopic photographs and described details of the ornamentation of the thecal plates as well as its geographic distribution.

The spindle of oocytes observed by polarized light microscope can predict embryo quality

Background: The aim is to evaluate spindle position of metaphase II oocyte and the development of embryos originated from oocytes with spindle and without spindle.Methods: Cross-sectional analysis Research: 250 MII oocytes were analyzed with polarized microscope in Military Institute of Clinical Embryology and Histology, Vietnam Military Medical University.Results: Spindles were detected in 170 (77.98%) of 218 metaphase II oocytes, 115 spindles (67.65%) of MII oocytes is beneath or adjacent to the first polar body, 55 oocytes had the spindle located between 300 and 1800 away from the first polar body. Fertilization rate and the rate of good quality embryos in oocytes with a visible spindle (77.98% and 61.02%) were higher than those in oocytes without a visible spindle (22.02% and 36.84%), the difference was statistically significant with p <0.001 and p <0.05.Conclusions: The spindle position of metaphase II oocytes is not always beneath or adjacent to the first polar body. Fertilization rate and the rate of good quality embryos in oocytes with a visible spindle were higher than those in oocytes without a visible spindle

Evolutionary tracks for Betelgeuse

We have constructed a series of non-rotating quasi-hydrostatic evolutionary models for the M2 Iab supergiant Betelgeuse ($\alpha~Orionis$). Our models are constrained by multiple observed values for the temperature, luminosity, surface composition and mass loss for this star, along with the parallax distance and high resolution imagery that determines its radius. We have then applied our best-fit models to analyze the observed variations in surface luminosity and the size of detected surface bright spots as the result of up-flowing convective material from regions of high temperature in the surface convective zone. We also attempt to explain the intermittently observed periodic variability in a simple radial linear adiabatic pulsation model. Based upon the best fit to all observed data, we suggest a best progenitor mass estimate of $20 ^{+5}_{-3} M_\odot$ and a current age from the start of the zero-age main sequence of $8.0 - 8.5$ Myr based upon the observed ejected mass while on the giant branch.Comment: 27 pages, 11 figures, Revised per referee suggestions, Accepted for publication in the Astrophysical Journa

A Model for the Prediction of Harmful Algae Blooms in the Vietnamese Upwelling Area

Satellite pictures and in situ observations indicate strong phytoplankton blooms including harmful algae blooms (HABs) during southwest (SW) summer monsoon in the Vietnamese upwelling area. In this period, nutrients are provided by coastal upwelling and by the very high river runoff from the Mekong River. During SW monsoon, in general two circulation patterns exist which allow the prediction of advection and diffusion of HAB patches. A Lagrangian HAB model that is driven by a circulation model and applied to HABs in Vietnamese waters is presented. Advection which is the most complicated part in modelling transport of passive substances is validated with a Lagrangian sediment trap experiment. The model produces realistic results compared to in situ observations and satellite images and might be used for real time forecast in the future

Abstractive Text Summarization Using the BRIO Training Paradigm

Summary sentences produced by abstractive summarization models may be coherent and comprehensive, but they lack control and rely heavily on reference summaries. The BRIO training paradigm assumes a non-deterministic distribution to reduce the model's dependence on reference summaries, and improve model performance during inference. This paper presents a straightforward but effective technique to improve abstractive summaries by fine-tuning pre-trained language models, and training them with the BRIO paradigm. We build a text summarization dataset for Vietnamese, called VieSum. We perform experiments with abstractive summarization models trained with the BRIO paradigm on the CNNDM and the VieSum datasets. The results show that the models, trained on basic hardware, outperform all existing abstractive summarization models, especially for Vietnamese.Comment: 6 pages, Findings of the Association for Computational Linguistics: ACL 202

Identification et caractérisation des déterminants physico-chimiques et biologiques mis en jeu dans l’adhésion de Lactococcus lactis à la mucine modèle PGM

Dans le tractus gastro-intestinal, l'adhésion des bactéries commensales à l’épithélium permet leur maintien, ce qui aide à contrôler l’implantation de germes indésirables par des mécanismes de concurrence (effets nutritionnels, sites spécifiques d'adhésion ...). Bien que le rôle de la couche du mucus (principalement composée de glycoprotéines à haut poids moléculaire, appelées mucines) recouvrant la muqueuse soit connu et décrit depuis de nombreuses années, notamment pour sa fonction de barrière protectrice, l'intérêt pour décrypter les mécanismes précis d’interaction(s) avec le microbiote (bactéries commensales, pathogènes ou probiotiques) n’a que récemment émergé. Dans ce cadre, l'objectif de cette thèse, menée en collaboration entre le Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés de Toulouse et le Laboratoire d’Analyse et d’Architecture des Systèmes de Toulouse, est de caractériser in vitro le comportement muco-adhésif de Lactococcus lactis, le modèle des bactéries lactiques, en utilisant des approches de quantification multi-échelles (du niveau moléculaire à l’échelle multicellulaire) sur un large panel de souches naturelles et recombinantes. Une attention particulière est accordée au rôle des mucines, en utilisant le modèle PGM (mucine gastrique de porc ou « Pig Gastric Mucin »).\ud La première partie du travail a porté sur la quantification à l'échelle de la cellule unique des interactions entre L. lactis et une surface abiotique (polystyrène) recouverte de PGM, en utilisant la microscopie à force atomique (AFM). La faisabilité de la méthode a tout d'abord été démontrée sur la souche modèle L. lactis ssp. cremoris MG1820. La couche de PGM a été caractérisée en utilisant des méthodes analytiques complémentaires (AFM, XPS - spectroscopie de photoélectrons induits par rayons X, QCM-D - Microbalance à Quartz à mesure de Dissipation...). En parallèle, les bactéries L. lactis ont été immobilisées sur la pointe AFM et utilisées comme « sonde de force », en considérant la souche naturelle IBB477 (L. lactis ssp. cremoris), d’origine laitière et présentant une forte persistance dans le tractus digestif du rat lors d’essais réalisés in vivo (collaboration avec l’Institut de Biochimie et de Biophysique de Varsovie, Pologne). Comparé aux conditions contrôle (i.e., surface de polystyrène sans PGM), les niveaux de force d'adhésion enregistrés entre L. lactis et PGM sont inférieurs, ceci en raison des répulsions électrostatiques, hydrophiles et stériques s’établissant entre la couche de PGM et la paroi cellulaire. La forme des courbes représentant l’évolution de la force au retrait en fonction de la distance est également différente. Une analyse détaillée souligne la contribution, conjointe et différente selon les souches testées, d’événements (i) non adhésifs, (ii) adhésifs non spécifiques (interactions électrostatiques, hydrophobes, de van der Waals) et (iii) adhésifs spécifiques (liaison de type ligand/récepteur). La contribution spécifique a ensuite été explorée plus finement en termes de constantes cinétiques d’association et de dissociation. \ud Nous avons, par ailleurs, poursuivi notre exploitation de la biodiversité naturelle chez les lactocoques en étudiant la souche TIL448 (L. lactis ssp. lactis) d’origine végétale, en collaboration avec l’Institut MICALIS de Jouy-en-Josas. Nous avons ainsi démontré, pour la première fois chez L. lactis, le rôle combiné des protéines à domaine(s) MUB (« Mucus-Binding ») et des pili, à travers l'analyse approfondie des données AFM (force d'adhésion, répartition des événements adhésifs spécifiques/non spécifiques, distances d'interaction...). Le rôle des pili a été confirmé sur des souches recombinantes piliées (L. lactis ssp. lactis IL1403), toujours en partenariat avec l’Institut MICALIS de Jouy-en-Josas. En parallèle, en collaboration avec l’Unité de Glycobiologie Structurale et Fonctionnelle de Villeneuve d'Ascq, nous avons cherché à identifier les O-glycannes de PGM (fractions neutre et acide), impliqués dans le processus d'interaction avec la surface bactérienne. \ud Pour confirmer l’ensemble des résultats obtenus à l'échelle de la cellule unique et en mode statique par AFM (effet anti-adhésif de PGM, comportement muco-adhésif différent selon les souches de L. lactis), la deuxième partie du travail a été consacrée à des expérimentations à l’échelle de l’ensemble de la population bactérienne, en conditions dynamiques (QCM-D, chambre à écoulement cisaillé). Nous avons évalué par QCM-D chez les souches IBB477 et MG1820 les propriétés viscoélastiques des dépôts bactériens, en relation avec le comportement bio-adhésif vis-à-vis de la couche de PGM. Les données obtenues par AFM et chambre à écoulement cisaillé sur ces mêmes souches ont été confrontées pour accéder plus finement au mode d’interaction avec PGM (densité de liaisons sur la surface bactérienne). Enfin, nous avons évalué chez IL1403 l’effet des pili sur la dynamique de détachement et d’orientation sous cisaillement contrôlé.\ud En conclusion, la combinaison des échelles d'observation et d’analyse, aussi bien au niveau de la cellule unique qu’à celui de l’ensemble de la population bactérienne, nous permet désormais de disposer de nouvelles connaissances sur les mécanismes diversifiés d'interaction entre L. lactis et PGM, visant à une meilleure compréhension des fonctionnalités de cette bactérie au niveau du tractus gastro-intestinal.---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------In the gastrointestinal tract, adhesion of commensal bacteria to epithelial cells allows their retention, which helps to control the implementation of unwanted germs through mechanisms of competition (nutritional effects, specific sites of adhesion ...). Indeed, bacterial adhesion to the intestinal epithelium seems to be important for the balance of intestinal microbiota. Although the role of the mucus layer lining the mucosa, which is mainly composed of large glycoproteins termed mucins, is known and described for many years, particularly for its protective barrier function, the interest for unraveling precise mechanisms of interaction with bacteria (commensal, pathogens or probiotics) has just recently emerged. In this framework, the aim of the PhD thesis was to characterize in vitro muco-adhesive behavior of Lactococcus lactis, the model of Lactic Acid Bacteria, using multi-scale approaches (from molecular to multicellular levels) on a large set of natural and recombinant strains. A particular attention was paid to the role of mucins, using the PGM model (Pig Gastric Mucin).\ud The first part of the work was focused on the quantification at nanoscale of interactions between L. lactis and adsorbed PGM, using AFM. The feasibility of the method was first demonstrated on the reference strain MG1820. PGM coating was characterized using a complementary set of analytical methods (AFM, XPS, quartz crystal microbalance with dissipation monitoring…). In parallel, L. lactis cells were immobilized onto the AFM tip and used as a living force probe, considering the natural strain IBB477 (L. lactis subsp. cremoris), isolated from Polish artisanal dairy products and previously shown to display in vivo retention in the rat gut (collaboration with the Institute of Biochemistry and Biophysics of Warsaw, Poland). Compared to control conditions (i.e., no PGM coating), adhesion force levels recorded for PGM were lower, due to the interplay of electrostatic, hydrophilic and steric repulsions. The shape of retraction force-distance curves for L. lactis/PGM interactions was also different. The detailed analysis of curve shape highlighted the contribution of non-adhesive, non-specific (electrostatic, hydrophobic, van der Waals interactions) and specific adhesive events (ligand/receptor bonding), depending on the strain under study. Specific forces were analyzed in terms of dissociation/association kinetic constants.\ud We then explored the natural biodiversity among lactococci by studying the natural strain of L. lactis (subsp. lactis) TIL448 from plant origin, in collaboration with MICALIS (Jouy-en-Josas). We demonstrated, for the first time for L. lactis, the combined role played by “MUB-like” domain-containing protein and pili, through the thorough analysis of AFM data (adhesion force, repartition of specific/non-specific adhesive events and distances of interaction…). The role of pili was also confirmed with recombinant piliated strains (L. lactis subsp. lactis IL1403), in partnership with MICALIS (Jouy-en-Josas). In parallel, in collaboration with the “Unité de Glycobiologie Structurale et Fonctionnelle de Villeneuve d'Ascq”, a first attempt was done to identify the O-glycans of PGM (neutral and acid fractions), involved in interactions with the bacterial surface.\ud To confirm these results achieved at single-cell scale and under static mode by AFM (anti-adhesive of PGM, different muco-adhesive properties among several strains of L. lactis), the second part of the work was devoted to experiments at multicellular scale under dynamic conditions (quartz crystal microbalance with dissipation monitoring – QCM-D, shear stress flow chamber). We evaluated by QCM-D, for MG1820 and IBB477 strains, the viscoelastic properties of the cell layers, in relation with the bio-adhesive behavior towards PGM. The data obtained by AFM and shear stress flow chamber were combined to access more precisely to the interaction mode with PGM (density of bonds over the cell surface). Finally, using the recombinant piliated strain (IL1403), we focused on the effect of pili on detachment and re-orientation dynamics under shear flow.\ud As a conclusion, the combination of complementary scales of observation and analysis, including single-cell and multicellular targeted experiments, let us now to get new insights into the interplay of interaction mechanisms between L. lactis and mucins, aiming at a better understanding of the behavior of this bacteria within the gastrointestinal tract.\ud \u