Indexing arbitrary-length kk-mers in sequencing reads

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments

A shopping centre as a traffic-generating factor in car transport as exemplified by Port Łódź, Poland

Artykuł przedstawia wyniki badań dotyczących roli centrum handlowego jako czynnika ruchotwórczego w indywidualnym transporcie samochodowym, na przykładzie Portu Łódź – jednego z trzynastu tego typu obiektów w granicach Łodzi. Głównym celem opracowania jest określenie udziału ruchu samochodowego generowanego przez Port Łódź w potokach ruchu na lokalnej sieci dróg. Analiza została oparta na danych pochodzących z miejskiego systemu sterowania ruchem, a dokładnie z pętli indukcyjnych rozmieszczonych na sieci miejskich skrzyżowań.The article presents results of research devoted to the role of the shopping centre as a traffic-generating factor in individual-car transport. The research procedure was conducted in relation to Port Łódź, one of thirteen shopping centres within the boundaries of the Polish city of Łódź. The main aim has been to determine the share of car traffic generated by Port Łódź in the totality of traffic flows in the network of roads leading to the shopping centre. The analysis was based on data from the urban traffic control system or, to be precise, one of its subsystems which has access to information on spatial and time accessibility of the number of vehicles, transmitted from induction loops situated in the network of urban crossroads. The research focuses on defi ning potential and real traffic generation for weekdays and weekends, as well as during public holidays and festival days. The research allowed for verifi cation of one of the model approaches to the correlation between selected characteristics of shopping centres and the volume of traffic they generate. Results show that shopping centres located along exit roads on the city outskirts affect the road transport system, particularly by exciting car traffic (also during rush hours), retaining it during afternoon rush hours (thus contributing to an alleviation and extension in time) and, to a lesser extent, serving as an informal element of the Park&Ride system (in the case of centres characterised by good accessibility to public transport and a free car park)

Dostępność transportowa łódzkich centrów handlowych

The main factors of the location of shopping centres are as follows: road network, customer remoteness and free investment areas. Transport accessibility is the connecting element between the transport component and the market component. By means of accessibility, we can indicate the potential for interaction between the client and the shopping mall and their locations, and to what extent they can meet the needs of the residents. The main aim of the article is to show transport accessibility to shopping centres in Łódź, as well as to indicate the tendencies that determine their accessibility to distribution. The study included extremely precise information that illustrates the demographic potential of various transport basins. The analyses used research methods based on recognition and presentation of spatial phenomena in the ArcMap environment and statistical methods. The analyses included accessibility by: walking, cycling, individual car and public transport. The studies showed the diversification of transport accessibility to shopping centres according to their location. It was also shown which malls presented the greatest potential in terms of market size.Основные факторы детального размещения торговых центров включают: сеть дорог, близость клиентов и свободные территории застройки. Связующим звеном, соединяющим транспортный компонент с рыночным, является тран- спортная доступность. С его помощью можно указать, каким потенциалом для возникновения интеракции вдоль оси клиент-торговый центр располагают от- дельные локализации и в какой мере они могут удовлетворять потребности жителей. Основная цель статьи – указать транспортную доступность лодзин- ских торговых центров, а также тенденции, определяющие их достигаемость по отношению к размещению. В исследованиях учли необыкновенно четкую информацию, представляющую демографический потенциал отдельных тран- спортных бассейнов. В анализах использовали методы изучения, основанные на способах распознания и представления пространственных явлений в среде ArcMap, а также статистические методы. В анализы доступности включили сферы достигаемости: пешеходную, велосипедную, частную автомобильную и с использованием коммунального транспорта. Исследования указали диф- ференциацию транспортной доступности торговых центров в зависимости от их размещения. Указали тоже, что торговые центры демонстрируют самый высокий потенциал в отношении объема местного рынка

Daily mobility of the elderly: An example from Łódź, Poland

Recently, numerous countries have been facing the issue of population ageing, which poses a formidable challenge for many sectors, including transportation. Alas, there are no detailed or insightful studies that involve the analysis of the elderly, which is why the authors of this paper decided to research the issue to determine which features of mobility are common among senior citizens (aged 60+). In our study, we focused on Bałuty, a district located in Łódź. The applied research tool was an interview questionnaire which consisted of eight questions. Since transportation is a fundamental human need, maintenance of the mobility of the elderly at an acceptable level is crucial as it directly impacts the quality of their life. What is more, a change of motivation and mode of transport is recommended for this age group

Suffix Arrays with a Twist

The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show that i) the way how we search for the right interval boundary impacts significantly the overall search speed, ii) a B-tree data layout easily wins over the standard one, iii) the well-known idea of a lookup table for the prefixes of the suffixes can be refined with using compression, iv) caching prefixes of the suffixes in a helper array can pose another practical space-time tradeoff

Particle production properties at SPS energy range - recent results from the NA61/SHINE experiment

One of the main physics goals of the NA61/SHINE programme on strong interactions is the study of the properties of the onset of deconfinement. This goal is pursued by performing an energy- (beam momentum 13A–158A GeV/c) and system-size (p+p, p+Pb, Be+Be, Ar+Sc, Xe+La) scan. In particular, recent inclusive spectra of identified hadrons in inelastic p+p and centrality selected Be+Be and Ar+Sc interactions at the SPS energies. The energy dependence of quantities inspired by the Statistical Model of the Early Stage (kink, horn and step) are shown

Recent results from NA61/SHINE

The research programme of the NA61 Collaboration covers a wide range of hadronic physics in the CERN SPS energy range, encompassing measurements of hadron–hadron, hadron–nucleus as well as nucleus–nucleus collisions. The latter are analysed to better understand the properties of hot and dense nuclear matter. In this paper, recent results of particle production properties as well as event-by-event fluctuations in proton–proton, as signatures of the critical point of strongly interacting matter, in Be+Be and Ar+Sc interactions at beam energies of 19A/20A, 30A, 40A, 75A/80A and 158A GeV/c are presented