Miracle-dz/UniFAR-FTUs huggingface dataset:
Various Algorithms for High Throughput Sequencing

Various Algorithms for High Throughput Sequencing Vladimir Yanovsky Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2014 The growing volume of generated DNA sequencing data makes the problem of its long term storage increasingly important. In the first chapter we present ReCoil – an I/O efficient external memory algorithm designed for compression of very large datasets of short reads DNA data. Typically each position of DNA sequence is covered by multiple reads of a short read dataset and our algorithm makes use of resulting redundancy to achieve high compression rate. While compression based on encoding mismatches between the dataset and a similar reference can yield high compression rate, good quality reference sequence may be unavailable. Instead, ReCoil’s compression is based on encoding the differences between similar or overlapping reads. As such reads may appear at large distances from each other in the dataset and since random access memory is a limited resource, ReCoil is designed to work efficiently in external memory, leveraging high bandwidth of modern hard disk drives. The next problem we address is the problem of mapping sequencing data to the reference genome. We revisit the basic problem of mapping a dataset of reads to the reference, developing a fast, memory-efficient algorithm for mapping of the new generation of long high error rate reads. We introduce a novel approach to hash based indexing which is both succinct and can be constructed very efficiently, avoiding the need to build the index in advance. Using our new index, we design a cache oblivious algorithm that makes an efficient use of the modern hardware to quickly cluster the reads in the dataset according to their position on the reference. Next, we show an algorithm for aligning two-pass Single Molecule Sequencing reads. Single Molecule Sequencing technologies such as the Heliscope simplify the preparation of DNA for sequencing, while sampling millions of reads in a day. The technology suffers from a high error rate, ameliorated by the ability to sample multiple reads from the same location. We develop novel rapid alignment algorithms for two-pass Single Molecule Sequencing methods. We combine the Weighted Sequence Graph representation of all optimal and near optimal alignments between the two reads sampled from a piece of DNA
EXPLORING SIMILARITIES AND VARIATIONS OF HUMAN MOBILITY PATTERNS IN THE CITY OF LONDON

Abstract. The availability of new spatial data represents an unprecedented opportunity to better understand and plan cities. In particular, extensive data sets of human mobility data supply new information that can empower urbanism research to unveil how people use and visit urban places over time, overcoming traditional limitations related to the lack of large, detailed data sets. In this work, we explore patterns of similarities and spatial differences in human mobility flows in London, analysing their temporal variations in relation to the liveliness measured in a number of places. Using data sourced from the Oyster smart card and Twitter, we perform a time-series cluster analysis, exploring the similarity of temporal trends amongst places assigned to each cluster. Results suggest that differences in patterns appear to be related to the central and peripheral location of places, which present two or more temporal trends over the week. The type of transport network connecting the places (Tube, Railways, etc.) also appears to be a factor in determining significant differences. This work contributes to current urbanism research investigating the daily rhythms in cities. It also explores how to use mobility data to classify places according to their temporal features, with the aim of enhancing conventional analysis tools and integrating them with new quantitative information and methods.
Safety assessment of steel framework of a utility boiler

KEYWORD: safety assessment, steel framework, finite element analysis, seismic loads. ABSTRACT: The steel framework of a utility boiler was an important structure sustained loads, and its strength and stiffness were primary factors in structural design. Stiffness was assessed by measuring perpendicularity of pillars. For this steel framewok seismic loads was significant to the entire strength. In order to refer to the influence of seismic loads, finite element method was adopted to analyze the strength of the whole steel framework. According to the results of finite element analysis, the maximum equivalent stress was 102.9MPa, which could satisfy the strength requirement. It indicated that this steel framework could satisfy the requirement of practical working conditions.
γδ T cells and IL-17/IL-17R signaling axis in CNS inflammation

Correspondence: Jayasri Das Sarma Department of Biological Sciences, Indian Institute of Science education and Research – Kolkata, Mohanpur Campus, PO: BCKV Campus Main Office, Mohanpur, Nadia, west Bengal 741252, India Tel +91 33 25873019 Fax +91 33 25873020 email dassarmaj@iiserkol.ac. in Abstract: Lymphocytes expressing γδ T-cell receptors constitute an entire system of functionally specialized subsets that have been implicated in the regulation of immune responses, including responses to pathogens and allergens, and in tissue repair. γδ T cells represent a small subpopulation of T cells that, unlike αβ T cells, function more as cells of the innate immune system. γδ T cells are known to mediate the production of inflammatory cytokines, including interferon-γ, tumor necrosis factor-α, and interleukin (IL)-17, and thus enable the activation of other subsets of infiltrating effector cells. However, not much attention was paid to γδ T cells until the recent discovery of a distinct CD4+ T helper (T H ) cell, T H 17 cell. CD4+ T cells, upon activation and expansion, develop into different T H -cell subsets with different cytokine profiles and distinct effector functions. T cells were earlier divided into T H 1 or T H 2 cells, depending on the cytokines they produce. A third subset of IL-17-producing effector T H cells, called T H 17 cells, has been discovered and characterized recently. Since then the literature on IL-17-producing cells has grown steadily, and several studies have focused on γδ T cells. Cytokine-mediated modulation of central nervous system (CNS) inflammatory diseases by γδ T cells in humans or in animal models is currently the subject of many studies. IL-17 and its receptor IL-17R have been implicated in the pathogenesis of immune-mediated CNS diseases, and attention has been paid to understand the mechanisms by which IL-17 cytokines and it receptor (IL-17R) family mediate the effects at a molecular level. This article reviews the studies that cover earlier aspects of γδ T cell/IL-17 biology and the new dimension of γδ T cells, IL-17, and IL-17/IL-17R signaling axis in CNS inflammation. Understanding the role of γδ T cells, IL-17, and IL-17/IL-17R signaling axis in infection and immunity could open a new avenue for immunomodulation.
A prototype of a dinamically expandable Virtual Analysis Facility

Current Grid deployments for LHC computing do not allow efficient parallel interactive processing of data. In order to allow physicists to access interactively subsets of data, for tasks like algorithm tuning or debugging before running over a full dataset, parallel Analysis Facilities based on PROOF have been deployed by the ALICE experiment at CERN and elsewhere. Whereas large Tier-1 centres can afford to build such facilities at the expense of their Grid computing clusters, this is likely not to be true for smaller Tier-2 centres. Leveraging on the virtualisation of highly performant multi-core machines, it is possible to build a fully virtual Analysis Facility on the same Worker Nodes that compose an existing Grid cluster. Using the Xen paravirtualisation hypervisor, it is then possible to dynamically move resources from the batch instance to the interactive one when needed. We present the status of the prototype being developed.
Flow, food supply and acorn barnacle population dynamics

While it is widely believed that oceanographic conditions influence benthic filter-feeding organisms, linkages between water column and population processes on rocky shores have been difficult to document. Here we combine laboratory and field studies to explore the relationship between water column conditions and the feeding, growth and population dynamics of the northern acorn barnacle Semibalanus balanoides. S. balanoides feeding behavior in a flow tank was strongly dictated by flow speeds, food concentrations, and temperatures. The percentage of barnacles feeding increased with both flow speed and food concentrations, but was depressed at high temperatures. These patterns were accurately reflected in S. balanoides feeding in the field. Moreover, within and among populat ion~ , variation in barnacle growth over a wide geographic area directly reflected corresponding variation in flow speed, food abundance, and water temperature. Flow effects on barnacles also had conspicuous population consequences. Since barnacle recruitment and growth are both enhanced at high flow speeds, barnacle density-dependent dynamics may often be strongly affected by flow conditions. Our results suggest that water column processes can powerfully affect passive filter feeding organisms on rocky shores and that oceanographic conditions may often leave a strong signature on the distribution, abundance, and dynamics of assemblages of sessile marine organisms.
A Polytropic Solution of the Expanding Universe – Constraining Relativistic and Non-Relativistic Matter Densities Using Astronomical Results

Important programs are being pursued currently to collect distance and recession velocity data from supernovae type Ia of several groups collecting and analyzing data (SNe Ia) (Astier et al., 2006; Hicken et al., 2009; Wood-Vasey et al., 2007) and from gamma ray bursts (GRB) (Schaefer, 2007) and most recently from other supernovae types. These events are our best hope of "standard candles" looking back in a quantitative manner towards the epochs of recombination and early galaxy formation, to nearly to the beginning of time (Leibundgut, 2008). While some optical data have been obtained from orbiting observatories, data of good quality have been collected from grounded telescopes with the hope to collect several thousand distance/velocity pairs of ever increasing quality over the next few years. Likewise, interpretation of the cosmic microwave background (CMB), which consists of signals remaining from the very primitive Universe after 13 billion years of cooling, may provide another independent source of data for estimating these parameters (Komatsu et al., 2009). Interpretation of the Sloan Digital Sky Survey (SDSS) data are being continually refined and the interpretations broadened to include analysis for the baryonic acoustic oscillations (BAO) remnant signals (Eisenstein et al., 2005). Another tool for estimation of gross Universe structure is the X-ray emissions from galaxy clusters (Vikhlinin et al., 2008) with future data collections planned to answer several cosmological questions (Vikhlinin et al., 2009). Data from dozens of studies have been used to estimate the Hubble constant, the Universe age and to support the new idea of Dark Energy (DE) assisted universe expansion (Carroll et al., 1992). Many decades ago Chandrasekhar successfully investigated the nature of white dwarf stars with gravitational fields large enough to quickly accrete considerable surrounding gas (Chandrasekhar, 1964). He predicted that as the object mass increases, Pauli instability of the dwarf star constituents is approached with a thermonuclear critical mass dependent both on the nature of the matter, the energy contained within and by the repulsive pressure exerted from the various nuclear species. When the instability limit is reached the object suffers collapse quickly followed by thermonuclear explosionwhichwe gaze at in awe as a supernova (Chandrasekhar & Trooper, 1964). This very successful description, which has been confirmed many times by observation, is dependent on the polytropic generalizations of matter and energy. The useful relationships of Chandrasekhar demand unique constants which differ A Polytropic Solution of the Expanding Universe – Constraining Relativistic and Non-Relativistic Matter Densities Using Astronomical Results
The Role of Demographic and Cost-Related Factors in Determining Where Plants Locate

In the environmental justice literature, evidence of disproportionate siting in poor or minority neighborhoods is decidedly mixed. Some allege this is due to the difference in whether the study looks at evidence at the national, state, or city level. Here, I compare results from two of the largest cities in Texas to results for the state overall to discern whether important demographic or other differences are evident at the city level that may be masked at a more aggregate level of analysis. I examine four possible hypotheses for why plants may locate in poor or minority neighborhoods: profit maximization (or cost minimization); relatively low willingness-to-pay for environmental amenities; a lower propensity for collective action by the community; and finally, the desire on the part of the firm to discriminate against particular groups of people. Specifically, I match the location of manufacturing plants that reported to the Toxic Release Inventory to US Census information at the census tract level at the time when the siting decision occurred. I then combine this information with a variety of other data, including voter participation, wages, and crime rates at the county-level. The main findings of this paper is that the principle driver of plant location decisions is profit maximization and that variables associated with the collective action and discrimination hypotheses are largely not significant, population density excepted. These findings appear to hold both at the city and state level. Variables associated with willingness-to-pay for environmental amenities appear somewhat sensitive to geographic scope: poverty is sometimes significant at the state level but never significant at the level of the city.
Perceived Organizational Support and Affective Commitment: A Demographic Analysis

This descriptive research is conducted to study perceived organizational support and affective commitment with respect to demographic variables (gender, marital status, education etc.) and to study the relation between these variables. To realize this purpose the data on these variables was collected from 120 employees working in banking sectors with the help of standardized questionnaires. Statistical techniques of mean, standard deviation, correlation and regression and ANOVA were applied on data to test the hypothesis. Collected data was analyzed with the help of SPSS. The results highlight that perceived organizational support is positively related to affective commitment and POS accounts for 22% contribution to AC. The limitations of the study are discussed and future research areas are also highlighted.
A New Child Protection Strategy for Aboriginal Communities in Western Australia

Abstract Despite numerous government inquiries and reforms, child sexual abuse in remote Aboriginal communities is a well-documented, ongoing problem. Established in Western Australia in 2009, Operation RESET is a multi-agency proactive community engagement initiative designed to improve the ability of communities and supporting agencies to detect, respond to and prevent child sexual abuse through the implementation of community engagement, capacity building and educational strategies. This comment describes the three core principles of Operation RESET: tackling child sexual abuse requires a collaborative, proactive approach between government and communities; the underlying causes and context of child sexual abuse must be recognised; and children's overall safety and wellbeing must be enhanced through integrated services that strengthen and empower families and communities. It also enumerates the seven phases of the operation's implementation, from identifying target communities to deploying an exit strategy. The comment ends by addressing the importance of empirical evaluation.
Training of support vector regressors based on the steepest ascent method

In this paper, we propose a new method for training support vector regressors. In our method, we partition all the variables into two sets: a working set that consists of more than two variables and a set in which variables are fixed. Then we optimize the variables in the working set using the steepest ascent method. If the Hessian matrix associated with the working set is not positive definite, we calculate corrections only for the independent variable in the working set. We test our method by two benchmark data sets, and show that by increasing the working set size, we can speed up training of support vector regressors.
Job Insecurity and Affective Commitment in Seasonal Versus Permanent Workers

The purpose of the present study is to compare seasonal with permanent workers in terms of job insecurity and affective commitment. We also investigate whether job insecurity mediates the relationship between contract type and affective commitment. Surveys from 161 seasonal and 107 permanent workers in the tourism sector in Turkey were analyzed using MANOVA and mediated regression analysis. The results demonstrate that seasonal workers perceive higher job insecurity compared to permanent workers. They are also affectively less committed to their organizations than permanent workers. Furthermore, job insecurity does not mediate the relationship between contract type and affective commitment. Most of the existing empirical research has focused on temporary and fixed-term workers. We examine seasonal workers, a category that is rarely studied.
Observation of Laser Wakefield Acceleration of Electrons

The acceleration of electrons injected in a plasma wave generated by the laser wakefield mechanism has been observed. A maximum energy gain of 1.6 MeV has been measured and the maximum longitudinal electric field is estimated to 1.5 GV/m. The experimental data agree with theoretical predictions when 3D effects are taken into account. The duration of the plasma wave inferred from the number of accelerated electrons is of the order of 1 ps
A laboratory experiment on the evolution of a sand gravel reach under a lack of sediment supply

A flume experiment was conducted to examine the evolution of a sand-gravel reach under a lack of sediment supply. A bed composed of a bimodal sediment mixture was installed with a uniform slope and an gradual fining pattern. At the upstream end of the flume the initial bed consisted of 100% gravel, which decreased stepwise (10% steps) in downstream direction until the location where the initial bed consisted of 100% sand. The water discharge and downstream water level were constant and the sediment feed rate was equal to zero. New image analysis equipment was used to frequently measure the grain size distribution of the bed surface during the experiment over the entire length of the flume. The experiment was governed by bedload transport and subcritical flow. The flow rate was such that only sand was mobile (partial transport). This led to the washing out of sand from the upstream bimodal reach and its gradual coarsening. In this reach we observed the formation of a static armour layer, which resulted in a more abrupt transition in the mean grain size of the bed surface. The total amount of bed degradation slightly increased in streamwise direction over the bimodal reach, which was due to the streamwise increase of the sand fraction in the initial bed. The sand reach adjusted to the lack of sand supply by decreasing its slope and so its sand transport capacity (i.e. through decreasing the flow velocity). Consequently, the sand transport rate at the downstream end of the flume gradually reduced during the experiment. A morphodynamic steady state over a movable bed is generally governed by normal flow. In the present case, governed by partial transport conditions, the morphodynamic steady state is dominated by a backwater curve. This happens because under partial transport conditions the bed cannot (fully) adjust to the upstream water and sediment discharge. These experimental results were reproduced using a one-dimensional numerical model based on the St Venant-Hirano equations, although the effects of the temporal change in bed porosity were not considered in the model.
A Perfect Storm for Consumer Misbehavior: Shopping on Black Friday

Consumer misbehavior that harms other consumers and/or retailers has occurred recently during Black Friday (BF) sales. Using a combination of theoretical perspectives, the purpose of our research was to gather information about BF shopping to use in questionnaire development, to investigate potential relationships among the variables identified, and to suggest ideas for future research. From a survey of BF shoppers, we found shoppers who perceived they expended effort planning for and shopping on BF were likely to misbehave. We also found BF shoppers who expended effort planning and executing their BF shopping tended to score high on trait impulsivity. While this may seem contradictory, it can be explained by considering that people who expend effort in their BF planning may cognitively plan their BF activities and then take advantage of unplanned deals along the way. Our results support premises of the general aggression model to explain consumer misbehavior on BF.
New materials for 193-nm trilayer imaging

This paper presents our progress in developing spin-on, thermosetting hardmasks and bottom antireflective coatings (BARCs) for 193-nm trilayer usage. Binder materials that were used in preparing the silicon-containing hardmasks include polymers with pendant alkylsilane function and various polyhedral oligomeric silsesquioxane (POSS) substances, with the hardmasks being very transparent at both 193 and 248 nm. The second generation hardmasks (POSS-containing) offer significant improvements over earlier materials in oxygen (O2) plasma etching resistance. The etching selectivity (O2 plasma) for a trilayer BARC relative to the best-case hardmask is about 31.5:1 (15-second etch), with the selectivity numbers being much higher for longer etching times. The preferred hardmask is both spin-bowl and solution compatible. The new trilayer BARCs use binders that are rich in aromatic content for halogen plasma etching resistance, but the antireflective products also feature optical parameters that allow low reflectivity into the photoresist. The BARCs are very spin-bowl compatible. At about 500-nm film thickness, selected BARCs have provided 80-95% planarity over 200-nm topography. Combining the two thermosetting products (hardmask and BARC) with a thin 193-nm photoresist in a trilayer configuration has given excellent 80-nm L/S (1:1) after exposure and wet-development. A conventional resist has provided 100-nm L/S (1:1.4).
ROLE OF BORON IN FORMATION OF SECONDARY RADIATION DEFECTS IN

Ґрунтуючись на колишні роботи авторів, досліджено роль домішок бору (B) у формуванні вторинних радіаційних дефектів в кристалах кремнію (Si). Залежності цих про-цесів від температури ізохронного відпалу (в інтервалі 80–600 °C) вив-чені з використанням холлівських вимірювань температурних залеж-ностей (в інтервалі 100–300 К) концентрації і рухливості дірок в кремній до і після опромінення елек-тронами з енергією близько 8 МеВ при дозі 5∙10