SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding

Scaffolding is an important subproblem in "de novo" genome assembly in which mate pair data are used to construct a linear sequence of contigs separated by gaps. Here we present SLIQ, a set of simple linear inequalities derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a preprocessing step for any scaffolding algorithm. We tested the SLIQ inequalities on five real data sets ranging in complexity from simple bacterial genomes to complex mammalian genomes and compared the results to the majority voting procedure used by many other scaffolding algorithms. SLIQ predicted the relative positions and orientations of the contigs with high accuracy in all cases and gave more accurate position predictions than majority voting for complex genomes, in particular the human genome. Finally, we present a simple scaffolding algorithm that produces linear scaffolds given a contig digraph. We show that our algorithm is very efficient compared to other scaffolding algorithms while maintaining high accuracy in predicting both contig positions and orientations for real data sets.Comment: 16 pages, 6 figures, 7 table

Write-limited sorts and joins for persistent memory

To mitigate the impact of the widening gap between the memory needs of CPUs and what standard memory technology can deliver, system architects have introduced a new class of memory technology termed persistent memory. Persistent memory is byteaddressable, but exhibits asymmetric I/O: writes are typically one order of magnitude more expensive than reads. Byte addressability combined with I/O asymmetry render the performance profile of persistent memory unique. Thus, it becomes imperative to find new ways to seamlessly incorporate it into database systems. We do so in the context of query processing. We focus on the fundamental operations of sort and join processing. We introduce the notion of write-limited algorithms that effectively minimize the I/O cost. We give a high-level API that enables the system to dynamically optimize the workflow of the algorithms; or, alternatively, allows the developer to tune the write profile of the algorithms. We present four different techniques to incorporate persistent memory into the database processing stack in light of this API. We have implemented and extensively evaluated all our proposals. Our results show that the algorithms deliver on their promise of I/O-minimality and tunable performance. We showcase the merits and deficiencies of each implementation technique, thus taking a solid first step towards incorporating persistent memory into query processing. 1

Weaving Entities into Relations: From Page Retrieval to Relation Mining on the Web

With its sheer amount of information, the Web is clearly an important frontier for data mining. While Web mining must start with content on the Web, there is no effective ``search-based'' mechanism to help sifting through the information on the Web. Our goal is to provide a such online search-based facility for supporting query primitives, upon which Web mining applications can be built. As a first step, this paper aims at entity-relation discovery, or E-R discovery, as a useful function-- to weave scattered entities on the Web into coherent relations. To begin with, as our proposal, we formalize the concept of E-R discovery. Further, to realize E-R discovery, as our main thesis, we abstract tuple ranking-- the essential challenge of E-R discovery-- as pattern-based cooccurrence analysis. Finally, as our key insight, we observe that such relation mining shares the same core functions as traditional page-retrieval systems, which enables us to build the new E-R discovery upon today's search engines, almost for free. We report our system prototype and testbed, WISDM-ER, with real Web corpus. Our case studies have demonstrated a high promise, achieving 83%-91% accuracy for real benchmark queries-- and thus the real possibilities of enabling ad-hoc Web mining tasks with online E-R discovery

The first successful use of the Levitronix PediMag ventricular support device as a biventricular bridge to transplant in an infant

Numeración errónea en el original, se ha corregido

Numerical investigation of the energy performance of a guideless irregular heat and mass exchanger with corrugated heat transfer surface for dew point cooling

© 2016 The Author(s) The paper presents an investigation into the energy performance of a novel irregular heat and mass exchanger for dew point cooling which, compared to the existing flat-plate heat exchangers, removed the use of the channel supporting guides and implemented the corrugated heat transfer surface, thus expecting to achieve the reduced air flow resistance, increased heat transfer area, and improved energy efficiency (i.e. Coefficient of Performance (COP)) of the air cooling process. CFD simulation was carried out to determine the flow resistance (K) factors of various elements within the dry and wet channels of the exchanger, while the ‘finite-element’ based ‘Newton-iteration’ numerical simulation was undertaken to investigate its cooling capacity, cooling effectiveness and COP at various geometrical and operational conditions. Compared to the existing flat-plate heat and mass exchangers with the same geometrical dimensions and operational conditions, the new irregular exchanger could achieve 32.9%–37% higher cooling capacity, dew-point and wet-bulb effectiveness, 29.7%–33.3% higher COP, and 55.8%–56.2% lower pressure drop. While undertaking dew point air cooling, the irregular heat and mass exchanger had the optimum air velocity of 1 m/s within the flow channels and working-to-intake air ratio of 0.3, which allowed the highest cooling capacity and COP to be achieved. In terms of the exchanger dimensions, the optimum height of the channel was 5 mm while its length was in the range 1–2 m. Overall, the proposed irregular heat and mass exchanger could lead to significant enhanced energy performance compared to the existing flat-plate dew point cooling heat exchanger of the same geometrical dimensions. To achieve the same amount cooling output, the irregular heat and mass exchanger had the reduced size and cost against the flat-plate ones