Online algorithms for 1-space bounded multi dimensional bin packing and hypercube packing

In this paper, we study 1-space bounded multi-dimensional bin packing and hypercube packing. A sequence of items arrive over time, each item is a d-dimensional hyperbox (in bin packing) or hypercube (in hypercube packing), and the length of each side is no more than 1. These items must be packed without overlapping into d-dimensional hypercubes with unit length on each side. In d-dimensional space, any two dimensions i and j define a space P ij. When an item arrives, we must pack it into an active bin immediately without any knowledge of the future items, and 90 {ring operator}-rotation on any plane P ij is allowed. The objective is to minimize the total number of bins used for packing all these items in the sequence. In the 1-space bounded variant, there is only one active bin for packing the current item. If the active bin does not have enough space to pack the item, it must be closed and a new active bin is opened. For d-dimensional bin packing, an online algorithm with competitive ratio 4 d is given. Moreover, we consider d-dimensional hypercube packing, and give a 2 d+1-competitive algorithm. These two results are the first study on 1-space bounded multi dimensional bin packing and hypercube packing. © 2012 The Author(s).published_or_final_versionSpringer Open Choice, 28 May 201

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

Since the read lengths of high throughput sequencing (HTS) technologies are short, de novo assembly which plays significant roles in many applications remains a great challenge. Most of the state-of-the-art approaches base on de Bruijn graph strategy and overlap-layout strategy. However, these approaches which depend on k-mers or read overlaps do not fully utilize information of paired-end and single-end reads when resolving branches. Since they treat all single-end reads with overlapped length larger than a fix threshold equally, they fail to use the more confident long overlapped reads for assembling and mix up with the relative short overlapped reads. Moreover, these approaches have not been special designed for handling tandem repeats (repeats occur adjacently in the genome) and they usually break down the contigs near the tandem repeats. We present PERGA (Paired-End Reads Guided Assembler), a novel sequence-reads-guided de novo assembly approach, which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds using paired-end reads and different read overlap size ranging from Omax to Omin to resolve the gaps and branches. By constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. When the correct extension cannot be determined, PERGA will try to extend the contig by all feasible extensions and determine the correct extension by using look-ahead approach. Many difficult-resolved branches are due to tandem repeats which are close in the genome. PERGA detects such different copies of the repeats to resolve the branches to make the extension much longer and more accurate. We evaluated PERGA on both Illumina real and simulated datasets ranging from small bacterial genomes to large human chromosome, and it constructed longer and more accurate contigs and scaffolds than other state-of-the-art assemblers. PERGA can be freely downloaded at https://github.com/hitbio/PERGA.published_or_final_versio

CO2 capture by dry alkanolamines and an efficient microwave regeneration process

Removal of acidic gases such as H2S and CO2 is performed during the purification of raw natural gas, most commonly using amine gas treatment. However, this industrially entrenched method is limited by significant shortcomings including low operational capture efficiency, amine pipeline corrosion and a large energy penalty due to the sorbent regeneration process. To address these shortcomings, we have studied the use of perfluorinated silica-stabilized dry alkanolamines (DAf) for CO2 capture. Due to their micronized liquid domains, DAf display high operational CO2 capture efficiency. Further, to minimize energy requirements for sorbent regeneration, microwave-assisted regeneration of the spent DAf sorbent was also studied and shown to decrease the energy requirements by about ten times. In contrast to very recent work, our results show that the use of DAf exhibits extraordinary recyclability, with a negligible decrease in absorption capacity over at least ten absorption–regeneration cycles, indicating the potential of this material for gas treatment applications

Microfluidic droplet grating for reconfigurable optical diffraction

Author name used in this publication: X. M. Zhang2009-2010 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

In Search of the Vortex Loop Blowout Transition for a type-II Superconductor in a Finite Magnetic Field

The 3D uniformly frustrated XY model is simulated to search for a predicted "vortex loop blowout" transition within the vortex line liquid phase of a strongly type-II superconductor in an applied magnetic field. Results are shown to strongly depend on the precise scheme used to trace out vortex line paths. While we find evidence for a transverse vortex path percolation transition, no signal of this transition is found in the specific heat.Comment: 11 pages, 17 figure

Simulation of the many-body dynamical quantum Hall effect in an optical lattice

We propose an experimental scheme to simulate the many-body dynamical quantum Hall effect with ultra-cold bosonic atoms in a one-dimensional optical lattice. We first show that the required model Hamiltonian of a spin-1/2 Heisenberg chain with an effective magnetic field and tunable parameters can be realized in this system. For dynamical response to ramping the external fields, the quantized plateaus emerge in the Berry curvature of the interacting atomic spin chain as a function of the effective spin-exchange interaction. The quantization of this response in the parameter space with the interaction-induced topological transition characterizes the many-body dynamical quantum Hall effect. Furthermore, we demonstrate that this phenomenon can be observed in practical cold-atom experiments with numerical simulations.Comment: 8 pages, 3 figures; accepted in Quantum Information Processin

Senescent stromal cells promote cancer resistance through SIRT1 loss-potentiated overproduction of small extracellular vesicles

Cellular senescence is a potent tumor-suppressive program that prevents neoplastic events. Paradoxically, senescent cells develop an inflammatory secretome, termed the senescence-associated secretory phenotype (SASP), which is implicated in age-related pathologies including cancer. Here we report that senescent cells actively synthesize and release small extracellular vesicles (sEVs) with a distinctive size distribution. Mechanistically, SIRT1 loss supported accelerated sEV production despite enhanced proteome-wide ubiquitination, a process correlated with ATP6V1A downregulation and defective lysosomal acidification. Once released, senescent stromal sEVs significantly altered the expression profile of recipient cancer cells and enhanced their aggressiveness, specifically drug resistance mediated by expression of ATP binding cassette subfamily B member 4 (ABCB4). Targeting SIRT1 with agonist SRT2104 prevented development of cancer resistance by restraining sEV production by senescent stromal cells. In clinical oncology, sEVs in peripheral blood of posttreatment cancer patients were readily detectable by routine biotechniques, presenting an exploitable biomarker to monitor therapeutic efficacy and predict long-term outcome. Together, this study identifies a distinct mechanism supporting pathological activities of senescent cells and provides a potent avenue to circumvent advanced human malignancies by co-targeting cancer cells and their surrounding microenvironment, which contributes to drug resistance via secretion of sEVs from senescent stromal cells

Hydrodynamic Modes in a Trapped Strongly Interacting Fermi Gases of Atoms

The zero-temperature properties of a dilute two-component Fermi gas in the BCS-BEC crossover are investigated. On the basis of a generalization of the variational Schwinger method, we construct approximate semi-analytical formulae for collective frequencies of the radial and the axial breathing modes of the Fermi gas under harmonic confinement in the framework of the hydrodynamic theory. It is shown that the method gives nearly exact solutions.Comment: 11 page

Versatile transporter apparatus for experiments with optically trapped Bose-Einstein condensates

We describe a versatile and simple scheme for producing magnetically and optically-trapped Rb-87 Bose-Einstein condensates, based on a moving-coil transporter apparatus. The apparatus features a TOP trap that incorporates the movable quadrupole coils used for magneto-optical trapping and long-distance magnetic transport of atomic clouds. As a stand-alone device, this trap allows for the stable production of condensates containing up to one million atoms. In combination with an optical dipole trap, the TOP trap acts as a funnel for efficient loading, after which the quadrupole coils can be retracted, thereby maximizing optical access. The robustness of this scheme is illustrated by realizing the superfluid-to-Mott insulator transition in a three-dimensional optical lattice