Detecting Multiple Communities Using Quantum Annealing on the D-Wave System

A very important problem in combinatorial optimization is partitioning a network into communities of densely connected nodes; where the connectivity between nodes inside a particular community is large compared to the connectivity between nodes belonging to different ones. This problem is known as community detection, and has become very important in various fields of science including chemistry, biology and social sciences. The problem of community detection is a twofold problem that consists of determining the number of communities and, at the same time, finding those communities. This drastically increases the solution space for heuristics to work on, compared to traditional graph partitioning problems. In many of the scientific domains in which graphs are used, there is the need to have the ability to partition a graph into communities with the ``highest quality'' possible since the presence of even small isolated communities can become crucial to explain a particular phenomenon. We have explored community detection using the power of quantum annealers, and in particular the D-Wave 2X and 2000Q machines. It turns out that the problem of detecting at most two communities naturally fits into the architecture of a quantum annealer with almost no need of reformulation. This paper addresses a systematic study of detecting two or more communities in a network using a quantum annealer

A 5'-region polymorphism modulates promoter activity of the tumor suppressor gene MFSD2A

<p>Abstract</p> <p>Background</p> <p>The MFSD2A gene maps within a linkage disequilibrium block containing the MYCL1-<it>EcoRI </it>polymorphism associated with prognosis and survival in lung cancer patients. Survival discrepancies between Asians and Caucasians point to ethnic differences in allelic frequencies of the functional genetic variations.</p> <p>Results</p> <p>Analysis of three single-nucleotide polymorphisms (SNPs) mapping in the MFSD2A 5'-regulatory region using a luciferase reporter system showed that SNP rs12072037, in linkage disequilibrium with the MYCL1-<it>EcoRI </it>polymorphism and polymorphic in Asians but not in Caucasians, modulated transcriptional activity of the MFSD2A promoter in cell lines expressing AHR and ARNT transcription factors, which potentially bind to the SNP site.</p> <p>Conclusion</p> <p>SNP rs12072037 modulates MFSD2A promoter activity and thus might affect MFSD2A levels in normal lung and in lung tumors, representing a candidate ethnically specific genetic factor underlying the association between the MYCL1 locus and lung cancer patients' survival.</p

Multilevel Combinatorial Optimization Across Quantum Architectures

Emerging quantum processors provide an opportunity to explore new approaches for solving traditional problems in the post Moore's law supercomputing era. However, the limited number of qubits makes it infeasible to tackle massive real-world datasets directly in the near future, leading to new challenges in utilizing these quantum processors for practical purposes. Hybrid quantum-classical algorithms that leverage both quantum and classical types of devices are considered as one of the main strategies to apply quantum computing to large-scale problems. In this paper, we advocate the use of multilevel frameworks for combinatorial optimization as a promising general paradigm for designing hybrid quantum-classical algorithms. In order to demonstrate this approach, we apply this method to two well-known combinatorial optimization problems, namely, the Graph Partitioning Problem, and the Community Detection Problem. We develop hybrid multilevel solvers with quantum local search on D-Wave's quantum annealer and IBM's gate-model based quantum processor. We carry out experiments on graphs that are orders of magnitudes larger than the current quantum hardware size, and we observe results comparable to state-of-the-art solvers in terms of quality of the solution

Expanding the Direct HetR Regulon in Anabaena sp. Strain PCC 7120

In response to a lack of environmental combined nitrogen, the filamentous cyanobacterium Anabaena sp. strain PCC 7120 differentiates nitrogen-fixing heterocyst cells in a periodic pattern. HetR is a transcription factor that coordinates the regulation of this developmental program. An inverted repeat-containing sequence in the hepA promoter required for proheterocyst-specific transcription was identified based on sequence similarity to a previously characterized binding site for HetR in the promoter of hetP. The binding affinity of HetR for the hepA site is roughly an order of magnitude lower than that for the hetP binding site. A BLAST search of the Anabaena genome identified 166 hepA-like sites that occur as single or tandem sites (two binding sites separated by 13 bp). The vast majority of these sites are present in predicted intergenic regions. HetR bound five representative single binding sites in vitro, and binding was abrogated by transversions in the binding sites that conserved the inverted repeat nature of the sites. Binding to four representative tandem sites was not observed. Transcriptional fusions of the green fluorescent protein gene gfp with putative promoter regions associated with the representative binding sites indicated that HetR could function as either an activator or repressor and that activation was cell-type specific. Taken together, we have expanded the direct HetR regulon and propose a model in which three categories of HetR binding sites, based on binding affinity and nucleotide sequence, contribute to three of the four phases of differentiation

Involvement of RET oncogene in human tumours: specificity of RET activation to thyroid tumours.

Non-thyroid neoplasia were analysed by Southern blot of genomic DNA and DNA prepared by reverse transcription and amplification by polymerase chain reaction (RT/PCR) for the activation of the RET oncogene. It is known that the rearrangement of RET occurs in about 10%-20% of human thyroid papillary carcinomas. None of 528 non-thyroid tumours showed rearrangement of the RET proto-oncogene, whereas three out of 30 thyroid papillary carcinomas were positive for RET activation. Therefore the activation of RET seems to be a somatic cell mutation specific to human thyroid carcinomas

Gene Expression Response to Stony Coral Tissue Loss Disease Transmission in M. cavernosa and O. faveolata From Florida

Since 2014, corals within Florida’s Coral Reef have been dying at an unprecedented rate due to stony coral tissue loss disease (SCTLD). Here we describe the transcriptomic outcomes of three different SCTLD transmission experiments performed at the Smithsonian Marine Station and Mote Marine Laboratory between 2019 and 2020 on the corals Orbicella faveolata and Montastraea cavernosa. Overall, diseased O. faveolata had 2194 differentially expressed genes (DEGs) compared with healthy colonies, whereas diseased M. cavernosa had 582 DEGs compared with healthy colonies. Many significant DEGs were implicated in immunity, extracellular matrix rearrangement, and apoptosis. These included, but not limited to, peroxidases, collagens, Bax-like, fibrinogen-like, protein tyrosine kinase, and transforming growth factor beta. A gene module was identified that was significantly correlated to disease transmission. This module possessed many apoptosis and immune genes with high module membership indicating that a complex apoptosis and immune response is occurring in corals during SCTLD transmission. Overall, we found that O. faveolata and M. cavernosa exhibit an immune, apoptosis, and tissue rearrangement response to SCTLD. We propose that future studies should focus on examining early time points of infection, before the presence of lesions, to understand the activating mechanisms involved in SCTLD

A comparison of buoy meteorological systems

During May and June 2000, an intercomparison was made of buoy meteorological systems from the Woods Hole Oceanographic Institution (WHOI), the National Oceanographic and Atmospheric Administration (NOAA), Pacific Marine Environmental Laboratory (PMEL), and the Japanese Marine Science and Technology Center (JAMSTEC). Two WHOI systems mounted on a 3 m discus buoy, two PMEL systems mounted on separate buoy tower tops and one JAMSTEC system mounted on a wooden platform were lined parallel to, and 25 m from Nantucket Sound in Massachusetts. All systems used R. M. Young propeller anemometers, Rotronic relative humidity and air temperature sensors and Eppley short-wave radiation sensors. The PMEL and WHOI systems used R. M.Young self-siphoning rain gauges, while the JAMSTEC system used a Scientific Technology ORG-115 optical rain gauge. The PMEL and WHOI systems included an Eppley PIR long-wave sensor, while the JAMSTEC had no longwave sensor. The WHOI system used an AIR DB-1A barometric pressure sensor. PMEL and JAMSTEC systems used Paroscientific Digiquartz sensors. The Geophysical Instruments and Measurements Group (GIM) from Brookhaven National Laboratory (BNL) installed two Portable Radiation Package (PRP) systems that include Eppley short-wave and long-wave sensors on a platform near the site. It was apparent from the data that for most of the sensors, the correlation between data sets was better than the absolute agreement between them. The conclusions made were that the sensors and associated electronics from the three different laboratories performed comparably.Funding was provided by the National Oceanic and Atmospheric Administration under Grant Number NA96GPO429

Ocean warming and acidification have complex interactive effects on the dynamics of a marine fungal disease

Diseases threaten the structure and function of marine ecosystems and are contributing to the global decline of coral reefs. We currently lack an understanding of how climate change stressors, such as ocean acidification (OA) and warming, may simultaneously affect coral reef disease dynamics, particularly diseases threatening key reef-building organisms, for example crustose coralline algae (CCA). Here, we use coralline fungal disease (CFD), a previously described CCA disease from the Pacific, to examine these simultaneous effects using both field observations and experimental manipulations. We identify the associated fungus as belonging to the subphylum Ustilaginomycetes and show linear lesion expansion rates on individual hosts can reach 6.5 mm per day. Further, we demonstrate for the first time, to our knowledge, that ocean-warming events could increase the frequency of CFD outbreaks on coral reefs, but that OA-induced lowering of pH may ameliorate outbreaks by slowing lesion expansion rates on individual hosts. Lowered pH may still reduce overall host survivorship, however, by reducing calcification and facilitating fungal bio-erosion. Such complex, interactive effects between simultaneous extrinsic environmental stressors on disease dynamics are important to consider if we are to accurately predict the response of coral reef communities to future climate change