Adiabatic Quantum Graph Matching with Permutation Matrix Constraints

Matching problems on 3D shapes and images are challenging as they are frequently formulated as combinatorial quadratic assignment problems (QAPs) with permutation matrix constraints, which are NP-hard. In this work, we address such problems with emerging quantum computing technology and propose several reformulations of QAPs as unconstrained problems suitable for efficient execution on quantum hardware. We investigate several ways to inject permutation matrix constraints in a quadratic unconstrained binary optimization problem which can be mapped to quantum hardware. We focus on obtaining a sufficient spectral gap, which further increases the probability to measure optimal solutions and valid permutation matrices in a single run. We perform our experiments on the quantum computer D-Wave 2000Q (2^11 qubits, adiabatic). Despite the observed discrepancy between simulated adiabatic quantum computing and execution on real quantum hardware, our reformulation of permutation matrix constraints increases the robustness of the numerical computations over other penalty approaches in our experiments. The proposed algorithm has the potential to scale to higher dimensions on future quantum computing architectures, which opens up multiple new directions for solving matching problems in 3D computer vision and graphics

Q-{M}atch: {I}terative Shape Matching via Quantum Annealing

Finding shape correspondences can be formulated as an NP-hard quadratic assignment problem (QAP) that becomes infeasible for shapes with high sampling density. A promising research direction is to tackle such quadratic optimization problems over binary variables with quantum annealing, which allows for some problems a more efficient search in the solution space. Unfortunately, enforcing the linear equality constraints in QAPs via a penalty significantly limits the success probability of such methods on currently available quantum hardware. To address this limitation, this paper proposes Q-Match, i.e., a new iterative quantum method for QAPs inspired by the alpha-expansion algorithm, which allows solving problems of an order of magnitude larger than current quantum methods. It implicitly enforces the QAP constraints by updating the current estimates in a cyclic fashion. Further, Q-Match can be applied iteratively, on a subset of well-chosen correspondences, allowing us to scale to real-world problems. Using the latest quantum annealer, the D-Wave Advantage, we evaluate the proposed method on a subset of QAPLIB as well as on isometric shape matching problems from the FAUST dataset

Predicting Future Changes in Muskegon River Watershed Game Fish Distributions under Future Land Cover Alteration and Climate Change Scenarios

Future alterations in land cover and climate are likely to cause substantial changes in the ranges of fish species. Predictive distribution models are an important tool for assessing the probability that these changes will cause increases or decreases in or the extirpation of species. Classification tree models that predict the probability of game fish presence were applied to the streams of the Muskegon River watershed, Michigan. The models were used to study three potential future scenarios: (1) land cover change only, (2) land cover change and a 3°C increase in air temperature by 2100, and (3) land cover change and a 5°C increase in air temperature by 2100. The analysis indicated that the expected change in air temperature and subsequent change in water temperatures would result in the decline of coldwater fish in the Muskegon watershed by the end of the 21st century while cool‐ and warmwater species would significantly increase their ranges. The greatest decline detected was a 90% reduction in the probability that brook trout Salvelinus fontinalis would occur in Bigelow Creek. The greatest increase was a 276% increase in the probability that northern pike Esox lucius would occur in the Middle Branch River. Changes in land cover are expected to cause large changes in a few fish species, such as walleye Sander vitreus and Chinook salmon Oncorhynchus tshawytscha, but not to drive major changes in species composition. Managers can alter stream environmental conditions to maximize the probability that species will reside in particular stream reaches through application of the classification tree models. Such models represent a good way to predict future changes, as they give quantitative estimates of the n‐dimensional niches for particular species.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141570/1/tafs0396.pd

Burbot Early Life History Strategies in the Great Lakes

Burbot Lota lota exhibit four previously known reproductive strategies in the Great Lakes region. In this paper we review those strategies and provide evidence for a fifth one—delayed deepwater spawning. The four known, shallow‐water strategies are as follows: (1) spawning by self‐sustaining, landlocked populations, (2) spawning in tributaries in winter and the exit of larvae to a Great Lake, (3) spawning by residents in a spawning stream with access to a Great Lake, and (4) spawning on unconsolidated and rocky areas in shallow water in winter in the lake proper. Resident, landlocked populations exist in some Michigan and Wisconsin rivers (e.g., the Muskegon River in Michigan). The evidence for winter tributary spawning is the appearance of newly hatched Burbot in the St. Marys and Bark rivers during April–June. Evidence for Burbot juveniles leaving spawning streams is U.S. Fish and Wildlife Service tributory mouth trap data. The evidence for winter nearshore spawning comes from power plant monthly entrainment studies (Mansfield et al. 1983). Our proposed fifth strategy is spring and summer spawning at deep reefs, where there is probably cobble or boulder habitat. Our evidence comes from midlake reefs in Lake Michigan and offshore areas of Lake Huron: (1) we collected adult Burbot at midlake reefs in Lake Michigan, (2) we collected many Burbot larvae (many of which were newly hatched) from Lakes Michigan and Huron in June–August, and (3) we collected a Burbot egg in a PONAR grab in mid‐July from 73 m in southern Lake Huron. An important question remains, namely, which life history strategy provides the highest recruitment success for this species. It may be that adaptability ensures the survival of this important, top‐predator fish during periods of crisis (e.g., encounters with dams, Sea Lamprey Petromyzon marinus predation).Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141895/1/tafs1733.pd

Engineering yield and rate of reductive biotransformation in Escherichia coli by partial cyclization of the pentose phosphate pathway and PTS-independent glucose transport

Optimization of yields and productivities in reductive whole-cell biotransformations is an important issue for the industrial application of such processes. In a recent study with Escherichia coli, we analyzed the reduction of the prochiral β-ketoester methyl acetoacetate by an R-specific alcohol dehydrogenase (ADH) to the chiral hydroxy ester (R)-methyl 3-hydroxybutyrate (MHB) using glucose as substrate for the generation of NADPH. Deletion of the phosphofructokinase gene pfkA almost doubled the yield to 4.8 mol MHB per mole of glucose, and it was assumed that this effect was due to a partial cyclization of the pentose phosphate pathway (PPP). Here, this partial cyclization was confirmed by 13C metabolic flux analysis, which revealed a negative net flux from glucose 6-phosphate to fructose 6-phosphate catalyzed by phosphoglucose isomerase. For further process optimization, the genes encoding the glucose facilitator (glf) and glucokinase (glk) of Zymomonas mobilis were overexpressed in recombinant E. coli strains carrying ADH and deletions of either pgi (phosphoglucose isomerase), or pfkA, or pfkA plus pfkB. In all cases, the glucose uptake rate was increased (30–47%), and for strains Δpgi and ΔpfkA also, the specific MHB production rate was increased by 15% and 20%, respectively. The yield of the latter two strains slightly dropped by 11% and 6%, but was still 73% and 132% higher compared to the reference strain with intact pgi and pfkA genes and expressing glf and glk. Thus, metabolic engineering strategies are presented for improving yield and rate of reductive redox biocatalysis by partial cyclization of the PPP and by increasing glucose uptake, respectively

Matrix Metalloproteinase-2 and -9 Secreted by Leukemic Cells Increase the Permeability of Blood-Brain Barrier by Disrupting Tight Junction Proteins

Central nervous system (CNS) involvement remains an important cause of morbidity and mortality in acute leukemia, the mechanisms of leukemic cell infiltration into the CNS have not yet been elucidated. The blood-brain barrier (BBB) makes CNS become a refugee to leukemic cells and serves as a resource of cells that seed extraneural sites. How can the leukemic cells disrupt this barrier and invasive the CNS, even if many of the currently available chemotherapies can not cross the BBB? Tight junction in endothelial cells occupies a central role in the function of the BBB. Except the well known role of degrading extracellular matrix in metastasis of cancer cells, here we show matrix metalloproteinase (MMP)-2 and -9, secreted by leukemic cells, mediate the BBB opening by disrupting tight junction proteins in the CNS leukemia. We demonstrated that leukemic cells impaired tight junction proteins ZO-1, claudin-5 and occludin resulting in increased permeability of the BBB. However, these alterations reduced when MMP-2 and -9 activities were inhibited by RNA interference strategy or by MMP inhibitor GM6001 in an in vitro BBB model. We also found that the disruption of the BBB in company with the down-regulation of ZO-1, claudin-5 and occludin and the up-regulation of MMP-2 and -9 in mouse brain tissues with leukemic cell infiltration by confocal imaging and the assay of in situ gelatin zymography. Besides, GM6001 protected all mice against CNS leukemia. Our findings suggest that the degradation of tight junction proteins ZO-1, claudin-5 and occludin by MMP-2 and -9 secreted by leukemic cells constitutes an important mechanism in the BBB breakdown which contributes to the invasion of leukemic cells to the CNS in acute leukemia

Violent aggression predicted by multiple pre-adult environmental hits

Early exposure to negative environmental impact shapes individual behavior and potentially contributes to any mental disease. We reported previously that accumulated environmental risk markedly decreases age at schizophrenia onset. Follow-up of matched extreme group individuals (≤1 vs. ≥3 risks) unexpectedly revealed that high-risk subjects had >5 times greater probability of forensic hospitalization. In line with longstanding sociological theories, we hypothesized that risk accumulation before adulthood induces violent aggression and criminal conduct, independent of mental illness. We determined in 6 independent cohorts (4 schizophrenia and 2 general population samples) pre-adult risk exposure, comprising urbanicity, migration, physical and sexual abuse as primary, and cannabis or alcohol as secondary hits. All single hits by themselves were marginally associated with higher violent aggression. Most strikingly, however, their accumulation strongly predicted violent aggression (odds ratio 10.5). An epigenome-wide association scan to detect differential methylation of blood-derived DNA of selected extreme group individuals yielded overall negative results. Conversely, determination in peripheral blood mononuclear cells of histone-deacetylase1 mRNA as 'umbrella mediator' of epigenetic processes revealed an increase in the high-risk group, suggesting lasting epigenetic alterations. Together, we provide sound evidence of a disease-independent unfortunate relationship between well-defined pre-adult environmental hits and violent aggression, calling for more efficient prevention