Unleashing Quantum Simulation Advantages: Hamiltonian Subspace Encoding for Resource Efficient Quantum Simulations

Number-conserved subspace encoding for fermionic Hamiltonians, which exponentially reduces qubit cost, is necessary for quantum advantages in variational quantum eigensolver (VQE). However, optimizing the trade-off between qubit compression and increased measurement cost poses a challenge. By employing the Gilbert-Varshamov bound on linear code, we optimize qubit scaling $\mathcal{O}(N\log_2M)$ and measurement cost $\mathcal{O}(M^4)$ for $M$ modes $N$ electrons chemistry problems. The compression is implemented with the Randomized Linear Encoding (RLE) algorithm on VQE for $\text{H}_2$ and LiH in the 6-31G* and STO-3G/6-31G* basis respectively. The resulting subspace circuit expressivity and trainability are enhanced with less circuit depth and higher noise tolerance

Comparative Multi-Epitope-Ligand-Cartography reveals essential immunological alterations in Barrett's metaplasia and esophageal adenocarcinoma

<p>Abstract</p> <p>Background</p> <p>Barrett's esophagus (BE) is caused by gastroesophageal reflux with consecutive mucosal inflammation, predisposing patients to the development of esophageal adenocarcinoma (EAC). We investigated changes in T cell-related mucosal combinatorial molecular protein patterns in both diseases using the novel Multi-Epitope-Ligand-Cartography, a unique robotic whole-cell imaging technology that simultaneously visualizes dozens of proteins in structurally intact tissues and correlates cellular localization of proteins with function.</p> <p>Results</p> <p>Biopsies were taken during endoscopy from BE, EAC, and normal control tissue, and proteomic microscopy was performed on 32 different epitopes. When the significance level was set to p < 0.0005 and the search depth to five antibody combinations, controls and BE can be differentiated by 63, controls and EAC by 3222, and BE from EAC by 1521 distinct protein combinations.</p> <p>For example, the number of activated apoptotic naïve and memory T cells was significantly increased only in BE, whereas the number of activated apoptotic helper and regulatory T cells was significantly elevated in BE and EAC. In contrast, the number of activated apoptotic cytotoxic T cells was significantly elevated only in EAC. Confirming different pathways in BE and EAC, the number of T lymphocytes with p53 expression and downregulation of bcl2 expression (CD3⁺p53⁺Bcl2^-NfkB^-) was significantly increased in EAC compared to BE and controls. Interestingly, the number of precursor T cells (CD7⁺) was significantly elevated only in EAC. These cells lack Bax and caspase-8, suggesting impaired apoptosis in the early stages of T cell differentiation.</p> <p>Conclusion</p> <p>Proteomic analysis showed for the first time that proteins, which are critically involved in the mucosal immune system of the esophagus, are distinctly expressed in BE and EAC, whereas others are comparably altered in both diseases, suggesting that many pathogenic events might be shared by both diseases. Topological proteomic analysis, therefore, helps us to understand the different pathogenic events in the underlying disease pathways.</p

Assessment of long-range correlation in animal behaviour time series: the temporal pattern of locomotor activity of Japanese quail (Coturnix coturnix) and mosquito larva (Culex quinquefasciatus)

The aim of this study was to evaluate the performance of a classical method of fractal analysis, Detrended Fluctuation Analysis (DFA), in the analysis of the dynamics of animal behavior time series. In order to correctly use DFA to assess the presence of long-range correlation, previous authors using statistical model systems have stated that different aspects should be taken into account such as: 1) the establishment by hypothesis testing of the absence of short term correlation, 2) an accurate estimation of a straight line in the log-log plot of the fluctuation function, 3) the elimination of artificial crossovers in the fluctuation function, and 4) the length of the time series. Taking into consideration these factors, herein we evaluated the presence of long-range correlation in the temporal pattern of locomotor activity of Japanese quail ({\sl Coturnix coturnix}) and mosquito larva ({\sl Culex quinquefasciatus}). In our study, modeling the data with the general ARFIMA model, we rejected the hypothesis of short range correlations (d=0) in all cases. We also observed that DFA was able to distinguish between the artificial crossover observed in the temporal pattern of locomotion of Japanese quail, and the crossovers in the correlation behavior observed in mosquito larvae locomotion. Although the test duration can slightly influence the parameter estimation, no qualitative differences were observed between different test durations

Constant sign and nodal solutions for a class of nonlinear Dirichlet problems

We consider a nonlinear Dirichlet problem with a Carathéodory reaction which has arbitrary growth from below. We show that the problem has at least three nontrivial smooth solutions, two of constant sign and the third nodal. In the semilinear case (i.e., p =2), with the reaction f(z, .)being C1and with subcritical growth, we show that there is a second nodal solution, for a total of four nontrivial smooth solutions. Finally,when the reaction has concave terms and is subcritical and for the nonlinear problem (i.e., 1 <p <∞) we show that again we can have the existence of three nontrivial smooth solutions, two of constant sign and a third nodal

The nuclear immune receptor RPS4 is required for RRS1SLH1-dependent constitutive defense activation in Arabidopsis thaliana

Plant nucleotide-binding leucine-rich repeat (NB-LRR) disease resistance (R) proteins recognize specific ‘‘avirulent’’ pathogen effectors and activate immune responses. NB-LRR proteins structurally and functionally resemble mammalian Nod-like receptors (NLRs). How NB-LRR and NLR proteins activate defense is poorly understood. The divergently transcribed Arabidopsis R genes, RPS4 (resistance to Pseudomonas syringae 4) and RRS1 (resistance to Ralstonia solanacearum 1), function together to confer recognition of Pseudomonas AvrRps4 and Ralstonia PopP2. RRS1 is the only known recessive NBLRR R gene and encodes a WRKY DNA binding domain, prompting suggestions that it acts downstream of RPS4 for transcriptional activation of defense genes. We define here the early RRS1-dependent transcriptional changes upon delivery of PopP2 via Pseudomonas type III secretion. The Arabidopsis slh1 (sensitive to low humidity 1) mutant encodes an RRS1 allele (RRS1SLH1) with a single amino acid (leucine) insertion in the WRKY DNA-binding domain. Its poor growth due to constitutive defense activation is rescued at higher temperature. Transcription profiling data indicate that RRS1SLH1-mediated defense activation overlaps substantially with AvrRps4- and PopP2-regulated responses. To better understand the genetic basis of RPS4/RRS1-dependent immunity, we performed a genetic screen to identify suppressor of slh1 immunity (sushi) mutants. We show that many sushi mutants carry mutations in RPS4, suggesting that RPS4 acts downstream or in a complex with RRS1. Interestingly, several mutations were identified in a domain C-terminal to the RPS4 LRR domain. Using an Agrobacterium-mediated transient assay system, we demonstrate that the P-loop motif of RPS4 but not of RRS1SLH1 is required for RRS1SLH1 function. We also recapitulate the dominant suppression of RRS1SLH1 defense activation by wild type RRS1 and show this suppression requires an intact RRS1 P-loop. These analyses of RRS1SLH1 shed new light on mechanisms by which NB-LRR protein pairs activate defense signaling, or are held inactive in the absence of a pathogen effector

Gravitational Lensing

Gravitational lensing has developed into one of the most powerful tools for the analysis of the dark universe. This review summarises the theory of gravitational lensing, its main current applications and representative results achieved so far. It has two parts. In the first, starting from the equation of geodesic deviation, the equations of thin and extended gravitational lensing are derived. In the second, gravitational lensing by stars and planets, galaxies, galaxy clusters and large-scale structures is discussed and summarised.Comment: Invited review article to appear in Classical and Quantum Gravity, 85 pages, 15 figure

Evidence for a Role of srGAP3 in the Positioning of Commissural Axons within the Ventrolateral Funiculus of the Mouse Spinal Cord

Slit-Robo signaling guides commissural axons away from the floor-plate of the spinal cord and into the longitudinal axis after crossing the midline. In this study we have evaluated the role of the Slit-Robo GTPase activating protein 3 (srGAP3) in commissural axon guidance using a knockout (KO) mouse model. Co-immunoprecipitation experiments confirmed that srGAP3 interacts with the Slit receptors Robo1 and Robo2 and immunohistochemistry studies showed that srGAP3 co-localises with Robo1 in the ventral and lateral funiculus and with Robo2 in the lateral funiculus. Stalling axons have been reported in the floor-plate of Slit and Robo mutant spinal cords but our axon tracing experiments revealed no dorsal commissural axon stalling in the floor plate of the srGAP3 KO mouse. Interestingly we observed a significant thickening of the ventral funiculus and a thinning of the lateral funiculus in the srGAP3 KO spinal cord, which has also recently been reported in the Robo2 KO. However, axons in the enlarged ventral funiculus of the srGAP3 KO are Robo1 positive but do not express Robo2, indicating that the thickening of the ventral funiculus in the srGAP3 KO is not a Robo2 mediated effect. We suggest a role for srGAP3 in the lateral positioning of post crossing axons within the ventrolateral funiculus

Direct Observation of Dimerization between Different CREB1 Isoforms in a Living Cell

Cyclic AMP-responsive element binding protein 1 (CREB1) plays multiple functions as a transcription factor in gene regulation. CREB1 proteins are also known to be expressed in several spliced isoforms that act as transcriptional activators or repressors. The activator isoforms, possessing the functional domains for kinase induction and for interaction with other transcriptional regulators, act as transcriptional activators. On the other hand, some isoforms, lacking those functional domains, are reported to be repressors that make heterodimers with activator isoforms. The complex and ingenious function for CREB1 arises in part from the variation in their spliced isoforms, which allows them to interact with each other. To date, however, the dimerization between the activator and repressor isoforms has not yet been proved directly in living cells. In this study, we applied fluorescence cross-correlation spectroscopy (FCCS) to demonstrate direct observation of dimerization between CREB1 activator and repressor. The FCCS is a well established spectroscopic method to determine the interaction between the different fluorescent molecules in the aqueous condition. Using differently labeled CREB1 isoforms, we successfully observed the interaction of CREB1 activator and repressor via dimerization in the nuclei of cultured cells. As a result, we confirmed the formation of heterodimer between CREB1 activator and repressor isoforms in living cells

Reduction of nucleosome assembly during new DNA synthesis impairs both major pathways of double-strand break repair

Assembly of new chromatin during S phase requires the histone chaperone complexes CAF-1 (Cac2p, Msi1p and Rlf2p) and RCAF (Asf1p plus acetylated histones H3 and H4). Cells lacking CAF-1 and RCAF are hypersensitive to DNA-damaging agents, such as methyl methanesulfonate and camptothecin, suggesting a possible defect in double-strand break (DSB) repair. Assays developed to quantitate repair of defined, cohesive-ended break structures revealed that DSB-induced plasmid:chromosome recombination was reduced ∼10-fold in RCAF/CAF-1 double mutants. Recombination defects were similar with both chromosomal and plasmid targets in vivo, suggesting that inhibitory chromatin structures were not involved. Consistent with these observations, ionizing radiation-induced loss of heterozygosity was abolished in the mutants. Nonhomologous end-joining (NHEJ) repair proficiency and accuracy were intermediate between wild-type levels and those of NHEJ-deficient yku70 and rad50 mutants. The defects in NHEJ, but not homologous recombination, could be rescued by deletion of HMR-a1, a component of the a1/alpha2 transcriptional repressor complex. The findings are consistent with the observation that silent mating loci are partially derepressed. These results demonstrate that defective assembly of nucleosomes during new DNA synthesis compromises each of the known pathways of DSB repair and that the effects can be indirect consequences of changes in silenced chromatin structure

Infrastructure for Detector Research and Development towards the International Linear Collider

The EUDET-project was launched to create an infrastructure for developing and testing new and advanced detector technologies to be used at a future linear collider. The aim was to make possible experimentation and analysis of data for institutes, which otherwise could not be realized due to lack of resources. The infrastructure comprised an analysis and software network, and instrumentation infrastructures for tracking detectors as well as for calorimetry.Comment: 54 pages, 48 picture