Efficient Decoding of Topological Color Codes

Color codes are a class of topological quantum codes with a high error threshold and large set of transversal encoded gates, and are thus suitable for fault tolerant quantum computation in two-dimensional architectures. Recently, computationally efficient decoders for the color codes were proposed. We describe an alternate efficient iterative decoder for topological color codes, and apply it to the color code on hexagonal lattice embedded on a torus. In numerical simulations, we find an error threshold of 7.8% for independent dephasing and spin flip errors.Comment: 7 pages, LaTe

Medical Home Implementation and Follow-Up of Cancer-Related Abnormal Test Results in the Veterans Health Administration

IMPORTANCE: Lack of timely follow-up of cancer-related abnormal test results can lead to delayed or missed diagnoses, adverse cancer outcomes, and substantial cost burden for patients. Care delivery models, such as the Veterans Affairs\u27 (VA) Patient-Aligned Care Team (PACT), which aim to improve patient-centered care coordination, could potentially also improve timely follow-up of abnormal test results. PACT was implemented nationally in the VA between 2010 and 2012. OBJECTIVE: To evaluate the long-term association between PACT implementation and timely follow-up of abnormal test results related to the diagnosis of 5 different cancers. DESIGN, SETTING, AND PARTICIPANTS: This multiyear retrospective cohort study used 14 years of VA data (2006-2019), which were analyzed using panel data-based random-effects linear regressions. The setting included all VA clinics and facilities. The participants were adult patients who underwent diagnostic testing related to 5 different cancers and had abnormal test results. Data extraction and statistical analyses were performed from September 2021 to December 2023. EXPOSURE: Calendar years denoting preperiods and postperiods of PACT implementation, and the PACT Implementation Progress Index Score denoting the extent of implementation in each VA clinic and facility. MAIN OUTCOME AND MEASURE: Percentage of potentially missed timely follow-ups of abnormal test results. RESULTS: This study analyzed 6 data sets representing 5 different types of cancers. During the initial years of PACT implementation (2010 to 2013), percentage of potentially missed timely follow-ups decreased between 3 to 7 percentage points for urinalysis suggestive of bladder cancer, 12 to 14 percentage points for mammograms suggestive of breast cancer, 19 to 22 percentage points for fecal tests suggestive of colorectal cancer, and 6 to 13 percentage points for iron deficiency anemia laboratory tests suggestive of colorectal cancer, with no statistically significant changes for α-fetoprotien tests and lung cancer imaging. However, these beneficial reductions were not sustained over time. Better PACT implementation scores were associated with a decrease in potentially missed timely follow-up percentages for urinalysis (0.3-percentage point reduction [95% CI, -0.6 to -0.1] with 1-point increase in the score), and laboratory tests suggestive of iron deficiency anemia (0.5-percentage point reduction [95% CI,-0.8 to -0.2] with 1-point increase in the score). CONCLUSIONS AND RELEVANCE: This cohort study found that implementation of PACT in the VA was associated with a potential short-term improvement in the quality of follow-up for certain test results. Additional multifaceted sustained interventions to reduce missed test results are required to prevent care delays

Sparse Quantum Codes from Quantum Circuits

Sparse quantum codes are analogous to LDPC codes in that their check operators require examining only a constant number of qubits. In contrast to LDPC codes, good sparse quantum codes are not known, and even to encode a single qubit, the best known distance is O(√n log(n)), due to Freedman, Meyer and Luo. We construct a new family of sparse quantum subsystem codes with minimum distance n[superscript 1 - ε] for ε = O(1/√log n). A variant of these codes exists in D spatial dimensions and has d = n[superscript 1 - ε - 1/D], nearly saturating a bound due to Bravyi and Terhal. Our construction is based on a new general method for turning quantum circuits into sparse quantum subsystem codes. Using this prescription, we can map an arbitrary stabilizer code into a new subsystem code with the same distance and number of encoded qubits but where all the generators have constant weight, at the cost of adding some ancilla qubits. With an additional overhead of ancilla qubits, the new code can also be made spatially local.National Science Foundation (U.S.) (Grant CCF-1111382)United States. Army Research Office (Contract W911NF-12-1-0486

From Skew-Cyclic Codes to Asymmetric Quantum Codes

We introduce an additive but not $\mathbb{F}_4$-linear map $S$ from $\mathbb{F}_4^{n}$ to $\mathbb{F}_4^{2n}$ and exhibit some of its interesting structural properties. If $C$ is a linear $[n,k,d]_4$-code, then $S(C)$ is an additive $(2n,2^{2k},2d)_4$-code. If $C$ is an additive cyclic code then $S(C)$ is an additive quasi-cyclic code of index $2$. Moreover, if $C$ is a module $\theta$-cyclic code, a recently introduced type of code which will be explained below, then $S(C)$ is equivalent to an additive cyclic code if $n$ is odd and to an additive quasi-cyclic code of index $2$ if $n$ is even. Given any $(n,M,d)_4$-code $C$, the code $S(C)$ is self-orthogonal under the trace Hermitian inner product. Since the mapping $S$ preserves nestedness, it can be used as a tool in constructing additive asymmetric quantum codes.Comment: 16 pages, 3 tables, submitted to Advances in Mathematics of Communication

Drosophila Condensin II subunit Chromosome-associated protein D3 regulates cell fate determination through non-cell-autonomous signaling

Citation: Klebanow, L. R., Peshel, E. C., Schuster, A. T., De, K., Sarvepalli, K., Lemieux, M. E., . . . Longworth, M. S. (2016). Drosophila Condensin II subunit Chromosome-associated protein D3 regulates cell fate determination through non-cell-autonomous signaling. Development, 143(15), 2791-2802. doi:10.1242/dev.133686The pattern of the Drosophila melanogaster adult wing is heavily influenced by the expression of proteins that dictate cell fate decisions between intervein and vein during development. dSRF (Blistered) expression in specific regions of the larval wing disc promotes intervein cell fate, whereas EGFR activity promotes vein cell fate. Here, we report that the chromatin-organizing protein CAP-D3 acts to dampen dSRF levels at the anterior/posterior boundary in the larval wing disc, promoting differentiation of cells into the anterior crossvein. CAP-D3 represses KNOT expression in cells immediately adjacent to the anterior/posterior boundary, thus blocking KNOT-mediated repression of EGFR activity and preventing cell death. Maintenance of EGFR activity in these cells depresses dSRF levels in the neighboring anterior crossvein progenitor cells, allowing them to differentiate into vein cells. These findings uncover a novel transcriptional regulatory network influencing Drosophila wing vein development, and are the first to identify a Condensin II subunit as an important regulator of EGFR activity and cell fate determination in vivo

Generalized Toric Codes Coupled to Thermal Baths

We have studied the dynamics of a generalized toric code based on qudits at finite temperature by finding the master equation coupling the code's degrees of freedom to a thermal bath. As a consequence, we find that for qutrits new types of anyons and thermal processes appear that are forbidden for qubits. These include creation, annihilation and diffusion throughout the system code. It is possible to solve the master equation in a short-time regime and find expressions for the decay rates as a function of the dimension $d$ of the qudits. Although we provide an explicit proof that the system relax to the Gibbs state for arbitrary qudits, we also prove that above a certain crossing temperature, qutrits initial decay rate is smaller than the original case for qubits. Surprisingly this behavior only happens with qutrits and not with other qudits with $d>3$.Comment: Revtex4 file, color figures. New Journal of Physics' versio

Integrative analysis of multimodal mass spectrometry data in MZmine 3

3 Pág.We thank Christopher Jensen and Gauthier Boaglio for their contributions to the MZmine codebase. We thank Jianbo Zhang and Zachary Russ for their donations to MZmine development. The MZmine 3 logo was designed by the Bioinformatics & Research Computing group at the Whitehead Institute for Biomedical Research. T.P. is supported by Czech Science Foundation (GA CR) grant 21-11563M and by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement 891397. Support for P.C.D. was from US NIH U19 AG063744, P50HD106463, 1U24DK133658 and BBSRC-NSF award 2152526. T.S. acknowledges funding by Deutsche Forschungsgemeinschaft (441958208). M. Wang acknowledges the US Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 , a DOE Office of Science User Facility) and is supported by the Office of Science of the US Department of Energy operated under subcontract No. 7601660. E.R. and H.H. thank Wen Jiang (HILICON AB) for providing the iHILIC Fusion(+) column for HILIC measurements. M.F., K.D. and S.B. are supported by Deutsche Forschungsgemeinschaft (BO 1910/20). L.-F.N. is supported by the Swiss National Science Foundation (project 189921). D.P. was supported through the Deutsche Forschungsgemeinschaft (German Research Foundation) through the CMFI Cluster of Excellence (EXC-2124 — 390838134 project-ID 1-03.006_0) and the Collaborative Research Center CellMap (TRR 261 - 398967434). J.-K.W. acknowledges the US National Science Foundation (MCB-1818132), the US Department of Agriculture, and the Chan Zuckerberg Initiative. MZmine developers have received support from the European COST Action CA19105 — Pan-European Network in Lipidomics and EpiLipidomics (EpiLipidNET). We acknowledge the support of the Google Summer of Code (GSoC) program, which has funded the development of several MZmine modules through student projects. We thank Adam Tenderholt for introducing MZmine to the GSoC program.Peer reviewe

The Prevalence of Co-Infections in Hospitalized Patients with COVID-19

Introduction: The Coronavirus disease 2019 (COVID-19) pandemic emerged in early 2020 and significantly altered the landscape of healthcare delivery. With the absence of a cure, treatment of hospitalized patients with COVID-19 has been particularly challenging. Physicians often treat hospitalized patients empirically with broad-spectrum antibiotics on admission due to concerns of missing an underlying, treatable co-infection. In this study, we aim to determine the rate of co-infections in hospitalized patients with SARS-CoV-2. Methods: We conducted a retrospective study which included all patients who had a nasopharyngeal swab sample positive for SARS-CoV-2 infection detected by the Cepheid Real-Time Polymerase Chain Reaction (RT-PCT) test at the Detroit Medical Center in April 2020. Of 409 patients with SARS-CoV-2 infection, 390 had sputum or blood cultures ordered during their hospitalization. The results of each culture were examined, and the isolated organisms and date of the culture positivity were documented. We analyzed the results of non-culture tests such as urine legionella antigen, urine pneumococcal antigen, and influenza A and B PCR. Results: Ninety four patients had a respiratory culture ordered, out of which 38 (40%) returned positive. Of these 38 patients, 12 patients had a positive culture within three days of admission. A total of 296 patients had a blood culture ordered out of which 30 (10%) returned positive. Of these 30 patients, 21 patients had a positive culture within the first three days of admission. A total of 126 urine legionella antigen tests were obtained, 0 of which returned positive. Out of the 125 urine pneumococcal antigens ordered, only 4 (3.1%) were positive. 221 patients were tested for Influenza A and B PCR, and 0 tested positive. Conclusions: Based on our findings, respiratory co-infections appear to be uncommon on initial presentation to the hospital in patients with the COVID-19 infection. Although only 10% of the total blood cultures obtained during hospitalization returned positive, around 70% of those (21 out of 30) were positive on admission. Based on our data, urine pneumococcal and urine legionella antigens appear to have no role in the evaluation of secondary bacterial infections in patients with SARS-CoV-2 infection. When in doubt, physicians should obtain respiratory and blood cultures to better guide management. Empiric antibiotic therapy on admission does not appear to be warranted in the majority of patients and discontinuation of empiric antibiotics should be guided based on culture results

The reign of religion in contemporary philosophy.

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