Unrolled algorithms for group synchronization

The group synchronization problem involves estimating a collection of group elements from noisy measurements of their pairwise ratios. This task is a key component in many computational problems, including the molecular reconstruction problem in single-particle cryo-electron microscopy (cryo-EM). The standard methods to estimate the group elements are based on iteratively applying linear and non-linear operators. Motivated by the structural similarity to deep neural networks, we adopt the concept of algorithm unrolling, where training data is used to optimize the algorithm. We design unrolled algorithms for several group synchronization instances, including synchronization over the group of 3-D rotations: the synchronization problem in cryo-EM. We also apply a similar approach to the multi-reference alignment problem. We show by numerical experiments that the unrolling strategy outperforms existing synchronization algorithms in a wide variety of scenarios

A Heap-Based Concurrent Priority Queue with Mutable Priorities for Faster Parallel Algorithms

Existing concurrent priority queues do not allow to update the priority of an element after its insertion. As a result, algorithms that need this functionality, such as Dijkstra\u27s single source shortest path algorithm, resort to cumbersome and inefficient workarounds. We report on a heap-based concurrent priority queue which allows to change the priority of an element after its insertion. We show that the enriched interface allows to express Dijkstra\u27s algorithm in a more natural way, and that its implementation, using our concurrent priority queue, outperform existing algorithms

On the Automated Verification of Web Applications with Embedded SQL

A large number of web applications is based on a relational database together with a program, typically a script, that enables the user to interact with the database through embedded SQL queries and commands. In this paper, we introduce a method for formal automated verification of such systems which connects database theory to mainstream program analysis. We identify a fragment of SQL which captures the behavior of the queries in our case studies, is algorithmically decidable, and facilitates the construction of weakest preconditions. Thus, we can integrate the analysis of SQL queries into a program analysis tool chain. To this end, we implement a new decision procedure for the SQL fragment that we introduce. We demonstrate practical applicability of our results with three case studies, a web administrator, a simple firewall, and a conference management system

Image-Processing Software for High-Throughput Quantification of Colony Luminescence

Luminescent markers are widely used as reporters for various biologically interesting traits. In colony luminescence assays, the levels of luminescence around each colony can be used to compare the levels of traits of interest for different strains, treatments, etc., using quantitative measurements of the luminescence. However, automatic methods of obtaining this data are underdeveloped, making this a laborious manual process, especially in analyzing large numbers of colonies. The significance of this work is in developing an automatic, high-throughput tool for quantitative analysis of colony luminescence assays, which will allow fast collection of qualitative data from these assays and thus increase their overall usability.Many microbiological assays include colonies that produce a luminescent or fluorescent (here generalized as “luminescent”) signal, often in the form of luminescent halos around the colonies. These signals are used as reporters for a trait of interest; therefore, exact measurements of the luminescence are often desired. However, there is currently a lack of high-throughput methods for analyzing these assays, as common automatic image analysis tools are unsuitable for identifying these halos in the presence of the inherent biological noise. In this work, we have developed CFQuant—automatic, high-throughput software for the analysis of images from colony luminescence assays. CFQuant overcomes the problems of automatic identification by relying on the luminescence halo's expected shape and provides measurements of several features of the colonies and halos. We examined the performance of CFQuant using one such colony luminescence assay, where we achieved a high correlation (R = 0.85) between the measurements of CFQuant and known protein expression levels. This demonstrates CFQuant's potential as a fast and reliable tool for analysis of colony luminescence assays

Costs of pediatric liver transplantation among commercially insured and Medicaid-insured patients with cholestasis in the US.

Children with rare cholestatic liver diseases, such as Alagille syndrome, progressive familial intrahepatic cholestasis, and biliary atresia typically require liver transplantation (LT). The objective of this analysis was to assess the economic burden of LT on these patients. Health care resource utilization and costs associated with pediatric LT were retrospectively assessed using insurance claims data from the US IBM MarketScan Commercial and Medicaid databases collected between October 2015 and December 2019. Inclusion criteria were as follows: ≥1 procedure code for LT, <18 years old at transplant, and ≥6 months of insurance eligibility at baseline. A cholestatic liver disease population who received LT was selected in the absence of specific diagnosis codes by excluding other severe liver conditions (ie, acute liver failure, malignancy) and by excluding severely decompensated individuals requiring ICU admission before LT. Annualized rates were reported. Over a mean study duration of 1.8 years, 53 commercially insured and 100 Medicaid-insured children received LT, with mean (SD) ages at baseline of 6.9 (6.0) and 5.7 (5.4) years, respectively. During this period, commercially insured and Medicaid-insured patients had annualized means of 65.3 and 52.8 medical visits, respectively. Most were outpatient visits, although the burden of inpatient visits was also high, with mean inpatient stays (inclusive of LT stay) of 37.2 and 31.6 days per year, respectively. Commercially insured and Medicaid-insured patients averaged US$512,124 and$211,863 in medical costs and $26,998 and$15,704 in pharmacy costs, respectively. These costs remained substantial throughout the first year after transplant. Overall, pediatric LT resulted in substantial health care resource utilization and cost burden in both commercially- and Medicaid-insured patients. Novel targeted medications that negate the need for pediatric LT could decrease the associated morbidity and costs

Induction of Innate Immune Response by TLR3 Agonist Protects Mice against SARS-CoV-2 Infection

SARS-CoV-2, a member of the coronavirus family, is the causative agent of the COVID-19 pandemic. Currently, there is still an urgent need in developing an efficient therapeutic intervention. In this study, we aimed at evaluating the therapeutic effect of a single intranasal treatment of the TLR3/MDA5 synthetic agonist Poly(I:C) against a lethal dose of SARS-CoV-2 in K18-hACE2 transgenic mice. We demonstrate here that early Poly(I:C) treatment acts synergistically with SARS-CoV-2 to induce an intense, immediate and transient upregulation of innate immunity-related genes in lungs. This effect is accompanied by viral load reduction, lung and brain cytokine storms prevention and increased levels of macrophages and NK cells, resulting in 83% mice survival, concomitantly with long-term immunization. Thus, priming the lung innate immunity by Poly(I:C) or alike may provide an immediate, efficient and safe protective measure against SARS-CoV-2 infection

Cancer and mortality in relation to traffic-related air pollution among coronary patients: Using an ensemble of exposure estimates to identify high-risk individuals

Background: Moderate correlations were previously observed between individual estimates of traffic-related air pollution (TRAP) produced by different exposure modeling approaches. This induces exposure misclassification for a substantial fraction of subjects.Aim: We used an ensemble of well-established modeling approaches to increase certainty of exposure classification and reevaluated the association with cancers previously linked to TRAP (lung, breast and prostate), other cancers, and all-cause mortality in a cohort of coronary patients.Methods: Patients undergoing percutaneous coronary interventions in a major Israeli medical center from 2004 to 2014 (n = 10,627) were followed for cancer (through 2015) and mortality (through 2017) via national registries. Residential exposure to nitrogen oxides (NOx) a proxy for TRAP was estimated by optimized dispersion model (ODM) and land use regression (LUR) (r(pearson) = 0.50). Mutually exclusive groups of subjects classified as exposed by none of the methods (high-certainty low-exposed), ODM alone, LUR alone, or both methods (high-certainty high-exposed) were created. Associations were examined using Cox regression models.Results: During follow-up, 741 incident cancer cases were diagnosed and 3051 deaths occurred. Using a >= 25 ppb cutoff, compared with high-certainty low exposed, the multivariable-adjusted hazard ratios (95% confidence intervals) for lung, breast and prostate cancer were 1.56 (1.13-2.15) in high-certainty exposed, 1.27 (0.86-1.86) in LUR-exposed alone, and 1.13 (0.77-1.65) in ODM-exposed alone. The association of the former category was strengthened using more extreme NOx cutoffs. A similar pattern, albeit less strong, was observed for mortality, whereas no association was shown for cancers not previously linked to TRAP.Conclusions: Use of an ensemble of TRAP exposure estimates may improve classification, resulting in a stronger association with outcomes

Chronic exposure to traffic-related air pollution and cancer incidence among 10,000 patients undergoing percutaneous coronary interventions: A historical prospective study

Background Exposure to traffic-related air pollution (TRAP) is considered to have a carcinogenic effect. The authors previously reported a nonsignificant association between TRAP and cancer risk in a relatively small cohort of myocardial infarction survivors. This study assessed whether TRAP exposure is associated with subsequent cancer in a large cohort of coronary patients.Methods & results Consecutive patients undergoing percutaneous coronary interventions in a major medical centre in central Israel from 2004 to 2014 were followed for cancer through 2015. Residential levels of nitrogen oxides (NOx) - a proxy for TRAP - were estimated based on a high-resolution national land use regression model. Cox proportional hazards models were constructed to study relationships with cancer. Among 12,784 candidate patients, 9816 had available exposure data and no history of cancer (mean age, 68 years; 77% men). During a median (25th-75th percentiles) follow-up of 7.0 (3.9-9.3) years, 773 incident cases of cancer (8%) were diagnosed. In a multivariable-adjusted model, a 10-ppb increase in mean NOx exposure was associated with hazard ratios (HRs) of 1.07 (95% confidence interval [CI] 1.00-1.15) for all-site cancer and 1.16 (95% CI 1.05-1.28) for cancers previously linked to TRAP (lung, breast, prostate, kidney and bladder). A stronger association was observed for breast cancer (HR=1.43; 95% CI 1.12-1.83). Associations were slightly strengthened after limiting the cohort to patients with more precise exposure assessment.Conclusion Coronary patients exposed to TRAP are at increased risk of several types of cancer, particularly lung, prostate and breast. As these cancers are amenable to prevention strategies, identifying highly exposed patients may provide an opportunity to improve clinical care