Efficient local strategies for vaccination and network attack

We study how a fraction of a population should be vaccinated to most efficiently top epidemics. We argue that only local information (about the neighborhood of specific vertices) is usable in practice, and hence we consider only local vaccination strategies. The efficiency of the vaccination strategies is investigated with both static and dynamical measures. Among other things we find that the most efficient strategy for many real-world situations is to iteratively vaccinate the neighbor of the previous vaccinee that has most links out of the neighborhood

The Primary Pretenders

We call a composite number q such that there exists a positive integer b with b^p == b (mod q) a prime pretender to base b. The least prime pretender to base b is the primary pretender q_b. It is shown that there are only 132 distinct primary pretenders, and that q_b is a periodic function of b whose period is the 122-digit number 19568584333460072587245340037736278982017213829337604336734362- 294738647777395483196097971852999259921329236506842360439300.Comment: 7 page

Outcome of renal grafts after simultaneous kidney/ pancreas transplantation

Nineteen patients with endstage renal failure due to Type 1 (insulin-dependent) diabetes mellitus received simultaneous pancreas/kidney transplants using bladder drainage technique. Another group of 25 Type 1 diabetic patients received pancreas/kidney transplants by the duct occlusion technique. We observed a higher incidence of rejection episodes in the patients of the bladder drainage group than those in the duct occlusion group, 14 of 19 patients (74%) vs 7 of 25 (28%) respectively. Anti CD3 antibodies (Orthoclone, OKT3) as a part of induction treatment was used more often in the bladder drainage group (58%) than in the control group (20%)

Kinetics of antibody response to Coxiella burnetii infection (Q fever): Estimation of the seroresponse onset from antibody levels

AbstractBackgroundFrom 2007 to 2009, the Netherlands experienced a major Q fever epidemic. Long-term serological follow-up of acute Q fever patients enabled the investigation of longitudinal antibody responses and estimating the onset of the seroresponse in individual patients.MethodsAll available IgG and IgM phase I and II antibody measurements determined by immunofluorescence assay at month 3, 6, 12, and 48 from 2321 acute Q fever patients were retrospectively analyzed. Characteristic features of the antibody response were calculated. To model the seroresponse onset, serological data from patients diagnosed with a positive C. burnetii PCR test (n=364), and therefore with a known time of infection, were used as reference.ResultsIn 9083 IgG samples and 3260 IgM samples large heterogeneity in shape and magnitude of antibody responses was observed. Phase II reached higher levels than phase I, and IgG antibodies were more persistent than IgM. The estimated seroresponse latency allowed for determining the time since start of the seroresponse from the concentrations of the different antibodies against C. burnetii.ConclusionsThe extraordinary large serological dataset provides new insight into the kinetics of the immunoglobulins against C. burnetii antigens. This knowledge is useful for seroprevalence studies and helps to better understand infection dynamics

The Longest Run Subsequence Problem

Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing the scaffolding phase, in which contigs need to be linked and ordered to obtain larger pseudo-chromosomes, by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. In particular, they can solve realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time. Our source code and all data used in the experiments are freely available

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding

Cardiac Arrest Disrupts Caspase-1 and Patterns of Inflammatory Mediators Differently in Skin and Muscle Following Localized Tissue Injury in Rats: Insights from Data-Driven Modeling

Background: Trauma often co-occurs with cardiac arrest and hemorrhagic shock. Skin and muscle injuries often lead to significant inflammation in the affected tissue. The primary mechanism by which inflammation is initiated, sustained, and terminated is cytokine-mediated immune signaling, but this signaling can be altered by cardiac arrest. The complexity and context sensitivity of immune signaling in general has stymied a clear understanding of these signaling dynamics. Methodology/Principal findings: We hypothesized that advanced numerical and biological function analysis methods would help elucidate the inflammatory response to skin and muscle wounds in rats, both with and without concomitant shock. Based on multiplexed analysis of inflammatory mediators, we discerned a differential interleukin (IL)-1α and IL-18 signature in skin vs. muscle, which was suggestive of inflammasome activation in the skin. Immunoblotting revealed caspase-1 activation in skin but not muscle. Notably, IL-1α and IL-18, along with caspase-1, were greatly elevated in the skin following cardiac arrest, consistent with differential inflammasome activation. Conclusions/Significance: Tissue-specific activation of Caspase-1 and the NLRP3 inflammasome appear to be key factors in determining the type and severity of the inflammatory response to tissue injury, especially in the presence of severe shock, as suggested via data-driven modeling