Tangled Paths: A Random Graph Model from Mallows Permutations

We introduce the random graph $\mathcal{P}(n,q)$ which results from taking the union of two paths of length $n\geq 1$, where the vertices of one of the paths have been relabelled according to a Mallows permutation with real parameter $0<q(n)\leq 1$. This random graph model, the tangled path, goes through an evolution: if $q$ is close to $0$ the graph bears resemblance to a path and as $q$ tends to $1$ it becomes an expander. In an effort to understand the evolution of $\mathcal{P}(n,q)$ we determine the treewidth and cutwidth of $\mathcal{P}(n,q)$ up to log factors for all $q$. We also show that the property of having a separator of size one has a sharp threshold. In addition, we prove bounds on the diameter, and vertex isoperimetric number for specific values of $q$.Comment: 40 pages, 7 figure

The complexity of finding optimal subgraphs to represent spatial correlation

Understanding spatial correlation is vital in many fields including epidemiology and social science. Lee, Meeks and Pettersson (Stat. Comput. 2021) recently demonstrated that improved inference for areal unit count data can be achieved by carrying out modifications to a graph representing spatial correlations; specifically, they delete edges of the planar graph derived from border-sharing between geographic regions in order to maximise a specific objective function. In this paper we address the computational complexity of the associated graph optimisation problem. We demonstrate that this problem cannot be solved in polynomial time unless P = NP; we further show intractability for two simpler variants of the problem. We follow these results with two parameterised algorithms that exactly solve the problem in polynomial time in restricted settings. The first of these utilises dynamic programming on a tree decomposition, and runs in polynomial time if both the treewidth and maximum degree are bounded. The second algorithm is restricted to problem instances with maximum degree three, as may arise from triangulations of planar surfaces, but is an FPT algorithm when the maximum number of edges that can be removed is taken as the parameter.Comment: Numerous new results adde

FOOD INSECURITY AMONG LOW-INCOME FAMILIES AS AN ECONOMIC SOCIAL DETERMINANT OF HEALTH IN DURHAM COUNTY, NORTH CAROLINA

Economic stability in Durham County, North Carolina, includes household food insecurity. Food insecurity is a lack of consistent access to healthy, affordable foods. County initiatives to increase food security exist, but many low-income families still suffer from food insecurity. Food insecurity is associated with various short- and long-term health effects, including poor academic performance, malnutrition in children, and increased susceptibility to obesity, diabetes, and heart disease. To alleviate this, an evidence-based ridesharing program that transports County residents to and from participating grocery stores at a reduced cost is proposed to reduce transportation barriers for low-income families. The ridesharing proposal will be designed, evaluated, and implemented through partnerships with various educational, community, and nonprofit stakeholders.Master of Public Healt

Molecular analyses of fecal bacteria and hydrodynamic modeling for microbial risk assessment of a drinking water source

Safe water is a global concern, and methods to accurately monitor quality of water are vital. To assess the risks related to bacterial pathogen load in Lake Vomb that provides drinking water to the southern part of Sweden, this study combined molecular analyses of enterobacteria and bacterial pathogens in water using quantitiative real-time PCR with hydrodynamic modeling and quantitative microbial risk assessment (QMRA). A real-time PCR assay to detect enterobacteria was set up by primers targeting ssrA. Between February 2015 and May 2016, presence of ssrA gene copies as well as Campylobacter spp., Salmonella spp., and EHEC O157 DNA was analyzed by real-time PCR at several locations in the catchment of Lake Vomb and its tributaries Bjorkaan, Borstbacken, and Torpsbacken. Bjorkaan had the highest detected concentrations of the ssrA gene and, according to the results of hydrodynamic modeling, contributed most to the contamination of the water intake in the lake. None of the water samples were positive for genes encoding EHEC O157 and Campylobacter spp., while invA (Salmonella spp.) was present in 11 samples. The QMRA showed that the suggested acceptable risk level (daily probability of infection &lt;2.7 x 10-7) is achieved with a 95% probability, if the Salmonella concentrations in the water intake are below 101 bacteria/100 mL. If a UV-disinfection step is installed, the Salmonella concentration at the water intake should not exceed 106 bacteria/100 mL

The Third Workshop on Population of the RDBES Data Model (WKRDB-POP3)

The aims of this workshop were to explain the data model developed for the commercial fisheries Regional Database and Estimation System (RDBES), assist in populating it with real data for the second test data call for the RDBES, and encourage participants to take part in ongoing testing of the RDBES data submission system. This report documents the progress that participants have done to prepare their institutes for future use of the RDBES system. Some issues with data conversion have been identified and are documented in this report. None of the identified issues are thought to be serious impediments to moving forward with the RDBES development according to the roadmap decided by the Steering Committee of the Regional Fisheries Database in 2020. The RDBES Core Group (the group of people developing the RDBES data model) and ICES Data Centre will look at the results of this workshop and either respond to individual questions or adapt the data model and documentation as required. The workshop concluded and reported before the deadline of the test data call. For a complete test of the data model, all participants were encouraged to complete the data call. A report on the degree of completion of the data call may be expected from WGRDBESGOV which convenes after the data call deadline

Regulation of cellular contractile force, shape and migration of fibroblasts by oncogenes and Histone deacetylase 6

The capacity of cells to adhere to, exert forces upon and migrate through their surrounding environment governs tissue regeneration and cancer metastasis. The role of the physical contractile forces that cells exert in this process, and the underlying molecular mechanisms are not fully understood. We, therefore, aimed to clarify if the extracellular forces that cells exert on their environment and/or the intracellular forces that deform the cell nucleus, and the link between these forces, are defective in transformed and invasive fibroblasts, and to indicate the underlying molecular mechanism of control. Confocal, Epifluorescence and Traction force microscopy, followed by computational analysis, showed an increased maximum contractile force that cells apply on their environment and a decreased intracellular force on the cell nucleus in the invasive fibroblasts, as compared to normal control cells. Loss of HDAC6 activity by tubacin-treatment and siRNA-mediated HDAC6 knockdown also reversed the reduced size and more circular shape and defective migration of the transformed and invasive cells to normal. However, only tubacin-mediated, and not siRNA knockdown reversed the increased force of the invasive cells on their surrounding environment to normal, with no effects on nuclear forces. We observed that the forces on the environment and the nucleus were weakly positively correlated, with the exception of HDAC6 siRNA-treated cells, in which the correlation was weakly negative. The transformed and invasive fibroblasts showed an increased number and smaller cell-matrix adhesions than control, and neither tubacin-treatment, nor HDAC6 knockdown reversed this phenotype to normal, but instead increased it further. This highlights the possibility that the control of contractile force requires separate functions of HDAC6, than the control of cell adhesions, spreading and shape. These data are consistent with the possibility that defective force-transduction from the extracellular environment to the nucleus contributes to metastasis, via a mechanism that depends upon HDAC6. To our knowledge, our findings present the first correlation between the cellular forces that deforms the surrounding environment and the nucleus in fibroblasts, and it expands our understanding of how cells generate contractile forces that contribute to cell invasion and metastasisis

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.</p

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.</p

Care in subsequent pregnancies following stillbirth: An international survey of parents

Objective: To assess the frequency of additional care, and parents' perceptions of quality, respectful care in pregnancies subsequent to stillbirth. Design: Multi-language web-based survey. Setting: International. Population: 2,716 parents, from 40 high- and middle-income countries. Methods: Data were obtained from a broader survey of parentsâ experiences of stillbirth. Data were analyzed using descriptive statistics and stratified by geographical region. Subgroup analyses explored variation in additional care by gestational age at index stillbirth. Main outcome measures: Frequency of additional care, and perceptions of quality, respectful care. Results: The majority (66%) of parents conceived their subsequent pregnancy within one year of stillbirth. Additional antenatal care visits and ultrasound scans were provided for 67% and 70% of all parents, respectively, although there was wide variation across geographical regions. Care addressing psychosocial needs was less frequently provided, such as visits to a bereavement counsellor (10%) and access to named care provider's phone number (27%). Compared to parents whose stillbirth occurred at 29 weeks' gestation or less, parents whose stillbirth occurred at 30 weeksâ gestation or greater were more likely to receive various forms of additional care, particularly the option for early delivery after 37 weeks. Around half (47-63%) of all parents felt that elements of quality, respectful care were consistently applied, such as spending enough time with parents and involving parents in decision-making. Conclusions: Care in pregnancies subsequent to stillbirth appears inconsistent. Greater attention is required to providing thoughtful, empathic, and collaborative care in all pregnancies following stillbirth. Training for health professionals is needed

Habitat properties are key drivers of Borrelia burgdorferi (s.l.) prevalence in Ixodes ricinus populations of deciduous forest fragments

Background: The tick Ixodes ricinus has considerable impact on the health of humans and other terrestrial animals because it transmits several tick-borne pathogens (TBPs) such as B. burgdorferi (sensu lato), which causes Lyme borreliosis (LB). Small forest patches of agricultural landscapes provide many ecosystem services and also the disservice of LB risk. Biotic interactions and environmental filtering shape tick host communities distinctively between specific regions of Europe, which makes evaluating the dilution effect hypothesis and its influence across various scales challenging. Latitude, macroclimate, landscape and habitat properties drive both hosts and ticks and are comparable metrics across Europe. Therefore, we instead assess these environmental drivers as indicators and determine their respective roles for the prevalence of B. burgdorferi in I. ricinus. Methods: We sampled I. ricinus and measured environmental properties of macroclimate, landscape and habitat quality of forest patches in agricultural landscapes along a European macroclimatic gradient. We used linear mixed models to determine significant drivers and their relative importance for nymphal and adult B. burgdorferi prevalence. We suggest a new prevalence index, which is pool-size independent. Results: During summer months, our prevalence index varied between 0 and 0.4 per forest patch, indicating a low to moderate disservice. Habitat properties exerted a fourfold larger influence on B. burgdorferi prevalence than macroclimate and landscape properties combined. Increasingly available ecotone habitat of focal forest patches diluted and edge density at landscape scale amplified B. burgdorferi prevalence. Indicators of habitat attractiveness for tick hosts (food resources and shelter) were the most important predictors within habitat patches. More diverse and abundant macro- and microhabitat had a diluting effect, as it presumably diversifies the niches for tick-hosts and decreases the probability of contact between ticks and their hosts and hence the transmission likelihood.[br/] Conclusions: Diluting effects of more diverse habitat patches would pose another reason to maintain or restore high biodiversity in forest patches of rural landscapes. We suggest classifying habitat patches by their regulating services as dilution and amplification habitat, which predominantly either decrease or increase B. burgdorferi prevalence at local and landscape scale and hence LB risk. Particular emphasis on promoting LB-diluting properties should be put on the management of those habitats that are frequently used by humans. In the light of these findings, climate change may be of little concern for LB risk at local scales, but this should be evaluated further