SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding

Scaffolding is an important subproblem in "de novo" genome assembly in which mate pair data are used to construct a linear sequence of contigs separated by gaps. Here we present SLIQ, a set of simple linear inequalities derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a preprocessing step for any scaffolding algorithm. We tested the SLIQ inequalities on five real data sets ranging in complexity from simple bacterial genomes to complex mammalian genomes and compared the results to the majority voting procedure used by many other scaffolding algorithms. SLIQ predicted the relative positions and orientations of the contigs with high accuracy in all cases and gave more accurate position predictions than majority voting for complex genomes, in particular the human genome. Finally, we present a simple scaffolding algorithm that produces linear scaffolds given a contig digraph. We show that our algorithm is very efficient compared to other scaffolding algorithms while maintaining high accuracy in predicting both contig positions and orientations for real data sets.Comment: 16 pages, 6 figures, 7 table

Accounting for the effect of heterogeneous plastic deformation on the formability of aluminium and steel sheets

Forming Limit Curves characterise ‘mean’ failure strains of sheet metals. Safety levels from the curves define the deterministic upper limit of the processing and part design window, which can be small for high strength, low formability materials. Effects of heterogeneity of plastic deformation, widely accepted to occur on the microscale, are neglected. Marciniak tests were carried out on aluminium alloys (AA6111-T4, NG5754-O), dual-phase steel (DP600) and mild steel (MS3). Digital image correlation was used to measure the effect of heterogeneity on failure. Heterogeneity, based on strain variance was modelled with the 2-component Gaussian Mixture Model and a framework was proposed to 1) identify the onset of necking and to 2) re-define formability as a probability to failure. The result were ‘forming maps’ in major-minor strain space of contours of constant probability (from probability, P=0 to P=1), which showed how failure risk increased with major strain. The contour bands indicated the unique degree of heterogeneity in each material. NG5754-O had the greatest width (0.07 strain) in plane strain and MS3 the lowest (0.03 strain). This novel characterisation will allow engineers to balance a desired forming window for a component design with the risk to failure of the material

Microstructural evolution, recovery and recrystallization kinetics of isothermally annealed ultra low carbon steel

The recovery and recrystallization kinetics of 80%cold rolled ultra low carbon steel are investigated during isothermally annealing for temperature ranges 350–640 °C as a function of different annealing time. The recovery is assessed by magnetic coercivity (Hc),while the recrystallization is determined by mechanical hardness.At low temperature (350 to 520 °C) annealing, recovery dominates for long time (∼12 000 s),while the annealing at 550 °C/ 900s and 580 °C/ 300s causes the recrystallized nuclei formation . The recovery kinetics is introduced by differential rate equation, explaining the reduction in coercivity with the recovery progress and the variation of an activation energy from41–113 kJmol−1. The recrystallization kinetics is found faster at high annealing temperature 640 °C than 550 and 580 °C based on hardness measurement, justifying by apparent activation energy within 114–190 kJ/mol. Furthermore, the recovery and recrystallization rate increase with different annealing time, consistent to the change of microstructures and grain boundary characteristics evaluated by the orientation imaging microscopy (OIM) of electron backscattered diffraction (EBSD)

Giant Magnetoimpedance Sensor for Structural Integrity Assessment of Engineering Components

Investigation is focused on the development of sensor based on giant magnetoimpedance (GMI) effect using soft magnetic Co66Fe2Si13B15Cr4 amorphous wire as sensing (core) element. The GMI property of the sensing element was utilized for fabrication of the sensor which is sensitive to the minute variation of the local magnetic field. The sensor output signal is calibrated with respect to external applied magnetic field and the sensitivity is found to be 56.11 mV/µT. The sensor shows a good linear response and its repeatability and reproducibility are observed to be satisfactory. The sensor is very much useful for detection of the localized magnetic field of service exposed engineering components within an external magnetic field using GMI sensor, and more specifically, to develop a GMI sensor for efficient monitoring of structural integrity of engineering components. The conventional non-destructive techniques like ultrasonic, eddy current, magnetic particle inspection are very useful to identify the defects or cracks. However, these methods are unsuitable for monitoring structural degradation. Since most of the structural components used in the industry are of ferromagnetic steel, the microstructural properties of the components due to their long service period influence the magnetic and mechanical properties. Therefore, the developed sensor could be used to detect the local magnetic field of the aging structure which changes with the microstructure of the component and thereby, assessing the integrity of the components

Development of GMI Based Sensing Device for Identification of Magnetic Phases in Steel

A giant magnetoimpedance (GMI) sensor based on CoFeSiBCr soft magnetic amorphous microwire of diameter 100 µm as a sensing element has been developed and the performances of the GMI sensor are carefully studied. The sensor measures the phase shift of the modulated signal in terms of voltage using balanced modulator/demodulator topology which has been calibrated in terms of localized magnetic field. The sensor shows a good linear response with the magnetic field. It has been tested at different conditions and repeatable of data has been observed. The sensitivity of the sensor has been observed to be 0.12 mV/Am-1. The sensor can be used to identify various magnetic phases in semi finished steel products. For an example, in duplex stainless steel where the material has austenite and ferrite components, the developed sensor can be utilized for the evaluation of volume fraction of each phase. Similarly, in 304 SS which undergoes stress induced martensite transformation can also be evaluated using the developed sensor

Prevalence of chronic kidney disease in South Asia: a systematic review

Background: Chronic kidney disease (CKD) is becoming a major public health problem around the world. But the prevalence has not been reported in South Asian region as a whole. This study aimed to systematically review the existing data from population based studies in this region to bridge this gap. Methods Articles published and reported prevalence of CKD according to K/DOQI practice guideline in eight South Asian countries between December 1955 and April 2017 were searched, screened and evaluated from seven electronic databases using the PRISMA checklist. CKD was defined as creatinine clearance (CrCl) or GFR less than 60 ml/min/1.73 m2. Results Sixteen population-based studies were found from four South Asian countries (India, Bangladesh, Pakistan and Nepal) that used eGFR to measure CKD. No study was available from Sri Lanka, Maldives, Bhutan and Afghanistan. Number of participants ranged from 301 in Pakistan to 12,271 in India. Majority of the studies focused solely on urban population. Different studies used different equations for measuring eGFR. The prevalence of CKD ranged from 10.6% in Nepal to 23.3% in Pakistan using MDRD equation. This prevalence was higher among older age group people. Equal number of studies reported high prevalence among male and female each. Conclusions This systematic review reported high prevalence of CKD in South Asian countries. The findings of this study will help pertinent stakeholders to prepare suitable policy and effective public health intervention in order to reduce the burden of this deadly disease in the most densely populated share of the globe

Mapping 123 million neonatal, infant and child deaths between 2000 and 2017

Since 2000, many countries have achieved considerable success in improving child survival, but localized progress remains unclear. To inform efforts towards United Nations Sustainable Development Goal 3.2—to end preventable child deaths by 2030—we need consistently estimated data at the subnational level regarding child mortality rates and trends. Here we quantified, for the period 2000–2017, the subnational variation in mortality rates and number of deaths of neonates, infants and children under 5 years of age within 99 low- and middle-income countries using a geostatistical survival model. We estimated that 32% of children under 5 in these countries lived in districts that had attained rates of 25 or fewer child deaths per 1,000 live births by 2017, and that 58% of child deaths between 2000 and 2017 in these countries could have been averted in the absence of geographical inequality. This study enables the identification of high-mortality clusters, patterns of progress and geographical inequalities to inform appropriate investments and implementations that will help to improve the health of all populations

Mapping child growth failure across low- and middle-income countries

Child growth failure (CGF), manifested as stunting, wasting, and underweight, is associated with high 5 mortality and increased risks of cognitive, physical, and metabolic impairments. Children in low- and middle-income countries (LMICs) face the highest levels of CGF globally. Here we illustrate national and subnational variation of under-5 CGF indicators across LMICs, providing 2000–2017 annual estimates mapped at a high spatial resolution and aggregated to policy-relevant administrative units and national levels. Despite remarkable declines over the study period, many LMICs remain far from the World Health 10 Organization’s ambitious Global Nutrition Targets to reduce stunting by 40% and wasting to less than 5% by 2025. Large disparities in prevalence and rates of progress exist across regions, countries, and within countries; our maps identify areas where high prevalence persists even within nations otherwise succeeding in reducing overall CGF prevalence. By highlighting where subnational disparities exist and the highest-need populations reside, these geospatial estimates can support policy-makers in planning locally 15 tailored interventions and efficient directing of resources to accelerate progress in reducing CGF and its health implications

Mapping disparities in education across low- and middle-income countries

Analyses of the proportions of individuals who have completed key levels of schooling across all low- and middle-income countries from 2000 to 2017 reveal inequalities across countries as well as within populations. Educational attainment is an important social determinant of maternal, newborn, and child health(1-3). As a tool for promoting gender equity, it has gained increasing traction in popular media, international aid strategies, and global agenda-setting(4-6). The global health agenda is increasingly focused on evidence of precision public health, which illustrates the subnational distribution of disease and illness(7,8); however, an agenda focused on future equity must integrate comparable evidence on the distribution of social determinants of health(9-11). Here we expand on the available precision SDG evidence by estimating the subnational distribution of educational attainment, including the proportions of individuals who have completed key levels of schooling, across all low- and middle-income countries from 2000 to 2017. Previous analyses have focused on geographical disparities in average attainment across Africa or for specific countries, but-to our knowledge-no analysis has examined the subnational proportions of individuals who completed specific levels of education across all low- and middle-income countries(12-14). By geolocating subnational data for more than 184 million person-years across 528 data sources, we precisely identify inequalities across geography as well as within populations.Peer reviewe

Spatial, temporal, and demographic patterns in prevalence of smoking tobacco use and attributable disease burden in 204 countries and territories, 1990-2019 : a systematic analysis from the Global Burden of Disease Study 2019

Background Ending the global tobacco epidemic is a defining challenge in global health. Timely and comprehensive estimates of the prevalence of smoking tobacco use and attributable disease burden are needed to guide tobacco control efforts nationally and globally. Methods We estimated the prevalence of smoking tobacco use and attributable disease burden for 204 countries and territories, by age and sex, from 1990 to 2019 as part of the Global Burden of Diseases, Injuries, and Risk Factors Study. We modelled multiple smoking-related indicators from 3625 nationally representative surveys. We completed systematic reviews and did Bayesian meta-regressions for 36 causally linked health outcomes to estimate non-linear dose-response risk curves for current and former smokers. We used a direct estimation approach to estimate attributable burden, providing more comprehensive estimates of the health effects of smoking than previously available. Findings Globally in 2019, 1.14 billion (95% uncertainty interval 1.13-1.16) individuals were current smokers, who consumed 7.41 trillion (7.11-7.74) cigarette-equivalents of tobacco in 2019. Although prevalence of smoking had decreased significantly since 1990 among both males (27.5% [26. 5-28.5] reduction) and females (37.7% [35.4-39.9] reduction) aged 15 years and older, population growth has led to a significant increase in the total number of smokers from 0.99 billion (0.98-1.00) in 1990. Globally in 2019, smoking tobacco use accounted for 7.69 million (7.16-8.20) deaths and 200 million (185-214) disability-adjusted life-years, and was the leading risk factor for death among males (20.2% [19.3-21.1] of male deaths). 6.68 million [86.9%] of 7.69 million deaths attributable to smoking tobacco use were among current smokers. Interpretation In the absence of intervention, the annual toll of 7.69 million deaths and 200 million disability-adjusted life-years attributable to smoking will increase over the coming decades. Substantial progress in reducing the prevalence of smoking tobacco use has been observed in countries from all regions and at all stages of development, but a large implementation gap remains for tobacco control. Countries have a dear and urgent opportunity to pass strong, evidence-based policies to accelerate reductions in the prevalence of smoking and reap massive health benefits for their citizens. Copyright (C) 2021 The Author(s). Published by Elsevier Ltd.Peer reviewe