High—throughput and automated screening for COVID-19

The COVID-19 pandemic has become a global challenge for the healthcare systems of many countries with 6 million people having lost their lives and 530 million more having tested positive for the virus. Robust testing and a comprehensive track and trace process for positive patients are essential for effective pandemic control, leading to high demand for diagnostic testing. In order to comply with demand and increase testing capacity worldwide, automated workflows have come into prominence as they enable high-throughput screening, faster processing, exclusion of human error, repeatability, reproducibility and diagnostic precision. The gold standard for COVID-19 testing so far has been RT-qPCR, however, different SARS-CoV-2 testing methods have been developed to be combined with high throughput testing to improve diagnosis. Case studies in China, Spain and the United Kingdom have been reviewed and automation has been proven to be promising for mass testing. Free and Open Source scientific and medical Hardware (FOSH) plays a vital role in this matter but there are some challenges to be overcome before automation can be fully implemented. This review discusses the importance of automated high-throughput testing, the different equipment available, the bottlenecks of its implementation and key selected case studies that due to their high effectiveness are already in use in hospitals and research centres

Gross-Neveu Models, Nonlinear Dirac Equations, Surfaces and Strings

Recent studies of the thermodynamic phase diagrams of the Gross-Neveu model (GN2), and its chiral cousin, the NJL2 model, have shown that there are phases with inhomogeneous crystalline condensates. These (static) condensates can be found analytically because the relevant Hartree-Fock and gap equations can be reduced to the nonlinear Schr\"odinger equation, whose deformations are governed by the mKdV and AKNS integrable hierarchies, respectively. Recently, Thies et al have shown that time-dependent Hartree-Fock solutions describing baryon scattering in the massless GN2 model satisfy the Sinh-Gordon equation, and can be mapped directly to classical string solutions in AdS3. Here we propose a geometric perspective for this result, based on the generalized Weierstrass spinor representation for the embedding of 2d surfaces into 3d spaces, which explains why these well-known integrable systems underlie these various Gross-Neveu gap equations, and why there should be a connection to classical string theory solutions. This geometric viewpoint may be useful for higher dimensional models, where the relevant integrable hierarchies include the Davey-Stewartson and Novikov-Veselov systems.Comment: 27 pages, 1 figur

High prevalence of potential biases threatens the interpretation of trials in patients with chronic disease

BACKGROUND: The complexity of chronic diseases is a challenge for investigators conducting randomized trials. The causes for this include the often difficult control for confounding, the selection of outcomes from many potentially important outcomes, the risk of missing data with long follow-up and the detection of heterogeneity of treatment effects. Our aim was to assess such aspects of trial design and analysis for four prevalent chronic diseases. METHODS: We included 161 randomized trials on drug and non-drug treatments for chronic obstructive pulmonary disease, type 2 diabetes mellitus, stroke and heart failure, which were included in current Cochrane reviews. We assessed whether these trials defined a single outcome or several primary outcomes, statistically compared baseline characteristics to assess comparability of treatment groups, reported on between-group comparisons, and we also assessed how they handled missing data and whether appropriate methods for subgroups effects were used. RESULTS: We found that only 21% of all chronic disease trials had a single primary outcome, whereas 33% reported one or more primary outcomes. Two of the fifty-one trials that tested for statistical significance of baseline characteristics adjusted the comparison for a characteristic that was significantly different. Of the 161 trials, 10% reported a within-group comparison only; 17% (n = 28) of trials reported how missing data were handled (50% (n = 14) carried forward last values, 27% (n = 8) performed a complete case analysis, 13% (n = 4) used a fixed value imputation and 10% (n = 3) used more advanced methods); and 27% of trials performed a subgroup analysis but only 23% of them (n = 10) reported an interaction test. Drug trials, trials published after wide adoption of the CONSORT (CONsolidated Standards of Reporting Trials) statement (2001 or later) and trials in journals with higher impact factors were more likely to report on some of these aspects of trial design and analysis. CONCLUSION: Our survey showed that an alarmingly large proportion of chronic disease trials do not define a primary outcome, do not use appropriate methods for subgroup analyses, or use naïve methods to handle missing data, if at all. As a consequence, biases are likely to be introduced in many trials on widely prescribed treatments for patients with chronic disease

Mineralogical evolution of cement pastes at early ages based on thermogravimetric analysis (TGA)

[EN] Ordinary thermogravimetric analysis (TG) and high-resolution TG tests were carried out on three different Portland cement pastes to study the phases present during the first day of hydration. Tests were run at 1, 6, 12 and 24 h of hydration, in order to determine the phases at these ages. High-resolution TG tests were used to separate decompositions presented in the 100¿200 C interval. The non-evaporable water determined by TG was used to determine hydration degree for the different ages. The effect of particle size distribution (PSD) on mineralogical evolution was established, as well as the addition of calcite as mineralogical filler. Finer PSD and calcite addition accelerate the hydration process, increasing the hydration degree on the first day of eaction between water and cement. According to high-resolution TG results, it was demonstrated that ettringite was the only decomposed phase in the 100¿200 C interval during the first 6 h of hydration for all studied cements. C-S-H phase starts to appear in all cements after 12 h of hydration.Funding was provided by Colciencias (Grant No. Convocatoria 567-2012).Gaviria, X.; Borrachero Rosado, MV.; Paya Bernabeu, JJ.; Monzó Balbuena, JM.; Tobón, J. (2018). Mineralogical evolution of cement pastes at early ages based on thermogravimetric analysis (TGA). Journal of Thermal Analysis and Calorimetry. 132(1):39-46. https://doi.org/10.1007/s10973-017-6905-0S39461321Benboudjema F, Meftah JM, Torernti F. Interaction between drying, shrinkage, creep and cracking phenomena in concrete. Eng Struct. 2005;27:239–50.Holt E. Contribution of mixture design to chemical and autogenous shrinkage of concrete at early ages. Cem Concr Res. 2005;35:464–72.Darquennes A, Staquet S, Delplancke-Ogletree MP, Espion B. Effect of autogenous deformation on the cracking risk of slag cement concretes. Cem Concr Compos. 2011;33:368–79.Slowik V, Schmidt M, Fritzsch R. Capillary pressure in fresh cement-based materials and identification of the air entry value. Cem Concr Compos. 2008;30(7):557–65.Evju C, Hansen S. Expansive properties of ettringite in a mixture of calcium aluminate cement, Portland cement and ß-calcium sulfate hemihydrates. Cem Concr Res. 2001;31:257–61.Bentz DP, Jensen OM, Hansen KK. Olesen, Stang, H. Haecker, C.J. Influence of cement particle-size distribution on early age autogenous strain and stresses in cement-based materials. J Am Ceram Soc. 2001;84(1):129–35.Barcelo L, Moranville M, Clavaud B. Autogenous shrinkage of concrete: a balance between autogenous swelling and self-desiccation. Cem Concr Res. 2005;35(1):177–83.Bouasker M, Mounanga P, Turcry P, Loukili A, Khelidj A. Chemical shrinkage of cement pastes and mortars at very early age: effect of limestone filler and granular inclusions. Cem Concr Compos. 2008;30(1):13–22.Bentz DP. A review of early-age properties of cement-based materials. Cem Concr Res. 2008;38(2):196–204.Ozawa T. Controlled rate thermogravimetry. New usefulness of controlled rate thermogravimetry revealed by decomposition of polyimide. J Therm Anal Calorim. 2000;59:375–84.Ramachandran VS, Paroli RM, Beaudoin JJ, Delgado AH. Thermal analysis of construction materials. Building materials series. New York: Noyes Publications; 2003.Zanier A. High-resolution TG for the characterization of diesel fuel additives. J Therm Anal Calorim. 2001;64:377–84.Tobón JI, Payá J, Borrachero MV, Restrepo OJ. Mineralogical evolution of Portland cement blended with silica nanoparticles and its effect on mechanical strength. Constr Build Mater. 2012;36:736–42.Singh M, Waghmare S, Kumar V. Characterization of lime plasters used in 16th century Mughal Monument. J Archeol Sci. 2014;42:430–4.Majchrzak-Kuçeba I. Thermogravimetry applied to characterization of fly ash-based MCM-41 mesoporous materials. J Therm Anal Calorim. 2012;107:911–21.Silva ACM, Gálico DA, Guerra RB, Legendre AO, Rinaldo D, Galhiane MS, Bannach G. Study of some volatile compounds evolved from the thermal decomposition of atenolol. J Therm Anal Calorim. 2014;115:2517–20.Rios-Fachal M, Gracia-Fernández C, López-Beceiro J, Gómez-Barreiro S, Tarrío-Saavedra J, Ponton A, Artiaga R. Effect of nanotubes on the thermal stability of polystyrene. J Therm Anal Calorim. 2013;113:481–7.Yamarte L, Paxman D, Begum S, Sarkar P, Chambers A. TG measurement of reactivity of candidate oxygen carrier materials. J Therm Anal Calorim. 2014;116:1301–7.Borrachero MV, Payá J, Bonilla M, Monzó J. The use of thermogravimetric analysis technique for the characterization of construction materials. The gypsum case. J Therm Anal Calorim. 2008;91(2):503–9.Tobón JI, Payá J, Borrachero MV, Soriano L, Restrepo OJ. Determination of the optimum parameters in the high resolution thermogravimetric analysis (HRTG) for cementitious materials. J Therm Anal Calorim. 2012;107:233–9.Kuzielova E, Žemlička M, Másilko, J, Palou, M.T. Effect of additives on the performance of Dyckerhoff cement, Class G, submitted to simulated hydrothermal curing. J Therm Anal Calorim. Accepted 29 Oct 2017Genc M, Genc ZK. Microencapsulated myristic acid–fly ash with TiO2 shell as a novel phase change material for building application. J Therm Anal Calorim. Accepted 24 Oct 2017.Singh M, Kumar SV, Waghmare SA. The composition and technology of the 3–4th century CE decorative earthen plaster of Pithalkhora caves, India. J Archeol Sci. 2016;7:224–37.Liu L, Liu Q, Cao Y, Pan WP. The isothermal studies of char-CO2 gasification using the high-pressure thermo-gravimetric method. J Therm Anal Calorim. 2015;120:1877–82.Majchrzak-Kuce I, Bukalak-Gaik D. Regeneration performance of metal–organic frameworks TG-vacuum tests. J Therm Anal Calorim. 2016;125:1461–6.Ion RM, Radovici C, Fierascu RC, Fierascu I. Thermal and mineralogical investigations of iron archaeological Materials. J Therm Anal Calorim. 2015;121:1247–53.Rupasinghe M, San Nicolas R, Mendis P, Sofi M, Ngo T. Investigation of strength and hydration characteristics in nano-silica incorporated cement paste. Cem Concr Compos. 2017;80:17–30.Esteves PL. On the hydration of water-entrained cement–silica systems: combined SEM, XRD and thermal analysis in cement pastes. Thermochim Acta. 2011;518:27–35.Riesen R. Adjustment of heating rate for maximum resolution in TG and TMA (MaxRes). J Therm Anal. 1998;53:365–74.Lim S, Mondal P. Micro- and nano-scale characterization to study the thermal degradation of cement-based materials. Mater Charact. 2014;92:15–25.Gill PS, Sauerbrunn SR, Crowe BS. High resolution thermogravimetry. J Therm Anal. 1992;38:255–66.Mounanga P, Khelidj A, Loukili A, Baroghel-Bouny V. Predicting Ca(OH)2 content and chemical shrinkage of hydrating cement pastes using analytical approach. Cem Concr Res. 2004;34:255–65.Zeng Q, Li K, Fen-chong T, Dangla P. Determination of cement hydration and pozzolanic reaction extents for fly-ash cement pastes. Constr Build Mater. 2012;27:560–9.Parrott LP, Geiker M, Gutteridge WA, Killoh D. Monitoring Portland cement hydration: Comparison of methods. Cem Concr Res. 1990;20:919–26.Hewlett PC. Lea’s chemistry of cement and concrete. 4th ed. Oxford: Elsevier Science & Technology Books; 2004.ASTM C305 Standard practice for mechanical mixing of hydraulic cement pastes and mortars of plastic consistency. ASTM International, West Conshohocken, PA; 2012.Taylor HF. Cement chemistry. 2nd ed. Westminster: Thomas Telford; 1997.Nadelman EI, Freas DJ, Kurtis KE. Nano- and microstructural characterization of Portland limestone cement paste. In: Nanotechnology in construction. Proceedings of NICOM 5. 2015. p. 87–92

Ecological study of socio-economic indicators and prevalence of asthma in schoolchildren in urban Brazil

BACKGROUND: There is evidence of higher prevalence of asthma in populations of lower socio-economic status in affluent societies, and the prevalence of asthma is also very high in some Latin American countries, where societies are characterized by a marked inequality in wealth. This study aimed to examine the relationship between estimates of asthma prevalence based on surveys conducted in children in Brazilian cities and health and socioeconomic indicators measured at the population level in the same cities. METHODS: We searched the literature in the medical databases and in the annals of scientific meeting, retrieving population-based surveys of asthma that were conducted in Brazil using the methodology defined by the International Study of Asthma and Allergies in Childhood. We performed separate analyses for the age groups 6-7 years and 13-14 years. We examined the association between asthma prevalence rates and eleven health and socio-economic indicators by visual inspection and using linear regression models weighed by the inverse of the variance of each survey. RESULTS: Six health and socioeconomic variables showed a clear pattern of association with asthma. The prevalence of asthma increased with poorer sanitation and with higher infant mortality at birth and at survey year, GINI index and external mortality. In contrast, asthma prevalence decreased with higher illiteracy rates. CONCLUSION: The prevalence of asthma in urban areas of Brazil, a middle income country, appears to be higher in cities with more marked poverty or inequality

Seasonality in pulmonary tuberculosis among migrant workers entering Kuwait

<p>Abstract</p> <p>Background</p> <p>There is paucity of data on seasonal variation in pulmonary tuberculosis (TB) in developing countries contrary to recognized seasonality in the TB notification in western societies. This study examined the seasonal pattern in TB diagnosis among migrant workers from developing countries entering Kuwait.</p> <p>Methods</p> <p>Monthly aggregates of TB diagnosis results for consecutive migrants tested between January I, 1997 and December 31, 2006 were analyzed. We assessed the amplitude (<it>α</it>) of the sinusoidal oscillation and the time at which maximum (<it>θ</it>°) TB cases were detected using Edwards' test. The adequacy of the hypothesized sinusoidal curve was assessed by <it>χ</it>²goodness-of-fit test.</p> <p>Results</p> <p>During the 10 year study period, the proportion (per 100,000) of pulmonary TB cases among the migrants was 198 (4608/2328582), (95% confidence interval: 192 – 204). The adjusted mean monthly number of pulmonary TB cases was 384. Based on the observed seasonal pattern in the data, the maximum number of TB cases was expected during the last week of April (<it>θ</it>° = 112°; <it>P </it>< 0.001). The amplitude (± se) (<it>α </it>= 0.204 ± 0.04) of simple harmonic curve showed 20.4% difference from the mean to maximum TB cases. The peak to low ratio of adjusted number of TB cases was 1.51 (95% CI: 1.39 – 1.65). The <it>χ</it>²goodness-of-test revealed that there was no significant (<it>P </it>> 0.1) departure of observed frequencies from the fitted simple harmonic curve. Seasonal component explained 55% of the total variation in the proportions of TB cases (100,000) among the migrants.</p> <p>Conclusion</p> <p>This regularity of peak seasonality in TB case detection may prove useful to institute measures that warrant a better attendance of migrants. Public health authorities may consider re-allocation of resources in the period of peak seasonality to minimize the risk of <it>Mycobacterium tuberculosis </it>infection to close contacts in this and comparable settings in the region having similar influx of immigrants from high TB burden countries. Epidemiological surveillance for the TB risk in the migrants in subsequent years and required chemotherapy of detected cases may contribute in global efforts to control this public health menace.</p

Retinoids cause apoptosis in pancreatic cancer cells via activation of RAR-γ and altered expression of Bcl-2/Bax

All-trans-retinoic acid and 9-cis-retinoic acid have been reported to have inhibitory effects on pancreatic adenocarcinoma cells and we have shown that this is partly due to induction of apoptosis. In this study, the mechanisms whereby 9-cis-retinoic acid induces apoptosis in these cells were investigated. An involvement of the Bcl-2 family of proteins was shown, such that 9-cis-retinoic acid causes a decrease in the Bcl-2/Bax ratio. Overexpression of Bcl-2 also resulted in inhibition of apoptosis induced by 9-cis-retinoic acid. Furthermore, two broad-range caspase inhibitors blocked DNA fragmentation induced by 9-cis-retinoic acid, but had no effect on viability defined by mitochondrial activity. Using synthetic retinoids, which bind selectively to specific retinoic acid receptor subtypes, we further established that activation of retinoic acid receptor-γ is essential for induction of apoptosis. Only pan-retinoic acid receptor and retinoic acid receptor-γ selective agonists reduced viability and a cell line expressing very low levels of retinoic acid receptor-γ is resistant to the effects of 9-cis-retinoic acid. A retinoic acid receptor-β/γ selective antagonist also suppressed the cytotoxic effects of 9-cis-retinoic acid in a dose-dependent manner. This study provides important insight into the mechanisms involved in suppression of pancreatic tumour cell growth by retinoids. Our results encourage further work evaluating the clinical use of receptor subtype selective retinoids in pancreatic carcinoma

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal