Stochastic analysis of surface roughness

For the characterization of surface height profiles we present a new stochastic approach which is based on the theory of Markov processes. With this analysis we achieve a characterization of the complexity of the surface roughness by means of a Fokker-Planck or Langevin equation, providing the complete stochastic information of multiscale joint probabilities. The method was applied to different road surface profiles which were measured with high resolution. Evidence of Markov properties is shown. Estimations for the parameters of the Fokker-Planck equation are based on pure, parameter free data analysis

Detection of Neutralizing Antibodies in COVID-19 Patients from Steve Biko Academic Hospital Complex: A Pilot Study

A correlation between neutralization activity after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination and protection against coronavirus disease 2019 (COVID-19) has been demonstrated by several studies. Here, we detect SARS-CoV-2 neutralizing antibody (NAB) production in COVID-19 patients from the Steve Biko Academic Hospital complex (SBAH), South Africa (SA). Samples from COVID-19 patients (mild to severe) were collected. SARS-CoV-2 rapid assays, genotyping (Delta and Omicron variants) and enzyme-linked immunosorbent assays (ELISA) were performed. IBM® Statistical Package for the Social Sciences (SPSS®) version 28 was used for inferential statistical analysis, and the data were presented using the Prism9 software (version 9.4.1). A total of 137 laboratory-confirmed COVID-19 patients, 12 vaccine recipients and 8 unvaccinated participants were evaluated. The production of SARS-CoV-2 NABs was observed in some of the COVID-19 cases, mainly in severe cases, although this should be noted with caution due to the small sample size of this pilot study. NABs were also observed in asymptomatic participants, with the most being found in recipients (n = 6) of the BNT162b2 (Pfizer-BioNTech) COVID-19 vaccine. We found a strong presence of NABs in COVID-19 patients, specifically in mild and severe cases. Severe infection was associated with higher NAB production (82%).P.M thanks H2020-WIDESPREAD-2018-951921-ImmunoHUB for the financial support

The lung microbiome in HIV‑positive patients with active pulmonary tuberculosis

Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIVpositive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.DATA AVAILABILITY : The datasets generated and analysed during the current study are available in the University of Pretoria data repository and can be accessed at https://doi.org/10.25403/UPresearchdata.19491317.v1.The Infectious diseases Research Fund.http://www.nature.com/scientificreportsam2023BiochemistryGeneticsInternal MedicineMedical MicrobiologyMicrobiology and Plant Patholog

Severe porphyric neuropathy - importance of screening for porphyria in Guillain-Barré syndrome

The hepatic porphyrias are a group of rare metabolic disorders, each of which is associated with a specific enzymatic alteration in the haem biosynthesis pathway. In South Africa (SA), a high incidence of variegate porphyria (VP) is seen as a result of a founder effect, but acute intermittent porphyria (AIP) is also encountered. The development of acute neurovisceral attacks is related to environmental factors, including medications, hormones and diet. A possible manifestation of a severe attack is rapidly progressing quadriparesis, which may mimic Guillain-Barré syndrome. We present four such cases, highlighting that acute porphyria should be considered in the differential diagnosis of Guillain-Barré syndrome. Three patients presented to Steve Biko Academic Hospital, Pretoria, SA, with progressive quadriparesis, and one to a private hospital with acute abdominal pain followed by rapidly progressive quadriparesis. Two patients had started antiretroviral therapy before the development of symptoms, and one had started antituberculosis therapy. All patients had marked weakness with depressed reflexes, and showed varying degrees of confusion. An initial diagnosis of Guillain-Barré syndrome led to administration of intravenous immunoglobulins in two patients. On testing for porphyria, it was found that two patients had AIP and two VP. Electrophysiological investigations revealed severe mainly motor axonal neuropathy in all. Two patients deteriorated to the point of requiring mechanical ventilation, and one of them died due to complications of critical illness. Haemin was administered to three patients, but the process of obtaining this medication was slow, which delayed the recommended early administration. The surviving patients showed minimal recovery and remained severely disabled. Porphyric neuropathy should always be considered as a differential diagnosis in a patient with an acute neuropathy, especially in SA. Absence of abdominal pain does not exclude the possibility of porphyria, and attacks may be precipitated by antiretroviral and antituberculosis medication. The outcome of our patients was not favourable; specifically, obtaining haemin was a challenge in the state hospital setting

Drive counts as a method of estimating ungulate density in forests: mission impossible?

Although drive counts are frequently used to estimate the size of deer populations in forests, little is known about how counting methods or the density and social organization of the deer species concerned influence the accuracy of the estimates obtained, and hence their suitability for informing management decisions. As these issues cannot readily be examined for real populations, we conducted a series of ‘virtual experiments’ in a computer simulation model to evaluate the effects of block size, proportion of forest counted, deer density, social aggregation and spatial auto-correlation on the accuracy of drive counts. Simulated populations of red and roe deer were generated on the basis of drive count data obtained from Polish commercial forests. For both deer species, count accuracy increased with increasing density, and decreased as the degree of aggregation, either demographic or spatial, within the population increased. However, the effect of density on accuracy was substantially greater than the effect of aggregation. Although improvements in accuracy could be made by reducing the size of counting blocks for low-density, aggregated populations, these were limited. Increasing the proportion of the forest counted led to greater improvements in accuracy, but the gains were limited compared with the increase in effort required. If it is necessary to estimate the deer population with a high degree of accuracy (e.g. within 10% of the true value), drive counts are likely to be inadequate whatever the deer density. However, if a lower level of accuracy (within 20% or more) is acceptable, our study suggests that at higher deer densities (more than ca. five to seven deer/100 ha) drive counts can provide reliable information on population size

Combining isotopic signatures of n(87Sr)/n(86Sr) and light stable elements (C, N, O, S) with multi-elemental profiling for the authentication of provenance of European cereal samples

The aim of this work (from the FP6 project TRACE) was to develop methods based on the use of geochemical markers for the authentication of the geographical origin of cereal samples in Europe (cf. EC regulations 2081/92 and 1898/06). For the first time, the potential usefulness of combining n(87Sr)/n(86Sr) and δ13C, δ15N, δ18O and δ34S isotopic signatures, alone or with key element concentrations ([Na], [K], [Ca], [Cu] and [Rb], progressively identified out of 31 sets of results), was investigated through multiple step multivariate statistics for more than 500 cereal samples collected over 2 years from 17 sampling sites across Europe representing an extensive range of geographical and environmental characteristics. From the classification categories compared (north/south; proximity to the Atlantic Ocean/to the Mediterranean Sea/to else; bed rock geologies) the first two were the most efficient (particularly with the ten variables selected together). In some instances element concentrations made a greater impact than the isotopic tracers. Validation of models included external prediction tests on 20% of the data randomly selected and, rarely done, a study on the robustness of these multivariate data treatments to uncertainties on measurement results. With the models tested it was possible to individualise 15 of the sampling sites

Why Are Outcomes Different for Registry Patients Enrolled Prospectively and Retrospectively? Insights from the Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF).

Background: Retrospective and prospective observational studies are designed to reflect real-world evidence on clinical practice, but can yield conflicting results. The GARFIELD-AF Registry includes both methods of enrolment and allows analysis of differences in patient characteristics and outcomes that may result. Methods and Results: Patients with atrial fibrillation (AF) and ≥1 risk factor for stroke at diagnosis of AF were recruited either retrospectively (n = 5069) or prospectively (n = 5501) from 19 countries and then followed prospectively. The retrospectively enrolled cohort comprised patients with established AF (for a least 6, and up to 24 months before enrolment), who were identified retrospectively (and baseline and partial follow-up data were collected from the emedical records) and then followed prospectively between 0-18 months (such that the total time of follow-up was 24 months; data collection Dec-2009 and Oct-2010). In the prospectively enrolled cohort, patients with newly diagnosed AF (≤6 weeks after diagnosis) were recruited between Mar-2010 and Oct-2011 and were followed for 24 months after enrolment. Differences between the cohorts were observed in clinical characteristics, including type of AF, stroke prevention strategies, and event rates. More patients in the retrospectively identified cohort received vitamin K antagonists (62.1% vs. 53.2%) and fewer received non-vitamin K oral anticoagulants (1.8% vs . 4.2%). All-cause mortality rates per 100 person-years during the prospective follow-up (starting the first study visit up to 1 year) were significantly lower in the retrospective than prospectively identified cohort (3.04 [95% CI 2.51 to 3.67] vs . 4.05 [95% CI 3.53 to 4.63]; p = 0.016). Conclusions: Interpretations of data from registries that aim to evaluate the characteristics and outcomes of patients with AF must take account of differences in registry design and the impact of recall bias and survivorship bias that is incurred with retrospective enrolment. Clinical Trial Registration: - URL: http://www.clinicaltrials.gov . Unique identifier for GARFIELD-AF (NCT01090362)

Improved risk stratification of patients with atrial fibrillation: an integrated GARFIELD-AF tool for the prediction of mortality, stroke and bleed in patients with and without anticoagulation.

OBJECTIVES: To provide an accurate, web-based tool for stratifying patients with atrial fibrillation to facilitate decisions on the potential benefits/risks of anticoagulation, based on mortality, stroke and bleeding risks. DESIGN: The new tool was developed, using stepwise regression, for all and then applied to lower risk patients. C-statistics were compared with CHA2DS2-VASc using 30-fold cross-validation to control for overfitting. External validation was undertaken in an independent dataset, Outcome Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT-AF). PARTICIPANTS: Data from 39 898 patients enrolled in the prospective GARFIELD-AF registry provided the basis for deriving and validating an integrated risk tool to predict stroke risk, mortality and bleeding risk. RESULTS: The discriminatory value of the GARFIELD-AF risk model was superior to CHA2DS2-VASc for patients with or without anticoagulation. C-statistics (95% CI) for all-cause mortality, ischaemic stroke/systemic embolism and haemorrhagic stroke/major bleeding (treated patients) were: 0.77 (0.76 to 0.78), 0.69 (0.67 to 0.71) and 0.66 (0.62 to 0.69), respectively, for the GARFIELD-AF risk models, and 0.66 (0.64-0.67), 0.64 (0.61-0.66) and 0.64 (0.61-0.68), respectively, for CHA2DS2-VASc (or HAS-BLED for bleeding). In very low to low risk patients (CHA2DS2-VASc 0 or 1 (men) and 1 or 2 (women)), the CHA2DS2-VASc and HAS-BLED (for bleeding) scores offered weak discriminatory value for mortality, stroke/systemic embolism and major bleeding. C-statistics for the GARFIELD-AF risk tool were 0.69 (0.64 to 0.75), 0.65 (0.56 to 0.73) and 0.60 (0.47 to 0.73) for each end point, respectively, versus 0.50 (0.45 to 0.55), 0.59 (0.50 to 0.67) and 0.55 (0.53 to 0.56) for CHA2DS2-VASc (or HAS-BLED for bleeding). Upon validation in the ORBIT-AF population, C-statistics showed that the GARFIELD-AF risk tool was effective for predicting 1-year all-cause mortality using the full and simplified model for all-cause mortality: C-statistics 0.75 (0.73 to 0.77) and 0.75 (0.73 to 0.77), respectively, and for predicting for any stroke or systemic embolism over 1 year, C-statistics 0.68 (0.62 to 0.74). CONCLUSIONS: Performance of the GARFIELD-AF risk tool was superior to CHA2DS2-VASc in predicting stroke and mortality and superior to HAS-BLED for bleeding, overall and in lower risk patients. The GARFIELD-AF tool has the potential for incorporation in routine electronic systems, and for the first time, permits simultaneous evaluation of ischaemic stroke, mortality and bleeding risks. CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier for GARFIELD-AF (NCT01090362) and for ORBIT-AF (NCT01165710)

Two-year outcomes of patients with newly diagnosed atrial fibrillation: results from GARFIELD-AF.

AIMS: The relationship between outcomes and time after diagnosis for patients with non-valvular atrial fibrillation (NVAF) is poorly defined, especially beyond the first year. METHODS AND RESULTS: GARFIELD-AF is an ongoing, global observational study of adults with newly diagnosed NVAF. Two-year outcomes of 17 162 patients prospectively enrolled in GARFIELD-AF were analysed in light of baseline characteristics, risk profiles for stroke/systemic embolism (SE), and antithrombotic therapy. The mean (standard deviation) age was 69.8 (11.4) years, 43.8% were women, and the mean CHA2DS2-VASc score was 3.3 (1.6); 60.8% of patients were prescribed anticoagulant therapy with/without antiplatelet (AP) therapy, 27.4% AP monotherapy, and 11.8% no antithrombotic therapy. At 2-year follow-up, all-cause mortality, stroke/SE, and major bleeding had occurred at a rate (95% confidence interval) of 3.83 (3.62; 4.05), 1.25 (1.13; 1.38), and 0.70 (0.62; 0.81) per 100 person-years, respectively. Rates for all three major events were highest during the first 4 months. Congestive heart failure, acute coronary syndromes, sudden/unwitnessed death, malignancy, respiratory failure, and infection/sepsis accounted for 65% of all known causes of death and strokes for <10%. Anticoagulant treatment was associated with a 35% lower risk of death. CONCLUSION: The most frequent of the three major outcome measures was death, whose most common causes are not known to be significantly influenced by anticoagulation. This suggests that a more comprehensive approach to the management of NVAF may be needed to improve outcome. This could include, in addition to anticoagulation, interventions targeting modifiable, cause-specific risk factors for death. CLINICAL TRIAL REGISTRATION: http://www.clinicaltrials.gov. Unique identifier: NCT01090362