Automated spectrometer alignment via machine learning.

During beam time at a research facility, alignment and optimization of instrumentation, such as spectrometers, is a time-intensive task and often needs to be performed multiple times throughout the operation of an experiment. Despite the motorization of individual components, automated alignment solutions are not always available. In this study, a novel approach that combines optimisers with neural network surrogate models to significantly reduce the alignment overhead for a mobile soft X-ray spectrometer is proposed. Neural networks were trained exclusively using simulated ray-tracing data, and the disparity between experiment and simulation was obtained through parameter optimization. Real-time validation of this process was performed using experimental data collected at the beamline. The results demonstrate the ability to reduce alignment time from one hour to approximately five minutes. This method can also be generalized beyond spectrometers, for example, towards the alignment of optical elements at beamlines, making it applicable to a broad spectrum of research facilities.

Unsupervised real-world knowledge extraction via disentangled variational autoencoders for photon diagnostics.

We present real-world data processing on measured electron time-of-flight data via neural networks. Specifically, the use of disentangled variational autoencoders on data from a diagnostic instrument for online wavelength monitoring at the free electron laser FLASH in Hamburg. Without a-priori knowledge the network is able to find representations of single-shot FEL spectra, which have a low signal-to-noise ratio. This reveals, in a directly human-interpretable way, crucial information about the photon properties. The central photon energy and the intensity as well as very detector-specific features are identified. The network is also capable of data cleaning, i.e. denoising, as well as the removal of artefacts. In the reconstruction, this allows for identification of signatures with very low intensity which are hardly recognisable in the raw data. In this particular case, the network enhances the quality of the diagnostic analysis at FLASH. However, this unsupervised method also has the potential to improve the analysis of other similar types of spectroscopy data.

Seroprevalence and effect of HBV and HCV co-infections on the immuno-virologic responses of adult HIV-infected persons on anti-retroviral therapy.

Chronic hepatitis negatively affects persons living with HIV. While varying in their transmission efficiency, HIV, HBV, and HCV have shared routes of transmission. Available data suggest widely variable rates of HBV and HCV infections in HIV-infected populations across sub-Saharan Africa. With prolonged survival rates due to increased accessibility to antiretroviral drugs, HBV and HCV have the potential to complicate the prognosis of HIV co-infected patients by contributing significantly to continued morbidity and mortality. The study sought to determine the seroprevalence of HIV/HBV and HIV/HCV co-infections among HIV patients on antiretroviral therapy and to evaluate the effect of HIV/HBV and HIV/HCV co-infections on the immunologic and virologic responses of patients. A cross-sectional study in which samples were taken from 500 people living with HIV and attending ART clinic at the Fevers unit of the Korle Bu Teaching Hospital and tested for Hepatitis B Surface Antigen (HBsAg) and Hepatitis C virus antibody (HCV). CD4 cell counts and HIV-1 RNA levels were estimated as well. Data generated were analysed using IBM SPSS version 22. The seroprevalence of HIV/HBV and HIV/HCV co-infections among people living with HIV was 8.4% and 0.2% respectively. HIV/HBV coinfection included 15/42 (35.7%) males and 27/42 (64.3%) females out of which the majority (97.6%) were in the 21-60 years old bracket. HIV/HBV and HIV/HCV co-infections have varied effects on the immunological and virological response of HIV patients on ART. The mean CD cell count was 361.0 ± 284.0 in HIV/HBV co-infected patients and 473.8 ± 326.7 in HIV mono-infected patients. The mean HIV-1 RNA level was not significantly different (X2 [df] = .057 [1]; P = .811) among HIV/HBV co-infected patients (Log102.9±2.0 copies/mL), compared to that of HIV mono-infected patients (Log102.8±2.1 copies/mL) although HIV mono-infected patients had lower viral load levels. One-third (14/42) of HIV/HBV co-infected patients had virologic failure and the only HIV/HCV co-infected patient showed viral suppression. 336/500 (67.2%) patients had HIV-1 viral suppression (females [66.1%]; males [33.9%]) while 164/500 (32.8%) had virologic failure (females [67.7%]; males [32.3%]). The mean CD4 count of patients with viral suppression and patients with virologic failure was 541.2 cells/µL (95% CI 508.5-573.8) and 309.9 cell/µL (95% CI 261.9-357.9) respectively.The study concludes that, HIV/HBV and HIV/HCV coinfections do not significantly affect the immunologic and virologic responses of patients who have initiated highly active antiretroviral therapy, and treatment outcomes were better in females than in males. There was no HBV/HCV co-infection among patients.

Persistent Urogenital Schistosomiasis and Its Associated Morbidity in Endemic Communities within Southern Ghana: Suspected Praziquantel Resistance or Reinfection?

BACKGROUND: schistosomiasis is a neglected tropical disease caused by helminths of the genus Schistosoma. The disease has a worldwide distribution, with more cases occurring in Africa. Urogenital schistosomiasis caused by S. haematobium with its associated morbidity is prevalent in many areas of Ghana. Praziquantel is still the recommended drug of choice for schistosomiasis treatment, although a number of studies have reported sub-therapeutic effects and associated treatment failure. The current study, therefore, assessed whether persistent schistosomiasis, with its associated morbidity among children living in endemic areas within the Greater Accra Region of Ghana, is as a result of reinfection or suspected praziquantel resistance. METHODOLOGY: this was a longitudinal study involving a baseline and follow-up sampling after praziquantel treatment. Urine samples were collected from school children (whose parents had also consented) for the detection of S. haematobium ova using a sedimentation technique. The morbidity parameters were examined with urine chemistry strips, as well as microscopy. Viability was assessed using a modified hatchability technique, vital staining (0.4% trypan blue and 1% neutral red) and fluorescent (Hoechst 33258) microscopy. Infected individuals were treated with a single dose of praziquantel (40mg/kg). Resampling to determine reinfection was done sixth months post-treatment, after evidence of total egg clearance. For possible resistance assessment, egg counts and viability testing were conducted on the positive samples at the baseline, as well as weekly post-treatment follow-ups for 12 weeks. RESULTS: out of the 420 school children sampled, 77 were initially positive but, after the sixth month sampling for reinfection assessment, eight out of the initial positives were infected again, giving a reinfection percentage of 10.4%. No suspected praziquantel resistance was recorded in the 21 positives detected out of the 360 sampled for suspected resistance assessment. The egg reduction rate increased weekly in the follow-up samples with a gradual reduction in the egg count. The study also recorded a gradual decrease in the percentage of live eggs after the first week; with all viability testing methods used complimenting each other. The morbidity parameters (proteinuria, haematuria and pyuria) changed between the baseline and post-treatment samples, eventually reducing to zero. CONCLUSIONS: the outcome of this study suggests that the persistent schistosomiasis, with its associated morbidity observed in these endemic communities, is not likely to be as a result of praziquantel resistance, but reinfection. Even though there was no suspected resistance observed in the study, there remains the need to continuously intensify the monitoring of praziquantel in other endemic communities.

Ability of Vital and Fluorescent Staining in the Differentiation of Schistosoma haematobium Live and Dead Eggs.

This study reports (for the first time) the staining ability of vital (0.4% trypan blue and 1% neutral red) and fluorescent (Hoechst 33258) dyes to differentiate between live and dead Schistosoma haematobium (S. haematobium) eggs in human urine samples. Since S. haematobium egg is important in disease pathology, diagnosis, transmission, and drug development research, it is essential to be able to easily distinguish live eggs from dead ones. Staining is considered a way of enhancing the identification of live and dead eggs. Urine samples from school children were examined for the presence of S. haematobium eggs. Vital and fluorescent dyes were used to stain the samples that contained S. haematobium eggs, after which they were observed using light and fluorescent microscopes, respectively. The Hoechst 33258 provided a good staining outcome for differentiation between live and dead eggs, followed by 0.4% Trypan blue. Regarding the 1% neutral red stain, even though it provided some evidence of which egg was alive or dead, the distinction was not very clear; therefore, it could be useful when used in combination with other stains for egg viability determination. The benefits of this study will include assessing the effect of drugs on S. haematobium eggs in Schistosomiasis research.

Comorbidity of Glucose-6-Phosphate Dehydrogenase Deficiency and Sickle Cell Disease Exert Significant Effect on RBC Indices.

BACKGROUND: Glucose-6-phosphate dehydrogenase (G6PD) converts glucose-6-phosphate into 6-phosphogluconate in the pentose phosphate pathway and protects red blood cells (RBCs) from oxidative damage. Their deficiency therefore makes RBCs prone to haemolysis. Sickle cell disease (SCD) on the other hand is a hereditary blood disorder in which there is a single nucleotide substitution in the codon for amino acid 6 substituting glutamic acid with valine. SCD patients are prone to haemolysis due to the shape of their red blood cells and if they are deficient in G6PD, the haemolysis may escalate. Reported studies have indicated variations in the prevalence of G6PD deficiency in SCD patients and as such further work is required. The aim of this study was therefore to estimate the incidence of G-6-PD deficiency among SCD patients and to determine its impact on their RBC parameters as a measure of incidence of anaemia. METHODS: A total of 120 clinically diagnosed SCD patients of genotypes HbSS and HbSC were recruited into the study. About 5ml of blood was collected via venipuncture from each patient and used to run G6PD, full blood count, and haemoglobin (Hb) electrophoresis tests. The data were analyzed using SPSS version 20 and Graphpad prism. RESULT: G6PD deficiency was detected in 43 (35.83%) of the participants made up of 16 (13.33%) males and 27 (22.50%) females of whom 17 (14.17%) had partial deficiency and 10 (8.33%) full deficiency. Statiscally significant differences p=0.036 and p=0.038 were established between the Hb concentration of the participants having a G6PD deficiency and those with normal G6PD activity for males and females, respectively. CONCLUSION: From the results obtained, it implies that G6PD deficiency may increase the severity of anaemia in SCD patients. There is therefore the need to screen all SCD patients for G6PD deficiency to ensure that their condition is not exacerbated during treatment.