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A further study comparing forward search multivariate outlier methods including ATLA with an application to clustering
Get PDFThis paper makes comparisons of automated procedures for robust multivariate outlier detection through discussion and simulation. In particular, automated procedures that use the forward search along with Mahalanobis distances to identify and classify multivariate outliers subject to predefined criteria are examined. Procedures utilizing a parametric model criterion based on a χ2-distribution are among these, whereas the multivariate Adaptive Trimmed Likelihood Algorithm (ATLA) identifies outliers based on an objective function that is derived from the asymptotics of the location estimator assuming a multivariate normal distribution. Several criterion including size (false positive rate), sensitivity, and relative efficiency are canvassed. To illustrate relative efficiency in a multivariate setting in a new way, measures of variability of the multivariate location parameter when the underlying distribution is chosen from a multivariate generalization of the Tukey–Huber ϵ-contamination model are used. Mean slippage models are also entertained. The simulation results here are illuminating and demonstrate there is no broadly accepted procedure that outperforms in all situations, albeit one may ascertain circumstances for which a particular method may be best if implemented. Finally the paper explores graphical monitoring for existence of clusters and the potential of classification through occurrence of multiple minima in the objective function using ATLA
Assessing the activity of antimicrobial peptides against common marine bacteria located in rotifer (Brachionus plicatilis) cultures
Get PDFRotifers are used as the first feed for marine fish larvae and are grown in large cultures that have high loads of organic matter and heterotrophic bacteria; these bacteria are passed on to the developing fish larvae and can potentially lead to bacterial infections. A modified minimum inhibitory concentration (MIC) protocol for antimicrobial peptides was used to determine the potency of ten antimicrobial peptides (AMPs) in artificial seawater relevant to a rotifer culture (salinity of 25‰) against common marine pathogens. All of the AMPs had antimicrobial activity against the bacterial isolates when the salt concentration was approximately zero. However, in high salt concentrations, the majority of the AMPs had an MIC value greater than 65 µg mL−1 in artificial seawater (25‰). The only exceptions were 2009 (32.5 µg mL−1) and 3002 (32.5 µg mL−1) against Vibrio rotiferianus and Tenacibaculum discolor, respectively. The selected synthetic AMPs were not effective at reducing the bacterial load in brackish salt concentrations of a typical commercial rotifer culture (25‰)
Microalgal culture to treat food waste digestate
Get PDFA significant proportion of all waste generated in the world is food waste, contributing up to 8% of global CO2 emissions. Conventional ways of food waste disposal including landfilling and incineration are simply inadequate and unsustainable, emphasizing the need for efficient ways recycling / valorizing food waste. Anaerobic digestion is a way to treat and valorize food waste with significantly less emission of greenhouse gases. However, anaerobic digestion itself produces a waste in the form of anaerobic digestate that is difficult to manage. Microalgae cultivation has been used for the treatment and valorization of a wide range of waste effluents and has been identified as a potentially viable option for the treatment and valorization of food waste anaerobic digestate. On the other hand, food waste digestate as a feed stock for the cultivation of microalgae has its challenges. Food waste digestate is a very high strength effluent having ammonia nitrogen concentration of up to 4000 mg L-1, which is extremely toxic to most microalgae species. Food waste digestate is also very turbid, making microalgae cultivation in this effluent extremely difficult without an unsustainably excessive amount of dilution, as light / irradiance is the most limiting factor in any microalgae cultivation system. Previous efforts to treat and valorize food waste digestate have been less than successful due to the reasons stated above. Considering these, we have identified possible solutions to mitigate the challenges involved in treatment and valorization of food waste digestate using microalgae. These are: the identification and application of microalgae species tolerant to high concentration of ammonia nitrogen as found in food waste digestion to tackle the problem of excessive dilution of the digestate before use; and the use of an inclined thin layer pond with a much shorter light path than conventional microalgae cultivation systems allowing for better utilization of incident irradiance in culture systems.
Three microalgae (Scenedesmus quadricauda, MUR 268, Chlorella sp, Mur 269, and Oocystis sp, MUR 273) were capable of growth in up to 600 mg L-1 of ammonia nitrogen in food waste digestate. Further experimentation was done at indoor bench scale laboratory conditions using the most tolerant and robust of the 3 identified species, Chlorella sp, Mur 269. To gain insight into the mechanisms required for tolerance of ammonia with the identified species, especially in relation to its response to light profiles imposed by turbidity, their photosynthetic response was studied using pulse amplitude modulation (PAM) fluorometry. Indicators including electron transport rate (ETR), maximum quantum yield in actinic light (fv’/fm’) and alpha (α), alongside oxygenesis as an indicator of photosynthesis, were used to study the state of the photosystem of the organism. Maximum specific growth (μmax) rates and in-situ irradiance profiles were also studied. The effect of turbidity was accounted for by studying the above response variables in clear synthetic medium (Bolds basal medium, BBM) and food waste digestate medium. Maximum specific growth rate (μmax) and biomass productivities were 63% and 47% higher in anaerobic digestate of food waste (ADF) than in BBM, maintaining values of 0.681 ± 0.03 d-1 and 165 ± 8 mg L-1 d-1 respectively, even at high irradiance intensities of 1500 μmol m-2s-1, validating their suitability to outdoor conditions. However, Chlorella sp, Mur 269 photosystem II at optimum irradiance, as reflected in Fv’/Fm’ values, was reduced by 16% in food waste digestate in comparison to BBM. A critical look at the photosynthesis of this algae shows that adaptive tolerance methods of Chlorella sp, MUR 269 to toxicity includes adjustment of the photosynthetic unit to maximize absorption of light and compensation mechanisms for reductions in PSII activity including switching to mixotrophic growth mode.
Application of Chlorella sp, Mur 269 for growth in food waste digestate was carried out using an inclined thin layer pond under outdoor conditions. Previous studies using the inclined thin layer pond had shown that though volumetric productivities and biomass densities could be improved by using the inclined thin layer pond for the treatment and valorization of digestates, areal productivities were significantly lower than paddle wheel driven raceway ponds because of the higher surface area to volume ratio in the inclined thin layer pond. To that end, depth optimisation of a 11 m2 surface area inclined thin layer pond was conducted, tailored towards its utilization for the treatment and valorization of food waste digestate using microalgae. Depth optimizations were performed by stepwise increments of the depth of the culture on the surface of the inclined thin layer pond through 0.005, 008, 0.011, 0.0145 and 0.02 m. The kinetics of electron flow around photosystem II of microalgae in-situ culture was used as descriptives for light utilization and limitations of the optimizations via variables including relative electron transfer rate, rETR, and maximum quantum yield, Fv/Fm, and derived parameters including functional relative electron transfer rate (FrETR) and functional relative electron transfer rate ratio (FrETR-ratio). Optimal culture depth determined for the inclined thin layer pond was 0.011 m, with average biomass density of 4.319 ± 0.18 g L-1 and areal productivity of 21.134 ± 1.83 g m-2 d, at an operational volume of 140 L. The most important parameters affecting growth rates and productivity were the mean irradiance inside the culture and the FrETR of photons for phytochemistry. Compared to previous study using anaerobic digestate of piggery waste effluent of similar turbidity, areal productivity was improved 9.5 times.
Further, the use of food waste digestate as a source of nutrients for the cultivation of high value species of microalgae such as Dunaliella salina, that are highly sensitive to ammonia nitrogen was explored. The main aim of this study was to assess the possibility of utilizing nutrients from food waste digestate for growing D. salina. Dunaliella salina was cultivated in modified F-medium with partial to complete replacement of the nitrogen (0 – 100 % digestate nitrogen) source under high salinity (150 - 250 ‰) conditions to study both cell growth and carotenogenesis. It was found that the growth and productivity of Dunaliella salina was not inhibited by ammonia nitrogen found in the food waste digestate. Irradiance above 400 μmol photons m-2 s-1 and higher salinity had combined negative effects on growth and carotenogenesis. However, under increased irradiation and temperature, in comparison with cultures grown in synthetic medium with nitrate salts as nitrogen source, there was no significant difference in biomass productivity when D. salina was cultivated using food waste digestate as sole nitrogen source.
Finally, a comparative study was performed between the depth optimized inclined thin layer pond and an open raceway pond, both occupying a surface area of 11 m2 under outdoor conditions, to ascertain and demonstrate the advantage of the inclined thin layer pond for the treatment and valorization of food waste digestate using Chlorella sp, Mur 269. The inclined thin layer pond supported a much higher average biomass density of 6.807 ± 0.15 g L-1, 7 times more in comparison to the open raceway pond, without severe photolimitation. Volumetric and areal productivities of the inclined thin layer pond were 0.563 ± 0.1 g L-1 d-1 and 31.916 ± 1.11 g m-2 d-1 respectively, 17 and 3 times higher than observed in the open raceway pond. Areal nutrient removal by the microalgae biomass were 2359.759 ± 64.75 mg m-2 d-1 and 260.815 ± 7.16 mg m-2 d-1 for nitrogen and phosphorous respectively in the inclined thin layer pond, 2.8 times higher than observed in the open raceway pond for both nutrients.
The results described above show that employing tolerant species of microalgae like Chlorella sp, Mur 269 offer an advantage for the treatment of high strength effluents, reducing excessive dilution, and unequivocally shows that the inclined thin layer pond is the more performant system for the treatment of highly turbid waste effluents such as food waste digestate
Artificial intelligence for right whale photo identification: From data science competition to worldwide collaboration
Get PDFPhoto identification is an important tool in the conservation management of endangered species, and recent developments in artificial intelligence are revolutionizing existing workflows to identify individual animals. In 2015, the National Oceanic and Atmospheric Administration hosted a Kaggle data science competition to automate the identification of endangered North Atlantic right whales (Eubalaena glacialis). The winning algorithms developed by Deepsense.ai were able to identify individuals with 87% accuracy using a series of convolutional neural networks to identify the region of interest, create standardized photographs of uniform size and orientation, and then identify the correct individual. Since that time, we have brought in many more collaborators as we moved from prototype to production. Leveraging the existing infrastructure by Wild Me, the developers of Flukebook, we have created a web-based platform that allows biologists with no machine learning expertise to utilize semi-automated photo identification of right whales. New models were generated on an updated dataset using the winning Deepsense.ai algorithms. Given the morphological similarity between the North Atlantic right whale and closely related southern right whale (Eubalaena australis), we expanded the system to incorporate the largest long-term photo identification catalogs around the world including the United States, Canada, Australia, South Africa, Argentina, Brazil, and New Zealand. The system is now fully operational with multi-feature matching for both North Atlantic right whales and southern right whales from aerial photos of their heads (Deepsense), lateral photos of their heads (Pose Invariant Embeddings), flukes (CurvRank v2), and peduncle scarring (HotSpotter). We hope to encourage researchers to embrace both broad data collaborations and artificial intelligence to increase our understanding of wild populations and aid conservation efforts
Prevalence and antimicrobial susceptibility pattern of Campylobacter jejuni in raw retail chicken meat in Metropolitan Accra, Ghana
No full textAlthough, Campylobacter spp. are a major cause of foodborne gastroenteritis, its occurrence and antimicrobial resistance traits have not been well defined in low income countries, particularly in Africa. In this study, retail chicken was sampled (n = 400) between February 2019 to January 2020 in Metropolitan Accra, Ghana, to determine the prevalence and antimicrobial susceptibility pattern of Campylobacter jejuni. Raw chicken samples were obtained in wet markets (n = 315) and supermarkets (n = 85) and each subjected to direct plating and broth enrichment according to standard culture methods for Campylobacter spp. with the identity of presumptive positive colonies confirmed by MALDI-TOF. The susceptibility of isolates to antibiotics commonly used for campylobacteriosis in humans (in order to reflect the One Health significance of Campylobacter at the human-food interface) were then assessed by disc diffusion. A prevalence of 38.3% was recorded and all isolates were confirmed as Campylobacter jejuni. Enrichment yielded 127 positives while direct plating yielded 55 positives with low level of agreement in detection between these assays (Kappa = 0.15). Among samples positive by direct plating, the mean Campylobacter count was 1.9 log10 CFU/g (sd ±0.8). About 13% (7/55) of the samples positive by direct plating contained counts of 3log and above. Samples from the wet market yielded more positives than those from the supermarket with the rate of isolation from wet markets being 1.6 times that of the supermarket. Among 182 isolates characterized for their antimicrobial susceptibility, resistance to fluoroquinolones was 99.5%, tetracyclines 100% and macrolides 26.9%. Multi-drug resistance was also observed in 26.9% of the screened isolates. The findings point to a potential high level of exposure of humans to Campylobacter jejuni through chicken meat and thus the need for education on hygienic preparation and handling of raw chicken. High rates of resistance to classes of antimicrobials critically important for treating Campylobacter infections in humans; fluroquinolones and macrolides, affirm the need for stronger regulatory control of antimicrobials and enhanced antimicrobial stewardship in chicken production
Efficiency and stability improvement of natural dye‐sensitized solar cells using the electrospun composite of TiO 2 nanofibres doped by the bio‐Ca nanoparticles
No full textThe dye-sensitized solar cells (DSSCs) can be effectively improved and stabilized by outstanding electrical and morphological characteristics of TiO2 nanofibres combined with bio-calcium doping. The pristine and bio-Ca-doped TiO2 nanofibres were fabricated using a cost-effective electrospinning technique. Biocompatible calcium carbonate nanoparticles (bio-Ca) were synthesized from the cuttlebone of Sepia Pharaonis. Moreover, a facile one-step procedure was employed to fabricate efficient TiO2 nanofibres-based DSSCs using a Pechini-type sol. This approach produced a highly porous dense film of TiO2 upon sintering without the need for the hot-pressing or adhesion layer steps. Based on the results, the DSSCs fabricated by the bio-Ca-doped TiO2 nanofibres showed the highest Isc, Voc, and η of 2.19 mA, 0.41 V, and 1.48% respectively. This superiority could be due to the higher specific surface area and the relatively smaller average diameter observed for bio-Ca-doped TiO2 nanofibres, which improved dye-loading and guided electron transport respectively. In addition, Ca2+ doping significantly suppressed the photocatalytic activity in the bio-Ca-doped TiO2 nanofibres owing to the formation of the TiO2 rutile-anatase combined phase. Besides, the substitution of Ti4+ with Ca2+ positively affects the conduction band of TiO2 and causes trap sites that retard the charge recombination. Our results also demonstrated that the bio-Ca-doped TiO2 nanofibres-based DSSC maintained about 78.38% of its initial efficiency after two weeks, while DSSCs fabricated by the TiO2 nanofibres and TiO2 nanoparticles retained 63.71% and 27.38% respectively. The superior stability could be due to the combined effect of nanoparticles into nanofibres transformation and bio-Ca doping
Rilzabrutinib, an Oral BTK Inhibitor, in Immune Thrombocytopenia
No full textBackground
Rilzabrutinib, an oral, reversible covalent inhibitor of Bruton’s tyrosine kinase, may increase platelet counts in patients with immune thrombocytopenia by means of dual mechanisms of action: decreased macrophage (Fcγ receptor)–mediated platelet destruction and reduced production of pathogenic autoantibodies.
Methods
In an international, adaptive, open-label, dose-finding, phase 1–2 clinical trial, we evaluated rilzabrutinib therapy in previously treated patients with immune thrombocytopenia. We used intrapatient dose escalation of oral rilzabrutinib over a period of 24 weeks; the lowest starting dose was 200 mg once daily, with higher starting doses of 400 mg once daily, 300 mg twice daily, and 400 mg twice daily. The primary end points were safety and platelet response (defined as at least two consecutive platelet counts of ≥50×103 per cubic millimeter and an increase from baseline of ≥20×103 per cubic millimeter without the use of rescue medication).
Results
Sixty patients were enrolled. At baseline, the median platelet count was 15×103 per cubic millimeter, the median duration of disease was 6.3 years, and patients had received a median of four different immune thrombocytopenia therapies previously. All the treatment-related adverse events were of grade 1 or 2 and transient. There were no treatment-related bleeding or thrombotic events of grade 2 or higher. At a median of 167.5 days (range, 4 to 293) of treatment, 24 of 60 patients (40%) overall and 18 of the 45 patients (40%) who had started rilzabrutinib treatment at the highest dose met the primary end point of platelet response. The median time to the first platelet count of at least 50×103 per cubic millimeter was 11.5 days. Among patients with a primary platelet response, the mean percentage of weeks with a platelet count of at least 50×103 per cubic millimeter was 65%.
Conclusions
Rilzabrutinib was active and associated with only low-level toxic effects at all dose levels. The dose of 400 mg twice daily was identified as the dose for further testing. Overall, rilzabrutinib showed a rapid and durable clinical activity that improved with length of treatment. (Funded by Sanofi; ClinicalTrials.gov number, NCT03395210. opens in new tab; EudraCT number, 2017-004012-19. opens in new tab.
Measuring the availability of human resources for health and its relationship to universal health coverage for 204 countries and territories from 1990 to 2019: A systematic analysis for the Global Burden of Disease Study 2019
Get PDFBackground
Human resources for health (HRH) include a range of occupations that aim to promote or improve human health. The UN Sustainable Development Goals (SDGs) and the WHO Health Workforce 2030 strategy have drawn attention to the importance of HRH for achieving policy priorities such as universal health coverage (UHC). Although previous research has found substantial global disparities in HRH, the absence of comparable cross-national estimates of existing workforces has hindered efforts to quantify workforce requirements to meet health system goals. We aimed to use comparable and standardised data sources to estimate HRH densities globally, and to examine the relationship between a subset of HRH cadres and UHC effective coverage performance.
Methods
Through the International Labour Organization and Global Health Data Exchange databases, we identified 1404 country-years of data from labour force surveys and 69 country-years of census data, with detailed microdata on health-related employment. From the WHO National Health Workforce Accounts, we identified 2950 country-years of data. We mapped data from all occupational coding systems to the International Standard Classification of Occupations 1988 (ISCO-88), allowing for standardised estimation of densities for 16 categories of health workers across the full time series. Using data from 1990 to 2019 for 196 of 204 countries and territories, covering seven Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) super-regions and 21 regions, we applied spatiotemporal Gaussian process regression (ST-GPR) to model HRH densities from 1990 to 2019 for all countries and territories. We used stochastic frontier meta-regression to model the relationship between the UHC effective coverage index and densities for the four categories of health workers enumerated in SDG indicator 3.c.1 pertaining to HRH: physicians, nurses and midwives, dentistry personnel, and pharmaceutical personnel. We identified minimum workforce density thresholds required to meet a specified target of 80 out of 100 on the UHC effective coverage index, and quantified national shortages with respect to those minimum thresholds.
Findings
We estimated that, in 2019, the world had 104·0 million (95% uncertainty interval 83·5–128·0) health workers, including 12·8 million (9·7–16·6) physicians, 29·8 million (23·3–37·7) nurses and midwives, 4·6 million (3·6–6·0) dentistry personnel, and 5·2 million (4·0–6·7) pharmaceutical personnel. We calculated a global physician density of 16·7 (12·6–21·6) per 10 000 population, and a nurse and midwife density of 38·6 (30·1–48·8) per 10 000 population. We found the GBD super-regions of sub-Saharan Africa, south Asia, and north Africa and the Middle East had the lowest HRH densities. To reach 80 out of 100 on the UHC effective coverage index, we estimated that, per 10 000 population, at least 20·7 physicians, 70·6 nurses and midwives, 8·2 dentistry personnel, and 9·4 pharmaceutical personnel would be needed. In total, the 2019 national health workforces fell short of these minimum thresholds by 6·4 million physicians, 30·6 million nurses and midwives, 3·3 million dentistry personnel, and 2·9 million pharmaceutical personnel.
Interpretation
Considerable expansion of the world's health workforce is needed to achieve high levels of UHC effective coverage. The largest shortages are in low-income settings, highlighting the need for increased financing and coordination to train, employ, and retain human resources in the health sector. Actual HRH shortages might be larger than estimated because minimum thresholds for each cadre of health workers are benchmarked on health systems that most efficiently translate human resources into UHC attainment.
Funding
Bill & Melinda Gates Foundation
Garmin wearable device offers reliable alternative for on-water stroke rate and velocity measurement in rowing
No full textPerformance tracking devices in the form of wrist-worn watches are common in rowing; however, the accuracy of relevant output variables (i.e. stroke rate [SR] and velocity) during on-water training is unknown. To assess the quality of wrist-watch data output, 16 rowing athletes recorded 118 on-water rowing sessions using a Garmin Forerunner 735XT, which was compared to a Catapult Optimeye R4 tracking device. Garmin recording function was set to ‘Every Second’ (N = 68 sessions) or ‘Smart’ (N = 50 sessions). Catapult velocity was calculated as the average velocity per stroke, while a 15 s velocity moving average was determined for Garmin data. Catapult and Garmin were filtered for training-specific data (SR = 14–50 strokes per minute [spm]; velocity = 2.1–7.0 m/s−1). Efficacy and reliability of the Garmin was assessed via the difference between devices (% error), intra-class correlation coefficient (ICC ± 95% confidence interval (CI)) and coefficient of variation (CV%). Error in 15 s smoothed velocity was 3.8% (‘Every Second’) and 8.2% (‘Smart’). Both recording functions demonstrated ‘good’ reliability (ICC = 0.75–0.9, CV < 10%) for SR and velocity; the exception was SR using ‘Smart’ recording. Our data suggests that when using the ‘Every Second’ recording function, data is filtered and velocity is smoothed over 15 s, the Garmin device can be reliable for SR and velocity measurement within 1 spm and <0.20 m/s−1 respectively
Growth and yield responses of sunflower to drainage in waterlogged saline soil are caused by changes in plant-water relations and ion concentrations in leaves
Get PDFPurpose
While well-designed drainage systems could improve crop growth and yield by mitigating waterlogging and salinity stresses, field evidence of the yield responses to changes in plant-water relations and ion concentrations in leaves is scarce. We investigated the changes in ion concentrations in leaves and plant-water relations of sunflower caused by drainage in waterlogged saline soil, and their relationships to growth and yield.
Methods
Over two growing seasons, we tested four drainage treatments: undrained, surface drains (SD; 0.1 m deep, 1.8 m apart), subsoil drains (SSD; 0.5 m deep, 4.5 m apart) and SSD + SD. All plots were inundated (2–3 cm depth; water salinity, ECw, 1.5–2.5 dS m–1) for 24 h at vegetative emergence and at the 8-leaf stage before opening drains.
Results
Relative to the most drained treatment (SSD + SD), the undrained treatment caused higher waterlogging at 0–30 cm depth, and decreased solute potential (Ψs) of soil at 7.5 cm to 52–374 kPa, leaf K+ by 5–20%, stomatal conductance by 5–37% and leaf greenness by 12–25%, but increased leaf Na+ by 25–70%, Na+/K+ ratio by 38–100% and leaf water potential by 90–250 kPa throughout the cropping season; these changes were closely related to reduced growth and yield.
Conclusions
The improved yield from the combination of shallow surface and sub-surface drains was attributed to an alleviation of salinity-waterlogging stress early in the season and to increased soil water late in the season that increased Ψs and decreased Na+/K+ ratio in leaves