Use of Multiple Irradiations and Reference Materials as Comparators in Quality Control of Neutron Activation Analysis Data of Biological Samples.

We propose that several different reactor irradiation times followed by assaying of activity for differential counting periods may be employed for quality control (QC) of neutron activation analysis (NAA) data of biological samples. It is also recommended that three to four reference materials (RMs) of similar matrix but from different agencies such as National Institute of Standards and Technology (NIST, USA), International Atomic Energy Agency (IAEA, Vienna), Institute of Nuclear Chemistry and Technology (INCT, Poland), and National Institute of Environmental Studies (NIES, Japan) including a synthetic multielemental primary standard should always be analyzed simultaneously along with the samples. Finally, the mean ± σ values so obtained may be considered as more reliable after statistical analysis. Our analytical data for Na and K in three RMs (SRM 1572, CRM H-9, and Bowen's Kale) using different irradiation periods of 15 m, 2 h, 6 h, and 1 day were comparable with the certified values within error range of + 0.2 to - 2.7%. We report our data for 20 elements in two candidate RMs corn flour (INCT-CF-3) and soya bean flour (INCT-SBF-4) from the INCT, Poland, where Z-score values for most elements are in reasonable range of certified values.

Exploring the association between microbiota and behaviour in suckling piglets.

It is increasingly recognised that the microbes residing in the gastrointestinal tract can influence brain physiology and behaviour, via the microbiota-gut-brain axis. Here, we made a first explorative evaluation at the association between the gut microbiota and behaviour in suckling piglets. 16S microbiota profiling information was obtained from two independent replicate experiments at 2 and 4 weeks of age. Piglets underwent a backtest to assess their personality or coping style at 2 weeks of age, and were subjected to a combined open field and novel object test at 3.5 weeks of age, recording anxiety-related and exploratory behaviour. The number of squeals vocalised during the open field test was associated with microbial groups such as Coprococcus 3 and CAG-873, whereas in the novel object test, explorative behaviour was significantly associated with microbial genera like Atopobium and Prevotella. Overall, this study explores the microbiota-behavioural relation by employing multivariate analysis and exemplifies the importance of individualised analyses when evaluating such relationships.

Role of Rotaviral Antigen Detection by ICT in Acute Diarrhoeic Children below 5 Years in a Tertiary Care Hospital of Bangladesh.

Rotavirus is responsible for acute severe watery diarrhoea in young children. Early and rapid detection of Rotavirus infection can help to reduce inappropriate administration of antibiotics and has future positive impact on prevention of drug resistance. This cross-sectional study was designed to determine the role of Rotaviral antigen detection by ICT from stool sample of acute diarrhoeal children below five years admitted in Sylhet MAG Osmani Medical College Hospital, Sylhet and was carried out in the Department of Microbiology in collaboration with the Department of Paediatrics during the period from 1st January 2018 to 31st December 2018. Total 184 children of under five years of age with acute watery diarrhoea were enrolled in this study. Rotaviral antigen was detected by ELISA (Enzyme Linked Immunosorbent Assay) and ICT (Immunochromatographic test) from stool samples. Out of 184 stool samples, Rotaviral antigen was found positive in 84 and 86 cases by ICT and ELISA methods, respectively. ICT showed sensitivity of 90.70% and specificity of 93.88% when compared with ELISA. The Rotavirus infection was found highest in male children (61.90%) and in age group of 7 to 12 months (51.89%). Considering the importance of Rotaviral diarrhoea, rapid detection of Rotavirus infection by ICT is essentially needed and might be practiced routinely as it is relatively reliable, easy to perform and cost-effective. It is particularly important in Bangladesh, where diarrhoea is still contributing a significant proportion of morbidity and mortality in under five children.

Efficacy of mupirocin, neomycin and octenidine for nasal Staphylococcus aureus decolonisation: a retrospective cohort study.

BACKGROUND: Periprosthetic joint infection (PJI) causes significant morbidity. Methicillin sensitive Staphylococcus aureus (MSSA) is the most frequent organism, and the majority are endogenous. Decolonisation reduces PJIs but there is a paucity of evidence comparing treatments. Aims; compare 3 nasal decolonisation treatments at (1) achieving MSSA decolonisation, (2) preventing PJI. METHODS: Our hospital prospectively collected data on our MSSA decolonisation programme since 2013, including; all MSSA carriers, treatment received, MSSA status at time of surgery and all PJIs. Prior to 2017 MSSA carriers received nasal mupirocin or neomycin, from August 2017 until August 2019 nasal octenidine was used. RESULTS: During the study period 15,958 primary hip and knee replacements were performed. 3200 (20.1%) were MSSA positive at preoperative screening and received decolonisation treatment, 698 mupirocin, 1210 neomycin and 1221 octenidine. Mupirocin (89.1%) and neomycin (90.9%) were more effective at decolonisation than octenidine (50.0%, P < 0.0001). There was no difference in PJI rates (P = 0.452). CONCLUSIONS: Mupirocin and neomycin are more effective than octenidine at MSSA decolonisation. There was poor correlation between the MSSA status after treatment (on day of surgery) and PJI rates. Further research is needed to compare alternative MSSA decolonisation treatments.

Where to Invest Project Efforts for Greater Benefit: A Framework for Management Performance Mapping with Examples for Potato Seed Health.

Policymakers and donors often need to identify the locations where technologies are most likely to have important effects, to increase the benefits from agricultural development or extension efforts. Higher-quality information may help to target the high-benefit locations, but often actions are needed with limited information. The value of information (VOI) in this context is formalized by evaluating the results of decision making guided by a set of specific information compared with the results of acting without considering that information. We present a framework for management performance mapping that includes evaluating the VOI for decision making about geographic priorities in regional intervention strategies, in case studies of Andean and Kenyan potato seed systems. We illustrate the use of recursive partitioning, XGBoost, and Bayesian network models to characterize the relationships among seed health and yield responses and environmental and management predictors used in studies of seed degeneration. These analyses address the expected performance of an intervention based on geographic predictor variables. In the Andean example, positive selection of seed from asymptomatic plants was more effective at high altitudes in Ecuador. In the Kenyan example, there was the potential to target locations with higher technology adoption rates and with higher potato cropland connectivity, i.e., a likely more important role in regional epidemics. Targeting training to high management performance areas would often provide more benefits than would random selection of target areas. We illustrate how assessing the VOI can contribute to targeted development programs and support a culture of continuous improvement for interventions.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Early life feeding accelerates gut microbiome maturation and suppresses acute post-weaning stress in piglets.

Early life microbiome perturbations can have important effects on host development, physiology and behaviour. In this longitudinal study, we evaluated the impact of early feeding on gut microbiome colonization in neonatal piglets. Early-fed (EF) piglets had access to a customized fibrous diet from 2 days after birth until weaning in addition to mother's milk, whereas control piglets suckled mother's milk only. Rectal swabs were collected at multiple time points until 6 weeks of age to investigate microbiota development using 16S rRNA gene profiling. The dynamic pre-weaning microbiota colonization was followed by a relatively stable post-weaning microbiota, represented by Prevotella, Roseburia, Faecalibacterium, Ruminococcus, Megasphaera, Catenibacterium and Subdoligranulum. EF piglets showed an accelerated microbiota maturation, characterized by increased microbial diversity, pre-weaning emergence of post-weaning-associated microbes and a more rapid decline of typical pre-weaning microbes. Furthermore, the individual eating behaviour scores of piglets quantitatively correlated with their accelerated microbiome. Importantly, EF piglets displayed a smoother relative weight gain and tended to reach a higher relative weight gain, in addition to reduced diarrhoea scores in the first week post-weaning. Overall, these findings demonstrate the beneficial impact of early feeding on microbiota development as well as pig health and performance during the weaning transition.

Impact of early-life feeding on local intestinal microbiota and digestive system development in piglets.

Early-life gut microbial colonisation is known to influence host physiology and development, shaping its phenotype. The developing gastro-intestinal tract of neonatal piglets provides a "window of opportunity" for programming their intestinal microbiota composition and corresponding intestinal development. Here, we investigated the impact of early feeding on jejunum and colon microbiota composition, and intestinal maturation in suckling piglets. From two days of age, early-fed (EF; n = 6 litters) piglets had access to solid feed containing a mixture of fibres till weaning (day29) in addition to sow's milk, whereas the control (CON; n = 6 litters) piglets exclusively fed on sow's milk. Early feeding elicited a significant impact on the colon microbiota, whereas no such effect was seen in the jejunal and ileal microbiota. Quantified eating behavioural scores could significantly explain the variation in microbiota composition of EF piglets and support their classification into good, moderate, and bad eaters. Members of the Lachnospiraceae family, and the genera Eubacterium, Prevotella, and Ruminococcus were quantitatively associated with eating scores. EF piglets were found to have a decreased pH in caecum and colon, which coincided with increased short-chain fatty acid (SCFA) concentrations. Moreover, they also had increased weights and lengths of several intestinal tract segments, as well as a decreased villus-crypt ratio in jejunal mucosa and an increased abundance of proliferative cells in colon mucosa. The approaches in this study indicate that early feeding of a mixed-fibre (pre-weaning) diet changes the microbiota composition, pH, and fermentation products in the distal gut of piglets, while it also alters both macroscopic and microscopic intestinal measurements. These results exemplify the potential of early feeding to modulate intestinal development in young piglets.

Risk factors associated with morbidity and mortality outcomes of COVID-19 patients on the 28th day of the disease course: a retrospective cohort study in Bangladesh.

Diverse risk factors intercede the outcomes of coronavirus disease 2019 (COVID-19). We conducted this retrospective cohort study with a cohort of 1016 COVID-19 patients diagnosed in May 2020 to identify the risk factors associated with morbidity and mortality outcomes. Data were collected by telephone-interview and reviewing records using a questionnaire and checklist. The study identified morbidity and mortality risk factors on the 28th day of the disease course. The majority of the patients were male (64.1%) and belonged to the age group 25-39 years (39.4%). Urban patients were higher in proportion than rural (69.3% vs. 30.7%). Major comorbidities included 35.0% diabetes mellitus (DM), 28.4% hypertension (HTN), 16.6% chronic obstructive pulmonary disease (COPD), and 7.8% coronary heart disease (CHD). The morbidity rate (not-cured) was 6.0%, and the mortality rate (non-survivor) was 2.5%. Morbidity risk factors included elderly (AOR = 2.56, 95% CI = 1.31-4.99), having comorbidity (AOR = 1.43, 95% CI = 0.83-2.47), and smokeless tobacco use (AOR = 2.17, 95% CI = 0.84-5.61). The morbidity risk was higher with COPD (RR = 2.68), chronic kidney disease (CKD) (RR = 3.33) and chronic liver disease (CLD) (RR = 3.99). Mortality risk factors included elderly (AOR = 7.56, 95% CI = 3.19-17.92), having comorbidity (AOR = 5.27, 95% CI = 1.88-14.79) and SLT use (AOR = 1.93, 95% CI = 0.50-7.46). The mortality risk was higher with COPD (RR = 7.30), DM (RR = 2.63), CHD (RR = 4.65), HTN (RR = 3.38), CKD (RR = 9.03), CLD (RR = 10.52) and malignant diseases (RR = 9.73). We must espouse programme interventions considering the morbidity and mortality risk factors to condense the aggressive outcomes of COVID-19.

Erratum: Evolution of π

This corrects the article DOI: 10.1103/PhysRevLett.109.152301.

Effective Altruism as an Ethical Lens on Research Priorities.

Effective altruism is an ethical framework for identifying the greatest potential benefits from investments. Here, we apply effective altruism concepts to maximize research benefits through identification of priority stakeholders, pathosystems, and research questions and technologies. Priority stakeholders for research benefits may include smallholder farmers who have not yet attained the minimal standards set out by the United Nations Sustainable Development Goals; these farmers would often have the most to gain from better crop disease management, if their management problems are tractable. In wildlands, prioritization has been based on the risk of extirpating keystone species, protecting ecosystem services, and preserving wild resources of importance to vulnerable people. Pathosystems may be prioritized based on yield and quality loss, and also factors such as whether other researchers would be unlikely to replace the research efforts if efforts were withdrawn, such as in the case of orphan crops and orphan pathosystems. Research products that help build sustainable and resilient systems can be particularly beneficial. The "value of information" from research can be evaluated in epidemic networks and landscapes, to identify priority locations for both benefits to individuals and to constrain regional epidemics. As decision-making becomes more consolidated and more networked in digital agricultural systems, the range of ethical considerations expands. Low-likelihood but high-damage scenarios such as generalist doomsday pathogens may be research priorities because of the extreme potential cost. Regional microbiomes constitute a commons, and avoiding the "tragedy of the microbiome commons" may depend on shifting research products from "common pool goods" to "public goods" or other categories. We provide suggestions for how individual researchers and funders may make altruism-driven research more effective.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Legitimate and Reliable Determination of the Age-Related Intestinal Microbiome in Young Piglets; Rectal Swabs and Fecal Samples Provide Comparable Insights.

A prerequisite for reliable microbiota analysis is having an effective and consistent sampling method. Fecal sampling, commonly used to study the intestinal microbiome, might not be suitable in all situations, especially considering the potential difficulties in obtaining fresh feces from young animals. Indeed, this study shows that the success rate of collecting fecal samples from young piglets (<2 weeks of age) was very low. Therefore, we evaluated rectal swabs as an alternative sample type (to feces) for studying porcine microbiome development and performed a comparative analysis of microbiome composition obtained from fresh fecal samples and rectal swabs in 15 healthy piglets at seven (6 piglets) and 20 (9 piglets) days of age. Three samples (fresh feces, rectal swab before and after defecation) were collected from individual piglets and microbiome composition was assessed by 16S rRNA gene sequencing. The results demonstrated that rectal swabs and fecal samples provide similar microbiome composition profiles, with samples clustering predominantly by individual animal rather than sample type. Furthermore, regardless of the sample type, the biological interpretation with respect to microbiota colonization patterns associated with different ages (7 and 20 days) was found to be comparable. Independent of sample type, we observed age-related changes like increasing microbiota diversity and alterations in relative abundances of the phyla Firmicutes, Bacteroidetes, and Fusobacteria, which was also reflected in consistent family- and genus-level microbiota changes. This study establishes that rectal swabs are a suitable alternative sample type to study the porcine microbiome development in early life, when fecal sampling is challenging.

Summary Measures of Predictive Power Associated with Logistic Regression Models of Disease Risk.

For an ordinary least-squares regression model, the coefficient of determination (R2) describes the proportion (or percentage) of variance of the response variable explained by the model, and is a widely accepted summary measure of predictive power. A number of R2-analogues are available as summary measures of predictive power associated with logistic regression models, including models of disease risk. Tjur's R2 and McFadden's R2 are of particular interest in this context. Both of these metrics have transparent derivations, which reveal that they apply to different aspects of model evaluation. Tjur's R2 is a measure of separation between (known) actual states (e.g., gold standard determinations of "healthy" or "diseased" status) whereas McFadden's R2 is a measure of separation between predicted states (e.g., forecasts of disease status based on models of disease risk). This clarifies their interpretation in the context of evaluation of logistic regression models of disease risk. In addition, versions of both Tjur's R2 and McFadden's R2 may be obtained from analyses of disease risk that are not preceded by logistic regression analysis. Tjur's R2 and McFadden's R2 are shown to be useful, distinct summary measures of predictive power for epidemiological models of disease risk.

Comparison among Different Culture Media for the Detection of Dermatophytes.

Dermatophytes are a group of closely related fungi that have the capacity of invading the keratinized tissue of human to produce infections known as dermatophytosis which is commonly referred to as ringworm. Other than routine microscopy, different culture media are available for the detection of dermatophytes from patient's specimen. This cross sectional study was designed to evaluate the outcome of three different culture media and microscopy for the detection of dermatophytes from clinical samples. Skin, hair and nail samples from 84 clinically suspected cases of dermatophytosis who attended at OPD of Dermatology Department, Sylhet MAG Osmani Medical College Hospital, Sylhet, Bangladesh from July 2014 to June 2015 were screened by direct microscopic examination using potassium hydroxide (KOH) mount. All the samples were inoculated for culture in Sabouraud's Dextrose Agar (SDA), Dermatophytes Test medium (DTM) and Sabouraud's Cycloheximide Chloramphenicol Agar (SCCA). The percentage of samples positive by microscopy was 37.5%, whereas the rate of positivity by culture was 47.6% which showed that culture was more sensitive than microscopy for the diagnosis of dermatophytosis. The efficiency of SDA and SCCA was found to be almost equal. There was no statistically significant difference between SDA and DTM in primary isolation of dermatophytes, though isolation rate was slightly higher in DTM. Though direct examination by microscopy is an efficient screening technique, culture should be done for accurate diagnosis. As DTM is easy to evaluate even without handling the growth of culture in the laboratory, it is recommended to use as screening medium for the detection of dermatophytes.

Network Analysis: A Systems Framework to Address Grand Challenges in Plant Pathology.

Plant pathology must address a number of challenges, most of which are characterized by complexity. Network analysis offers useful tools for addressing complex systems and an opportunity for synthesis within plant pathology and between it and relevant disciplines such as in the social sciences. We discuss applications of network analysis, which ultimately may be integrated together into more synthetic analyses of how to optimize plant disease management systems. The analysis of microbiome networks and tripartite phytobiome networks of host-vector-pathogen interactions offers promise for identifying biocontrol strategies and anticipating disease emergence. Linking epidemic network analysis with social network analysis will support strategies for sustainable agricultural development and for scaling up solutions for disease management. Statistical tools for evaluating networks, such as Bayesian network analysis and exponential random graph models, have been underused in plant pathology and are promising for informing strategies. We conclude with research priorities for network analysis applications in plant pathology.

The Impact of Aquifer Flushing on Groundwater Arsenic Across a 35-km Transect Perpendicular to the Upper Brahmaputra River in Assam, India.

Well testing in the floodplain of the Brahmaputra River in Golaghat and Jorhat districts of Assam, India, shows that groundwater arsenic (As) concentrations increase with distance from the river. To establish the origin of this pattern, an additional 900 wells <60 m deep were tested for As and 9 sites were drilled along a 35-km transect perpendicular to the river. The field data show no relation between groundwater As concentrations ranging from <1 to 660 µg/L along the transect and (a) As concentrations of <1-5 mg/kg in cuttings of aquifer sand recovered while drilling or (b) the degree of reduction of iron oxides in these cuttings. The drilling indicates, however, a marked increase in the thickness of a clay layer capping the aquifer starting from <1-5 m near the river to over 60 m at the most distant site towards the base of the Naga foothills. Organic radiocarbon ages of 18-46 kyr obtained from all but one of 13 clay samples indicate pre-Holocene deposition of the underlying sands across the entire transect. Radiocarbon ages of dissolved inorganic carbon of 0.2, 4.7, and 17.8 kyr were measured in groundwater from 3 monitoring wells installed to 30-60 m depth at distances of 10, 20, and 40 km from the river, respectively. A conceptual groundwater flow model consistent with monitored heads and groundwater ages suggests that thick clay layers capping the aquifer further from the river inhibited flushing of the aquifer and, as a result, preserved higher As levels in groundwater.

Effect of cationic substitution on the double-well hydrogen-bond potential in [K1-x(NH4)x]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study.

The structure of the mixed crystal [K1-x(NH4)x]3H(SO4)2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K3H(SO4)2. The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K+ with NH4+ has a significant influence on the short strong hydrogen bond connecting the two SO42- ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K1-x(NH4)x]3H(SO4)2 are much faster than in K3H(SO4)2; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

Spatiotemporal Patterns in the Airborne Dispersal of Spinach Downy Mildew.

Downy mildew is the most devastating disease threatening sustainable spinach production, particularly in the organic sector. The disease is caused by the biotrophic oomycete pathogen Peronospora effusa, and the disease results in yellow lesions that render the crop unmarketable. In this study, the levels of DNA from airborne spores of P. effusa were assessed near a field of susceptible plants in Salinas, CA during the winter months of 2013-14 and 2014/15 using rotating-arm impaction spore-trap samplers that were assessed with a species-specific quantitative polymerase chain reaction (qPCR) assay. Low levels of P. effusa DNA were detectable from December through February in both winters but increased during January in both years, in correlation with observed disease incidence; sharp peaks in P. effusa DNA detection were associated with the onset of disease incidence. The incidence of downy mildew in the susceptible field displayed logistic-like dynamics but with considerable interseason variation. Analysis of the area under the disease progress curves suggested that the 2013-14 epidemic was significantly more severe than the 2014-15 epidemic. Spatial analyses indicated that disease incidence was dependent within an average range of 5.6 m, approximately equivalent to the width of three planted beds in a typical production field. The spatial distribution of spores captured during an active epidemic most closely fit a power-law distribution but could also be fit with an exponential distribution. These studies revealed two important results in the epidemiology of spinach downy mildew in California. First, they demonstrated the potential of impaction spore-trap samplers linked with a qPCR assay for indicating periods of high disease risk, as well as the detection of long-distance dispersal of P. effusa spores. Second, at the scale of individual crops, a high degree of spatial aggregation in disease incidence was revealed.

Season-Long Dynamics of Spinach Downy Mildew Determined by Spore Trapping and Disease Incidence.

Peronospora effusa is an obligate oomycete that causes downy mildew of spinach. Downy mildew threatens sustainable production of fresh market organic spinach in California, and routine fungicide sprays are often necessary for conventional production. In this study, airborne P. effusa spores were collected using rotating arm impaction spore trap samplers at four sites in the Salinas Valley between late January and early June in 2013 and 2014. Levels of P. effusa DNA were determined by a species-specific quantitative polymerase chain reaction assay. Peronospora effusa was detected prior to and during the growing season in both years. Nonlinear time series analyses on the data suggested that the within-season dynamics of P. effusa airborne inoculum are characterized by a mixture of chaotic, deterministic, and stochastic features, with successive data points somewhat predictable from the previous values in the series. Analyses of concentrations of airborne P. effusa suggest both an exponential increase in concentration over the course of the season and oscillations around the increasing average value that had season-specific periodicity around 30, 45, and 75 days, values that are close to whole multiples of the combined pathogen latent and infectious periods. Each unit increase in temperature was correlated with 1.7 to 6% increased odds of an increase in DNA copy numbers, while each unit decrease in wind speed was correlated with 4 to 12.7% increased odds of an increase in DNA copy numbers. Disease incidence was correlated with airborne P. effusa levels and weather variables, and a receiver operating characteristic curve analysis suggested that P. effusa DNA copy numbers determined from the spore traps nine days prior to disease rating could predict disease incidence.

Recovery practice in community mental health teams: national survey.

BACKGROUND: There is consensus about the importance of 'recovery' in mental health services, but the link between recovery orientation of mental health teams and personal recovery of individuals has been underresearched. AIMS: To investigate differences in team leader, clinician and service user perspectives of recovery orientation of community adult mental health teams in England. METHOD: In six English mental health National Health Service (NHS) trusts, randomly chosen community adult mental health teams were surveyed. A random sample of ten patients, one team leader and a convenience sample of five clinicians were surveyed from each team. All respondents rated the recovery orientation of their team using parallel versions of the Recovery Self Assessment (RSA). In addition, service users also rated their own personal recovery using the Questionnaire about Processes of Recovery (QPR). RESULTS: Team leaders (n = 22) rated recovery orientation higher than clinicians (n = 109) or patients (n = 120) (Wald(2) = 7.0, P = 0.03), and both NHS trust and team type influenced RSA ratings. Patient-rated recovery orientation was a predictor of personal recovery (b = 0.58, 95% CI 0.31-0.85, P<0.001). Team leaders and clinicians with experience of mental illness (39%) or supporting a family member or friend with mental illness (76%) did not differ in their RSA ratings from other team leaders or clinicians. CONCLUSIONS: Compared with team leaders, frontline clinicians and service users have less positive views on recovery orientation. Increasing recovery orientation may support personal recovery.