Semi-quantitative Surveys Research Articles

Implementing SARS-CoV-2 antigen testing scale-up in Rwanda: retrospective analysis of national programme data and qualitative findings

ObjectivesReverse transcriptase PCR is the most sensitive test for SARS-CoV-2 diagnosis. However, the scale-up of these tests in low-income and middle-income countries (LMICs) has been limited due to infrastructure and...

A framework for evaluating health system surveillance sensitivity to support public health decision-making for malaria elimination: a case study from Indonesia

BackgroundThe effectiveness of a surveillance system to detect infections in the population is paramount when confirming elimination. Estimating the sensitivity of a surveillance system requires identifying key steps in the care-seeking cascade, from initial infection to confirmed diagnosis, and quantifying the probability of appropriate action at each stage. Using malaria as an example, a framework was developed to estimate the sensitivity of key components of the malaria surveillance cascade.MethodsParameters to quantify the sensitivity of the surveillance system were derived from monthly malaria case data over a period of 36 months and semi-quantitative surveys in 46 health facilities on Java Island, Indonesia. Parameters were informed by the collected empirical data and estimated by modelling the flow of an infected individual through the system using a Bayesian framework. A model-driven health system survey was designed to collect empirical data to inform parameter estimates in the surveillance cascade.ResultsHeterogeneity across health facilities was observed in the estimated probability of care-seeking (range = 0.01–0.21, mean ± sd = 0.09 ± 0.05) and testing for malaria (range = 0.00–1.00, mean ± sd = 0.16 ± 0.29). Care-seeking was higher at facilities regularly providing antimalarial drugs (Odds Ratio [OR] = 2.98, 95% Credible Intervals [CI]: 1.54–3.16). Predictably, the availability of functioning microscopy equipment was associated with increased odds of being tested for malaria (OR = 7.33, 95% CI = 20.61).ConclusionsThe methods for estimating facility-level malaria surveillance sensitivity presented here can help provide a benchmark for what constitutes a strong system. The proposed approach also enables programs to identify components of the health system that can be improved to strengthen surveillance and support public-health decision-making.

Influence of wastewater discharges on benthic macroinvertebrate communities in a cantabrian-atlantic coastal river

This paper studies the effect of wastewater discharges on benthic macroinvertebrates in the Furnia River (Pontevedra, NW Spain). Semiquantitative surveys were carried out in spring 2008 and 2017 in three different locations, upstream and downstream of a sewage treatment plant built in 2013. Different indexes were calculated based on benthic macroinvertebrate assemblages: abundance, richness, Shannon-Wiener, EPT, IASPT, IBMWP and several physicochemical variables were measured concurrently. Although the indexes values decreased slightly along the water course, the results indicate an optimal water quality of the Furnia River, supporting a very diverse community of aquatic macroinvertebrates.

A Framework for Evaluating Health System Surveillance Sensitivity to Support Public Health Decision-Making for Malaria Elimination: A Case Study from Indonesia

Background: The effectiveness of a surveillance system to detect infections in the population is paramount when confirming elimination. Estimating the sensitivity of a health system requires identifying key steps in the cascade, from initial infection to confirmed diagnosis, and quantifying the probability of appropriate action at each stage. Using malaria as an example, a framework was developed to estimate the sensitivity of key components of the malaria surveillance cascade. Methods: Parameters to quantify the sensitivity of the surveillance system were derived from monthly malaria case data over a period of 36 months and semi-quantitative surveys in 46 health facilities on Java Island, Indonesia. Parameters were estimated by modelling the flow of an infected individual through the system and the underlying expected malaria cases in the population using autoregressive spatio-temporal models in a joint inferential Bayesian framework. A model-driven health system survey was designed to collect empirical data to inform parameter estimates in the surveillance cascade. Findings: Heterogeneity across health facilities was observed in the estimated probability of care-seeking (Range=0.012 - 0.191) and testing for malaria (Range=0.000 - 0.630). Care-seeking was higher at facilities regularly providing antimalarial drugs (odds ratio = 1.48, credible intervals: 1.47/1.48). Predictably, the availability of functioning microscopy equipment was associated with increased odds of being tested for malaria (odds ratio = 136.0, credible intervals = 92.08/199.30). Interpretation: Methods for estimating facility-level malaria surveillance sensitivity, particularly in areas targeting elimination, can help provide a benchmark and identify components of the health system that can be improved to strengthen surveillance to support public-health decision-making. Funding Information: This study was funded by the Bill and Melinda Gates Foundation (grant OPP1177272) awarded to GS and CD and by the Indonesia Endowment Fund for Education (Lembaga Pengelola Dana Pendidikan Indonesia; grant: 20151022084537) awarded to HS. Declaration of Interests: We declare no competing interests.

Perception of ecosystem services and disservices on a peri-urban communal forest: Are landowners’ and visitors’ perspectives dissimilar?

Galician communal forests are private lands collectively owned by the neighbours of the rural settlement where they are located. Their societal role shifted from the support of the traditional agrarian system in the past, to a variety of situations nowadays. The intrinsic characteristics of these social-ecological units make them a promising opportunity for rural development in the region that calls for more scientific attention on the arena of ecosystem services. In this study, we investigated the social perception and valuation of a comprehensive range of ecosystem services and disservices on the peri-urban communal forests of Mount Xalo (NW Spain), distinguishing among the perspectives of landowners and various visitor types. For this, we used a socio-cultural approach consisting of 175 semi-quantitative surveys that included a basic Public Participation Geographic Information System. Our results showed that Mt. Xalo is a well recognised provider of ecosystem services that constitutes a local hotspot in the region. The most frequently perceived and most valued ecosystem services within ecosystem services classes were the provision of drinking water, the practice of sports, climate regulation and a group of three cognitive cultural ecosystem services: socializing, mythical features and sense of place. Nevertheless, nuances were noticed among landowners and visitor types following a rural–urban gradient where landowners and urban users presented the most significant differences. These findings address recognition to the actual role of these communal forests for society and call for collaboration with public institutions to facilitate the sustainable management of their resources.

An updated phytoplankton check-list for the Helgoland Roads time series station with eleven new records of diatoms and dinoflagellates

The Helgoland Roads time series is one of the longest and most detailed time series in the world. It comprises daily phytoplankton counts accompanied by physico-chemical measurements. As such, it provides valuable long-term record of changes and their underlying causes in the phytoplankton community around Helgoland. This work provides an updated check-list of the phytoplankton species encountered at the Helgoland Roads LTER station with additional taxonomic assessments from live net samples and scanning electron microscope surveys. Since the last check-list was published 11 additional taxa have been recorded for the first time comprising 9 diatom and 2 dinoflagellate species. Of the 9 diatom species 3 were Chaetoceros species: Chaetoceros anastomosans, C. pseudocurvisetus and C. lorenzianus (the latter identified by their resting cysts) which were all first recognised in September 2009. The toxic dinoflagellate Dinophysis tripos, and the bipolar centric diatom Odontella longicruris both were first observed in September 2015. The latest new record is the potentially toxic dinoflagellate Alexandrium ostenfeldii, first recorded in August 2017. All of the first records (with the exception of Dinophysis tripos) were first observed in semi-quantitative surveys based on live samples and SEM demonstrating that adding less frequent but very detailed assessments can complement high frequency counts of fixed samples as long as these data of different origin are linked efficiently to the individual sampling event and all metadata including representative pictorial metadata are recorded in a consistent manner. In this manner the enhanced checklist serves as a baseline against which long-term changes in phytoplankton potentially related to ecosystem state can be addressed.

Changes in Freshwater Mussel Communities Linked to Legacy Pollution in the Lower Delaware River

Freshwater mussels are among the most-imperiled organisms worldwide, although they provide a variety of important functions in the streams and rivers they inhabit. Among Atlantic-slope rivers, the Delaware River is known for its freshwater mussel diversity and biomass; however, limited data are available on the freshwater mussel fauna in the lower, non-tidal portion of the river. This section of the Delaware River has experienced decades of water-quality degradation from both industrial and municipal sources, primarily as a function of one of its major tributaries, the Lehigh River. We completed semi-quantitative snorkel surveys in 53.5 of the 121 km of the river to document mussel community composition and the continued impacts from pollution (particularly inputs from the Lehigh River) on mussel fauna. We detected changes in mussel catch per unit effort (CPUE) below the confluence of the Lehigh River, with significant declines in the dominant species Elliptio complanata (Eastern Elliptio) as we moved downstream from its confluence—CPUE dropped from 179 to 21 mussels/h. Patterns in mussel distribution around the Lehigh confluence matched chemical signatures of Lehigh water input. Specifically, Eastern Elliptio CPUE declined more quickly moving downstream on the Pennsylvania bank, where Lehigh River water input was more concentrated compared to the New Jersey bank. A definitive causal link remains to be established between the Lehigh River and the dramatic shifts in mussel community composition, warranting continued investigation as it relates to mussel conservation and restoration in the basin.

A comparison of mollusc diversity between the relatively pristine Marico River and the impacted Crocodile River, two major tributaries of the Limpopo River, South Africa

A study of the freshwater mollusc diversity was conducted at selected sites in the relatively pristine Marico River and the impacted Crocodile River, the major tributaries of the Limpopo River. Four surveys were conducted, two in an early (May 2013 and 2014) and two in a late (November 2013 and 2014) low-flow period. Semi-quantitative surveys were done by sampling the vegetation, as well as the substratum, with a standard SASS net for approximately 15 min each. Environmental parameters including water temperature, electrical conductivity (EC) and pH were measured at each site. Molluscs were identified up to species level, sorted, counted, and the presence of juvenile specimens recorded. Historical data for the 1/16 th degree square grids (loci), in which each of the sampling sites of the current study was located, were extracted from the National Freshwater Snail Collection at the Unit for Environmental Sciences and Management, Potchefstroom Campus of the North-West University. During this study, 20 and 9 species were recovered from the Marico and Crocodile Rivers, respectively, as compared to 13 and 12 species on record for these loci, respectively. Juvenile specimens were present during the four surveys at most of the sites. Canonical correspondence analyses were applied which revealed that biotopes, water temperature and EC played the most significant role in the distribution and abundance of species. The relatively high mollusc diversity and the fact that juveniles were present throughout the study, demonstrated that current habitat and environmental conditions were suitable to promote recruitment and the sustainability of diverse mollusc populations in the Marico River and its tributaries. However, in contrast to this, the exploitation of and habitat transformation in the Crocodile River has resulted in the decrease of biotopes which eventually could have led to the decrease in diversity and the establishment of P. acuta , an exotic invader species. Keywords : freshwater molluscs, biodiversity, Marico River, Crocodile River, environmental variables

Regulatory Monitoring of Fortified Foods: Identifying Barriers and Good Practices.

While fortification of staple foods and condiments has gained enormous global traction, poor performance persists throughout many aspects of implementation, most notably around the critical element of regulatory monitoring, which is essential for ensuring foods meet national fortification standards. Where coverage of fortified foods is high, limited nutritional impact of fortification programs largely exists due to regulatory monitoring that insufficiently identifies and holds producers accountable for underfortified products. Based on quality assurance data from 20 national fortification programs in 12 countries, we estimate that less than half of the samples are adequately fortified against relevant national standards. In this paper, we outline key findings from a literature review, key informant interviews with 11 fortification experts, and semi-quantitative surveys with 39 individuals from regulatory agencies and the food fortification industry in 17 countries on the perceived effectiveness of regulatory monitoring systems and barriers to compliance against national fortification standards. Findings highlight that regulatory agencies and industry disagree on the value that enforcement mechanisms have in ensuring compliance against standards. Perceived political risk of enforcement and poorly resourced inspectorate capacity appear to adversely reinforce each other within an environment of unclear legislation to create a major hurdle for improving overall compliance of fortification programs against national standards. Budget constraints affect the ability of regulatory agencies to create a well-trained inspector cadre and improve the detection and enforcement of non-compliant and underfortified products. Recommendations to improve fortification compliance include improving technical capacity; ensuring sustained leadership, accountability, and funding in both the private and the public sectors; and removing political barriers to ensure consistent detection of underfortified products and enforcement of applicable fortification standards. Only by taking concrete steps to improve the entire regulatory system that is built on a cooperative working relationship between regulatory agencies and food producers will a nutrition strategy that uses fortification see its intended health effects.

The invasive barnacle species, Austrominius modestus: Its status and competition with indigenous barnacles on the Isle of Cumbrae, Scotland

The invasive barnacle Austrominius (= Elminius) modestus has been present in Europe since the 1940s, and has recently been recorded to outnumber native barnacle species at some locations, including an Irish marine nature reserve. It has been suggested that these increases in abundance following a lag phase since establishment, represent the awakening of an ‘ecological sleeper’, due to changes in environmental conditions. Austrominius modestus was first recorded on the Isle of Cumbrae, Scotland in 1955, and was reported to be well established on the island by 2007. Since this location is close to the northern limit of the invaded range of A. modestus, it has been chosen as a site for the long term monitoring of this species. Quantitative and semi-quantitative surveys of the abundance of A. modestus, together with the native barnacle species Chthamalus montagui and Semibalanus balanoides, have been made on the island on a biannual basis since 2009. This study examined changes in the abundances of these three species from 2009 to 2013, and reports on the present status of this invasive species on the island. Austrominius modestus was found at all sites surveyed, but did not outnumber native barnacle species at any site. Semibalanus balanoides, a cold water boreal species, was the most abundant barnacle species at most sites from 2009 to 2013. All three barnacle species underwent a decline in 2011, but had increased in abundance by 2013. Despite undergoing the smallest increase in abundance between 2011 and 2013, S. balanoides remains the dominant barnacle species on the Isle of Cumbrae. Nearly sixty years after its initial discovery on the island, A. modestus is widespread, however it has not outnumbered native species, which continue to recruit at high densities. This competitive pressure makes it unlikely that A. modestus will outnumber native barnacle species at this location, close to its northern limit, in the near future.

A semi-quantitative survey of macroinvertebrates at selected sites to evaluate the ecosystem health of the Olifants River

This study was conducted to evaluate the ecosystem health of the Olifants River by means of semi-quantitative surveys of the macroinvertebrates at 7 selected sites in the catchment. These surveys were performed during the high- and low-flow seasons for 2 consecutive years. Macroinvertebrates were collected by using a net consisting of a 30 cm square steel frame with a sturdy handle, to which a Perlon gauze net with a mesh of 1 mm was attached. Semi-quantitative surveys were done by sampling the vegetation, as well as the substratum, with the net at each site for approximately 15 min. The pH, water temperature and conductivity were measured in situ at each site during the different surveys. Samples were fixed and preserved in 90% ethanol and thereafter sorted, identified up to family level and counted. The specimens were categorised as tolerant, moderately sensitive or highly sensitive, according to the guidelines set by the South African Scoring System Version 5 (SASS5). Although a total of 95 taxa were recovered during this study, only 7 of these taxa were categorised as highly sensitive, it can be concluded that the water of the Olifants River is in a poor state of health as revealed by the macroinvertebrate assemblages. Keywords : Olifants River, macroinvertebrates, river health

Insights into Patient and Clinician Concerns about Scar Appearance: Semiquantitative Structured Surveys

Insights into Patient and Clinician Concerns about Scar Appearance: Semiquantitative Structured Surveys

Insights into Patient and Clinician Concerns about Scar Appearance: Semiquantitative Structured Surveys

Few data are available regarding the psychological impact of scars arising from routine elective/aesthetic surgical procedures. To gain insight into both patients' and clinicians' concerns, the authors have undertaken structured semiquantitative surveys of (1) patients who had recently undergone a routine surgical procedure and (2) a cohort of plastic and aesthetic dermatological surgeons. All selected patients had undergone a surgical procedure within 6 to 24 months before survey and had a scar(s) that caused concern. Participants completed a previously validated Self Completion Form that aimed to investigate their concerns. Clinicians were surveyed via telephone interviews using a similar format of questionnaire but with questions tailored to clinicians. Ninety-seven patients and 24 clinicians were interviewed. Patients were dissatisfied with scars resulting from surgery, irrespective of gender, age, ethnicity, or geographical location, and 91 percent would value even small improvements in scarring. Patients had scar(s) that they wished were less noticeable over a wide range of body sites (both "visible" and "nonvisible"). Male and female respondents had similar rates of dissatisfaction about their own scars. The survey revealed issues in the communication between patients and clinicians regarding scars; 71 percent of patients felt that they were more concerned than their surgeon about the scar resulting from a recent surgical procedure. This preliminary study indicates that patients are highly concerned about scarring following routine surgery, with most patients valuing any improvement in scarring. These data also show that there are disparities in patient-clinician communication regarding expectations following surgery.

Surveying biodiversity of soil herpetofauna: towards a standard quantitative methodology

Soil herpetofauna biodiversity is conservatively estimated as 2775 species, made up of 10% and 28% of Amphibia and Squamata, respectively. Neglect in their taxonomy, ecology and standard sampling methodologies suggests that proportions, as well as numbers, are likely to be far higher. Like invertebrate soil macrofauna, the majority of species live within the first few centimetres of leaf litter and soil. Results of 30 quantitative and 52 semi-quantitative surveys in nine regions of three continents show that these are infrequently encountered, whereas dedicated subterranean burrowers can be found at high densities, up to 0.844 individuals m −2 ( x - = 0.26 ). This suggests that a two tier sampling approach may be most appropriate, with superficial excavations in a large quadrat (e.g. 25 m 2) in addition to a smaller deeper subsample. It is hoped that this contribution will stimulate further discussion towards a consensus, filling the gap for a standard method of quantitative surveying of soil herpetofauna biodiversity.

Mass spectrometry‐based profiling of phospholipids and sphingolipids in extracts from Saccharomyces cerevisiae

Lipids are rapidly moving to centre stage in many fields of biological sciences. Lipidomics, the systems-level scale analysis of lipids and their interacting factors, is thus an emerging field which holds great promise for drug and biomarker discovery. Here we present a mass spectrometry-based approach for profiling of polar lipids, in particular phospholipids and sphingolipids, in Saccharomyces cerevisiae. The first step includes semi-quantitative surveys of lipids in an untargeted fashion, which is particularly powerful for detection of changes that cannot easily be anticipated. This leads to the identification of ions with increased or decreased signal intensities. Comprehensive theoretical calculation of the masses of yeast phospholipid and sphingolipid molecular species, based on fatty acyl and headgroup heterogeneity, is next used to tentatively assign ions of interest. Subsequent targeted analysis using tandem mass spectrometry allows for characterization and quantification of phospholipids and sphingolipids. Given the high degree of conservation in pathways of lipid metabolism between different organisms, it can be expected that this method will lead to the discovery of novel enzymatic activities and modulators of known ones, particularly when used in combination with genetic and chemogenetic libraries and screens. We validated the method using the EUROSCARF library of non-essential deletion mutants. Mutants of SCS7, a lipid hydroxylase, and SLC1, a putative acyl transferase with unknown substrate specificity, were profiled for their phospholipid and sphingolipid content. The observed changes in lipid profiles are consistent with previous observations and extend our knowledge on in vivo substrate use under permissive growth conditions.