scholarly journals Fundamental identifiability limits in molecular epidemiology

2021 ◽  
Author(s):  
Stilianos Louca ◽  
Angela McLaughlin ◽  
Ailene MacPherson ◽  
Jeffrey B. Joy ◽  
Matthew W. Pennell
Keyword(s):  
Congruence Class ◽  
Entire Study Period ◽  
Reproduction Ratio ◽  
Entire Study ◽  
Phylogenetic Data ◽  
Pathogen Prevalence ◽  
Crucial Information ◽  
Mathematical Techniques ◽  
Over Time ◽  
Epidemiological Parameters

AbstractViral phylogenies provide crucial information on the spread of infectious diseases, and many studies fit mathematical models to phylogenetic data to estimate epidemiological parameters such as the effective reproduction ratio (Re) over time. Such phylodynamic inferences often complement or even substitute for conventional surveillance data, particularly when sampling is poor or delayed. It remains generally unknown, however, how robust phylodynamic epidemiological inferences are, especially when there is uncertainty regarding pathogen prevalence and sampling intensity. Here we use recently developed mathematical techniques to fully characterize the information that can possibly be extracted from serially collected viral phylogenetic data, in the context of the commonly used birth-death-sampling model. We show that for any candidate epidemiological scenario, there exist a myriad of alternative, markedly different and yet plausible “congruent” scenarios that cannot be distinguished using phylogenetic data alone, no matter how large the dataset. In the absence of strong constraints or rate priors across the entire study period, neither maximum-likelihood fitting nor Bayesian inference can reliably reconstruct the true epidemiological dynamics from phylogenetic data alone; rather, estimators can only converge to the “congruence class” of the true dynamics. We propose concrete and feasible strategies for making more robust epidemiological inferences from viral phylogenetic data.

scholarly journals Effects of liming and development of Curimbatá (Prochilodus lineatus) larvae on the abundance of zooplankton in fish ponds

2012 ◽  
Vol 23 (4) ◽  
pp. 386-393 ◽  
Author(s):  
Thécia Alfenas Silva Valente Paes ◽  
José Mauro Valente Paes ◽  
Nilton Eduardo Torres Rojas ◽  
Odete Rocha ◽  
Maria José dos Santos Wisniewski
Keyword(s):  
Sharp Decrease ◽  
Fish Predation ◽  
Fish Ponds ◽  
Initial Part ◽  
Entire Study Period ◽  
Neotropical Fish ◽  
Entire Study ◽  
Prochilodus Lineatus ◽  
Zooplankton Density ◽  
Over Time

AIM: We aimed to evaluate the influence of the correction of the water alkalinity in the fish ponds on the density of zooplankton under a period they were stocked with larvae of Prochilodus lineatus, a neotropical fish called "Curimbatá". METHODS: We used a factorial design completely randomized. In one plot (2 ponds) there was no correction of the alkalinity of the water (20 mg CaCO3.L-1) and in two others, this variable was adjusted weekly to values around 30 and 60 mg CaCO3.L-1 ¹, with two replicates each. Zooplankton was sampled weekly and the experiment lasted 63 days. RESULTS: Significant differences in the density of the zooplankton over time (F = 6.78, p < 0.05) were found and there was a sharp decrease in zooplankton density from first to second week, and successive small increases in density from the fourth week until the end of the experiment. When considering the entire study period, alkalinity correction 60 mg CaCO3.L-1 resulted in higher density of zooplankton. Great changes in zooplankton composition occurred. Rotifera were dominant at the beginning of the experiment and Cladocera and Copepoda in the later weeks possibly due to an interplay of dilution by rain and fish predation in the initial part of the experiment and due to both alkalinity correction and predation by both fish and predatory copepods from the fourth week until the end. CONCLUSION: The experiment corroborated the hypothesis that correction of water alkalinity in ponds does favor zooplankton development but also highlighted biotic and abiotic interaction of factors operating simultaneously.

Population biology and diet of the puffer fish Lagocephalus laevigatus (Tetraodontiformes: Tetraodontidae) in Caraguatatuba Bay, south-eastern Brazil

2011 ◽  
Vol 92 (2) ◽  
pp. 407-412 ◽  
Author(s):  
M.R. Denadai ◽  
F.B. Santos ◽  
E. Bessa ◽  
L.P. Bernardes ◽  
A. Turra
Keyword(s):  
Population Biology ◽  
Temporal Distribution ◽  
Late Winter ◽  
Entire Study Period ◽  
Entire Study ◽  
South Eastern ◽  
Eastern Brazil ◽  
Puffer Fish ◽  
Spatio Temporal ◽  
Sexually Mature

This study describes the spatio-temporal distribution, population biology, and diet of the puffer fish Lagocephalus laevigatus in Caraguatatuba Bay, south-eastern Brazil. Monthly samples were taken between August 2003 and October 2004 by trawls in two areas, south and north, at depths of 1 to 4 m. The fish were measured and their sex and reproductive stage determined. The abundance of this species was compared between areas and among months, and the items in the diet were identified and quantified. Lagocephalus laevigatus was rare in Caraguatatuba Bay, where only 199 small individuals (4.8 to 15.4 cm) were obtained in the entire study period, suggesting that this species uses the estuary as a nursery. None of the specimens of L. laevigatus captured in Caraguatatuba Bay were sexually mature. Higher densities of L. laevigatus in the bay were recorded in the south area and between October and December 2003, i.e. in the spring, suggesting that spawning may occur from late winter to spring (August through to November). The diet items consumed by L. laevigatus in Caraguatatuba Bay were, as expected from the current literature, crustaceans, mainly amphipods, and fish. However, the most-consumed item was the sea whip Leptogorgia setacea (Cnidaria). This feeding habit may be related to the presence of toxins (tetrodotoxin and saxitoxin) that are frequently found in the skin and viscera of L. laevigatus, which may be sequestered from the sea whip, which possibility still needs to be specifically evaluated.

scholarly journals Prevalence of the nematodes Eustrongylides exisus Jägerskiöld, 1909, – larvae (Nematoda: Dioctophymatidae) infection in the Rutilis rutilis, linnaeus 1758 and the seasonal dynamics of the infection in the waters of the Dnipro-Buh estuari in southern Ukrai

2020 ◽  
Vol 22 (97) ◽  
pp. 31-38
Author(s):  
S. L. Honcharov
Keyword(s):  
Entire Study Period ◽  
Sample Collection ◽  
Upward Trend ◽  
Entire Study ◽  
Total Prevalence ◽  
The Mean ◽  
Predatory Fishes ◽  
Two Peaks ◽  
The Village ◽  
Collection Sites

In this study, we determined the prevalence and seasonal dynamic of the infection of the Rutilis rutilis, Lіnnaeus 1758 with the nematode Eustrongylides excisus. The fish was caught in the waters of the Dnipro-Buh estuary in seven sample collection sites between 2016 and 2019. They all underwent ichthyopathological examination. Parasites, found during examination, undergone microscopy to determine their taxonomy. Overall 595 specimens were obtained. The mean prevalence of infection over entire study period (2016–2019) was 17.4 %. Ichthyopathological examination of the roach caught in the waters of the Dnipro-Buh estuary revealed the infection with larvae E. excises nematode. The parasitic larvae were found in the muscles of the ventral abdominal wall of the roach. There was more than two-fold difference in the prevalence of infection between sample collection sites – from 12 % in site 5 near Sofiivka to 28 % in site 3 near the village Oleksandrivka over the study period in 2016–2019. The total prevalence of infection in roaches in the Dnipro-Buh estuary was 17.4 %. Seasonal changes were not statistically significant and ranged from 12.8 % in summer to 20.1 % in spring. Annual changes suggested a possible upward trend, but more observations are needed to confirm it. Аnnual changes were not statistically significant. The prevalence of infection changed throughout the year: there were two peaks in spring (20.1 %) and autumn (18.3 %). In summer (12.8 %) and winter (15.1 %) the prevalence of infection was lower. Morphologically, the E. excisus larvae found in roaches were different compared to those found in predatory fishes: they had more pale color and were smaller in length. E. excisus is a prevalent infection of roach in Dnipro-Buh estuary. Considering seemingly increasing prevalence of E.excisus infection, further studies are required to understand a pathophysiology of E.excisus infection  in mammals and humans, since data remain limited.

Analysis of extreme rains through climate indicators in the context of climate change in southern Benin

2021 ◽  
Vol 2 (1b) ◽  
pp. C20A01-1-C20A01-33
Author(s):  
Ferdinand Sourou HOUNVOU ◽  
◽  
K. F. Guedje ◽  
Hilaire Kougbeagbede ◽  
Adebiyi Joseph Adechinan ◽  
...  
Keyword(s):  
Climate Change ◽  
Global Warming ◽  
West Africa ◽  
Economic System ◽  
Entire Study Period ◽  
Entire Study ◽  
Climate Indicators ◽  
Large Growth ◽  
Southern Benin ◽  
Heavy Rains

The recurrence of flooding in recent years in West Africa is dramatically affecting the socio-economic system of most countries in the region. This work is devoted to the analysis of the heavy rains of its last years in the context of global warming in subequatorial Benin through eight rainfall indicators. For this purpose, the daily rains collected at seventeen stations in the south of Benin between 1960 and 2018, the maximum and minimum daily temperatures of the two synoptic stations in the study area between 1970 and 2018 are used. Analysis of the results shows a non-uniform trend in rainfall indicators over the entire study period. The monthly trend is in accordance with the bimodal rain regime of southern Benin for each of the climatic indicators studied. After the break in the downward trend in rainfall in the 1980s or 1990s at the various stations, the last three decades have been marked above all by ten-year averages of the various indicators that are higher than those obtained over the entire study period. Despite the low proportion of extreme rains, their frequency has increased since the resumption of rainfall in the 1980s or 1990s, especially compared to the 1970s and 1980s. The highest heights are observed for the most part in the towns close to the sea Atlantic Ocean. Global warming in southern Benin is characterized above all by high decadal temperature variation rates in the 1990s. This significant global warming in this pivotal decade is accompanied by relatively large growth in all indicators in southern Benin.

scholarly journals Biological contamination of soils in urbanized ecosystems by Toxocara sp. eggs.

2020 ◽  
Vol 169 ◽  
pp. 04002
Author(s):  
Olga Maslennikova ◽  
Viktoriya Erofeeva
Keyword(s):  
Average Rate ◽  
50Th Anniversary ◽  
Entire Study Period ◽  
Entire Study ◽  
Fecal Samples ◽  
Biological Contamination ◽  
Dog Walking ◽  
Special Area ◽  
Contamination Of Soils ◽  
Study Sites

As a result of the study of three sites (two city parks and a special area for walking dogs) on the contamination of Toxocara sp. eggs it was found that 28.0±2.3% of the studied fecal samples from the territories of the Kirov Park were infected with Тохосаrа eggs, 21.0±3.6% of fecal samples from the territory of the Park of the 50th anniversary of the Komsomol and 7.0±0.4% of fecal samples were infected with Тохосаrа eggs selected at a specially equipped dog walking area in the Metrograd residential complex in Kirov. The average rate of dogs which were infected by Toxocara (EI) was 18.7±6.2%. The average rate of contamination of soil by eggs Тохосаrа in the study sites amounted to 34.6%. Contamination of soil samples with eggs of Toxocara sp. in parks was 45.6% and 45.8%, respectively, and in the dog walking area it was 12%. The largest number of dogs, including stray ones, were registered in the parks: 74.8±7.1 and 62.8±7.0 individuals, respectively. There were no stray individuals in the dog walking area, and there were 21.6±1.0 individuals over the entire study period.

scholarly journals Locating Seismo-Conductivity Anomaly before the 2017 MW 6.5 Jiuzhaigou Earthquake in China Using Far Magnetic Stations

2020 ◽  
Vol 12 (11) ◽  
pp. 1777
Author(s):  
Zhiqiang Mao ◽  
Chieh-Hung Chen ◽  
Suqin Zhang ◽  
Aisa Yisimayili ◽  
Huaizhong Yu ◽  
...  
Keyword(s):  
Transfer Function ◽  
Moving Window ◽  
Entire Study Period ◽  
Conductivity Anomaly ◽  
Promising Candidate ◽  
Jiuzhaigou Earthquake ◽  
Entire Study ◽  
Background Distribution ◽  
Geomagnetic Data ◽  
Magnetic Transfer

Changes in the underlying conductivity around hypocenters are generally considered one of the promising mechanisms of seismo-electromagnetic anomaly generation. Parkinson vectors are indicators of high-conductivity materials and were utilized to remotely monitor conductivity changes during the MW 6.5 Jiuzhaigou earthquake (103.82°E, 33.20°N) on 8 August 2017. Three-component geomagnetic data recorded in 2017 at nine magnetic stations with epicenter distances of 63–770 km were utilized to compute the azimuths of the Parkinson vectors based on the magnetic transfer function. The monitoring and background distributions at each station were constructed by using the azimuths within a 15-day moving window and over the entire study period, respectively. The background distribution was subtracted from the monitoring distribution to mitigate the effects of underlying inhomogeneous electric conductivity structures. The differences obtained at nine stations were superimposed and the intersection of a seismo-conductivity anomaly was located about 70 km away from the epicenter about 17 days before the earthquake. The anomaly disappeared about 7 days before and remained insignificant after the earthquake. Analytical results suggested that the underlying conductivity close to the hypocenter changed before the Jiuzhaigou earthquake. These changes can be detected simultaneously by using multiple magnetometers located far from the epicenter. The disappearance of the seismo-conductivity anomaly after the earthquake sheds light on a promising candidate of the pre-earthquake anomalous phenomena.

Evaluation of dosing and safety outcomes of low-dose prophylactic warfarin in children after cardiothoracic surgery

2020 ◽  
Vol 77 (13) ◽  
pp. 1018-1025
Author(s):  
Maura Harkin ◽  
Brittany Powers Shaddix ◽  
Stephen B Neely ◽  
Leigh A Peek ◽  
Katy Stephens ◽  
...  
Keyword(s):  
Low Dose ◽  
Warfarin Dose ◽  
International Normalized Ratio ◽  
Primary Objective ◽  
Cardiothoracic Surgery ◽  
Entire Study Period ◽  
Entire Study ◽  
Frequent Monitoring ◽  
Safety Outcomes ◽  
Warfarin Dosing

Abstract Purpose Prophylactic warfarin with an International Normalized Ratio (INR) goal of 1.5 to 2.0 is one antithrombotic therapy utilized in children after cardiothoracic surgery (CTS); published sources suggest a dose of 0.1 mg/kg per day to achieve this goal. However, few studies have evaluated dosing in this population. The purpose of this study was to evaluate dosing and safety outcomes in children receiving warfarin after CTS. Methods A descriptive, retrospective review was conducted to evaluate warfarin dosing and INR outcomes in patients 18 years of age or younger who underwent CTS and received prophylactic warfarin with an INR goal of 1.5 to 2.0 from January 2014 through December 2018. The primary objective was to determine the median initial warfarin dose. Secondary objectives included identifying the percentage of documented INR values that were outside the therapeutic range, the percentage of patients with therapeutic INRs at discharge, and the 30-day readmission rate. Results Twenty-six patients were included in the review. The median initial warfarin dosage was 0.07 mg/kg/d (interquartile range [IQR], 0.05-0.10 mg/kg/d). Of the total of 177 INR values collected during the entire study period, 67 (37.9%) were therapeutic, 64 (36.2%) were subtherapeutic, and 46 (26.0%) were supratherapeutic. Eighteen patients (69.2%) had at least 1 supratherapeutic INR at any point during the study period, most frequently on days 2 through 4 of therapy. At discharge, 11 patients (42.3%) had therapeutic INRs. Four patients (15.4%) were readmitted within 30 days, with bleeding documented in 2 patients during their readmission. Conclusion The majority of patients received an initial warfarin dose less than that specified in published recommendations but still had a supratherapeutic INR at least once during the study period. When initiating warfarin after CTS, a dosage of &lt;0.1 mg/kg per day and frequent monitoring may be needed to achieve an INR goal of 1.5 to 2.0.

scholarly journals Tick-Borne Encephalitis Virus: Seasonal and Annual Variation of Epidemiological Parameters Related to Nymph-to-Larva Transmission and Exposure of Small Mammals

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 518
Author(s):  
Laure Bournez ◽  
Gerald Umhang ◽  
Marie Moinet ◽  
Céline Richomme ◽  
Jean-Michel Demerson ◽  
...  
Keyword(s):  
Small Mammals ◽  
Temporal Variations ◽  
Encephalitis Virus ◽  
Myodes Glareolus ◽  
Mountain Forest ◽  
Annual Variations ◽  
Tick Borne Encephalitis ◽  
Tick Borne Encephalitis Virus ◽  
Over Time ◽  
Epidemiological Parameters

A greater knowledge of the ecology of the natural foci of tick-borne encephalitis virus (TBEV) is essential to better assess the temporal variations of the risk of tick-borne encephalitis for humans. To describe the seasonal and inter-annual variations of the TBEV-cycle and the epidemiological parameters related to TBEV nymph-to-larva transmission, exposure of small mammals to TBEV, and tick aggregation on small mammals, a longitudinal survey in ticks and small mammals was conducted over a 3-year period in a mountain forest in Alsace, eastern France. TBEV prevalence in questing nymphs was lower in 2013 than in 2012 and 2014, probably because small mammals (Myodes glareolus and Apodemus flavicollis) were more abundant in 2012, which reduced tick aggregation and co-feeding transmission between ticks. The prevalence of TBEV in questing nymphs was higher in autumn than spring. Despite these variations in prevalence, the density of infected questing nymphs was constant over time, leading to a constant risk for humans. The seroprevalence of small mammals was also constant over time, although the proportion of rodents infested with ticks varied between years and seasons. Our results draw attention to the importance of considering the complex relationship between small mammal densities, tick aggregation on small mammals, density of infected questing nymphs, and prevalence of infected nymphs in order to forecast the risk of TBEV for humans.

Characterizing the first wave of fish and invertebrate colonization on a new offshore petroleum platform

2019 ◽  
Vol 77 (3) ◽  
pp. 1127-1136 ◽  
Author(s):  
Victoria L G Todd ◽  
Laura D Williamson ◽  
Sophie E Cox ◽  
Ian B Todd ◽  
Peter I Macreadie
Keyword(s):  
Artificial Reef ◽  
Minimal Change ◽  
Entire Study Period ◽  
Survey Period ◽  
Entire Study ◽  
Ecological Connectivity ◽  
Marine Communities ◽  
Offshore Oil ◽  
Invertebrate Colonization ◽  
Insight Into

Abstract Offshore Oil & Gas (O&G) infrastructure creates artificial reef complexes that support marine communities in oceans. No studies have characterized the first wave of colonization, which can reveal information about habitat attraction and ecological connectivity. Here we used opportunistically-collected industrial Remotely Operated Vehicles (ROVs) to investigate fish and invertebrate colonization on a new North Sea O&G platform and trenching of an associated pipeline. We observed rapid colonization of fish communities, with increases in species richness (S), abundance (N), and diversity (H′) over the first four days (the entire study period). By contrast, there was minimal change in motile invertebrate communities over the survey period. After trenching, invertebrate S, N and H′ decreased significantly, whilst fish S, N and H′ increased. This study is the first to report on the pioneer wave of fish and invertebrate colonization on O&G infrastructure, thereby providing rare insight into formation of new reef communities in the sea. These short and opportunistic data are valuable in terms of showing what can be discovered from analysis of ‘pre-installation’ ROV footage of O&G structures, of which there are terabytes of data held by O&G companies waiting to be analyzed by environmental scientists.

scholarly journals Aldegondabreen glacier change since 1910 from structure-from-motion photogrammetry of archived terrestrial and aerial photographs: utility of a historic archive to obtain century-scale Svalbard glacier mass losses

2020 ◽  
pp. 1-10
Author(s):  
Erik Schytt Holmlund
Keyword(s):  
Loss Rate ◽  
Aerial Photographs ◽  
Volume Loss ◽  
Entire Study Period ◽  
Elevation Change ◽  
Entire Study ◽  
Mass Losses ◽  
Elevation Data ◽  
Manual Processing ◽  
Insight Into

Abstract Photogrammetric reconstructions of the Aldegondabreen glacier on Svalbard from 17 archival terrestrial oblique photographs taken in 1910 and 1911 reveal a past volume of 1373.7 ± 78.2 · 106 m3; almost five times greater than its volume in 2016. Comparisons to elevation data obtained from aerial and satellite imagery indicate a relatively unchanging volume loss rate of − 10.1 ± 1.6 · 106 m3 a−1 over the entire study period, while the rate of elevation change is increasing. At this rate of volume loss, the glacier may be almost non-existent within 30 years. If the changes of Aldegondabreen are regionally representative, it suggests that there was considerable ice loss over the entire 1900s for the low elevation glaciers of western Svalbard. The 1910/11 reconstruction was made from a few of the tens of thousands of archival terrestrial photographs from the early 1900s that cover most of Svalbard. Further analysis of this material would give insight into the recent history and future prospects of the archipelago's glaciers. Photogrammetric reconstructions of this kind of material require extensive manual processing to produce good results; for more extensive use of these archival imagery, a better processing workflow would be required.

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