DIRECT SALE AS ONE OF THE ORGANIZATIONAL FORMS OF LOCAL FOOD SYSTEMS. THE SPATIAL CONCENTRATION OF DIRECT SALE ENTITIES IN POLAND

Direct selling is one of the most common local activities in the agri-food sector. Contemporary trends in the production and consumption of food indicate a duality of food systems, in which the concept of industrialization of the agri-food sector is simultaneously developing together with a concept of local food systems. In this article, it was noticed that the direct sale of agri-food products is in a line with the contemporary trends in the agri-food sector, and that it is important to analyze its spatial patterns. Taking into account the spatial concentration of direct selling entities, it has been proved that their distribution is random and does not show clustering patterns.

Genetic Analysis of the Measles Virus From the Outbreaks in South Korea, 2019

Three genotypes (B3, D8, and H1) of the measles virus (MeV) have recently caused global outbreaks. In Korea, four measles outbreaks were reported during 2018–2019 and most patients were infants and health care workers in their 20s and 30s. To investigate the genetic characteristics and molecular epidemiology of the outbreaks, we analyzed the sequence of MeVs by targeting the N-450, MF-NCR, and/or H gene regions. Considering their phylogenetic relationships, besides the N-450 and MF-NCR sequences that are commonly used for genotyping MeVs, the MF-NCR-H sequence was related to the dynamics for identifying the transmission of MeVs. Phylogenetic clustering patterns reconstructed from the MF-NCR-H sequence set revealed that genotype D8 caused three of the four outbreaks, while B3 seemed to have induced the fourth outbreak. These results suggest that the MF-NCR-H sequence is useful for rapid confirmation of measles outbreaks and to identify the epidemiological routes of MeVs.

Visualizing Spatiotemporal Epidemic Clusters on a Map-based Dashboard: A case study of early COVID-19 cases in Singapore

Spatiotemporal distribution of the epidemic data plays an important role in its understanding and prediction. In order to understand the transmission patterns of infectious diseases in a more intuitive way, many works applied various visualizations to show the epidemic datasets. However, most of them focus on visualizing the epidemic information at the overall level such as the confirmed counts each country, while spending less effort on powering user to effectively understand and reason the very large and complex epidemic datasets through flexible interactions. In this paper, the authors proposed a novel map-based dashboard for visualizing and analyzing spatiotemporal clustering patterns and transmission chains of epidemic data. We used 102 confirmed cases officially reported by the Ministry of Health in Singapore as the test dataset. This experiment shown that the well-designed and interactive map-based dashboard is effective in shorten the time that users required to mine the spatiotemporal characteristics and transmission chains behind the textual and numerical epidemic data.

First Report on Detection and Molecular Characterization of Adenoviruses in the Small Indian Mongoose (Urva auropunctata)

Using a broad-range nested PCR assay targeting the DNA-dependent DNA polymerase (pol) gene, we detected adenoviruses in 17 (20.48%) out of 83 fecal samples from small Indian mongooses (Urva auropunctata) on the Caribbean island of St. Kitts. All 17 PCR amplicons were sequenced for the partial pol gene (~300 bp, hereafter referred to as Mon sequences). Fourteen of the 17 Mon sequences shared maximum homology (98.3–99.6% and 97–98.9% nucleotide (nt) and deduced amino acid (aa) sequence identities, respectively) with that of bovine adenovirus-6 (species Bovine atadenovirus E). Mongoose-associated adenovirus Mon-39 was most closely related (absolute nt and deduced aa identities) to an atadenovirus from a tropical screech owl. Mon-66 shared maximum nt and deduced aa identities of 69% and 71.4% with those of atadenoviruses from a spur-thighed tortoise and a brown anole lizard, respectively. Phylogenetically, Mon-39 and Mon-66 clustered within clades that were predominated by atadenoviruses from reptiles, indicating a reptilian origin of these viruses. Only a single mongoose-associated adenovirus, Mon-34, was related to the genus Mastadenovirus. However, phylogenetically, Mon-34 formed an isolated branch, distinct from other mastadenoviruses. Since the fecal samples were collected from apparently healthy mongooses, we could not determine whether the mongoose-associated adenoviruses infected the host. On the other hand, the phylogenetic clustering patterns of the mongoose-associated atadenoviruses pointed more towards a dietary origin of these viruses. Although the present study was based on partial pol sequences (~90 aa), sequence identities and phylogenetic analysis suggested that Mon-34, Mon-39, and Mon-66 might represent novel adenoviruses. To our knowledge, this is the first report on the detection and molecular characterization of adenoviruses from the mongoose.

Oxidation product characterization from ozonolysis of the diterpene ent-kaurene

Diterpenes (C20H32) are biogenically emitted volatile compounds that only recently have been observed in ambient air. They are expected to be highly reactive, and their oxidation is likely to form condensable vapors. However, until now, no studies have investigated gas-phase diterpene oxidation. In this paper, we explored the ozonolysis of a diterpene, ent-kaurene, in a simulation chamber. Using state-of-the-art mass spectrometry, we characterized diterpene oxidation products for the first time, and we identified several products with varying oxidation levels, including highly oxygenated organic molecules (HOM) monomers and dimers. The most abundant monomers measured using a nitrate chemical ionization mass spectrometer were C19H28O8 and C20H30O5, and dimers were C38H60O6 and C39H62O6. The exact molar yield of HOM from kaurene ozonolysis was hard to quantify due to uncertainties in both the kaurene and HOM concentrations, but our best estimate was a few percent, which is similar to values reported earlier for many monoterpenes. We also monitored the decrease of the gas-phase oxidation products in response to an increased condensation sink in the chamber to deduce their affinity to condense. The oxygen content was a critical parameter affecting the volatility of products, with 4–5 O-atoms needed for the main monomeric species to condense. Finally, we report on the observed fragmentation and clustering patterns of kaurene in a Vocus proton transfer reaction time-of-flight mass spectrometer. Our findings highlight similarities and differences between diterpenes and smaller terpenes during their atmospheric oxidation, but more studies on different diterpenes are needed for a broader view of their role in atmospheric chemistry.

The distribution of hepatitis C virus infection in Shanghai, China: a time-spatial study

Background Shanghai, as a pilot city of China to achieve the goal of eliminating hepatitis C, its strategy of allocating medical resources is a pressing problem to be solved. This study aims to infer the time-spatial clustering patterns of HCV-infected cases, and grasp the dynamic genotype distribution of HCV, thereby inform elimination strategies of HCV with efficacy and efficiency. Methods Reported HCV cases including their demographic information in Shanghai city from 2005 to 2018 were released from the National Infectious Disease Reporting Information System, population data at community scale, geographical layers of hospitals, communities and districts were gathered from former research. Blood samples of HCV-infected individuals were collected during 2014–2018 from 24 sentinel hospitals, HCV-antibody test, qualitative nucleic acid test and NS5B/5’UTR gene amplification were performed accordingly to determine the genotypes of the specimen. Furthermore, global and local spatial self-correlation analysis of both acute and chronic HCV infections were conducted at community scale year by year, then time-spatial clusters of acute and chronic HCV infections and HCV genotype distribution of specimen collected from sentinel hospitals by districts were mapped by using Arcmap10.1. Results A total of 2631 acute HCV cases and 15,063 chronic HCV cases were reported in Shanghai from 2005 to 2018, with a peak in 2010 and 2017, respectively. The mean age of chronic HCV patients was 49.70 ± 14.55 years, 3.34 ± 0.32 years older than the acute (t = 10.55, P-value < 0.01). The spatial distribution of acute HCV infection formed one primary cluster (Relative Risk = 2.71), and the chronic formed one primary cluster and three secondary clusters with Relative Risk ranged from 1.94 to 14.42, meanwhile, an overlap of 34 communities between acute and chronic HCV clusters were found with time period spans varied from 6 to 12 years. Genotype 1 (N = 257, 49.71%) was the most prevalent HCV genotype in Shanghai, genotype 3 infections have increased in recent years. Baoshan district presented cluster of acute HCV and the highest proportion of genotype 2, Pudong new area was the cluster of chronic HCV and occupied the highest proportion of genotype 3. Conclusions Despite the low prevalence of HCV infection, it is still needed to push forward the elimination process in Shanghai, as there is a certain amount of HCV infected people waiting to be treated. The time-spatial clustering patterns and the dynamic of HCV genotype distribution together indicated a changing constitution of different transmission routes of HCV infection, thus, a focused strategy may be needed for high-risk population related to genotype 3 infection like drug users, in addition to an enforcement of the existing measures of preventing the iatrogenic and hematogenic transmission of HCV.

Understanding the nature and dynamics of Mycobacterium ulcerans cytochrome P450 monooxygenases (CYPs) – a bioinformatics approach

Cytochrome P450 monooxygenases (CYPs or P450s) are catalytically versatile hemoproteins, associated with drug metabolism, substrate utilization and pathogenesis. Mycobacterium ulcerans is a human pathogen causing Buruli ulcer. The study intended to investigate frequency and diversity of CYPs from M. ulcerans strains, understand the pan-CYPome clustering patterns and interconnection of CYPs using bioinformatics tools. M. ulcerans strains demonstrated the presence of 261 CYPs categorized into 35 families and 38 subfamilies. CYP138, CYP140, CYP189 and CYP125 were the flourishing families. Around, 20 CYP families and 20 subfamilies were conserved. Flourishing and conserved CYP families/subfamilies were associated with lipid metabolism, substrate utilization etc. CYP140 had a role in pathogenesis. CYP279 was the least dominant family. CYP135, CYP183, CYP190, CYP271 and CYP276 were diagnostic markers for M. ulcerans subsp. shinshuense strain ATCC 33728 and M. ulcerans strain P7741. The pan-CYPome specified that M. ulcerans is evolving by gaining CYPs. CYP centric clustering revealed diversity and resemblances among M. ulcerans strains. More diverse nature of the M. ulcerans strain Harvey could be attributed to its larger size and geographical location. Co-occurrence network demonstrated mutual associations amongst substantial number of CYP families/subfamilies. This work provided comprehensive understanding of previously unexplored CYPs from M. ulcerans.

Geographical Clustering Analysis of Birth Defects in Guangxi

Birth defects (BD) is a big public health issue in Guangxi Zhuang Autonomous Region of China. The overall prevalence of BD in Guangxi is about 1% and higher than most other provinces of China. However, the geographical clustering variations in BD of Guangxi has not been described. Therefore, the aim of this study was to explore and detect the spatial clustering patterns of BD prevalence across a well-defined geographic space. The data were obtained from Guangxi birth defects monitoring network (GXBDMN) from 2016 to 2020, which collected socio-demographic and clinical information from perinatal infants between 28 weeks of gestation and 7 days postnatal. The spatial autocorrelation analysis and hot spot analysis will be used to explore the geographical clustering of BD prevalence in 70 counties and 41 districts of Guangxi in this study. A total of 44,418 perinatal infants were born with BD from 2016 to 2020. The overall prevalence of BD was 122.47/10,000 [95% confidence interval (CI): 121.34-123.60/10,000]. The local indicators of spatial association (LISA) statistic and Gi* statistic showed that the spatial clustering patterns of BD prevalence changed over time, and the largest High-High clustering area and hot spot area were both identified in the city of Nanning. Therefore, the spatial clustering patterns of BD prevalence in Guangxi is very significant. Spatial cluster analysis can provide reliable and accurate spatial distribution patterns in BD control and prevention.