Machine learning and XAI approaches highlight the strong connection between O 3 and N O 2 pollutants and Alzheimer's disease.

Alzheimer's disease (AD) is the most common type of dementia with millions of affected patients worldwide. Currently, there is still no cure and AD is often diagnosed long time after onset because there is no clear diagnosis. Thus, it is essential to study the physiology and pathogenesis of AD, investigating the risk factors that could be strongly connected to the disease onset. Despite AD, like other complex diseases, is the result of the combination of several factors, there is emerging agreement that environmental pollution should play a pivotal role in the causes of disease. In this work, we implemented an Artificial Intelligence model to predict AD mortality, expressed as Standardized Mortality Ratio, at Italian provincial level over 5 years. We employed a set of publicly available variables concerning pollution, health, society and economy to feed a Random Forest algorithm. Using methods based on eXplainable Artificial Intelligence (XAI) we found that air pollution (mainly O 3 and N O 2 ) contribute the most to AD mortality prediction. These results could help to shed light on the etiology of Alzheimer's disease and to confirm the urgent need to further investigate the relationship between the environment and the disease.

Signatures of disease outcome severity in the intestinal fungal and bacterial microbiome of COVID-19 patients.

Background: COVID-19, whose causative pathogen is the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic in March 2020. The gastrointestinal tract is one of the targets of this virus, and mounting evidence suggests that gastrointestinal symptoms may contribute to disease severity. The gut-lung axis is involved in the immune response to SARS-CoV-2; therefore, we investigated whether COVID-19 patients' bacterial and fungal gut microbiome composition was linked to disease clinical outcome. Methods: In May 2020, we collected stool samples and patient records from 24 hospitalized patients with laboratory-confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the MiSeq, Illumina's integrated next generation sequencing instrument. A cohort of 201 age- and sex-matched healthy volunteers from the project PRJNA661289 was used as a control group for the bacterial gut microbiota analysis. Results: We observed that female COVID-19 patients had a lower gut bacterial microbiota richness than male patients, which was consistent with a different latency in hospital admittance time between the two groups. Both sexes in the COVID-19 patient study group displayed multiple positive associations with opportunistic bacterial pathogens such as Enterococcus, Streptococcus, and Actinomyces. Of note, the Candida genus dominated the gut mycobiota of COVID-19 patients, and adult patients showed a higher intestinal fungal diversity than elderly patients. We found that Saccharomycetales unassigned fungal genera were positively associated with bacterial short-chain fatty acid (SCFA) producers and negatively associated with the proinflammatory genus Bilophila in COVID-19 patients, and we observed that none of the patients who harbored it were admitted to the high-intensity unit. Conclusions: COVID-19 was associated with opportunistic bacterial pathogens, and Candida was the dominant fungal taxon in the intestine. Together, we found an association between commensal SCFA-producers and a fungal genus that was present in the intestines of patients who did not experience the most severe outcome of the disease. We believe that this taxon could have played a role in the disease outcome, and that further studies should be conducted to understand the role of fungi in gastrointestinal and health protection.

A Dementia mortality rates dataset in Italy (2012-2019).

Dementia is on the rise in the world population and has been defined by the World Health Organization as a global public health priority. In Italy, according to demographic projections, in 2051 there will be 280 elderly people for every 100 young people, with an increase in all age-related chronic diseases, including dementia. Currently the total number of patients with dementia is estimated to be over 1 million (mainly with Alzheimer's disease (AD) and Parkinson's disease (PD)). In-depth studies of the etiology and physiology of dementia are complicated due to the complexity of these diseases and their long duration. In this work we present a dataset on mortality rates (in the form of Standardized Mortality Ratios, SMR) for AD e PD in Italy at provincial level over a period of 8 years (2012-2019). Access to long-term, spatially detailed and ready-to-use data could favor both health monitoring and the research of new treatments and new drugs as well as innovative methodologies for early diagnosis of dementia.

Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group.

BACKGROUND: Phylogenetic analyses of closely related species of mosquitoes are important for better understanding the evolution of traits contributing to transmission of vector-borne diseases. Six out of 41 dominant malaria vectors of the genus Anopheles in the world belong to the Maculipennis Group, which is subdivided into two Nearctic subgroups (Freeborni and Quadrimaculatus) and one Palearctic (Maculipennis) subgroup. Although previous studies considered the Nearctic subgroups as ancestral, details about their relationship with the Palearctic subgroup, and their migration times and routes from North America to Eurasia remain controversial. The Palearctic species An. beklemishevi is currently included in the Nearctic Quadrimaculatus subgroup adding to the uncertainties in mosquito systematics. RESULTS: To reconstruct historic relationships in the Maculipennis Group, we conducted a phylogenomic analysis of 11 Palearctic and 2 Nearctic species based on sequences of 1271 orthologous genes. The analysis indicated that the Palearctic species An. beklemishevi clusters together with other Eurasian species and represents a basal lineage among them. Also, An. beklemishevi is related more closely to An. freeborni, which inhabits the Western United States, rather than to An. quadrimaculatus, a species from the Eastern United States. The time-calibrated tree suggests a migration of mosquitoes in the Maculipennis Group from North America to Eurasia about 20-25 million years ago through the Bering Land Bridge. A Hybridcheck analysis demonstrated highly significant signatures of introgression events between allopatric species An. labranchiae and An. beklemishevi. The analysis also identified ancestral introgression events between An. sacharovi and its Nearctic relative An. freeborni despite their current geographic isolation. The reconstructed phylogeny suggests that vector competence and the ability to enter complete diapause during winter evolved independently in different lineages of the Maculipennis Group. CONCLUSIONS: Our phylogenomic analyses reveal migration routes and adaptive radiation timing of Holarctic malaria vectors and strongly support the inclusion of An. beklemishevi into the Maculipennis Subgroup. Detailed knowledge of the evolutionary history of the Maculipennis Subgroup provides a framework for examining the genomic changes related to ecological adaptation and susceptibility to human pathogens. These genomic variations may inform researchers about similar changes in the future providing insights into the patterns of disease transmission in Eurasia.

The spatial association between environmental pollution and long-term cancer mortality in Italy.

Tumours are nowadays the second world­leading cause of death after cardiovascular diseases. During the last decades of cancer research, lifestyle and random/genetic factors have been blamed for cancer mortality, with obesity, sedentary habits, alcoholism, and smoking contributing as supposed major causes. However, there is an emerging consensus that environmental pollution should be considered one of the main triggers. Unfortunately, all this preliminary scientific evidence has not always been followed by governments and institutions, which still fail to pursue research on cancer's environmental connections. In this unprecedented national-scale detailed study, we analyzed the links between cancer mortality, socio-economic factors, and sources of environmental pollution in Italy, both at wider regional and finer provincial scales, with an artificial intelligence approach. Overall, we found that cancer mortality does not have a random or spatial distribution and exceeds the national average mainly when environmental pollution is also higher, despite healthier lifestyle habits. Our machine learning analysis of 35 environmental sources of pollution showed that air quality ranks first for importance concerning the average cancer mortality rate, followed by sites to be reclaimed, urban areas, and motor vehicle density. Moreover, other environmental sources of pollution proved to be relevant for the mortality of some specific cancer types. Given these alarming results, we call for a rearrangement of the priority of cancer research and care that sees the reduction and prevention of environmental contamination as a priority action to put in place in the tough struggle against cancer.

A ten-year (2009-2018) database of cancer mortality rates in Italy.

In Italy, approximately 400.000 new cases of malignant tumors are recorded every year. The average of annual deaths caused by tumors, according to the Italian Cancer Registers, is about 3.5 deaths and about 2.5 per 1,000 men and women respectively, for a total of about 3 deaths every 1,000 people. Long-term (at least a decade) and spatially detailed data (up to the municipality scale) are neither easily accessible nor fully available for public consultation by the citizens, scientists, research groups, and associations. Therefore, here we present a ten-year (2009-2018) database on cancer mortality rates (in the form of Standardized Mortality Ratios, SMR) for 23 cancer macro-types in Italy on municipal, provincial, and regional scales. We aim to make easily accessible a comprehensive, ready-to-use, and openly accessible source of data on the most updated status of cancer mortality in Italy for local and national stakeholders, researchers, and policymakers and to provide researchers with ready-to-use data to perform specific studies.

Machine learning reveals that prolonged exposure to air pollution is associated with SARS-CoV-2 mortality and infectivity in Italy.

Air pollution can increase the risk of respiratory diseases, enhancing the susceptibility to viral and bacterial infections. Some studies suggest that small air particles facilitate the spread of viruses and also of the new coronavirus, besides the direct person-to-person contagion. However, the effects of the exposure to particulate matter and other contaminants on SARS-CoV-2 has been poorly explored. Here we examined the possible reasons why the new coronavirus differently impacted on Italian regional and provincial populations. With the help of artificial intelligence, we studied the importance of air pollution for mortality and positivity rates of the SARS-CoV-2 outbreak in Italy. We discovered that among several environmental, health, and socio-economic factors, air pollution and fine particulate matter (PM2.5), as its main component, resulted as the most important predictors of SARS-CoV-2 effects. We also found that the emissions from industries, farms, and road traffic - in order of importance - might be responsible for more than 70% of the deaths associated with SARS-CoV-2 nationwide. Given the major contribution played by air pollution (much more important than other health and socio-economic factors, as we discovered), we projected that, with an increase of 5-10% in air pollution, similar future pathogens may inflate the epidemic toll of Italy by 21-32% additional cases, whose 19-28% more positives and 4-14% more deaths. Our findings, demonstrating that fine-particulate (PM2.5) pollutant level is the most important factor to predict SARS-CoV-2 effects that would worsen even with a slight decrease of air quality, highlight that the imperative of productivity before health and environmental protection is, indeed, a short-term/small-minded resolution.

Certified "sustainable" palm oil took the place of endangered Bornean and Sumatran large mammals habitat and tropical forests in the last 30 years.

Tropical forests inhabited by endangered orangutans, rhinos, tigers, and elephants in South-east Asia are threatened by deforestation, including oil palm expansion. Certification has been proposed to label sustainable palm oil production. However, from a remotely sensed time-series and imagery analysis (1984-2020), we discovered that most of the currently certified grower supply bases and concessions in Sumatra and Borneo are located in the 1990s large mammals habitat and in areas that were biodiverse tropical forests less than 30 years ago. In light of this dramatic evidence, we suggest that certification schemes claim for the "sustainable" production of palm oil just because they neglect a very recent past of deforestation and habitat degradation.

Accelerating upward treeline shift in the Altai Mountains under last-century climate change.

Treeline shift and tree growth often respond to climatic changes and it is critical to identify and quantify their dynamics. Some regions are particularly sensitive to climate change and the Altai Mountains, located in Central and East Asia, are showing unequivocal signs. The mean annual temperature in the area has increased by 1.3-1.7 °C in the last century. As this mountain range has ancient and protected forests on alpine slopes, we focus on determining the treeline structure and dynamics. We integrated in situ fine-scale allometric data with analyses from dendrochronological samples, high-resolution 3D drone photos and new satellite images to study the dynamics and underlying causal mechanisms of any treeline movement and growth changes in a remote preserved forest at the Aktru Research Station in the Altai Mountain. We show that temperature increase has a negative effect on mountain tree growth. In contrast, only younger trees grow at higher altitudes and we document a relatively fast upward shift of the treeline. During the last 52 years, treeline moved about 150 m upward and the rate of movement accelerated until recently. Before the 1950s, it never shifted over 2150-2200 m a.s.l. We suggest that a continuous upward expansion of the treeline would be at the expense of meadow and shrub species and radically change this high-mountain ecosystem with its endemic flora. This documented treeline shift represents clear evidence of the increased velocity of climate change during the last century.

Sustainable palm oil may not be so sustainable.

The globalization of the palm oil trade poses a menace to the ecosystem integrity of Southeast Asia. In this short communication, we briefly discuss why palm oil certifications may have failed as an effective means to halt forest degradation and biodiversity loss. From a comparison of multiple new datasets, we analysed recent tree loss in Indonesia, Malaysia, and Papua New Guinea, and discovered that, from 2001 to 2016, about 40% of the area located in certified concessions suffered from habitat degradation, deforestation, fires, or other tree damages. Certified concessions have been subject to more tree removals than non-certified ones. We also detect significant tree loss before and after the start of certification schemes. Beyond non-governmental organisations' concern that Roundtable on Sustainable Palm Oil (RSPO) and Palm Oil Innovation Group (POIG) certifications allow ongoing clearance of any forest not identified as of high conservation values (HCV) or high carbon stock (HCS), we suggest an alarming and previously overlooked situation, such as that current "sustainable palm oil" is often associated with recent habitat degradation and forest loss. In other words, certified palm oil production may not be so sustainable.

The last 50 years of climate-induced melting of the Maliy Aktru glacier (Altai Mountains, Russia) revealed in a primary ecological succession.

In this article, we report and discuss the results obtained from a survey of plants, microorganisms (bacteria and fungi), and soil elements along a chronosequence in the first 600 m of the Maliy Aktru glacier's forefront (Altai Mountains, Russia). Many glaciers of the world show effects of climate change. Nonetheless, except for some local reports, the ecological effects of deglaciation have been poorly studied and have not been quantitatively assessed in the Altai Mountains. Here, we studied the ecological changes of plants, fungi, bacteria, and soil elements that take the form of a primary ecological succession and that took place over the deglaciated soil of the Maliy Aktru glacier during the last 50 year. According to our measurements, the glacier lost about 12 m per year during the last 50 years. Plant succession shows clear signs of changes along the incremental distance from the glacier forefront. The analysis of the plant α- and ß-diversity confirmed an expected increase of them with increasing distance from the glacier forefront. Moreover, the analysis of ß-diversity confirmed the hypothesis of the presence of three main stages of the plant succession: (a) initial (pioneer species) from 30 to 100 m; (b) intermediate (r-selected species) from 110 to 120-150 m; and (c) final (K-selected species) from 150 to 550. Our study also shows that saprotrophic communities of fungi are widely distributed in the glacier retreating area with higher relative abundances of saprotroph ascomycetes at early successional stages. The evolution of a primary succession is also evident for bacteria, soil elements, and CO 2 emission and respiration. The development of biological communities and the variation in geochemical parameters represent an irrefutable proof that climate change is altering soils that have been long covered by ice.

A standard photomap of the ovarian nurse cell chromosomes for the dominant malaria vector in Europe and Middle East Anopheles sacharovi.

BACKGROUND: Anopheles sacharovi is a dominant malaria vector species in South Europe and the Middle East which has a highly plastic behaviour at both adult and larval stages. Such plasticity has prevented this species from eradication by several anti-vector campaigns. The development of new genome-based strategies for vector control will benefit from genome sequencing and physical chromosome mapping of this mosquito. Although a cytogenetic photomap for chromosomes from salivary glands of An. sacharovi has been developed, no cytogenetic map suitable for physical genome mapping is available. METHODS: Mosquitoes for this study were collected at adult stage in animal shelters in Armenia. Polytene chromosome preparations were prepared from ovarian nurse cells. Fluorescent in situ hybridization (FISH) was performed using PCR amplified probes. RESULTS: This study constructed a high-quality standard photomap for polytene chromosomes from ovarian nurse cells of An. sacharovi. Following the previous nomenclature, chromosomes were sub-divided into 39 numbered and 119 lettered sub-divisions. Chromosomal landmarks for the chromosome recognition were described. Using FISH, 4 PCR-amplified genic probes were mapped to the chromosomes. The positions of the probes demonstrated gene order reshuffling between An. sacharovi and Anopheles atroparvus which has not been seen cytologically. In addition, this study described specific chromosomal landmarks that can be used for the cytotaxonomic diagnostics of An. sacharovi based on the banding pattern of its polytene chromosomes. CONCLUSIONS: This study constructed a high-quality standard photomap for ovarian nurse cell chromosomes of An. sacharovi and validated its utility for physical genome mapping. Based on the map, cytotaxonomic features for identification of An. sacharovi have been described. The cytogenetic map constructed in this study will assist in creating a chromosome-based genome assembly for this mosquito and in developing cytotaxonomic tools for identification of other species from the Maculipennis group.

A standard photomap of ovarian nurse cell chromosomes and inversion polymorphism in Anopheles beklemishevi.

BACKGROUND: Anopheles beklemishevi is a member of the Maculipennis group of malaria mosquitoes that has the most northern distribution among other members of the group. Although a cytogenetic map for the larval salivary gland chromosomes of this species has been developed, a high-quality standard cytogenetic photomap that enables genomics and population genetics studies of this mosquito at the adult stage is still lacking. METHODS: In this study, a cytogenetic map for the polytene chromosomes of An. beklemishevi from ovarian nurse cells was developed using high-resolution digital imaging from field collected mosquitoes. PCR-amplified DNA probes for fluorescence in situ hybridization (FISH) were designed based on the genome of An. atroparvus. The DNA probe obtained by microdissection procedures from the breakpoint region was labelled in a DOP-PCR reaction. Population analysis was performed on 371 specimens collected in 18 locations. RESULTS: We report the development of a high-quality standard photomap for the polytene chromosomes from ovarian nurse cells of An. beklemishevi. To confirm the suitability of the map for physical mapping, several PCR-amplified probes were mapped to the chromosomes of An. beklemishevi using FISH. In addition, we identified and mapped DNA probes to flanking regions of the breakpoints of two inversions on chromosome X of this species. Inversion polymorphism was determined in 13 geographically distant populations of An. beklemishevi. Four polymorphic inversions were detected. The positions of common chromosomal inversions were indicated on the map. CONCLUSIONS: The study constructed a standard photomap for ovarian nurse cell chromosomes of An. beklemishevi and tested its suitability for physical genome mapping and population studies. Cytogenetic analysis determined inversion polymorphism in natural populations of An. beklemishevi related to this species' adaptation.