Antibodies specific to SARS-CoV-2 proteins N, S and E in COVID-19 patients in the normal population and in historical samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally; recognition of immune responses to this virus will be crucial for coronavirus disease 2019 (COVID-19) control, prevention and treatment. We comprehensively analysed IgG and IgA antibody responses to the SARS-CoV-2 nucleocapsid protein (N), spike protein domain 1 (S1) and envelope protein (E) in: SARS-CoV-2-infected patient, healthy, historical and pre-epidemic samples, including patients’ medical, epidemiological and diagnostic data, virus-neutralizing capability and kinetics. N-specific IgG and IgA are the most reliable diagnostic targets for infection. Serum IgG levels correlate to IgA levels. Half a year after infection, anti-N and anti-S1 IgG decreased, but sera preserved virus-inhibitory potency; thus, testing for IgG may underestimate the protective potential of antibodies. Historical and pre-epidemic sera did not inhibit SARS-CoV-2, thus its circulation before the pandemic and a protective role from antibodies pre-induced by other coronaviruses cannot be confirmed by this study

Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.

Research on Geological Disaster Forecast Method Based on PCA Structure BP Model

The BP neural network prediction method constructed by PCA and the geological hazard prediction method based on the MM5 numerical model were used to establish geological hazard classification short-term objective forecast models. The calculation results show that these two objective forecast methods have a good fitting effect on historical samples. The independent sample’s trial report effect is also good; based on the above two objective forecasting methods, through correction, the comprehensive forecast product is finally obtained.

PSXII-1 Tracing the historical genetic components in turano-mongolian cattle breeds based on the microsatellite analysis of modern and museum samples

In their centuries-long history, the nomads of the south of Russia developed the local cattle breeds, which are well adapted to the harsh steppe conditions. In 20th century, the population size of such cattle breeds was dramatically decreased. At the same time, intensive cross breeding with high-producing transboundary breeds had been practiced on the small remaining part of population. The aim of our study was to trace the historical genetic components in modern populations of local cattle breeds of the turano-mongolian origin. The historical specimens of Kalmyk (n = 10), Kyrgyz (n = 11) and Kazakh (n = 3) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry and subjected to the study. The modern representatives of Kalmyk (n = 28), Kyrgyz (n = 20), Kazakh White-headed (n = 30), Hereford (n = 26), and Mongolian (n = 41) cattle were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst research Center for Animal Husbandry. The samples were genotyped for 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples, the PCR reactions were carried out in five replicates to determine the consensus genotypes. In total, 132 alleles were identified, including 97 alleles in historical samples and 124 alleles in modern samples. The values of unbiased expected heterozygosity were 0.767–0.776 and 0.653–0.778 for the historical and modern samples, respectively. The STRUCTURE clustering showed the visible differences in genetic structure between the historical and modern populations of Kalmyk, Kyrgyz and Kazakh cattle breeds; however, the historical genetic components were still maintained in modern representatives of all of studied breeds. The research results will be useful for the sustainable breeding and conservation of valuable local genetic resources. The study was funded by the RSF No. 19-76-20012.

PSXV-10 Study of allelic pattern of PLAG1 gene in the historical and modern populations of two oldest Russian dairy cattle breeds

Increasing animal stature is one of the goals of modern breeding programs for many dairy cattle breeds, because stature related to higher milk yield. The PLAG1 gene was shown to be a strong candidate responsible for stature in different cattle breeds. The polymorphic SNP BovineHD1400007259, located within PLAG1 gene, is considered as a causal mutation responsible for stature. The aim of our work was to evaluate the effect of long selection for the increased body height on the alterations of the allele’s frequencies of the PLAG1 gene in the historical and modern populations of the Russian Yaroslavl and Kholmogor dairy cattle breeds. The historical specimens of Yaroslavl (n = 22) and Kholmogor (n = 12) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry. The modern representatives of Yaroslavl (n = 31) and Kholmogor (n = 25) breeds were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst Research Center for Animal Husbandry. The samples were genotyped using high-density DNA arrays (Illumina Inc., USA). The historical DNA was treated by USER enzyme before genotyping to avoid the misincoporated nucleotides occurred due to postmortem DNA damage. We observed significant differences in allele frequencies of PLAG1 genes between historical and modern populations of both breeds. The frequencies of G allele, which is associated with higher stature, were increased from 0.114 in historical Yaroslavl cattle and from 0.167 in historical Kholmogor cattle to 0.633 and 0.860 in the modern breeds’ representatives, respectively. Our data suggest that PLAG1 gene was affected by artificial selection in studied cattle breeds. The research results will be useful for elucidation of the history of these two oldest Russian dairy cattle breeds. The study was funded by the RSF No. 21-66-00007.

Potential Impacts of Assimilating Every-10-Minute Himawari-8 Satellite Radiance with the POD-4DEnVar Method

The Advanced Himawari Imager (AHI) onboard the Himawari-8 geostationary satellite provides continuous observations every 10 min. This study investigates the assimilation of every-10-min radiance from the AHI with the POD-4DEnVar method. Cloud detection is conducted in the AHI quality control procedure to remove cloudy and precipitation-affected observations. Historical samples and physical ensembles are combined to construct four-dimensional ensembles according to the observed frequency of the Himawari-8 satellite. The purpose of this study was to test the potential impacts of assimilating high temporal resolution observations with POD-4DEnVar in a numerical weather prediction (NWP) system. Two parallel experiments were performed with and without Himawari-8 radiance assimilation during the entire month of July 2020. The results of the experiment with radiance assimilation show that it improves the analysis and forecast accuracy of geopotential, horizontal wind field and relative humidity compared to the experiment without radiance assimilation. Moreover, the equitable threat score (ETS) of 24-h accumulated precipitation shows that assimilating Himawari-8 radiance improves the rainfall forecast accuracy. Improvements were found in the structure, amplitude and location of the precipitation. In addition, the ETS of hourly accumulated precipitation indicates that assimilating high temporal resolution Himawari-8 radiance can improve the prediction of rapidly developed rainfall. Overall, assimilating every-10-min AHI radiance from Himawari-8 with POD-4DEnVar has positive impacts on NWP.

Analysis of red chalk drawings from the workshop of Giovanni Battista Piranesi using fiber optics reflectance spectroscopy

The viability of fiber optics reflectance spectroscopy (FORS) for the differentiation of red chalk drawing media was investigated, focusing on the group of drawings from the workshop of Giovanni Battista Piranesi (1720–1778) at the Staatliche Kunsthalle Karlsruhe, Germany. The evaluation of spectra was supported by principal component analysis (PCA). The method was tested on mock-up drawings made with recently acquired natural and synthetic red chalks of known origin. It was possible to sort these mock-up drawings according to chalk type and application technique. The compositional differences of these reference chalks were confirmed by X-ray diffraction (XRD) and scanning electron microscopy (SEM). Subsequent FORS analysis of selected original drawings revealed the existence of several closely grouped clusters, implying similarities on the basis of the underlying spectral features among the historical red chalks used in Rome. These similarities distinguished the historical drawings from the red chalk mock-up drawings, except for the drawings made with red chalk samples from the area near the town of Theley, Germany, which were shown to bear close similarities to those in the cluster of historical samples.

Artificial Intelligence for Pigment Classification Task in the Short-Wave Infrared Range

Hyperspectral reflectance imaging in the short-wave infrared range (SWIR, “extended NIR”, ca. 1000 to 2500 nm) has proven to provide enhanced characterization of paint materials. However, the interpretation of the results remains challenging due to the intrinsic complexity of the SWIR spectra, presenting both broad and narrow absorption features with possible overlaps. To cope with the high dimensionality and spectral complexity of such datasets acquired in the SWIR domain, one data treatment approach is tested, inspired by innovative development in the cultural heritage field: the use of a pigment spectral database (extracted from model and historical samples) combined with a deep neural network (DNN). This approach allows for multi-label pigment classification within each pixel of the data cube. Conventional Spectral Angle Mapping and DNN results obtained on both pigment reference samples and a Buddhist painting (thangka) are discussed.

Discoloration of Historical Plastic Objects: New Insight into the Degradation of β-Naphthol Pigment Lakes

Light is a determining factor in the discoloration of plastics, and photodegradation processes can affect the molecular structures of both the polymer and colorants. Limited studies focused on the discoloration of heritage plastics in conservation science. This work investigated the discoloration of red historical polyethylene (PE) objects colored with PR 48:2 and PR 53:1. High-density and low-density PE reference polymers, neat pigment powders, and historical samples were assessed before and after accelerated photoaging. The applied methodology provided insight into the individual light-susceptibility of polyethylenes, organic pigment lakes, and their combined effect in the photoaging of historical plastic formulations. After light exposure, both PE references and historical samples yellowed, PR53:1 faded, and PR 48:2 darkened; however, both organic pigments faded severely in the historical samples. This highlights the role played by the plastic binder likely facilitating the pigment photofading. Fourier transform infrared spectroscopy and mass spectrometry techniques—EGA-MS, PY-GC/MS, and TD-GC/MS—were successfully employed for characterizing the plastic formulations and degradation. The identification of phthalic compounds in both aged β-naphthol powders opens new venues for studies on their degradation. This work’s approach and analytical methods in studying the discoloration of historical plastics are novel, proving their efficacy, reliability, and potentiality.