Investigations of the lower and middle atmosphere at the Arecibo Observatory and a description of the new VHF radar project

The atmospheric science research at the Arecibo Observatory is performed by means of (active) radar methods and (passive) optical methods. The active methods utilize the 430 NHz radar, the S-band radar on 2380 MHz, and a recently constructed Very High Frequency (VHF) radar. The passive methods include measurements of the mesopause temperature by observing the rotational emissions from OH-bands. The VHF radar design is discussed

Method to determine the optimal parameters of the Arecibo 46.8-MHz antenna system

The spherical reflector at the Arecibo Observatory (AO) offers great advantages for the design of simple and inexpensive high performance steerable antennas at VHF. Light and small feeds have the added benefit that they can be quickly installed in the Arecibo platform. It is important to evaluate the performance of any given feed including the effects of the spherical reflector. The optimization is emphasized of two parameters, namely, the distance below the focal point of the reflector and the beam width of a point feed. For the design of the feed at 46.8 MHz at the AO there were other requirements independent of MST (mesosphere stratosphere troposphere) work. The design of the primary array is discussed along with its performance with the AO spherical reflector

CoryneRegNet 6.0—Updated database content, new analysis methods and novel features focusing on community demands

Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de

Cell-type-specific mechanistic drivers of progressive multiple sclerosis lesions

Understanding the drivers of compartmentalized and sustained inflammation in the brain of progressive multiple sclerosis (PMS) remains elusive. To investigate the interplay between inter- and intra-cellular molecular mechanisms in white matter (WM) lesions, we integrated single-cell transcriptome and chromatin accessibility data from PMS lesions with spatial transcriptomics of chronic active lesion borders. We identified a PMS-specific oligodendrocyte genetic program governed by the Krüppel-like factor and specificity protein (KLF/SP) gene family, implicated in myelination and stress-induced iron uptake. Additionally, we found high expression of transferrin gene (TF) and its receptor megalin (LRP2) across lesion types, suggesting autocrine communication of iron uptake potential related to iron rim lesion in smoldering MS. Additionally, inflammatory phenotype of oligodendrocytes expressing osteopontin gene and complement were observed at chronic active lesion edges. Inside the chronic active lesion, the axonal damage biomarker, neurofilament light (NFL) gene expression was upregulated, and an astrocytic-neuronal axis through fibroblast growth factor (FGF) signaling (FGFR3-FGF13) was present. Additionally, a metabolic astrocyte phenotype at the lesion border potentially segregates inflammation areas. We also identified two distinct B cell co-expression networks with different locations and gene expressions, preferring different lesion types. Overall, singlecell multi-omics enabled the identification of specific cell types with unique molecular profiles, cell-cell communications, and spatial context, contributing to lesion fate.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Quantitative estimates of relationships between geomagnetic activity and equatorial spread-F as determined by TID occurrence levels

Using a world-wide set of stations for 15 years, quantitative estimates of changes to equatorial spread-F (ESF) occurrence rates obtained from ionogram scalings, have been determined for a range of geomagnetic activity (GA) levels, as well as for four different levels of solar activity. Average occurrence rates were used as a reference. The percentage changes vary significantly depending on these subdivisions. For example for very high GA the inverse association is recorded by a change of -33% for R-z greater than or equal to 150, and -10% for R-z < 50. Using data for 9 years for the equatorial station, Huancayo, these measurements of ESF which indicate the presence of TIDs, have also been investigated by somewhat similar analyses. Additional parameters were used which involved the local times of GA, with the ESF being examined separately for occurrence pre-midnight (PM) and after-midnight (AM). Again the negative changes were most pronounced for high GA in R-z-max years (-21%). This result is for PM ESF for GA at a local time of 1700. There were increased ESF levels (+31%) for AM ESF in R-z-min years for high GA around 2300 LT. This additional knowledge of the influence of GA on ESF occurrence involving not only percentage changes, but these values for a range of parameter levels, may be useful if ever short-term forecasts are needed. There is some discussion on comparisons which can be made between ESF results obtained by coherent scatter from incoherent-scatter equipment and those obtained by ionosondes

Population genomics of mycobacterium ieprae reveals a new genotype in Madagascar and the Comoros

Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia, followed by migrations from Africa and the Middle East. Remains of these different cultural, genetic, and linguistic legacies are still present in Madagascar and other islands of the Indian Ocean. The close relationship between human migration and the introduction and spread of infectious diseases, a well-documented phenomenon, is particularly evident for the causative agent of leprosy, Mycobacterium leprae. In this study, we used whole-genome sequencing (WGS) and molecular dating to characterize the genetic background and retrace the origin of the M. leprae strains circulating in Madagascar (n = 30) and the Comoros (n = 3), two islands where leprosy is still considered a public health problem and monitored as part of a drug resistance surveillance program. Most M. leprae strains (97%) from Madagascar and Comoros belonged to a new genotype as part of branch 1, closely related to single nucleotide polymorphism (SNP) type 1D, named 1D-Malagasy. Other strains belonged to the genotype 1A (3%). We sequenced 39 strains from nine other countries, which, together with previously published genomes, amounted to 242 genomes that were used for molecular dating. Specific SNP markers for the new 1D-Malagasy genotype were used to screen samples from 11 countries and revealed this genotype to be restricted to Madagascar, with the sole exception being a strain from Malawi. The overall analysis thus ruled out a possible introduction of leprosy by the Austronesian settlers and suggests a later origin from East Africa, the Middle East, or South Asia.Immunogenetics and cellular immunology of bacterial infectious disease