Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust.

Biological soil crusts (biocrusts) are photosynthetic "hot spots" in deserts and cover ∼12% of the Earth's terrestrial surface, and yet they face an uncertain future given expected shifts in rainfall events. Laboratory wetting of biocrust communities is known to cause a bloom of Firmicutes which rapidly become dominant community members within 2 days after emerging from a sporulated state. We hypothesized that their bacteriophages (phages) would respond to such a dramatic increase in their host's abundance. In our experiment, wetting caused Firmicutes to bloom and triggered a significant depletion of cyanobacterial diversity. We used genome-resolved metagenomics to link phage to their hosts and found that the bloom of the genus Bacillus correlated with a dramatic increase in the number of Caudovirales phages targeting these diverse spore-formers (r = 0.762). After 2 days, we observed dramatic reductions in the relative abundances of Bacillus, while the number of Bacillus phages continued to increase, suggestive of a predator-prey relationship. We found predicted auxiliary metabolic genes (AMGs) associated with sporulation in several Caudovirales genomes, suggesting that phages may influence and even benefit from sporulation dynamics in biocrusts. Prophage elements and CRISPR-Cas repeats in Firmicutes metagenome-assembled genomes (MAGs) provide evidence of recent infection events by phages, which were corroborated by mapping viral contigs to their host MAGs. Combined, these findings suggest that the blooming Firmicutes become primary targets for biocrust Caudovirales phages, consistent with the classical "kill-the-winner" hypothesis.IMPORTANCE This work forms part of an overarching research theme studying the effects of a changing climate on biological soil crust (biocrust) in the Southwestern United States. To our knowledge, this study was the first to characterize bacteriophages in biocrust and offers a view into the ecology of phages in response to a laboratory wetting experiment. The phages identified here represent lineages of Caudovirales, and we found that the dynamics of their interactions with their Firmicutes hosts explain the collapse of a bacterial bloom that was induced by wetting. Moreover, we show that phages carried host-altering metabolic genes and found evidence of proviral infection and CRISPR-Cas repeats within host genomes. Our results suggest that phages exert controls on population density by lysing dominant bacterial hosts and that they further impact biocrust by acquiring host genes for sporulation. Future research should explore how dominant these phages are in other biocrust communities and quantify how much the control and lysis of blooming populations contributes to nutrient cycling in biocrusts

ifCNV: A novel isolation-forest-based package to detect copy-number variations from various targeted NGS datasets

Copy-number variations (CNVs) are an essential component of genetic variation distributed across large parts of the human genome. CNV detection from next-generation sequencing data and artificial intelligence algorithms have progressed in recent years. However, only a few tools have taken advantage of machine-learning algorithms for CNV detection, and none propose using artificial intelligence to automatically detect probable CNV-positive samples. The most developed approach is to use a reference or normal dataset to compare with the samples of interest, and it is well known that selecting appropriate normal samples represents a challenging task that dramatically influences the precision of results in all CNV-detecting tools. With careful consideration of these issues, we propose here ifCNV, a new software based on isolation forests that creates its own reference, available in R and python with customizable parameters. ifCNV combines artificial intelligence using two isolation forests and a comprehensive scoring method to faithfully detect CNVs among various samples. It was validated using targeted next-generation sequencing (NGS) datasets from diverse origins (capture and amplicon, germline and somatic), and it exhibits high sensitivity, specificity, and accuracy. ifCNV is a publicly available open-source software (https://github.com/SimCab-CHU/ifCNV) that allows the detection of CNVs in many clinical situations

The distribution of the species of the genus Deroceras Rafinesque, 1820 in Belgium (Gastropoda, Pulmonata, Agriolimacidae)

Four species belonging to the genus Deroceras are known from Belgium: D. reticulatum /MÜLLER, 1774/, D. laeve /MÜLLER, 1774/, D. caruanae /POLLONERA, 1891/ and D. agreste /LINNAEUS, 1758/. The distribution of D. reticulatum, P. laeve and D. caruanae as known at the end of 1971 is compared with a map showing all records of landsnail species in Belgium till then. A similar comparison is given for the year 1982. From the period 1972-1982 year to year maps- showing all records of each of these three Deroceras species are compared with a corresponding map compiling all landsnail records of the same year. At present P.reticulatum,D.laeve and D. caruanae are very widespread and common. D. caruanae was found for the first time in Belgium in 1968. As shown by means of a series of cumulative maps, D. caruanae became very rapidly widespread /1973 onwards/ presenting an explosive dispersal. Undoubtedly,man assisted in its introduction and dispersal. P. agreste seems to be very rare in Belgium with a limited number of local populations in the four southern provinces

Establishment of the New Particle Therapy Research Center (PARTREC) at UMCG Groningen

After 25 years of successful research in the nuclear and radiation physics domain, the KVI-CART research center in Groningen is upgraded and re-established as the PARticle Therapy REsearch Center (PARTREC). Using the superconducting cyclotron AGOR and being embedded within the University Medical Center Groningen, it operates in close collaboration with the Groningen Proton Therapy Center. PARTREC uniquely combines radiation physics, medical physics, biology and radiotherapy research with an R&D program to improve hadron therapy technology and advanced radiation therapy for cancer. A number of further upgrades, scheduled for completion in 2023, will establish a wide range of irradiation modalities, such as pencil beam scanning, shoot-through with high energy protons and SOBP for protons, helium and carbon ions. Delivery of spatial fractionation (GRID) and dose rates over 300 Gy/s (FLASH) are envisioned. In addition, PARTREC delivers a variety of ion beams and infrastructure for radiation hardness experiments conducted by scientific and commercial communities, and nuclear science research in collaboration with the Faculty of Science and Engineering of the University of Groningen

Synthesis–Structure–Activity Relations in Fe-CHA for C–H Activation: Control of Al Distribution by Interzeolite Conversion

The search for structurally relevant Al-arrangements in zeolites is an important endeavor for single site catalysis. Little is known about the mechanisms and zeolite dynamics during synthesis that are responsible for creating those Al-ensembles. Here, new synthetic strategies for creating Al-hosts in small-pore zeolites suitable for divalent cation catalysis are uncovered, leading to a mechanistic proposal for Al-organization during crystallization. As such, unique synthesis-structure-activity relations are demonstrated for the partial oxidation of methane on Fe-exchanged CHA-zeolites. With modified interzeolite conversions, the divalent cation capacity of the resulting high Si SSZ-13 zeolites (Si/Al ~ 35) can be reproducibly controlled in a range between 0.04 and 0.34 Co²⁺/Al. This capacity is a proxy for the distribution of framework aluminum in pairs and correlates with the methanol production per Al when these zeolites host the α-Fe^(II) redox active site. The uncovered IZC synthesis-structure relations paint an Al-distribution hypothesis, where incongruent dissolution of the starting USY zeolite and fast synthesis kinetics with atypical growth modes allow assembling specific Al-arrangements, resulting in a high divalent cation capacity. Prolonged synthesis times and high temperatures overcome the energetic barriers for T-atom reshuffling favoring Al-isolation. These mechanisms and the relations uncovered in this work will guide the search for relevant Al-ensembles in a range of zeolite catalysts where controlling the environment for a single active site is crucial

Thermal bremsstrahlung probing the thermodynamical state of multifragmenting systems

Inclusive and exclusive hard-photon (E$_\gamma >$ 30 MeV) production in five different heavy-ion reactions ($^{36}$Ar+$^{197}$Au, $^{107}$Ag, $^{58}$Ni, $^{12}$C at 60{\it A} MeV and $^{129}$Xe+$^{120}$Sn at 50{\it A} MeV) has been studied coupling the TAPS photon spectrometer with several charged-particle multidetectors covering more than 80% of 4$\pi$. The measured spectra, slope parameters and source velocities as well as their target-dependence, confirm the existence of thermal bremsstrahlung emission from secondary nucleon-nucleon collisions that accounts for roughly 20% of the total hard-photon yield. The thermal slopes are a direct measure of the temperature of the excited nuclear systems produced during the reaction.Comment: 4 pages, 3 figures, Proceedings CRIS 2000, 3rd Catania Relativistic Ion Studies, "Phase Transitions in Strong Interactions: Status and Perspectives", Acicastello, Italy, May 22-26, 2000 (to be published in Nuc. Phys. A

Stereotactic large-core needle breast biopsy: analysis of pain and discomfort related to the biopsy procedure

The purpose of this study was to determine the significance of variables such as duration of the procedure, type of breast tissue, number of passes, depth of the biopsies, underlying pathology, the operator performing the procedure, and their effect on women’s perception of pain and discomfort during stereotactic large-core needle breast biopsy. One hundred and fifty consecutive patients with a non-palpable suspicious mammographic lesions were included. Between three and nine 14-gauge breast passes were taken using a prone stereotactic table. Following the biopsy procedure, patients were asked to complete a questionnaire. There was no discomfort in lying on the prone table. There is no relation between type of breast lesion and pain, underlying pathology and pain and performing operator and pain. The type of breast tissue is correlated with pain experienced from biopsy (P = 0.0001). We found out that patients with dense breast tissue complain of more pain from biopsy than patients with more involution of breast tissue. The depth of the biopsy correlates with pain from biopsy (P = 0.0028). Deep lesions are more painful than superficial ones. There is a correlation between the number of passes and pain in the neck (P = 0.0188) and shoulder (P = 0.0366). The duration of the procedure is correlated with pain experienced in the neck (P = 0.0116) but not with pain experienced from biopsy

Hard photon and neutral pion production in cold nuclear matter

The production of hard photons and neutral pions in 190 MeV proton induced reactions on C, Ca, Ni, and W targets has been for the first time concurrently studied. Angular distributions and energy spectra up to the kinematical limit are discussed and the production cross-sections are presented. From the target mass dependence of the cross-sections the propagation of pions through nuclear matter is analyzed and the production mechanisms of hard photons and primordial pions are derived. It is found that the production of subthreshold particles proceeds mainly through first chance nucleon-nucleon collisions. For the most energetic particles the mass scaling evidences the effect of multiple collisions.Comment: submitted to Phys. Lett.

Federated causal inference based on real-world observational data sources:Application to a SARS-CoV-2 vaccine effectiveness assessment

Introduction Causal inference helps researchers and policy-makers to evaluate public health interventions. When comparing interventions or public health programs by leveraging observational sensitive individual-level data from populations crossing jurisdictional borders, a federated approach (as opposed to a pooling data approach) can be used. Approaching causal inference by re-using routinely collected observational data across different regions in a federated manner, is challenging and guidance is currently lacking. With the aim of filling this gap and allowing a rapid response in the case of a next pandemic, a methodological framework to develop studies attempting causal inference using federated cross-national sensitive observational data, is described and showcased within the European BeYond-COVID&nbsp;project. Methods A framework for approaching federated causal inference by re-using routinely collected observational data across different regions, based on principles of legal, organizational, semantic and technical interoperability, is proposed. The framework includes step-by-step guidance, from defining a research question, to establishing a causal model, identifying and specifying data requirements in a common data model, generating synthetic data, and developing an interoperable and reproducible analytical pipeline for distributed deployment. The conceptual and instrumental phase of the framework was demonstrated and an analytical pipeline implementing federated causal inference was prototyped using open-source software in preparation for the assessment of real-world effectiveness of SARS-CoV-2 primary vaccination in preventing infection in populations spanning different countries, integrating a data quality assessment, imputation of missing values, matching of exposed to unexposed individuals based on confounders identified in the causal model and a survival analysis within the matched&nbsp;population. Results The conceptual and instrumental phase of the proposed methodological framework was successfully demonstrated within the BY-COVID project. Different Findable, Accessible, Interoperable and Reusable (FAIR) research objects were produced, such as a study protocol, a data management plan, a common data model, a synthetic dataset and an interoperable analytical&nbsp;pipeline. Conclusions The framework provides a systematic approach to address federated cross-national policy-relevant causal research questions based on sensitive population, health and care data in a privacy-preserving and interoperable way. The methodology and derived research objects can be re-used and contribute to pandemic&nbsp;preparedness.</p