Beam Studies of the Segmented Resistive WELL: a Potential Thin Sampling Element for Digital Hadron Calorimetry

Thick Gas Electron Multipliers (THGEMs) have the potential of constituting thin, robust sampling elements in Digital Hadron Calorimetry (DHCAL) in future colliders. We report on recent beam studies of new single- and double-THGEM-like structures; the multiplier is a Segmented Resistive WELL (SRWELL) - a single-faced THGEM in contact with a segmented resistive layer inductively coupled to readout pads. Several 10$\times$10 cm$^2$ configurations with a total thickness of 5-6 mm (excluding electronics) with 1 cm$^2$ pads coupled to APV-SRS readout were investigated with muons and pions. Detection efficiencies in the 98$$ range were recorded with average pad-multiplicity of $\sim$1.1. The resistive anode resulted in efficient discharge damping, with potential drops of a few volts; discharge probabilities were $\sim10^{-7}$ for muons and $\sim10^{-6}$ for pions in the double-stage configuration, at rates of a few kHz/cm$^2$. Further optimization work and research on larger detectors are underway.Comment: Presented at the $13^{th}$ Vienna Conference on Instrumentation, February 2013 and submitted to its proceeding

Microbial community drivers of PK/NRP gene diversity in selected global soils

Background The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils. Results Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP. Conclusions The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites

A universal model for mobility and migration patterns

Introduced in its contemporary form by George Kingsley Zipf in 1946, but with roots that go back to the work of Gaspard Monge in the 18th century, the gravity law is the prevailing framework to predict population movement, cargo shipping volume, inter-city phone calls, as well as bilateral trade flows between nations. Despite its widespread use, it relies on adjustable parameters that vary from region to region and suffers from known analytic inconsistencies. Here we introduce a stochastic process capturing local mobility decisions that helps us analytically derive commuting and mobility fluxes that require as input only information on the population distribution. The resulting radiation model predicts mobility patterns in good agreement with mobility and transport patterns observed in a wide range of phenomena, from long-term migration patterns to communication volume between different regions. Given its parameter-free nature, the model can be applied in areas where we lack previous mobility measurements, significantly improving the predictive accuracy of most of phenomena affected by mobility and transport processes.Comment: Main text and supplementary informatio

Barrier and internal wave contributions to the quantum probability density and flux in light heavy-ion elastic scattering

We investigate the properties of the optical model wave function for light heavy-ion systems where absorption is incomplete, such as $\alpha + ^{40}$Ca and $\alpha + ^{16}$O around 30 MeV incident energy. Strong focusing effects are predicted to occur well inside the nucleus, where the probability density can reach values much higher than that of the incident wave. This focusing is shown to be correlated with the presence at back angles of a strong enhancement in the elastic cross section, the so-called ALAS (anomalous large angle scattering) phenomenon; this is substantiated by calculations of the quantum probability flux and of classical trajectories. To clarify this mechanism, we decompose the scattering wave function and the associated probability flux into their barrier and internal wave contributions within a fully quantal calculation. Finally, a calculation of the divergence of the quantum flux shows that when absorption is incomplete, the focal region gives a sizeable contribution to nonelastic processes.Comment: 16 pages, 15 figures. RevTeX file. To appear in Phys. Rev. C. The figures are only available via anonynous FTP on ftp://umhsp02.umh.ac.be/pub/ftp_pnt/figscat

Comparison of Pathway Analysis Approaches Using Lung Cancer GWAS Data Sets

Pathway analysis has been proposed as a complement to single SNP analyses in GWAS. This study compared pathway analysis methods using two lung cancer GWAS data sets based on four studies: one a combined data set from Central Europe and Toronto (CETO); the other a combined data set from Germany and MD Anderson (GRMD). We searched the literature for pathway analysis methods that were widely used, representative of other methods, and had available software for performing analysis. We selected the programs EASE, which uses a modified Fishers Exact calculation to test for pathway associations, GenGen (a version of Gene Set Enrichment Analysis (GSEA)), which uses a Kolmogorov-Smirnov-like running sum statistic as the test statistic, and SLAT, which uses a p-value combination approach. We also included a modified version of the SUMSTAT method (mSUMSTAT), which tests for association by averaging χ2 statistics from genotype association tests. There were nearly 18000 genes available for analysis, following mapping of more than 300,000 SNPs from each data set. These were mapped to 421 GO level 4 gene sets for pathway analysis. Among the methods designed to be robust to biases related to gene size and pathway SNP correlation (GenGen, mSUMSTAT and SLAT), the mSUMSTAT approach identified the most significant pathways (8 in CETO and 1 in GRMD). This included a highly plausible association for the acetylcholine receptor activity pathway in both CETO (FDR≤0.001) and GRMD (FDR = 0.009), although two strong association signals at a single gene cluster (CHRNA3-CHRNA5-CHRNB4) drive this result, complicating its interpretation. Few other replicated associations were found using any of these methods. Difficulty in replicating associations hindered our comparison, but results suggest mSUMSTAT has advantages over the other approaches, and may be a useful pathway analysis tool to use alongside other methods such as the commonly used GSEA (GenGen) approach

Utilização de indutor de fotossíntese na cultura da soja (glycine max L) implantada no sudoeste de Goiás / Use of photosynthesis inducer in soybean culture (glycine max L) implemented in the southwest of Goiás

A soja (Glycine max (L) Merrill) cultivada no Brasil, para a produção de grãos, é uma planta herbácea, da classe Rosideae, ordem Fabales, família Fabaceae, subfamília Papilionoideae, tribo Phaseoleae, gênero Glycine L., espécie max. Nesse contexto. Esse trabalho teve como objetivo de avaliar uso do indutor de fotossíntese (Start Foton), utilizando a cultura da soja. O experimento foi implantado no ano agrícola 2020/2021, na fazenda São Leopoldo, no Município de Rio Verde, estado de Goiás, em Sistema Plantio Direto na palha, pelo Núcleo de Estudos e Pesquisa em Fitotecnia. O cultivar de soja implantada foi HO APORE, e o delineamento experimental foi em blocos casualizados com quatro repetições, e uma única fatores de tratamento, com seis níveis, sendo descrito da seguinte forma: T1: 0,0 L ha-1 (controle negativo); T2: 3,0 L ha-1; T3: 6,0 L ha-1; T4: 9,0 L ha-1; T5: 12,0 L ha-1; T6: 15,0 L ha-1. As variáveis tecnológicas mensuradas foram: População de planta; Índice fotossintético; Altura de planta, Altura de inserção da primeira vagem; Número de galhos; Número de vagens por planta. Os dados foram analisados estatisticamente pelo programa Sisvar. As informações obtidas com a coleta de dados do experimento foram submetidas à análise de variância, sendo as médias comparadas pelo teste Tukey, quando detectada significância para a ANOVA a p=0,05% de probabilidade para a comparação de médias. Podemos concluir que, com a utilização do produto ocorreu um acréscimo na produtividade em quilogramas por hectare e manteve as características químicas dentro dos patamares desejados

Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for Future Outbreaks

Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on a single isolate of bat coronaviruses (bat CoVs) which does not adequately represent genetically related coronaviruses (CoVs) [...

Widespread Translocation from Autosomes to Sex Chromosomes Preserves Genetic Variability in an Endangered Lark

Species that pass repeatedly through narrow population bottlenecks (<100 individuals) are likely to have lost a large proportion of their genetic variation. Having genotyped 92 Raso larks Alauda razae, a Critically Endangered single-island endemic whose world population in the Cape Verdes over the last 100 years has fluctuated between about 15 and 130 pairs, we found variation at 7 of 21 microsatellite loci that successfully amplified, the remaining loci being monomorphic. At 6 of the polymorphic loci variation was sex-linked, despite the fact that these microsatellites were not sex-linked in the other passerine birds where they were developed. Comparative analysis strongly suggests that material from several different autosomes has been recently transferred to the sex chromosomes in larks. Sex-linkage might plausibly allow some level of heterozygosity to be maintained, even in the face of persistently small population sizes

Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution

Various lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have contributed to prolongation of the coronavirus disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown an evenly uneven distribution of unique protein variants of SARS-CoV-2 is geo-location or demography-specific. However, the correlation between the demographic transmutability of the SARS-CoV-2 infection and mutations in various proteins remains unknown due to hidden symmetry/asymmetry in the occurrence of mutations. This study tracked how these mutations are emerging in SARS-CoV-2 proteins in six model countries and globally. In a geo-location, considering the mutations having a frequency of detection of at least five hundred in each SARS-CoV-2 protein; we studied the country-wise percentage of invariant residues. Our data revealed that since October 2020, highly frequent mutations in SARS-CoV-2 have been observed mostly in the Open Reading Frames (ORF) 7b and ORF8, worldwide. No such highly frequent mutations in any of the SARS-CoV-2 proteins were found in the UK, India, and Brazil, which does not correlate with the degree of transmissibility of the virus in India and Brazil. However, we have found a signature that SARS-CoV-2 proteins were evolving at a higher rate, and considering global data, mutations are detected in the majority of the available amino acid locations. Fractal analysis of each protein's normalized factor time series showed a periodically aperiodic emergence of dominant variants for SARS-CoV-2 protein mutations across different countries. It was noticed that certain high-frequency variants have emerged in the last couple of months, and thus the emerging SARS-CoV-2 strains are expected to contain prevalent mutations in ORF3a, membrane, and ORF8 proteins. In contrast to other beta-coronaviruses, SARS-CoV-2 variants have rapidly emerged based on demographically dependent mutations. Characterization of the periodically aperiodic nature of the demographic spread of SARS-CoV-2 variants in various countries can contribute to the identification of the origin of SARS-CoV-2