Ionospheric research - The interaction of an obliquely incident p-polarized plane electromagnetic wave with a hot plasma half- space and plasma slab

Interaction of plane p-polarized electromagnetic wave obliquely incident on hot plasma half space and plasma sla

Clinton F. Thurlow Correspondence

Entries include a print brochure for a motion picture lecture series These United States with a biography of Stiles and photographic images of his Yankee subjects on the U.S. northern coastline, a typed letter that presumably maintains several pseudonyms, returned as from the wife of his editor, on The Sugar Ball Press stationery, typed letters from Stiles on personal stationery with plans to visit the Maine State Library and presenting the second edition of his book, and a typed letter in receipt of the book from the Maine State Library

Evaluating team dynamics in interdisciplinary science teams

Purpose – This article considers how the evaluation of research teams can better account for the challenges of transdisciplinarity, including their larger team size and more diverse and permeable membership, as well as the tensions between institutional pressures on individuals to publish and team goals. Design/methodology/approach – An evaluation team was retained from 2015 to 2020 to conduct a comprehensive external evaluation of a five-year EPSCoR-funded program undertaken by a transdisciplinary research team. The formative portion of the evaluation involved monitoring the program’s developmental progress, while the summative portion tracked observable program outputs and outcomes as evidence of progress toward short- and long-term goals. The evaluation team systematically reviewed internal assessments and gathered additional data for an external assessment via periodic participation in team meetings, participant interviews and an online formative team survey (starting in Year 2). Findings – Survey participants had a better understanding of the project’s “Goals and Vision” compared to other aspects. “Work Roles,” and particularly the timeliness of decision-making, were perceived to be a “Big Problem,” specifically in regard to heavy travel by key managers/leadership. For “Communication Channels,” Year 2 tensions included differing views on the extent to which management should be collaborative versus “hierarchical.” These concerns about communication demonstrate that differences in language, culture or status impact the efficiency and working relationship of the team. “Authorship Credit/Intellectual Property” was raised most consistently each year as an area of concern. Originality/value – The study involves the use of a unique survey approach

Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome

The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In this study, we have evaluated the reproducibility of the SAGE method and identified the factors that affect it. The determination coefficient (R(2)) for the reproducibility of SAGE is 0.96. However, there are some factors that can affect the reproducibility of SAGE, such as the replication of concatemers and ditags, the number of sequenced tags and double PCR amplification of ditags. Thus, corrections for these factors must be made to ensure the reproducibility and accuracy of SAGE results. A bioinformatic analysis of SAGE data is also presented in order to eliminate these artifacts. Finally, the current study shows that increasing the number of sequenced tags improves the power of the method to detect transcripts and their regulation by experimental conditions

Host-linked soil viral ecology along a permafrost thaw gradient

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling

efam: an expanded, metaproteome-supported HMM profile database of viral protein families

Motivation: Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Results: Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, panecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from 'conservative' to 'eXtremely Conservative' resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by similar to 24% on average (up to similar to 42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem

Structural basis of nSH2 regulation and lipid binding in PI3Kα

We report two crystal structures of the wild-type phosphatidylinositol 3-kinase α (PI3Kα) heterodimer refined to 2.9 Å and 3.4 Å resolution: the first as the free enzyme, the second in complex with the lipid substrate, diC4-PIP2, respectively. The first structure shows key interactions of the N-terminal SH2 domain (nSH2) and iSH2 with the activation loop that suggest a mechanism by which the enzyme is inhibited in its basal state. In the second structure, the lipid substrate binds in a positively charged pocket adjacent to the ATP-binding site, bordered by the P-loop, the activation loop and the iSH2 domain. An additional lipid-binding site was identified at the interface of the ABD, iSH2 and kinase domains. The ability of PI3Kα to bind an additional PIP2 molecule was confirmed in vitro by fluorescence quenching experiments. The crystal structures reveal key differences in the way the nSH2 domain interacts with wild-type p110α and with the oncogenic mutant p110αH1047R. Increased buried surface area and two unique salt-bridges observed only in the wild-type structure suggest tighter inhibition in the wild-type PI3Kα than in the oncogenic mutant. These differences may be partially responsible for the increased basal lipid kinase activity and increased membrane binding of the oncogenic mutant

About Attitudes and Perceptions: Finding the Proper Way to Consider Latent Variables in Discrete Choice Models

We provide an in-depth theoretical discussion about the differences between attitudes and perceptions, as well as an empirical exercise to analyze its effects. This discussion is of importance, as the large majority of papers considering attitudinal latent variables, just consider those as attributes affecting directly the utility of a certain alternative while systematic taste variations are rarely taken into account and perceptions are normally completely ignored. The results of our case study show that perceptions may indeed affect the decision making process and that they are able to capture a significant part of the variability that is normally explained by alternative specific constants. In the same line, our results indicate that attitudes may be a reason for systematic taste variations, and that a proper categorization of the latent variables, in accordance with the underlying theory, may outperform the customary assumption of linearity

Latent variables and route choice behavior

In the last decade, a broad array of disciplines has shown a general interest in enhancing discrete choice models by considering the incorporation of psychological factors affecting decision making. This paper provides insight into the comprehension of the determinants of route choice behavior by proposing and estimating a hybrid model that integrates latent variable and route choice models. Data contain information about latent variable indicators and chosen routes of travelers driving regularly from home to work in an urban network. Choice sets include alternative routes generated with a branch and bound algorithm. A hybrid model consists of measurement equations, which relate latent variables to measurement indicators and utilities to choice indicators, and structural equations, which link travelers' observable characteristics to latent variables and explanatory variables to utilities. Estimation results illustrate that considering latent variables (i.e., memory, habit, familiarity, spatial ability, time saving skills) alongside traditional variables (e.g., travel time, distance, congestion level) enriches the comprehension of route choice behavior