Beyond Sentiment: Leveraging Topic Metrics for Political Stance Classification

Sentiment analysis, widely critiqued for capturing merely the overall tone of a corpus, falls short in accurately reflecting the latent structures and political stances within texts. This study introduces topic metrics, dummy variables converted from extracted topics, as both an alternative and complement to sentiment metrics in stance classification. By employing three datasets identified by Bestvater and Monroe (2023), this study demonstrates BERTopic's proficiency in extracting coherent topics and the effectiveness of topic metrics in stance classification. The experiment results show that BERTopic improves coherence scores by 17.07% to 54.20% when compared to traditional approaches such as Dirichlet Allocation (LDA) and Non-negative Matrix Factorization (NMF), prevalent in earlier political science research. Additionally, our results indicate topic metrics outperform sentiment metrics in stance classification, increasing performance by as much as 18.95%. Our findings suggest topic metrics are especially effective for context-rich texts and corpus where stance and sentiment correlations are weak. The combination of sentiment and topic metrics achieve an optimal performance in most of the scenarios and can further address the limitations of relying solely on sentiment as well as the low coherence score of topic metrics

Characterization of Biochelators, Membrane Redox Systems, and Quinone Reductases from Wood Degrading Basidiomycetes

Biodegradation of wood by brown rot fungi is dependent upon a non-enzymatic system involving Fenton chemistry. Iron biochelators with molecular weights lower than 1kD are important components in this process. Phenolate biochelators drive a hydroxyl radical generating Fenton reaction by reducing ferric iron. Biochelators may be mineralized or alternately, in some cases oxidized biochelators may be regenerated via a quinone redox cycle. Electron donors for this postulated regeneration have not been identified. Extracellular cellobiose dehydrogenase has also been found to drive the Fenton reaction by generating ferrous iron and hydrogen peroxide. This research compared the production of biochelators and the cellobiose dehydrogenase in white rot, brown rot and non-decay fungi to elucidate the brown rot mechanisms. The transplasma membrane redox system and intracellular quinone reductases were also characterized in the brown rot fungus GloeophyIIum trabeum. All the tested fungi produced iron chelating compounds and cellobiose dehydrogenase. The chemical characteristics and iron-reducing abilities of the biochelators produced varied, with the brown rot fungi producing biochelators showing significant higher iron reducing ability. The brown rot fungus Fomitopsis pinicola produced biochelators with the greatest iron reducing activity. Gloeophyllum trabeum mycelia showed 1,4-benzoquinone reducing ability. The transplasma membrane redox system was characterized based on its ferricyanide reduction kinetics. The fungus also produced constitutive intracellular NAD(P)H dependent 1,4-benzoquinone reductases. Reduction of 1,4-benzoquinone by intact mycelia and the intracellular enzymes showed different characteristics. An intracellular NADH dependent flavin mononucleotide containing 1,4-benzoquinone reductase was purified from G. trabeum. The phy.sica1 and catalytical properties of the purified enzyme were characterized. The enzyme was highly inducible by 2,6-dimethoxy-1,4- benzoquinone and had a high turn over number for multiple quinones, which indicated it functioned efficiently in quinone metabolism. Quinone reductases can play an important role in pH regulation, protecting hyphae against free radicals, and may in some cases act as one type of electron carrier potentially capable of transporting electrons from the intracellular NADH pool to the extracellular Fenton reaction. The research described here contributes to the understanding of brown rot degradative mechanisms and to an enhanced understanding of the biochemistry and physiology of the brown rot fungus G. trabeum

Structure of Unsupported Small Palladium Nanoparticles

A tight binding molecular dynamics calculation has been conducted to study the size and coordination dependence of bond length and bond energy of Pd atomic clusters of 1.2–5.4 nm in diameter. It has been found that the bond contraction associated with bond energy increases in the outermost layer about 0.24 nm in a radial way, yet in the core interior the bond length and the bond energy remain their corresponding bulk values. This surface bond contraction is independent of the particle size

An Anomaly-Based Method for Identifying Signals of Spring and Autumn Low-Temperature Events in the Yangtze River Valley, China

June 2015 QIAN ET AL. Vol. 54 1216-123

Bias or Diversity? Unraveling Semantic Discrepancy in U.S. News Headlines

There is a broad consensus that news media outlets incorporate ideological biases in their news articles. However, prior studies on measuring the discrepancies among media outlets and further dissecting the origins of semantic differences suffer from small sample sizes and limited scope. In this study, we collect a large dataset of 1.8 million news headlines from major U.S. media outlets spanning from 2014 to 2022 to thoroughly track and dissect the semantic discrepancy in U.S. news media. We employ multiple correspondence analysis (MCA) to quantify the semantic discrepancy relating to four prominent topics - domestic politics, economic issues, social issues, and foreign affairs. Additionally, we compare the most frequent n-grams in media headlines to provide further qualitative insights into our analysis. Our findings indicate that on domestic politics and social issues, the discrepancy can be attributed to a certain degree of media bias. Meanwhile, the discrepancy in reporting foreign affairs is largely attributed to the diversity in individual journalistic styles. Finally, U.S. media outlets show consistency and high similarity in their coverage of economic issues

Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland

Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host

Comparative metagenomics of Daphnia symbionts

BACKGROUND: Shotgun sequences of DNA extracts from whole organisms allow a comprehensive assessment of possible symbionts. The current project makes use of four shotgun datasets from three species of the planktonic freshwater crustaceans Daphnia: one dataset from clones of D. pulex and D. pulicaria and two datasets from one clone of D. magna. We analyzed these datasets with three aims: First, we search for bacterial symbionts, which are present in all three species. Second, we search for evidence for Cyanobacteria and plastids, which had been suggested to occur as symbionts in a related Daphnia species. Third, we compare the metacommunities revealed by two different 454 pyrosequencing methods (GS 20 and GS FLX). RESULTS: In all datasets we found evidence for a large number of bacteria belonging to diverse taxa. The vast majority of these were Proteobacteria. Of those, most sequences were assigned to different genera of the Betaproteobacteria family Comamonadaceae. Other taxa represented in all datasets included the genera Flavobacterium, Rhodobacter, Chromobacterium, Methylibium, Bordetella, Burkholderia and Cupriavidus. A few taxa matched sequences only from the D. pulex and the D. pulicaria datasets: Aeromonas, Pseudomonas and Delftia. Taxa with many hits specific to a single dataset were rare. For most of the identified taxa earlier studies reported the finding of related taxa in aquatic environmental samples. We found no clear evidence for the presence of symbiotic Cyanobacteria or plastids. The apparent similarity of the symbiont communities of the three Daphnia species breaks down on a species and strain level. Communities have a similar composition at a higher taxonomic level, but the actual sequences found are divergent. The two Daphnia magna datasets obtained from two different pyrosequencing platforms revealed rather similar results. CONCLUSION: Three clones from three species of the genus Daphnia were found to harbor a rich community of symbionts. These communities are similar at the genus and higher taxonomic level, but are composed of different species. The similarity of these three symbiont communities hints that some of these associations may be stable in the long-term

Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil

Analysis of Plasmodium falciparum var Genes Expressed in Children from Papua New Guinea

Background The variable antigen P. falciparum erythrocyte membrane protein-1 (PfEMP1) is a major virulence factor in malaria. A large number of var genes encode PfEMP1, and we hypothesized that a restricted PfEMP1 repertoire determines clinical disease presentation. We conducted a case-control study in Papua New Guinea and analyzed transcribed var genes in naturally infected children. Methods var messenger RNA was isolated from 78 children with asymptomatic, mild, or severe malaria. We prepared complementary DNA from the upstream region into the DBL1α domain and picked, on average, 20 clones for sequencing. Results Twenty-five percent of centrally located var genes were shared between children, whereas only 5% of subtelomeric genes were shared, indicating lower diversity in the former group. Linkage between group B or C var upstream sequences and DBL1α groups was not observed, which impeded prediction by DBL1α analysis. A higher proportion of var group A sequences was detected in symptomatic malaria, and a subgroup of frequently encountered var genes with complex head structure seems to be associated with severe malaria. A subset of var group C genes was frequently expressed in older children with asymptomatic high levels of parasitemia. Conclusion Despite this vast diversity, restricted disease-associated var genes were identified and might be used for innovative interventions based on PfEMP

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

Longer reads and higher sequence yield per run provided by the 454 Titanium technology in comparison to earlier generations of pyrosequencing proved beneficial for the quality of assembly. An almost full representation of genes known to be expressed in the mouse heart was identified. Usage of the extensive genomic resources available for the house mouse, a moderately (20-40 mln years) divergent relative of the voles, enabled a comprehensive assessment of the transcript completeness. Transcript sequences generated in the present study allowed the identification of candidate SNPs associated with divergence of selection lines and constitute a valuable permanent resource forming a foundation for RNAseq experiments aiming at detection of adaptive changes both at the level of gene expression and sequence variants, that would facilitate studies of the genetic basis of evolutionary divergence