bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unprecedented enantio-selective live-cell mitochondrial DNA super-resolution imaging and photo-sensitizing by the chiral ruthenium polypyridyl DNA “light-switch”
Authors: Huang Rong , Huang Chun-Hua , Chen Jing , Yan Zhu-Ying , Tang Miao , Shao Jie , Cai Kaiyong , Zhu Ben-Zhan 
Published: November 2023

Abstract
Mitochondrial DNA (mtDNA) is known to play a critical role in cellular functions. However, the fluorescent probe enantio-selectively targeting live-cell mtDNA is rare. We recently found that the well-known DNA ‘light-switch’ [Ru(phen)2dppz]Cl2 can image nuclear DNA in live-cells with chlorophenolic counter-anions via forming lipophilic ion-pairing complex. Interestingly, after washing with fresh-medium, [Ru(phen)2dppz]Cl2 was found to re-localize from nucleus to mitochondria via ABC transporter proteins. Intriguingly, the two enantiomers of [Ru(phen)2dppz]Cl2 were found to bind enantio-selectively with mtDNA in live-cells not only by super-resolution optical microscopy techniques (SIM, STED), but also by biochemical methods (mitochondrial membrane staining with Tomo20-dronpa). Using [Ru(phen)2dppz]Cl2 as the new mtDNA probe, we further found that each mitochondrion containing 1–8 mtDNA molecules are distributed throughout the entire mitochondrial matrix, and there are more nucleoids near nucleus. More interestingly, we found enantio-selective apoptotic cell death was induced by the two enantiomers by prolonged visible light irradiation, and in-situ self-monitoring apoptosis process can be achieved by using the unique ‘photo-triggered nuclear translocation’ property of the Ru complex. This is the first report on enantio-selective targeting and super-resolution imaging of live-cell mtDNA by a chiral Ru complex via formation and dissociation of ion-pairing complex with suitable counter-anions.
NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update
Authors: Clough Emily , Barrett Tanya , Wilhite Stephen E , Ledoux Pierre , Evangelista Carlos , Kim Irene F , Tomashevsky Maxim , Marshall Kimberly A , Phillippy Katherine H , Sherman Patti M , Lee Hyeseung , Zhang Naigong , Serova Nadezhda , Wagner Lukas , Zalunin Vadim , Kochergin Andrey , Soboleva Alexandra 
Published: November 2023

Abstract
The Gene Expression Omnibus (GEO) is an international public repository that archives gene expression and epigenomics data sets generated by next-generation sequencing and microarray technologies. Data are typically submitted to GEO by researchers in compliance with widespread journal and funder mandates to make generated data publicly accessible. The resource handles raw data files, processed data files and descriptive metadata for over 200 000 studies and 6.5 million samples, all of which are indexed, searchable and downloadable. Additionally, GEO offers web-based tools that facilitate analysis and visualization of differential gene expression. This article presents the current status and recent advancements in GEO, including the generation of consistently computed gene expression count matrices for thousands of RNA-seq studies, and new interactive graphical plots in GEO2R that help users identify differentially expressed genes and assess data set quality. The GEO repository is built and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM), and is publicly accessible at https://www.ncbi.nlm.nih.gov/geo/.
Evaluation of input data modality choices on functional gene embeddings
Authors: Brechtmann Felix , Bechtler Thibault , Londhe Shubhankar , Mertes Christian , Gagneur Julien 
Published: November 2023

AbstractFunctional gene embeddings, numerical vectors capturing gene function, provide a promising way to integrate functional gene information into machine learning models. These embeddings are learnt by applying self-supervised machine-learning algorithms on various data types including quantitative omics measurements, protein–protein interaction networks and literature. However, downstream evaluations comparing alternative data modalities used to construct functional gene embeddings have been lacking. Here we benchmarked functional gene embeddings obtained from various data modalities for predicting disease-gene lists, cancer drivers, phenotype–gene associations and scores from genome-wide association studies. Off-the-shelf predictors trained on precomputed embeddings matched or outperformed dedicated state-of-the-art predictors, demonstrating their high utility. Embeddings based on literature and protein–protein interactions inferred from low-throughput experiments outperformed embeddings derived from genome-wide experimental data (transcriptomics, deletion screens and protein sequence) when predicting curated gene lists. In contrast, they did not perform better when predicting genome-wide association signals and were biased towards highly-studied genes. These results indicate that embeddings derived from literature and low-throughput experiments appear favourable in many existing benchmarks because they are biased towards well-studied genes and should therefore be considered with caution. Altogether, our study and precomputed embeddings will facilitate the development of machine-learning models in genetics and related fields.
Tumor and immune cell types interact to produce heterogeneous phenotypes of pediatric high-grade glioma
Authors: DeSisto John , Donson Andrew M , Griesinger Andrea M , Fu Rui , Riemondy Kent , Mulcahy Levy Jean , Siegenthaler Julie A , Foreman Nicholas K , Vibhakar Rajeev , Green Adam L 
Published: November 2023

Abstract

Background
Pediatric high-grade gliomas (PHGG) are aggressive brain tumors with 5-year survival rates ranging from &lt;2% to 20% depending upon subtype. PHGG presents differently from patient to patient and is intratumorally heterogeneous, posing challenges in designing therapies. We hypothesized that heterogeneity occurs because PHGG comprises multiple distinct tumor and immune cell types in varying proportions, each of which may influence tumor characteristics.

Methods
We obtained 19 PHGG samples from our institution’s pediatric brain tumor bank. We constructed a comprehensive transcriptomic dataset at the single-cell level using single-cell RNA-Seq (scRNA-Seq), identified known glial and immune cell types, and performed differential gene expression and gene set enrichment analysis. We conducted multi-channel immunofluorescence (IF) staining to confirm the transcriptomic results.

Results
Our PHGG samples included 3 principal predicted tumor cell types: astrocytes, oligodendrocyte progenitors (OPCs), and mesenchymal-like cells (Mes). These cell types differed in their gene expression profiles, pathway enrichment, and mesenchymal character. We identified a macrophage population enriched in mesenchymal and inflammatory gene expression as a possible source of mesenchymal tumor characteristics. We found evidence of T-cell exhaustion and suppression.

Conclusions
PHGG comprises multiple distinct proliferating tumor cell types. Microglia-derived macrophages may drive mesenchymal gene expression in PHGG. The predicted Mes tumor cell population likely derives from OPCs. The variable tumor cell populations rely on different oncogenic pathways and are thus likely to vary in their responses to therapy.
Endogenous learning in international environmental agreements: the impact of research spillovers and the degree of cooperation
Authors: André Francisco J , Finus Michael 
Published: November 2023

Abstract
We consider an endogenous learning-by-doing process where countries can invest in research that reduces the systematic uncertainty about climate change damages. We analyse a coalition model in which countries decide whether to join a treaty and then choose their level of research and abatement. Countries can cooperate on research and abatement or only on one of these items. We consider the entire range of possible research spillovers. Cooperation on all issues and large research spillovers are generally welfare improving, but lead to smaller coalitions, as they encourage free-riding. However, on balance, in equilibrium, we find that cooperation should not be confined to research and should include abatement, and research findings should freely travel.
Departmental Organization, Treasurer, House Servants, and Tradesmen
Authors: Milhous Judith , Dideriksen Gabridla , Hume Robert D 
Published: November 2023

Abstract
Turning from the physical premises to their inhabitants, we need to ask how the company was organized and how it conducted its operations. A flow chart would show Bedford and Salisbury as the concealed proprietors, linked to their minion O’Reilly by Sheldon. The company proper consisted of at least seven distinct ‘departments’: opera, ballet, costume, scenery, properties, lighting, and the treasurer’s office (which oversaw admission and housekeeping). The extent to which these were essentially separate and self contained units may surprise those accustomed to the concept of an ‘artistic director’ and present-day notions of opera-house management.
Canada
Authors: Djwa Sandra 
Published: November 2023

Abstract
In the past thirty years Canadian writing in English (with which I shall be exclusively concerned here: Quebec literature has a tradition of its own) has come of age. Up until the 1950s the major genre was poetry; the 1960s saw the rise of the novel; drama emerged in the 1970s; after 1980 there was a flurry of autobiographical writing. Nor should one forget literary criticism, strong in Canada thanks to the influence of two leading figures: Marshall McLuhan (1911-80), who was hailed as a guru of the new ‘information age’ after publication of The Gutenberg Galaxy (1962) and The Meium is the Message (1967); and Northrop Frye (1912-91), whose work has been extraordinarily influential, largely because of the synoptic intelligence of books such as his Anatomy of Criticism (1957), The Great Code (1982), and the ‘Conclusion’ to the first Literary History of Canada (1965), in which Frye established a paradigm for Canadian criticism when he asserted that the country’s poetry (and, by extension, writing) was characterized by a ‘deep note of terror’ and a ‘garrison mentality’-the response of the pioneer to the wilderness.
China, Taiwan, And Hong Kong
Authors: Bailey Alison 
Published: November 2023

Abstract
PRIOR to 1949, Chinese literature emanated from one major source: the Chinese mainland. After 1949, once the Communists had taken control of the mainland, the Nationalists fled to Taiwan. Radical ideological and cultural divergences between the rival Chinese states then played a significant role in the development of two literatures, even if there are, also, remarkable similarities, founded on responses to a shared heritage. Hong Kong represents yet a third source of Chinese literature, both creatively and as a conduit through which writing unobtainable elsewhere can be published or bought. Finally, after the Tiananmen Massacre in 1989, a new avenue for Chinese literature opened up through exile.
New Zealand
Authors: Sharp Iain 
Published: November 2023

Abstract
Before 1980 the literary forms at which New Zealand writers excelled were miniaturist—the short lyric poem and the short story. Consequently, much of the best writing of those years can be found within the covers of a single volume, The Oxford Anthology of New Zealand Writing since 1945 (1983). Since 1980 New Zealand writing has burgeoned, however, and the significant works of the 1980s and 1990s require a full shelf.
Wales
Authors: Thomas Ned 
Published: November 2023

Abstract
To understand contemporary writing in Wales requires a complex cultural map. We have to deal with two languages that are used in varying degrees across the whole country. An outsider might think that what is written in the more generally accessible language of the two, English, offers a way into the hidden world of the Welsh language, but that is seldom the case. Many Welsh writers in English have little knowledge of Welsh history, language, or tradition; others are steeped in them, but even they cannot be regarded as simple interpreters of Welsh-language culture, for languages and literary traditions are themselves important shaping elements, irrespective of the way individuals may use them for their own literary purposes. To this may be added the difficulty of defining a Welsh literature in English. Writing in Welsh defines itself by the medium used-a novel may be set in Prague or Italy and be no less Welsh in that sense; but what makes a novel written in English ‘Welsh’? Usually the fact that it deals with Wales.
Global warming in the pipeline
Authors: Hansen James E , Sato Makiko , Simons Leon , Nazarenko Larissa S , Sangha Isabelle , Kharecha Pushker , Zachos James C , von Schuckmann Karina , Loeb Norman G , Osman Matthew B , Jin Qinjian , Tselioudis George , Jeong Eunbi , Lacis Andrew , Ruedy Reto , Russell Gary , Cao Junji , Li Jing 
Published: November 2023

AbstractImproved knowledge of glacial-to-interglacial global temperature change yields Charney (fast-feedback) equilibrium climate sensitivity 1.2 ± 0.3°C (2σ) per W/m2, which is 4.8°C ± 1.2°C for doubled CO2. Consistent analysis of temperature over the full Cenozoic era—including ‘slow’ feedbacks by ice sheets and trace gases—supports this sensitivity and implies that CO2 was 300–350 ppm in the Pliocene and about 450 ppm at transition to a nearly ice-free planet, exposing unrealistic lethargy of ice sheet models. Equilibrium global warming for today’s GHG amount is 10°C, which is reduced to 8°C by today’s human-made aerosols. Equilibrium warming is not ‘committed’ warming; rapid phaseout of GHG emissions would prevent most equilibrium warming from occurring. However, decline of aerosol emissions since 2010 should increase the 1970–2010 global warming rate of 0.18°C per decade to a post-2010 rate of at least 0.27°C per decade. Thus, under the present geopolitical approach to GHG emissions, global warming will exceed 1.5°C in the 2020s and 2°C before 2050. Impacts on people and nature will accelerate as global warming increases hydrologic (weather) extremes. The enormity of consequences demands a return to Holocene-level global temperature. Required actions include: (1) a global increasing price on GHG emissions accompanied by development of abundant, affordable, dispatchable clean energy, (2) East-West cooperation in a way that accommodates developing world needs, and (3) intervention with Earth’s radiation imbalance to phase down today’s massive human-made ‘geo-transformation’ of Earth’s climate. Current political crises present an opportunity for reset, especially if young people can grasp their situation.
Big Little Election Lies: Cynical and Credulous Evaluations of Electoral Fraud
Authors: Norris Pippa 
Published: November 2023

Abstract
The ‘Big Lie’ in American politics has sparked intense concern about the erosion of public confidence in the integrity of US elections—raising questions about the legitimacy of the authorities, institutions, and principles of democratic governance. Cynicism generated from misinformation about trustworthy elections has attracted a growing body of individual-level social-psychological research in America and Europe. Another common problem found around the world, however, which has received far less attention, concerns credulous citizens who express considerable faith and confidence in flawed contests. This study theorises that at macro-level, the accuracy of any public judgments about trustworthy elections is likely to be mediated by the information environment in open and closed societies, as well as by the type of regime. To understand these issues, Part I summarises the conceptual and theoretical argument about trust and trustworthiness. Part II describes the sources of evidence. To apply the theory, data on public opinion is drawn from around 85 societies around the globe included in Waves 6 and 7 of the World Values Survey (2010–2022), with measures of electoral trust and subjective perceptions of electoral integrity among ordinary citizens. Institutional electoral performance indices are drawn from the Varieties of Democracy project (V-Dem 12.0). Part III analyses how far these independent estimates match public judgments of the trustworthiness of elections in each country – and how far such relationships are conditioned by the type of information society as well as by the type of regime. Part IV highlights the key findings and considers their broader implications for understanding the macro-level conditions for trust and trustworthiness.
The changing nitrogen landscape of United States streams: Declining deposition and increasing organic nitrogen
Authors: Lin Jiajia , Compton Jana E , Sabo Robert D , Herlihy Alan T , Hill Ryan A , Weber Marc H , Brooks J Renée , Paulsen Steve G , Stoddard John L 
Published: November 2023

Abstract
Air quality regulations have led to decreased nitrogen (N) and sulfur deposition across the conterminous United States (CONUS) during the last several decades, particularly in the eastern parts. But it is unclear if declining deposition has altered stream N at large scales. We compared watershed N inputs with N chemistry from over 2,000 CONUS streams where deposition was the largest N input to the watershed. Weighted change analysis showed that deposition declined across most watersheds, especially in the Eastern CONUS. Nationally, declining N deposition was not associated with significant large-scale declines in stream nitrate concentration. Instead, significant increases in stream dissolved organic carbon (DOC) and total organic N (TON) were widespread across regions. Possible mechanisms behind these increases include declines in acidity and/or ionic strength drivers, changes in carbon availability, and/or climate variables. Our results also reveal a declining trend of DOC/TON ratio over the entire study period, primarily influenced by the trend in the Eastern region, suggesting the rate of increase in stream TON exceeded the rate of increase in DOC concentration during this period. Our results illustrate the complexity of nutrient cycling that links long-term atmospheric deposition to water quality. More research is needed to understand how increased dissolved organic N could affect aquatic ecosystems and downstream riverine nutrient export.
Effectiveness of cloth face masks to prevent viral spread: a meta-analysis
Authors: Zeilinger Elisabeth L , Brunevskaya Nadine , Wurzer Jana , Oberleiter Sandra , Fries Jonathan , Fuchs Amelie , Herscovici Alma , Kum Lea , Masel Eva K , Pietschnig Jakob 
Published: November 2023

Abstract

Background
The effectiveness of cloth face masks to prevent viral spread has not yet been conclusively established. In this meta-analysis, we evaluate their effectiveness in comparison to standard medical/surgical and N95-typed masks against viral spread.

Methods
We identified literature through a systematic search in three databases and meta-analytically synthesized relevant studies by means of random-effects as well as multilevel modelling.

Results
Twelve studies comprising k = 28 effect sizes (N = 338) were included. Medical/surgical and N95-typed masks outperformed cloth masks, yielding a large effect (g = 1.40). This effect remained robust when data were grouped according to comparisons with medical/surgical masks (g = 1.25) and N95-typed masks (g = 1.29). However, effects were differentiated according to mask fit, indicating reversals of signs when cloth mask effects were compared with ill-fitting medical/surgical and N95-typed masks (gs = −12.50 and − 10.90, respectively).

Conclusions
Cloth face masks were found to have significantly poorer filtering performance than medical/surgical masks and N95 masks, but only if non-cloth masks were properly fitted. Our results illustrate the necessity of using well-fitting medical/surgical or N95-typed masks to prevent viral spread, although some allowance should be made in circumstances where higher compliance with cloth mask mandates are expected.
Interaction between hepatitis B, hepatitis C and smoking in the development of hepatocellular carcinoma: a systematic review and meta-analysis
Authors: Shadi Yahya , Heshmati Bahram , Poorolajal Jalal 
Published: November 2023

Abstract

Background
This meta-analysis reports the relationship between hepatitis B virus (HBV), hepatitis C virus (HCV), smoking and their combined impact on the development of hepatocellular carcinoma (HCC).

Methods
We conducted a systematic search of PubMed, Web of Science and Scopus databases up to 15 July 2023. Observational studies investigating the association between HBV, HCV and smoking in the development of HCC were included. We assessed between-study heterogeneity using the I2 statistics. The effect sizes were estimated as odds ratio (OR) with 95% confidence intervals (CIs) using a random-effects model.

Results
Out of 20 794 studies identified in the initial search, 32 observational studies involving 22 282 participants met the inclusion criteria. Our meta-analysis showed that the combined impact of HBV and smoking was associated with an OR of 19.81 (95% CI: 14.77, 26.58), HCV and smoking was associated with an OR of 24.86 (95% CI: 12.41, 49.79), and coinfection of HBV and HCV was associated with an OR of 32.58 (95% CI: 20.57, 51.60).

Conclusions
Our findings indicate a significant interaction between HBV, HCV and smoking in the development of HCC and highlight the importance of addressing smoking cessation and viral hepatitis prevention and treatment as potential strategies for reducing HCC.
Micrometre-sized ice particles for planetary science experiments – CoPhyLab cryogenic granular sample production and storage
Authors: Kreuzig C , Bischoff D , Molinski N S , Brecher J N , Kovalev A , Meier G , Oesert J , Gorb S N , Gundlach B , Blum J 
Published: November 2023

Abstract
In this work, we present a comprehensive investigation into the production, characteristics, handling, and storage of micrometre-sized granular water-ice. The focus of this research is to provide well-characterized analogue samples for laboratory experiments simulating icy bodies found in the Solar system, particularly comets. These experiments are conducted as part of the Comet Physics Laboratory (CoPhyLab) project, an international collaboration aimed at studying cometary processes to gain insights into the underlying physics of cometary activity. Granular water-ice, along with other less abundant but more volatile ices, plays a crucial role in the ejection of gas and dust particles when comets approach the Sun. To facilitate large-scale laboratory experiments, an ice-particle machine was developed, capable of autonomously producing sufficient quantities of granular water-ice. Additionally, a cryogenic desiccator was designed to remove any residual moisture from the ice using liquid nitrogen. The resulting ice particles can be mixed with other materials and stored within the desiccator or a cryogenic transport can, enabling easy shipment to any laboratory, including via air transport. To analyse the ice grains, cryogenic scanning electron microscopy was employed to determine their particle shape and size-frequency distribution. These analyses contribute to a better understanding of the properties of granular water-ice and its behaviour under cryogenic conditions, supporting the objectives of the CoPhyLab project.