bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glyoxal as an alternative fixative for single-cell RNA sequencing
Authors: Bageritz Josephine , Krausse Niklas , Yousefian Schayan , Leible Svenja , Valentini Erica , Boutros Michael 
Published: July 2023

Abstract
Single-cell RNA sequencing has become an important method to identify cell types, delineate the trajectories of cell differentiation in whole organisms, and understand the heterogeneity in cellular responses. Nevertheless, sample collection and processing remain a severe bottleneck for single-cell RNA sequencing experiments. Cell isolation protocols often lead to significant changes in the transcriptomes of cells, requiring novel methods to preserve cell states. Here, we developed and benchmarked protocols using glyoxal as a fixative for single-cell RNA sequencing applications. Using Drop-seq methodology, we detected a large number of transcripts and genes from glyoxal-fixed Drosophila cells after single-cell RNA sequencing. The effective glyoxal fixation of transcriptomes in Drosophila and human cells was further supported by a high correlation of gene expression data between glyoxal-fixed and unfixed samples. Accordingly, we also found highly expressed genes overlapping to a large extent between experimental conditions. These results indicated that our fixation protocol did not induce considerable changes in gene expression and conserved the transcriptome for subsequent single-cell isolation procedures. In conclusion, we present glyoxal as a suitable fixative for Drosophila cells and potentially cells of other species that allow high-quality single-cell RNA sequencing applications.
FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies
Authors: Zhao Roy , Lukacsovich Tamas , Gaut Rebecca , Emerson J J 
Published: July 2023

Abstract
The accurate determination of allele frequencies is crucially important across a wide range of problems in genetics, such as developing population genetic models, making inferences from genome-wide association studies, determining genetic risk for diseases, as well as other scientific and medical applications. Furthermore, understanding how allele frequencies change over time in populations is central to ascertaining their evolutionary dynamics. We present a precise, efficient, and economical method (FREQ-Seq2) for quantifying the relative frequencies of different alleles at loci of interest in mixed population samples. Through the creative use of paired barcode sequences, we exponentially increased the throughput of the original FREQ-Seq method from 48 to 2,304 samples. FREQ-Seq2 can be targeted to specific genomic regions of interest, which are amplified using universal barcoded adapters to generate Illumina sequencing libraries. Our enhanced method, available as a kit along with open-source software for analyzing sequenced libraries, enables the detection and removal of errors that are undetectable in the original FREQ-Seq method as well as other conventional methods for allele frequency quantification. Finally, we validated the performance of our sequencing-based approach with a highly multiplexed set of control samples as well as a competitive evolution experiment in Escherichia coli and compare the latter to estimates derived from manual colony counting. Our analyses demonstrate that FREQ-Seq2 is flexible, inexpensive, and produces large amounts of data with low error, low noise, and desirable statistical properties. In summary, FREQ-Seq2 is a powerful method for quantifying allele frequency that provides a versatile approach for profiling mixed populations.
A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs
Authors: Degen Bernd , Müller Niels A 
Published: July 2023

Abstract
Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection (GS)? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software “SNPscan breeder,” we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny testing, GS using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. GS increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. We discuss the practical implications for tree breeding programs. In conclusion, our analyses further support the potential of GS for forest tree breeding and improvement, although MAS may gain relevance with decreasing sequencing costs in the future.
Long-Term PM2.5 Exposure, Lung Function, and Cognitive Function Among Middle-Aged and Older Adults in China
Authors: Ye Zirong , Li Xueru , Lang Haoxiang , Fang Ya 
Published: July 2023

Abstract

Background
Long-term exposure to PM2.5 is related to poor lung function and cognitive impairment, but less is known about the pathway involved in this association. We aimed to explore whether the effect of PM2.5 on cognitive function was mediated by lung function.

Methods
A total of 7 915 adults older than 45 years old were derived from the China Health and Retirement Longitudinal Study (CHARLS) collected in 2011 and 2015. PM2.5 exposure was estimated using a geographically weighted regression model. Lung function was measured by peak expiratory flow (PEF). Cognitive function was evaluated through a structured questionnaire with 4 dimensions: episodic memory, attention, orientation, and visuoconstruction. Under the counterfactual framework, causal mediation analysis was applied to examine direct and indirect associations.

Results
An interquartile range (IQR) increase in PM2.5 change was significantly related to an 8.480 (95% confidence interval [CI]: 3.116, 13.845) decrease in PEF change and a 0.301 (95% CI: 0.100, 0.575) decrease in global cognitive score change. The direct and indirect effects of PM2.5 exposure on global cognitive performance were −0.279 (95% CI: −0.551, −0.060) and −0.023 (95% CI: −0.041, −0.010), respectively. The proportion of the indirect effect was 7.48% (p = .010). The same significant association appeared in only 2 dimensions, episodic memory and attention, which were both mediated by PEF.

Conclusions
Lung function played a partially mediating role in the association between long-term PM2.5 exposure and cognition. More clean air actions should be undertaken to improve lung function and cognitive function in older adults.
Determinants of initiation, continuation and cessation of smokeless tobacco use among pregnant and lactating women: a qualitative study from low-income communities in urban India
Authors: Singh Shalini , Jain Rupal , Joshi Isha , Chandra Rishita , Singh Lucky , Singh Prashant Kumar 
Published: July 2023

Abstract
Smokeless tobacco (SLT) consumption increases the risk of cardiovascular diseases and cancer and leads to adverse reproductive health outcomes among women and newborns. This study examines the factors associated with initiation, continuation and cessation of SLT use among women in the reproductive age so as to formulate and include prevention and cessation interventions from its inception. The study was conducted in urban low-income communities in India. Using snowball and purposive sampling techniques, in-depth interviews were conducted with 20 pregnant and 22 lactating women who currently used SLT products. Data were analysed using thematic analysis with the help of QSR NVivo software. Findings revealed that factors such as people influencing usage change with different life stages including pre-marital and post-marital periods. Perceived health benefits, altered taste preferences during pregnancy and social influences were also studied. Women were found to be more aware of the harmful effects of tobacco during pregnancy than during breastfeeding. Social stigma around women consuming tobacco acted as a major driving factor for cessation. Most of the participants were willing to quit but were not aware of any technique or programme for cessation. The findings of the study highlight the need to develop behavioural change intervention tools, which are culturally and locally appropriate and have a gender-sensitive approach. Different socio-cultural factors associated with initiation/cessation at different life stages should also be taken into consideration while developing these tools.
Socioeconomic inequalities in COVID-19 incidence during the first six waves in Barcelona
Authors: Martinez-Beneito Miguel Angel , Marí-Dell’Olmo Marc , Sánchez-Valdivia Nacho , Rodríguez-Sanz Maica , Pérez Glòria , Pasarín Maria Isabel , Rius Cristina , Artazcoz Lucía , Prieto Raquel , Pérez Katherine , Borrell Carme 
Published: July 2023

AbstractBackgroundThe emergence of SARS-CoV-2 affected urban areas. In Barcelona, six waves of COVID-19 hit the city between March 2020 and March 2022. Inequalities in the incidence of COVID-19 have been described. However, no studies have examined the daily trends of socioeconomic inequalities and how they changed during the different phases of the pandemic. The aim of this study is to analyse the dynamic socioeconomic inequalities in the incidence of COVID-19 during the six waves in Barcelona.MethodsWe examined the proportion of daily cases observed in the census tracts in the lower income tercile compared with the proportion of daily cases observed in the sum of the lower and higher income terciles. Daily differences in these proportions were assessed as a function of the epidemic waves, sex, age group, daily incidence and daily change in the incidence. A logistic regression model with an autoregressive term was used for statistical analysis.ResultsA time-dynamic effect was found for socioeconomic inequalities in the incidence of COVID-19. In fact, belonging to a lower-income area changed from being a risk factor (Waves 1, 2, 4 and 5) to being a protective factor in the sixth wave of the pandemic. Age also had a significant effect on incidence, which also changed over the different waves of the pandemic. Finally, the lower-income areas showed a comparatively lower incidence during the ascending phase of the epidemic waves.ConclusionSocioeconomic inequalities in COVID-19 changed by wave, age group and wave phase.
On Triple Product L-Functions and a Conjecture of Harris–Venkatesh
Authors: Lecouturier Emmanuel 
Published: July 2023

Abstract
Harris and Venkatesh made a conjecture relating the derived Hecke operators and the adjoint motivic cohomology in the setting of weight one modular forms. This conjecture was proved under some conditions in the dihedral case by Darmon–Harris–Rotger–Venkatesh. We use a new approach to prove more general cases of the conjecture (up to sign). Our approach relies on Waldspurger’s formula for the central value of Rankin L-series and Ichino’s formula for the triple product L-function.
Polynomial Volume Growth of Quasi-Unipotent Automorphisms of Abelian Varieties (with an Appendix in Collaboration with Chen Jiang)
Authors: Hu Fei 
Published: July 2023

Abstract
Let $X$ be an abelian variety over an algebraically closed field $\textbf{k}$ and $f$ a quasi-unipotent automorphism of $X$. When $\textbf{k}$ is the field of complex numbers, Lin, Oguiso, and D.-Q. Zhang provide an explicit formula for the polynomial volume growth of (or equivalently, for the Gelfand–Kirillov dimension of the twisted homogeneous coordinate ring associated with) the pair $(X, f)$, by an analytic argument. We give an algebraic proof of this formula that works in arbitrary characteristic. In the course of the proof, we obtain the following: (1) a new description of the action of endomorphisms on the $\ell $-adic Tate spaces, in comparison with recent results of Zarhin and Poonen–Rybakov; (2) a partial converse to a result of Reichstein, Rogalski, and J.J. Zhang on quasi-unipotency of endomorphisms and their pullback action on the rational Néron–Severi space $\textsf{N}^{1}(X)_{\textbf{Q}}$ of $\textbf{Q}$-divisors modulo numerical equivalence; and (3) the maximum size of Jordan blocks of (the Jordan canonical form of) $f^{*}|_{\textsf{N}^{1}(X)_{\textbf{Q}}}$ in terms of the action of $f$ on the Tate space $V_{\ell }(X)$.
Conductor-Discriminant Inequality for Hyperelliptic Curves in Odd Residue Characteristic
Authors: Obus Andrew , Srinivasan Padmavathi 
Published: July 2023

Abstract
We prove an inequality between the conductor and the discriminant for all hyperelliptic curves defined over discretely valued fields $K$ with perfect residue field of characteristic not $2$. Specifically, if such a curve is given by $y^{2} = f(x)$ with $f(x) \in \mathcal{O}_{K}[x]$, and if $\mathcal{X}$ is its minimal regular model over $\mathcal{O}_{K}$, then the negative of the Artin conductor of $\mathcal{X}$ (and thus also the number of irreducible components of the special fiber of $\mathcal{X}$) is bounded above by the valuation of $\operatorname{disc}(f)$. There are no restrictions on genus of the curve or on the ramification of the splitting field of $f$. This generalizes earlier work of Ogg, Saito, Liu, and the second author.
Effect of the L74I Polymorphism on Fitness of Cabotegravir-Resistant Variants of Human Immunodeficiency Virus 1 Subtype A6
Authors: Hu Zixin , Cordwell Trevor , Nguyen Hieu , Li Jialin , Jeffrey Jerry L , Kuritzkes Daniel R 
Published: July 2023

Abstract
The presence of human immunodeficiency virus (HIV) 1 subtype A6, characterized by the L74I integrase (IN) polymorphism, is associated with confirmed virologic failure in clinical trials of long-acting cabotegravir and rilpivirine. We investigated the effect of L74I on replication capacity (RC) of recombinant viruses carrying this polymorphism in combination with various IN stand-transfer inhibitor resistance mutations. The presence of L74I conferred greater RC to recombinant viruses expressing HIV-1 A6 IN when present together with G118R, G140R, Q148H, and R263K; no significant difference in RC was observed for the Q148K or R mutants. These findings may explain, in part, the association of HIV-1 subtype A6 with virologic failure.
Discussion of the 2022 Hansen Lecture: “The Evolution of the Use of Models in Survey Sampling”
Authors: Breidt F Jay 
Published: July 2023

Abstract
The 2022 Hansen Lecture gave a broad overview of the use of models in survey sampling, with emphasis on modeling approaches to incorporating auxiliary information in survey estimators. This discussion expands upon some issues in model-assisted estimation, exploring data needs and the availability of multipurpose weights for advanced modeling methods.
Roles of auxin pathways in maize biology
Authors: Cowling Craig L , Dash Linkan , Kelley Dior R 
Published: July 2023

AbstractPhytohormones play a central role in plant development and environmental responses. Auxin is a classical hormone that is required for organ formation, tissue patterning, and defense responses. Auxin pathways have been extensively studied across numerous land plant lineages, including bryophytes and eudicots. In contrast, our understanding of the roles of auxin in maize morphogenesis and immune responses is limited. Here, we review evidence for auxin-mediated processes in maize and describe promising areas for future research in the auxin field. Several recent transcriptomic and genetic studies have demonstrated that auxin is a key influencer of both vegetative and reproductive development in maize (namely roots, leaves, and kernels). Auxin signaling has been implicated in both maize shoot architecture and immune responses through genetic and molecular analyses of the conserved co-repressor RAMOSA ENHANCER LOCUS2. Polar auxin transport is linked to maize drought responses, root growth, shoot formation, and leaf morphogenesis. Notably, maize has been a key system for delineating auxin biosynthetic pathways and offers many opportunities for future investigations on auxin metabolism. In addition, crosstalk between auxin and other phytohormones has been uncovered through gene expression studies and is important for leaf and root development in maize. Collectively these studies point to auxin as a cornerstone for maize biology that could be leveraged for improved crop resilience and yield.
Chromosome-Aware Phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) Elucidates Ancient Gene Conflict
Authors: Knyshov Alexander , Gordon Eric R L , Masonick Paul K , Castillo Stephanie , Forero Dimitri , Hoey-Chamberlain Rochelle , Hwang Wei Song , Johnson Kevin P , Lemmon Alan R , Moriarty Lemmon Emily , Standring Samantha , Zhang Junxia , Weirauch Christiane 
Published: July 2023

Abstract
Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for nonvertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 anchored hybrid enrichment, 24 RNA-seq, and 70 whole-genome sequencing samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g., nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse (∼7,000 spp.) and old (&gt;180 Ma) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact the accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade.
Takayasu’s arteritis after a prolonged course of hypertrophic osteoarthropathy
Authors: Jubashi Takashi , Horai Yoshiro , Tomokawa Takuya , Hara Kazusato , Kawakami Atsushi 
Published: July 2023

ABSTRACT
A 71-year-old male with hypertrophic osteoarthropathy was referred to our hospital because of a nocturnal fever and tenderness stretching from the left parotid region to the left front neck, in which antibacterials were ineffective. He was diagnosed with Takayasu’s arteritis following findings of contrast-enhanced computed tomography and neck ultrasound. This is the first report to describe the development of Takayasu’s arteritis after a prolonged course of typical hypertrophic osteoarthropathy, and the proposed hypertrophic osteoarthropathy and Takayasu’s arteritis have common underlying pathophysiological factors.
Interactions between chromium species and DNA in vitro and their potential role in the toxicity of hexavalent chromium
Authors: Mezencev R , Gibbons C 
Published: July 2023

Abstract
Epidemiological and animal studies have supported the carcinogenicity of hexavalent chromium [Cr(VI)]; however, molecular changes responsible for the induction of cancer by Cr(VI) are not entirely understood. Numerous mechanistic studies suggested the role of oxidative stress and genotoxicity in Cr(VI)-mediated carcinogenesis; however, specific types of DNA damage have not yet been conclusively attributed to specific chromium species or other reactive byproducts generated in biological systems exposed to Cr(VI). Due to the remarkably complex chemistry and biological effects of chromium species generated through the intracellular reduction of Cr(VI), their relevance for Cr(VI)-mediated carcinogenesis has not yet been fully elucidated and continues to be a subject of ongoing discussions in the field. In this report, we describe a complex world of chromium species and their reactivity with DNA and other biologically relevant molecules in vitro to inform a more complete understanding of Cr(VI)-mediated toxicity. In addition, we discuss previous results in the context of in vitro models and analytical methods to reconcile some conflicting findings on the biological role of chromium species.
Single-cell reference mapping to construct and extend cell-type hierarchies
Authors: Michielsen Lieke , Lotfollahi Mohammad , Strobl Daniel , Sikkema Lisa , Reinders Marcel J T , Theis Fabian J , Mahfouz Ahmed 
Published: July 2023

Abstract
Single-cell genomics is now producing an ever-increasing amount of datasets that, when integrated, could provide large-scale reference atlases of tissue in health and disease. Such large-scale atlases increase the scale and generalizability of analyses and enable combining knowledge generated by individual studies. Specifically, individual studies often differ regarding cell annotation terminology and depth, with different groups specializing in different cell type compartments, often using distinct terminology. Understanding how these distinct sets of annotations are related and complement each other would mark a major step towards a consensus-based cell-type annotation reflecting the latest knowledge in the field. Whereas recent computational techniques, referred to as ‘reference mapping’ methods, facilitate the usage and expansion of existing reference atlases by mapping new datasets (i.e. queries) onto an atlas; a systematic approach towards harmonizing dataset-specific cell-type terminology and annotation depth is still lacking. Here, we present ‘treeArches’, a framework to automatically build and extend reference atlases while enriching them with an updatable hierarchy of cell-type annotations across different datasets. We demonstrate various use cases for treeArches, from automatically resolving relations between reference and query cell types to identifying unseen cell types absent in the reference, such as disease-associated cell states. We envision treeArches enabling data-driven construction of consensus atlas-level cell-type hierarchies and facilitating efficient usage of reference atlases.