bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between mitochondrial DNA copy number and production traits in pigs
Authors: Molinero Eduard , Pena Ramona N. , Estany Joan , Ros‐Freixedes Roger 
Published: August 2024

AbstractMitochondria are essential organelles in the regulation of cellular energetic metabolism. Mitochondrial DNA copy number (mtDNA_CN) can be used as a proxy for mitochondria number, size, and activity. The aims of our study are to evaluate the effect of mtDNA_CN and mitochondrial haploblocks on production traits in pigs, and to identify the genetic background of this cellular phenotype. We collected performance data of 234 pigs and extracted DNA from skeletal muscle. Whole‐genome sequencing data was used to determine mtDNA_CN. We found positive correlations of muscle mtDNA_CN with backfat thickness at 207 d (+0.14; p‐value = 0.07) and negative correlations with carcase loin thickness (−0.14; p‐value = 0.03). Pigs with mtDNA_CN values below the lower quartile had greater loin thickness (+4.1 mm; p‐value = 0.01) and lower backfat thickness (−1.1 mm; p‐value = 0.08), which resulted in greater carcase lean percentage (+2.4%; p‐value = 0.04), than pigs with mtDNA_CN values above the upper quartile. These results support the hypothesis that a reduction of mitochondrial activity is associated with greater feed efficiency. Higher mtDNA_CN was also positively correlated with higher meat ultimate pH (+0.19; p‐value <0.01) but we did not observe significant difference for meat ultimate pH between the two groups with extreme mtDNA_CN. We found no association of the most frequent mitochondrial haploblocks with mtDNA_CN or the production traits, but several genomic regions that harbour potential candidate genes with functions related to mitochondrial biogenesis and homeostasis were associated with mtDNA_CN. These regions provide new insights into the genetic background of this cellular phenotype but it is still uncertain if such associations translate into noticeable effects on the production traits.
The past, present, and future of tumour deposits in colorectal cancer: Advancing staging for improved prognosis and treatment decision‐making
Authors: Chang Zhengyan , Fu Huijun , Song Jiaqi , Kong Cheng , Xie Ruting , Pi Man , Sun Xuechen , Zhang Wentao , Liu Yifan , Huang Ruizhi , Yang Tingsong , Han Dongyan 
Published: August 2024

AbstractTumour deposits (TDs) significantly impact colorectal cancer (CRC) prognosis. Integrating TDs into the TNM staging system can enhance individualized disease management. Keeping abreast of evolving TDs research is pivotal for clinical advancement. We comprehensively reviewed both recent and popular literature to grasp the field's essence. Subsequently, a data retrieval sourced articles on TDs in CRC for bibliometric analysis, spanning from 1 January 1935 to 30 April 2023. Bibliometrix software facilitated paper analysis and visualization. Bibliometric indicators, the trends and hotspots were determined. A total of 2147 articles were successfully retrieved. Brown G emerged as the most productive author, and the USA as the most prolific country. Central South University and Memorial Sloan Kettering Cancer Center led productivity. Bradford's law categorized 48 journals into zone 1. Keywords co‐occurrence analysis identified three main clusters: the application of TDs in TNM staging, the pathogenesis of TDs, and the assessment of TDs. The trend topic analysis highlighted research focused on refining TDs incorporation into tumour staging. TDs wield enduring medical significance, shaping ongoing research. Much literature focused on confirming TD's prognostic value and optimizing TNM integration. Additionally, it is worth highlighting that TD's enigmatic pathogenesis demands research priority, as it holds the potential to unveil concealed knowledge regarding their development.
Oral microbiome diversity and diet quality in relation to mortality
Authors: Shen Jie , Chen Hui , Zhou Xiaofeng , Huang Qiumin , Garay Lucas Gonzalo , Zhao Mengjia , Qian Shujiao , Zong Geng , Yan Yan , Wang Xiaofeng , Wang Baohong , Tonetti Maurizio , Zheng Yan , Yuan Changzheng 
Published: August 2024

AbstractAimTo examine the independent and joint associations of oral microbiome diversity and diet quality with risks of all‐cause and cause‐specific mortality.Materials and MethodsWe included 7,055 eligible adults from the U.S. National Health and Nutrition Examination Survey (NHANES). Oral microbiome diversity was measured with α‐diversity, including the Simpson Index, observed amplicon sequence variants (ASVs), Faith's phylogenetic diversity, and Shannon–Weiner index. Dietary quality was assessed using the Healthy Eating Index‐2015 (HEI‐2015). Cox proportional hazard models were used to assess the corresponding associations.ResultsDuring a mean follow‐up of 9.0 years, we documented 382 all‐cause deaths. We observed independent associations of oral microbiome diversity indices and dietary quality with all‐cause mortality (hazard ratio [HR] = 0.63; 95% confidence interval [CI]: 0.49–0.82 for observed ASVs; HR = 0.68, 95% CI: 0.52–0.89 for HEI‐2015). Jointly, participants with the highest tertiles of both oral microbiome diversity (in Simpson index) and HEI‐2015 had the lowest hazard of mortality (HR = 0.37, 95% CI: 0.23–0.60). In addition, higher oral microbiome diversity was associated with lower risks of deaths from cardiometabolic disease and cancer.ConclusionsHigher oral microbiome α‐diversity and diet quality were independently associated with lower risk of mortality.
Applying Hegelian theory to contemporary family science
Authors: Cedeño Diana 
Published: August 2024

AbstractDespite Hegel's thorough exploration of the interplay between politics, family dynamics, and the role of self‐consciousness in family processes, his work has been notably absent from discussions within family science and human development. This paper aims to bridge this gap by conducting a comprehensive review of Hegel's contributions, addressing historical issues, and presenting arguments for the relevance of Hegelian concepts in family research, including an overview of methodological possibilities. The paper begins with a concise introduction to Hegel's views on family and society, examining key theoretical concepts such as marriage and family capital. Following this, the discussion delves into the application of Hegelian notions of spirit and develops a list of family values based on my interpretation of Hegel's works. The conclusion underscores the importance of Hegelian thought, emphasizing its potential as an epistemological foundation for advancing family science.
“I feel like a ‘cyber‐gypsy’”: BL fanfiction writers in China's changing landscape of fandom culture
Authors: Li Xiaomeng 
Published: August 2024

AbstractIn 2020, Archive of Our Own, a renowned fanfiction website, became inaccessible in China due to mass reporting by a celebrity's fans upset about him being portrayed as having a gender identity disorder in a fanfiction. This event led to increased regulation of Boys' Love (BL) content on many Chinese fanfiction platforms, posing challenges for writers. This study interviews Chinese BL fanfiction writers post‐incident and explores their strategies for navigating the shrinking creative space. It argues that China's current fandom culture is capital‐driven, data‐centric, and commercial, fostering a “fanquan (fan circle)” culture that redefines the meaning of “being a fan.”
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach
Authors: Wang Yiguan , Allen Scott L. , Reddiex Adam J. , Chenoweth Stephen F. 
Published: August 2024

AbstractThis study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (partialS/HIC) and a range of inferred demographic histories, we identified that approximately 14% of the genome is directly affected by sweeps, with soft sweeps being more prevalent (10.6%) than hard sweeps (2.1%), and partial sweeps being uncommon (1.3%). The algorithm demonstrated robustness to demographic assumptions in classifying complete sweeps but faced challenges in distinguishing neutral regions from partial sweeps and linked regions under demographic misspecification. The findings reveal the indirect influence of sweeps on nearly two‐thirds of the genome through linkage, with an over‐representation of putatively deleterious variants suggesting that positive selection drags deleterious variants to higher frequency due to hitchhiking with beneficial loci. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under positive selection due to evolutionary arms races (e.g. immunity) were detected in hard sweeps. This study provides valuable insights into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.
Strigolactone signalling inhibits trehalose 6‐phosphate signalling independently of BRC1 to suppress shoot branching
Authors: Fichtner Franziska , Humphreys Jazmine L. , Barbier Francois F. , Feil Regina , Westhoff Philipp , Moseler Anna , Lunn John E. , Smith Steven M. , Beveridge Christine A. 
Published: August 2024

Summary

The phytohormone strigolactone (SL) inhibits shoot branching, whereas the signalling metabolite trehalose 6‐phosphate (Tre6P) promotes branching. How Tre6P and SL signalling may interact and which molecular mechanisms might be involved remains largely unknown.

Transcript profiling of Arabidopsis SL mutants revealed a cluster of differentially expressed genes highly enriched in the Tre6P pathway compared with wild‐type (WT) plants or brc1 mutants. Tre6P‐related genes were also differentially expressed in axillary buds of garden pea (Pisum sativum) SL mutants.

Tre6P levels were elevated in the SL signalling mutant more axillary (max) growth 2 compared with other SL mutants or WT plants indicating a role of MAX2‐dependent SL signalling in regulating Tre6P levels.

A transgenic approach to increase Tre6P levels demonstrated that all SL mutant lines and brc1 flowered earlier, showing all of these mutants were responsive to Tre6P. Elevated Tre6P led to increased branching in WT plants but not in max2 and max4 mutants, indicating some dependency between the SL pathway and Tre6P regulation of shoot branching. By contrast, elevated Tre6P led to an enhanced branching phenotype in brc1 mutants indicating independence between BRC1 and Tre6P. A model is proposed whereby SL signalling represses branching via Tre6P and independently of the BRC1 pathway.
Differential contribution of Arabidopsis chitin receptor complex components to defense signaling and ubiquitination‐dependent endocytotic removal from the plasma membrane
Authors: Mittendorf Josephine , Niebisch Jule Meret , Pierdzig Leon , Sun Siqi , Petutschnig Elena Kristin , Lipka Volker 
Published: August 2024

Summary

In Arabidopsis, the enzymatically active lysin motif‐containing receptor‐like kinase (LysM‐RLK) CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) and the pseudokinases LYSIN MOTIF‐CONTAINING RECEPTOR‐LIKE KINASE 5 (LYK5) and LYK4 are the core components of the canonical chitin receptor complex. CERK1 dimerizes and autophosphorylates upon chitin binding, resulting in activation of chitin signaling.

In this study, we clarified and further elucidated the individual contributions of LYK4 and LYK5 to chitin‐dependent signaling using mutant (combination)s and stably transformed Arabidopsis plants expressing fluorescence‐tagged LYK5 and LYK4 variants from their endogenous promoters.

Our analyses revealed that LYK5 interacts with CERK1 upon chitin treatment, independently of LYK4 and vice versa. We show that chitin‐induced autophosphorylation of CERK1 is predominantly dependent on LYK5, whereas chitin‐triggered ROS generation is almost exclusively mediated by LYK4. This suggests specific signaling functions of these two co‐receptor proteins apart from their redundant function in mitogen‐activated protein kinase (MAPK) signaling and transcriptional reprogramming.

Moreover, we demonstrate that LYK5 is subject to chitin‐induced and CERK1‐dependent ubiquitination, which serves as a signal for chitin‐induced internalization of LYK5. Our experiments provide evidence that a combination of phosphorylation and ubiquitination events controls LYK5 removal from the plasma membrane via endocytosis, which likely contributes to receptor complex desensitization.
Current landscape of fertility induction in males with congenital hypogonadotropic hypogonadism
Authors: Dwyer Andrew A. , McDonald Isabella R. , Quinton Richard 
Published: August 2024

AbstractCongenital hypogonadotropic hypogonadism (CHH) is a rare reproductive disorder caused by deficient secretion or action of gonadotropin‐releasing hormone (GnRH) and is a hormonally treatable form of male infertility. Both pulsatile GnRH treatment and combined gonadotropin therapy effectively induce spermatogenesis in 75%–80% of males with CHH, albeit the ejaculate does not usually approach normal semen parameters by WHO criteria. This is in some contrast to the cumulative fertility outcomes in females with CHH on gonadotropin treatment that are indistinguishable from those of reproductively normal females. Emerging data provide insights into early life determinants of male fertility (i.e., minipuberty), and research has identified key predictors of outcomes for fertility‐inducing treatment in men with CHH. Such developments provide mounting evidence for tailoring approaches to maximize fertility potential in CHH, although there is no clear consensus to date on the optimal approach to fertility‐inducing treatment. This review provides an up‐to‐date review on the current evidence underpinning therapeutic approaches for inducing spermatogenesis in males with CHH. In the absence of evidence‐based clinical guidelines, this synthesis of current evidence provides guidance for clinicians working with males with CHH seeking fertility.
In‐silico identification of putatively functional intergenic small open reading frames in the cucumber genome and their predicted response to biotic and abiotic stresses
Authors: Ahmad Esraa M. , Abdelsamad Ahmed , El‐Shabrawi Hattem M. , El‐Awady Mohamed A. M. , Aly Mohammed A. M. , El‐Soda Mohamed 
Published: August 2024

AbstractThe availability of high‐throughput sequencing technologies increased our understanding of different genomes. However, the genomes of all living organisms still have many unidentified coding sequences. The increased number of missing small open reading frames (sORFs) is due to the length threshold used in most gene identification tools, which is true in the genic and, more importantly and surprisingly, in the intergenic regions. Scanning the cucumber genome intergenic regions revealed 420 723 sORF. We excluded 3850 sORF with similarities to annotated cucumber proteins. To propose the functionality of the remaining 416 873 sORF, we calculated their codon adaptation index (CAI). We found 398 937 novel sORF (nsORF) with CAI ≥ 0.7 that were further used for downstream analysis. Searching against the Rfam database revealed 109 nsORFs similar to multiple RNA families. Using SignalP‐5.0 and NLS, identified 11 592 signal peptides. Five predicted proteins interacting with Meloidogyne incognita and Powdery mildew proteins were selected using published transcriptome data of host‐pathogen interactions. Gene ontology enrichment interpreted the function of those proteins, illustrating that nsORFs' expression could contribute to the cucumber's response to biotic and abiotic stresses. This research highlights the importance of previously overlooked nsORFs in the cucumber genome and provides novel insights into their potential functions.
Resin acid δ13C and δ18O as indicators of intra‐seasonal physiological and environmental variability
Authors: Tang Yu , Sahlstedt Elina , Rissanen Kaisa , Bäck Jaana , Schiestl‐Aalto Pauliina , Angove Charlotte , Richter Andreas , Saurer Matthias , Aalto Juho , Dukat Paulina , Lintunen Anna , Rinne‐Garmston Katja T. 
Published: August 2024

AbstractUnderstanding the dynamics of δ13C and δ18O in modern resin is crucial for interpreting (sub)fossilized resin records and resin production dynamics. We measured the δ13C and δ18O offsets between resin acids and their precursor molecules in the top‐canopy twigs and breast‐height stems of mature Pinus sylvestris trees. We also investigated the physiological and environmental signals imprinted in resin δ13C and δ18O at an intra‐seasonal scale. Resin δ13C was c. 2‰ lower than sucrose δ13C, in both twigs and stems, likely due to the loss of 13C‐enriched C‐1 atoms of pyruvate during isoprene formation and kinetic isotope effects during diterpene synthesis. Resin δ18O was c. 20‰ higher than xylem water δ18O and c. 20‰ lower than δ18O of water‐soluble carbohydrates, possibly caused by discrimination against 18O during O2‐based diterpene oxidation and 35%–50% oxygen atom exchange with water. Resin δ13C and δ18O recorded a strong signal of soil water potential; however, their overall capacity to infer intraseasonal environmental changes was limited by their temporal, within‐tree and among‐tree variations. Future studies should validate the potential isotope fractionation mechanisms associated with resin synthesis and explore the use of resin δ13C and δ18O as a long‐term proxy for physiological and environmental changes.
A chloroplast sulphate transporter modulates glutathione‐mediated redox cycling to regulate cell division
Authors: Huang Pin‐jui , Lin Yen‐Ling , Chen Chun‐Han , Lin Hsiang‐Yin , Fang Su‐Chiung 
Published: August 2024

AbstractGlutathione redox cycling is important for cell cycle regulation, but its mechanisms are not well understood. We previously identified a small‐sized mutant, suppressor of mat3 15‐1 (smt15‐1) that has elevated cellular glutathione. Here, we demonstrated that SMT15 is a chloroplast sulphate transporter. Reducing expression of γ‐GLUTAMYLCYSTEINE SYNTHETASE, encoding the rate‐limiting enzyme required for glutathione biosynthesis, corrected the size defect of smt15‐1 cells. Overexpressing GLUTATHIONE SYNTHETASE (GSH2) recapitulated the small‐size phenotype of smt15‐1 mutant, confirming the role of glutathione in cell division. Hence, SMT15 may regulate chloroplast sulphate concentration to modulate cellular glutathione levels. In wild‐type cells, glutathione and/or thiol‐containing molecules (GSH/thiol) accumulated in the cytosol at the G1 phase and decreased as cells entered the S/M phase. While the cytosolic GSH/thiol levels in the small‐sized mutants, smt15‐1 and GSH2 overexpressors, mirrored those of wild‐type cells (accumulating during G1 and declining at early S/M phase), GSH/thiol was specifically accumulated in the basal bodies at early S/M phase in the small‐sized mutants. Therefore, we propose that GSH/thiol‐mediated redox signalling in the basal bodies may regulate mitotic division number in Chlamydomonas reinhardtii. Our findings suggest a new mechanism by which glutathione regulates the multiple fission cell cycle in C. reinhardtii.
The B‐box transcription factor BnBBX22.A07 enhances salt stress tolerance by indirectly activating BnWRKY33.C03
Authors: Zhang Yan , Liu Xiang , Shi Yiji , Lang Lina , Tao Shunxian , Zhang Qi , Qin Mengfan , Wang Kai , Xu Yu , Zheng Lin , Cao Hanming , Wang Han , Zhu Yunlin , Song Jia , Li Keqi , Xu Aixia , Huang Zhen 
Published: August 2024

AbstractSalt stress has a detrimental impact on both plant growth and global crop yields. B‐box proteins have emerged as pivotal players in plant growth and development regulation. Although the precise role of B‐box proteins orchestrating salt stress responses in B. napus (Brassica napus) is not well understood in the current literature, further research and molecular explorations are required. Here, we isolated the B‐box protein BnBBX22.A07 from B. napus. The overexpression of BnBBX22.A07 significantly improved the salt tolerance of Arabidopsis (Arabidopsis thaliana) and B. napus. Transcriptomic and histological analysis showed that BnBBX22.A07 enhanced the salt tolerance of B. napus by activating the expression of reactive oxygen species (ROS) scavenging‐related genes and decreasing salt‐induced superoxide anions and hydrogen peroxide. Moreover, BnBBX22.A07 interacted with BnHY5.C09, which specifically bound to and activated the promoter of BnWRKY33.C03. The presence of BnBBX22.A07 enhanced the activation of BnHY5.C09 on BnWRKY33.C03. Overexpression of BnHY5.C09 and BnWRKY33.C03 improved the salt tolerance of Arabidopsis. Functional analyses revealed that BnBBX22.A07‐mediated salt tolerance was partly dependent on WRKY33. Taken together, we demonstrate that BnBBX22.A07 functions positively in salt responses not only by activating ROS scavenging‐related genes but also by indirectly activating BnWRKY33.C03. Notably, our study offers a promising avenue for the identification of candidate genes that could be harnessed in breeding endeavours to develop salt‐resistant transgenic crops.
Logic and conventions
Authors: Büttner Kai Michael , Glock Hans‐Johann 
Published: August 2024

AbstractWittgenstein and the logical positivists attempted to explain logical necessity in terms of linguistic conventions. It is often thought that their respective accounts have been conclusively refuted by objections from Quine, Dummett and others. We argue that this verdict is premature. Several of the most popular anti‐conventionalist arguments fail, partly because they misconstrue the idea of truth by convention in Wittgenstein and/or logical positivism. Correctly understood, conventionalism claims that, given certain linguistic conventions, some sentences are unconditionally true, that is true irrespective of how the world happens to be. This claim is difficult to deny, and the corresponding conventionalism about logical necessity remains a viable position.
KGF‐2 ameliorates UVB‐triggered skin photodamage in mice by attenuating DNA damage and inflammatory response and mitochondrial dysfunction
Authors: Li Xuenan , Cheng Jinli , Guo Keke , Wan Jianwei , Wang Cuihong , Chen Lu , Xu Nuo , Chen Min 
Published: August 2024

AbstractBackgroundLong‐term exposure to UVB induces DNA damage, inflammatory response, mitochondrial dysfunction, and apoptosis in skin cells, thus causing skin photodamage. Research has demonstrated the noteworthy antioxidant, anti‐inflammatory, DNA repair, and mitochondrial protective properties of keratinocyte growth factor‐2 (KGF‐2).MethodsTo examine the impact of KGF‐2 on UVB‐triggered skin photodamage in mice, hair‐removed mice were initially exposed under UVB radiation and subsequently treated with KGF‐2 hydrogel and repeated for 6 days. On day 7, the assessment of histopathological alterations, inflammation, DNA damage, mitochondrial function, and apoptosis in mouse skin was assessed.ResultsIt was found that KGF‐2 could effectively relieve cutaneous photodamage symptoms and inhibit epidermal proliferation in mice. Meanwhile, KGF‐2 was found to significantly reduce DNA damage, attenuate the inflammatory response, and inhibit the mitochondria‐mediated intrinsic apoptotic pathway in the UVB‐exposed mouse skin photodamage model.ConclusionTo summarize, our results indicated that KGF‐2 reduces the severity of mouse skin photodamage caused by UVB rays by attenuating DNA damage and the inflammatory response, besides inhibiting the mitochondria‐mediated intrinsic apoptosis pathway.