bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term effects of vaginal surgery and endogenous ovarian hormones on the vagina and bladder
Authors: Ho Tam , Zhang Jerry , Wen Yan , Guo Song , Dobberfuhl Amy Diane , Chen Bertha 
Published: December 2023

Abstract

Background
Surgery is a common treatment for pelvic organ prolapse (POP); however, risk of recurrence and reoperation is high, resulting in a negative impact on quality of life and sexual function.

Aim
To examine the long-term effects of POP surgery and endogenous circulating ovarian hormones on the vagina and bladder.

Methods
Our animal model simulated surgical injury of the vagina and bladder during POP surgery. Female Rowett nude rats were divided into 4 groups: intact control (IC), vaginal surgery only (V), ovariectomy only (O), and ovariectomy + vaginal surgery (OV). Rats were euthanized 10 weeks postsurgery. Proximal vagina and bladder dome/trigone underwent (1) organ bath myography to assess smooth muscle contractility; (2) real-time quantitative polymerase chain reaction to quantify mRNA expression of elastin, collagen I and III, and PGP9.5 (protein gene product 9.5); (3) enzyme-linked immunosorbent assay for protein quantification of elastin and collagen I and III; and (4) hematoxylin-eosin/immunohistochemistry staining.

Outcomes
The primary outcome was tissue contractility as measured by organ bath myography. Secondary outcomes included gene and protein expression of collagen I and III and elastin.

Results
O and OV showed reduced vaginal wall contractility vs IC and V (P &lt; .002). Bladder dome and trigone displayed different contractile patterns, with significant differences between O and OV (P &lt; .05), suggesting a negative effect from surgery rather than ovariectomy. OV demonstrated consistent reductions in contractility and elastin/collagen protein expression for the vagina and bladder vs IC. V had similar contractility and increased collagen I expression vs IC, suggesting a protective effect of ovarian hormones. Vaginal epithelium thinning was confirmed in the ovariectomized groups (P = .001), although there was no statistical significance in muscularis thinning with surgery or ovariectomy. O, V, and OV showed significant downregulation of PGP9.5 mRNA expression vs IC.

Clinical Translation
These data allow researchers to gain insights into the long-term effects of surgery and deprivation of ovarian hormones. Future studies can use this animal model to investigate other mechanisms that may affect long-term tissue changes due to surgical intervention.

Strengths and Limitations
Major strengths are long-term data on the effects of POP surgery and development of an animal model for future studies. However, the animal model limits our ability to extrapolate to humans, where tissue healing is modulated by many factors.

Conclusion
Our animal model provides evidence that ovarian hormone deprivation and POP surgery result in negative long-term effects on tissue function and extracellular matrix.
How Will the Retained EU Law (Revocation and Reform) Act 2023 Affect the Principle of EU-Law Conforming Construction in UK Law?
Authors: Barth Fabian 
Published: December 2023

Abstract
Following prolonged political controversy, the provisions from the initial Retained EU Law (Revocation and Reform) Bill which abolish general principles of EU law, as well as its supremacy, have been enacted. This article investigates whether this is likely to affect the principle of EU-law conforming construction, and contemplates three scenarios how EU-derived UK law might be interpreted in the future.
Division-Independent Differentiation of Muscle Stem Cells During a Growth Stimulus
Authors: Ismaeel Ahmed , Goh Jensen , Mobley C Brooks , Murach Kevin A , Brett Jamie O , de Morrée Antoine , Rando Thomas A , Peterson Charlotte A , Wen Yuan , McCarthy John J 
Published: December 2023

Abstract
Adult muscle stem cells (MuSCs) are known to replicate upon activation before differentiating and fusing to regenerate myofibers. It is unclear whether MuSC differentiation is intrinsically linked to cell division, which has implications for stem cell population maintenance. We use single-cell RNA-sequencing to identify transcriptionally diverse subpopulations of MuSCs after 5 days of a growth stimulus in adult muscle. Trajectory inference in combination with a novel mouse model for tracking MuSC-derived myonuclei and in vivo labeling of DNA replication revealed an MuSC population that exhibited division-independent differentiation and fusion. These findings demonstrate that in response to a growth stimulus in the presence of intact myofibers, MuSC division is not obligatory.
Does transport stress have any effect on carcass quality of Nellore cattle (Bos taurus indicus) in Brazil? — A case study
Authors: da Silva Rodrigues Mendes Nathalia , Rodrigues Silva Renato , Ferreira de Oliveira Tatianne , Ellies-Oury Marie-Pierre , Hocquette Jean-François , Chriki Sghaier 
Published: December 2023

Abstract
With the increasing concomitant demands for Brazilian beef and in particular high-quality beef, there is a need for observational studies of the effects of pre- and post-slaughter practices on beef carcass traits. We hypothesized in our case study that pre-slaughter transport of bovines over significant distances would induce stress in animals, and that this would reduce carcass quality because of higher pH resulting from long-distance transportation. To test this hypothesis, 30,230 Nellore carcasses from a private slaughterhouse were evaluated 24 h postmortem. Analysis showed correlations between animal maturity, ultimate pH, distance, and carcass weight. More precisely, there was a slight positive correlation between ultimate pH and weight (but not with transportation distance) and a slight positive correlation between maturity and weight. A linear regression model (R2 = 0.016) failed to show distance having a significant effect on ultimate pH (P = 0.63), while carcass weight significantly affected ultimate pH (P &lt; 0.001) with a low coefficient of 0.0003. Maturity negatively affected ultimate pH also (P &lt; 0.001) but with also a small effect (−0.0008). Results (from 95% confidence intervals of variance of the random effects and of the random errors) showed that the variability within farms was higher than between farms. The linear mixed model showed that maturity had a significant effect on carcass weight value (P &lt; 0.001) with a large coefficient of 2.90. The R2 of the linear mixed model was 46.03%. In conclusion, while weight and maturity both affect ultimate pH, long distances did not significantly impact ultimate pH and therefore the beef quality from Nellore cattle. This could be because of low stress during transport, as well as the physical characteristics of the Nellore breed that favor greater resistance to tropical climatic conditions.
Flying singers: spatio-temporal distribution and acoustic dynamics of two species of Carinetini (Hemiptera: Cicadidae) cicadas in sympatry
Authors: Acosta Riuler C , Ruschel Tatiana P , Kaminski Lucas A 
Published: December 2023

Abstract
The natural history of Neotropical cicadas is poorly understood. Here, we describe comparatively the spatio-temporal distribution and acoustic dynamics of two Carinetini cicadas in sympatry: colourful-cicada, Carineta diardi, and eryngo-cicada, Guaranisaria llanoi. Males of both species emit conspicuous acoustic signals during flight, a rare behaviour in cicadas. Although sympatric and synchronic, these species are not syntopic, occurring in different habitats: colourful-cicada occurs in Atlantic Forest and eryngo-cicada in native Pampean grasslands. Vertical stratification also occurs: colourful-cicada flies, sings, and copulates along the forest edge and canopy (above 2 m), while eryngo-cicada flies, sings, and copulates only in open areas (below 1 m), performing directional flights between the ‘Gravatá’ eryngo patches—a keystone plant species used as shelter, and calling and reproduction site. Acoustic repertoires vary between species: colourful-cicada presents two types of signals (flying and calling songs) and eryngo-cicada has four types (flying, calling, courtship, and wing-flicks emitted by the females). Furthermore, acoustic differences between species were found in the flying songs, but no specific differences were found in the peak frequency of their calling songs. These results show that spatial use of ‘flying singer’ cicadas can vary in habitat, providing coexistence in sympatry.
The cadmium-hypertolerant fern,Athyrium yokoscense, exhibits two cadmium stress mitigation strategies in the roots and the aerial parts
Authors: Ukai Yuko , Taoka Hiroki , Kamada Manaka , Wakui Yuko , Goto Fumiyuki , Kitazaki Kazuyoshi , Abe Tomoko , Hokura Akiko , Yoshihara Toshihiro , Shimada Hiroaki 
Published: December 2023

AbstractAthyrium yokoscenseis hypertolerant to cadmium (Cd) and can grow normally under a high Cd concentration despite Cd being a highly toxic heavy metal. To mitigate Cd stress in general plant species, Cd is promptly chelated with a thiol compound and is isolated into vacuoles. Generated active oxygen species (ROS) in the cytoplasm are removed by reduced glutathione. However, we found many differences in the countermeasures inA. yokoscense. Thiol compounds accumulated in the stele of the roots, although a long-term Cd exposure induced Cd accumulation in the aerial parts. Synchrotron radiation-based X-ray fluorescence (SR-XRF) analysis indicated that a large amount of Cd was localized in the cell walls of the roots. Overexpression ofAyNramp5a, encoding a representative Fe and Mn transporter ofA. yokoscense, increased both Cd uptake and iron and manganese uptake in rice calli under the Cd exposure conditions. Organic acids were abundantly detected inA. yokoscenseroots. Investigating the chemical forms of the Cd molecules by X-ray absorption fine structure (XAFS) analysis detected many compounds with Cd-oxygen (Cd-O) binding inA. yokoscenseroots, whereas in the aerial parts, the ratio of the compounds with Cd-sulfur (Cd-S) binding was increased. Together, our results imply that the strong Cd tolerance ofA. yokoscenseis an attribute of the following two mechanisms: Cd-O compound formation in the cell wall is a barrier to reduce Cd uptake into aerial parts. Thiol compounds in the region of root stele are involved in detoxication of Cd by formation of Cd-S compounds.Statements and DeclarationsNo potential conflict of interest was reported by the authors.
Spatial and temporal detection of root exudates with a paper-based microfluidic device
Authors: Patko Daniel , Gunatilake Udara Bimendra , Dupuy Lionel X. , Basabe-Desmonts Lourdes , Benito-Lopez Fernando 
Published: December 2023

AbstractRoot exudates control critical processes in the rhizosphere, retaining water, selecting for beneficial microorganisms or solubilising nutrients prior to uptake by the plant. Analysing root exudation patterns however is challenging because existing methods are often destructive and unable to resolve spatial and temporal variations in the production of root exudates. Here, we present a paper-based microfluidic device with integrated colorimetric sensors for the continuous extraction of root exudates along plant roots. The microfluidic device used standard filter paper wax printer to create channels for water to carry the exudates towards the sensors. TiO2nanotubes/alginate hydrogel-based sensors were used to analyse the glucose content of the root exudates of living plants. The study shows that the paper microfluidic substrate successfully extracts the released glucose from the root, and transfers it to the hydrogel-based sensor to be calorimetrically detected from independent sections of the root at different times, up to 7 days. The method was tested on two different wheat varietiesTriticum aestivum(rgt Tocayo and Filon varieties), where significant differences in exudation patterns were recorded. The researchdemonstrates the feasibility of low cost technological solution for high precision screening and diagnostic of the biochemical composition of root exudates.
scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis
Authors: Liu Tianyu , Chen Tianqi , Zheng Wangjie , Luo Xiao , Zhao Hongyu 
Published: December 2023

AbstractVarious Foundation Models (FMs) have been built based on the pre-training and fine-tuning framework to analyze single-cell data with different degrees of success. In this manuscript, we propose a method named scELMo (Single-cell Embedding from Language Models), to analyze single-cell data that utilizes Large Language Models (LLMs) as a generator for both the description of metadata information and the embeddings for such descriptions. We combine the embeddings from LLMs with the raw data under the zero-shot learning framework to further extend its function by using the fine-tuning framework to handle different tasks. We demonstrate that scELMo is capable of cell clustering, batch effect correction, and cell-type annotation without training a new model. Moreover, the fine-tuning framework of scELMo can help with more challenging tasks including in-silico treatment analysis or modeling perturbation. scELMo has a lighter structure and lower requirements for resources. Our method also outperforms recent large-scale FMs (such as scGPT [1], Geneformer [2]) and other LLM-based single-cell data analysis pipelines (such as GenePT [3] and GPTCelltype [4]) based on our evaluations, suggesting a promising path for developing domain-specific FMs.
Rapid integration of face detection and task set in visually guided reaching
Authors: Mekhaiel David Y. , Goodale Melvyn A. , Corneil Brian D. 
Published: December 2023

ABSTRACTThe superior colliculus (SC) has been increasingly implicated in the rapid processing of evolutionarily relevant visual stimuli like faces, but the behavioural relevance of such processing is not clear. The SC has also been implicated in the generation of upper-limb Express Visuomotor Responses (EVRs) on upper limb muscles, which are very short-latency (within ∼80 ms) bursts of muscle activity time-locked to visual target presentation. This reasoning led us to investigate the influence of faces on EVRs.We recorded upper limb muscle activity from young healthy participants as they reached toward left or right targets in the presence of a distractor stimulus presented on the opposite side. Across blocks of trials, we varied the instruction as to which stimulus served as the target or distractor. Doing so allowed us to assess the impact of instruction on muscle recruitment by examining trials when the exact same stimuli required a reach to either the left or right. We found that EVRs were uniquely modulated in tasks involving face selection, promoting reaches toward or away from faces depending on instruction. Follow-up experiments confirmed that this phenomenon required highly salient repeated faces, and was not observed to non-facial salient stimuli nor to faces expressing different affect. We conclude that our results attest to an integration of top-down task set and bottom-up feature detection to promote rapid motor responses to faces at latencies that match or precede the arrival of face information in human cortex.STATEMENT OF SIGNIFICANCEThe tecto-reticulo-spinal pathway is hypothesized to mediate the express visuomotor response (EVR). This study extends this hypothesis by demonstrating that face detection in the subcortex impacts low-latency movement via the EVR at latencies preceding cortical activity for face perception. To date, this constitutes the most direct evidence for direct behavioural relevance of rapid face detection in the brainstem. Further, we find that this response can be modulated by task context, allowing for different instruction-based responses given the exact same visual stimulus and implicating top-down cortical control of the EVR.
The gut microbiome-linked long chain fatty acid stearate suppresses colorectal cancer
Authors: Tsenkova Mina , Brauer Madita , Pozdeev Vitaly , Kasakin Marat , Busi Susheel Bhanu , Schmoetten Maryse , Cheung Dean , Meyers Marianne , Rodriguez Fabien , Gaigneaux Anthoula , Koncina Eric , Gilson Cedric , Schlicker Lisa , Herebian Diran , Schmitz Martine , Nies Laura de , Mayatepek Ertan , Haan Serge , Beaufort Carine de , Cramer Thorsten , Meiser Johannes , Linster Carole L. , Wilmes Paul , Letellier Elisabeth 
Published: December 2023

AbstractColorectal cancer (CRC) patients have been shown to possess an altered gut microbiome. Diet is a well-established modulator of the microbiome, and thus, dietary interventions might have a beneficial effect on CRC. An attenuating effect of the ketogenic diet (KD) on CRC cell growth has been previously observed, however the role of the gut microbiome in driving this effect remains unknown. Here, we describe a reduced colonic tumor burden upon KD consumption in a CRC mouse model with a humanized microbiome. Importantly, we demonstrate a causal relationship through microbiome transplantation into germ-free mice, whereby alterations in the gut microbiota were maintained in the absence of continued selective pressure from the KD. Specifically, we identify a shift toward bacterial species that produce stearic acid in ketogenic conditions, whereas consumers were depleted, resulting in elevated levels of free stearate in the gut lumen. This microbial product demonstrated tumor-suppressing properties by inducing apoptosis in cancer cells and decreasing colonic Th17 immune cell populations. Taken together, the beneficial effects of the KD are mediated through alterations in the gut microbiome, including, among others, increased stearic acid production, which in turn significantly reduces intestinal tumor growth.
Newly obtained genome of fungi-related amoeba is enriched with genes shared with animals-related protists
Authors: Pozdnyakov Igor R. , Potapenko Evgeny V. , Kalashnikova Vera A. , Barzasekova Christina O. , Zlatogursky Vasily V. , Selyuk Alexey O. , Sukhanova Ksenia M. , Babenko Vladislav V. , Boldyreva Daria I. 
Published: December 2023

AbstractNuclearariids are a group of Opisthokonta, forming the deepest branch in Holomycota - one of the two major Opisthokonta clades, containing Fungi as a crawn group. They are the only members of Holomycota retaining the filose amoeboid state ancestral for Opisthokonta. The newly assembled genome ofNuclearia thermophila(Holomycota, Rotosphaerida) had a total length of 49 Mb, 15 321 protein-coding genes and a GC percentage of 44%. This is the first sequenced genome for this genus and the the third for Rotosphaerida as a whole. It was shown that N. thermophila shares more protein domains with Holozoa, than with the rest of Holomycota. Protein domains that were presumably acquired or lost by the common ancestors of the Holomycota and Holozoa groups were identified. The Holomycota ancestor had probably more gains and losses of protein domains compared to the Holozoa ancestor, which is particularly true for metabolism-related domains. However, this trend should be confirmed by studying the genomes of free-living organisms of the Teretosporea group.
INHBA/Activin A promotes tumor growth and induces resistance to anti-PD-L1 therapy by suppressing IFN-γ signaling
Authors: Li Fanglin , Gu Longhua , Tong Yongliang , Yu Xiaolu , Chen Runqiu , Liu Nan , Chen Shiyi , Lu Jiangling , Si Yuan , Sun Jianhua , Chen Jing , Long Yiru , Gong Likun 
Published: December 2023

AbstractInhibin beta A (INHBA) and its homodimer activin A have pleiotropic effects on modulation of immune responses and tumor progression, respectively, but it remains uncertain whether tumors may release activin A to regulate anti-tumor immunity. As evidenced by our RNA-Seq and in vitro results, the interferon-γ (IFN-γ) signaling pathway was significantly down-regulated by tumor intrinsic activin A. Tumor INHBA deficiency led to lower expression of PD-L1 induced by IFN-γ, resulting in poor responsiveness to anti-PD-L1 therapy. On the other hand, decreased secretion of IFN-γ-stimulated chemokines, including C-X-C motif chemokine 9 (CXCL9) and 10 (CXCL10), impaired the infiltration of effector T cells into the tumor microenvironment. Furthermore, the activin A-specific antibody garetosmab improved anti-tumor immunity and its combination with the anti-PD-L1 antibody atezolizumab showed a superior therapeutic effect to monotherapy. Our findings reveal that INHBA/activin A is involved in anti-tumor immunity by inhibiting the IFN-γ signaling pathway and considered to be a potential target to overcome anti-PD-L1 resistance in clinical cancer treatment.
Solution to what? Global assessment of nature-based solutions, urban challenges, and outcomes
Authors: Li Meng , Remme Roy P. , Van Bodegom Peter M. , Van Oudenhoven Alexander P.E. 
Published: December 2023

AbstractIn response to multiple societal challenges faced in cities, nature-based solutions (NbS) are gaining prominence as means to support sustainable and resilient urban planning. However, NbS are being implemented in cities around the globe without comprehensive evidence on their effectiveness in addressing urban challenges. Based on a systematic mapping methodology, we synthesized 547 empirical cases of NbS in 197 cities globally, yielding 799 outcomes encompassing biodiversity, health well-being, and regulating ecosystem services. To structure this evidence we developed an urban NbS classification and categories of urban challenges and outcomes. Effectiveness of NbS was assessed through synthesizing which urban challenges are addressed by NbS, which outcomes are generated, and how these outcomes perform compared to alternative solutions. Our analysis suggests that specific urban challenges were mostly linked to closely related outcomes, but rarely to multiple outcomes. Specifically, forests & trees and general parks were commonly used to enhance health and well-being, while grassland and gardens were applied to mitigate biodiversity loss. Furthermore, urban NbS generally yielded positive effects compared to non-NbS, particularly in relation to microclimate mitigation and mental health outcomes. However, we note a scarcity of evidence on multifunctional NbS, especially on studies that report multiple outcomes related to biodiversity and well-being simultaneously. Our study provides a foundation for further understanding NbS effectiveness and can inform urban planners and policymakers with measurable evidenced-based targets for the application of NbS.
Cryptic endogenous retrovirus subfamilies in the primate lineage
Authors: Chen Xun , Zhang Zicong , Yan Yizhi , Goubert Clement , Bourque Guillaume , Inoue Fumitaka 
Published: December 2023

ABSTRACTMany endogenous retroviruses (ERVs) in the human genome are primate-specific and have contributed novel cis-regulatory elements and transcripts. However, current approaches for classifying and annotating ERVs and their long terminal repeats (LTRs) have limited resolution and are inaccurate. Here, we developed a new annotation based on phylogenetic analysis and cross-species conservation. Focusing on the evolutionary young MER11A/B/C subfamilies, we revealed the presence of 4 ‘new subfamilies’, that better explained the epigenetic heterogeneity observed within the MER11 instances, suggesting a new annotation for 412 (19.8%) of these repeat elements. Furthermore, we functionally validated the regulatory potential of these four new subfamilies using a massively parallel reporter assay (MPRA), which also identified motifs associated with their differential activities. Combining MPRA with new annotations across primates revealed an apes-specific gain of SOX related motifs through a single-nucleotide deletion. Lastly, by applying our approach across 53 simian-enriched LTR subfamilies, we defined a total of 75 new subfamilies and found that 3,807 (30.0%) instances from 26 LTR subfamilies could be categorized into a novel annotation, many of which with a distinct epigenetic profile. Thus, with our refined annotation of simian-enriched LTRs, it will be possible to better understand the evolution in primate genomes and potentially identify new roles for ERVs and their LTRs in the hosts.