bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microglial heterogeneity in amyotrophic lateral sclerosis
Authors: Takahashi Kazuya 
Published: November 2022

Abstract
Amyotrophic lateral sclerosis (ALS) is an intractable neurodegenerative disease of the central nervous system that is pathologically characterized by motor neuron loss. Although the cause of the disease is still unknown, its pathophysiology is considered heterogeneous. In recent years, there have been a series of reports on the existence of disease-associated microglia (DAM) in the lesions of various neurodegenerative diseases. DAM have also been reported in SOD1-deficient mice, a disease model of ALS. However, the role of DAM in sporadic ALS remains unclear. This study revealed that spinal cord lesions in ALS can be pathologically distinguished into 2 subgroups (TMEM119+ and TMEM119− microglia) according to the type of microglia. Expression of the microglial activation marker CD68 and endothelial activation were also observed in the TMEM119+ microglia group, suggesting the presence of inflammatory processes in ALS lesions. Since DAM suppress the expression of TMEM119, the TMEM119+ microglia group may indicate DAM-independent inflammatory neurodegeneration. These results may explain why, in some clinical trials of anti-inflammatory drugs for ALS, only some cases showed suppression of disease progression.
Massive pulmonary embolism and intra-cardiac thrombus requiring systemic thrombolysis 9-hours post emergency laparotomy
Authors: Beatty Andrew Stafford , Simpson Fraser Hugh , Chandrasegaram Manju D 
Published: November 2022

Abstract
The link between abdominal surgery and venous thromboembolism (VTE) has been well established with recent evidence exploring the optimal VTE risk reducing strategy. However, despite these strategies pulmonary embolisms (PEs) do occur, which in the immediate post-operative setting creates a dilemma; to treat the VTE with anticoagulation but balance against the risk of hemorrhage. Treatment guidelines often do not include post-operative patients leaving the decision up to the treating physician to weigh the relative risks on an individual basis. We present a 59-year-old lady who developed a life-threatening submassive PE within 9 h of an emergency laparotomy for a perforated rectal cancer. She was treated with systemic thrombolysis after alternative interventions had been excluded. She responded well to therapy with no major bleeding. She was successfully discharged home after a short period of inpatient rehabilitation.
Evolutionary implications of C2 photosynthesis: how complex biochemical trade-offs may limit C4 evolution
Authors: Walsh Catherine A , Bräutigam Andrea , Roberts Michael R , Lundgren Marjorie R 
Published: November 2022

AbstractThe C2 carbon-concentrating mechanism increases net CO2 assimilation by shuttling photorespiratory CO2 in the form of glycine from mesophyll to bundle sheath cells, where CO2 concentrates and can be re-assimilated. This glycine shuttle also releases NH3 and serine into the bundle sheath, and modelling studies suggest that this influx of NH3 may cause a nitrogen imbalance between the two cell types that selects for the C4 carbon-concentrating mechanism. Here we provide an alternative hypothesis outlining mechanisms by which bundle sheath NH3 and serine play vital roles to not only influence the status of C2 plants along the C3 to C4 evolutionary trajectory, but to also convey stress tolerance to these unique plants. Our hypothesis explains how an optimized bundle sheath nitrogen hub interacts with sulfur and carbon metabolism to mitigate the effects of high photorespiratory conditions. While C2 photosynthesis is typically cited for its intermediary role in C4 photosynthesis evolution, our alternative hypothesis provides a mechanism to explain why some C2 lineages have not made this transition. We propose that stress resilience, coupled with open flux tricarboxylic acid and photorespiration pathways, conveys an advantage to C2 plants in fluctuating environments.
A novel rat model of denture stomatitis and the role of antibiotics in the development of the disease
Authors: Moraes Gustavo Simão , Albach Thaís , Sugio Carolina Yoshi Campos , Cachoeira Victoria Schlumberger , Kiratcz Falyne , Claudino Marcela , Campagnoli Eduardo Bauml , Pochapski Márcia Thaís , dos Santos Fabio André , Neppelenbroek Karin Hermana , Urban Vanessa Migliorini 
Published: November 2022

Abstract
This study compared different conditions to establish a rat model of denture stomatitis. Immunocompetent Wistar rats were divided into two groups (n = 35): Tetracycline = administration of 0.83 mg/ml of tetracycline hydrochloride 7 days before induction of denture stomatitis and amoxicillin = administration of 0.156 mg/ml of amoxicillin with clavulanic acid 4 days before induction of denture stomatitis. A suspension of Candida albicans was inoculated on the palate followed by the use of a palatal device contaminated with C. albicans inoculum for 4 days to induce denture stomatitis. As controls, some rats were not submitted to any procedure or used a sterile palatal device for 4 days. The development of denture stomatitis was confirmed by visual analysis, colony-forming units per milliliter (CFU/ml) count, histopathological and immunohistochemical analyses, and through myeloperoxidase (MPO) and N-acetylglucosaminidase (NAG) assays. Rats were euthanized right after device removal (T0), 4 (T4), or 6 (T6) days after device removal. Tetracycline improved the development of the disease, with more severe clinical signs at T0. Similar results were observed in the CFU/ml count and in the histometric and immunohistochemical analyses. Higher MPO expression was detected in the palates of the tetracycline group (P = .006). Despite the subtle differences between antibiotics, tetracycline showed better results in inducing and maintaining denture stomatitis for at least 4 days after device removal.
Probing the tidal disruption event iPTF16axa with cloudy and disc-wind models
Authors: Mageshwaran T , Shaw Gargi , Bhattacharyya Sudip 
Published: November 2022

ABSTRACT
We present both a disc-wind model on the optical/ultraviolet (UV) emission continuum and cloudy modelling on the spectral lines of the tidal disruption event (TDE) intermediate Palomar Transient Factory (iPTF)16axa to understand the disc-wind emission and the properties of the atmosphere that impacts the line luminosity of the TDE. Assuming the optical/UV emission from the wind due to the disc super-Eddington phase, we use the steady structured disc-wind model with a spherical wind with constant velocity to fit the observations on multiple days. The extracted parameters are stellar-mass M⋆ = 6.20 ± 1.19M⊙, disc radiative efficiency log10(η) = −1.22 ± 1.327, wind inner radius rl = (2.013 ± 0.551) × 1014 cm, and velocity vw = 18999.4 ± 1785.1 km s−1. The photosphere temperature for wind emission is ∼2 × 104 K and the disc single blackbody temperature is ∼0.995 × 105 K. We also perform cloudy modelling to explain the observed He and H line luminosities that estimate a wind inner radius rl = 7.07 × 1014 cm and velocity vw = 1.3 × 104 km s−1. The independent analyses of iPTF16axa using cloudy and disc-wind models show comparable results that agree with observations. The cloudy modelling finds that both the super-solar abundance of He and a smaller He II line optical depth is responsible for the enhancement of He II line luminosity over the Hα line luminosity. The super-solar abundance of He II agrees with a relatively large stellar mass and suggests that the disrupted star might have been a red giant.
Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling
Authors: Liu Qi , Peng Xin , Shen Mengyuan , Qian Qian , Xing Junlian , Li Chen , Gregory Richard I 
Published: November 2022

Abstract
Upstream open reading frames (uORFs) are typically defined as translation sites located within the 5′ untranslated region upstream of the main protein coding sequence (CDS) of messenger RNAs (mRNAs). Although uORFs are prevalent in eukaryotic mRNAs and modulate the translation of downstream CDSs, a comprehensive resource for uORFs is currently lacking. We developed Ribo-uORF (http://rnainformatics.org.cn/RiboUORF) to serve as a comprehensive functional resource for uORF analysis based on ribosome profiling (Ribo-seq) data. Ribo-uORF currently supports six species: human, mouse, rat, zebrafish, fruit fly, and worm. Ribo-uORF includes 501 554 actively translated uORFs and 107 914 upstream translation initiation sites (uTIS), which were identified from 1495 Ribo-seq and 77 quantitative translation initiation sequencing (QTI-seq) datasets, respectively. We also developed mRNAbrowse to visualize items such as uORFs, cis-regulatory elements, genetic variations, eQTLs, GWAS-based associations, RNA modifications, and RNA editing. Ribo-uORF provides a very intuitive web interface for conveniently browsing, searching, and visualizing uORF data. Finally, uORFscan and UTR5var were developed in Ribo-uORF to precisely identify uORFs and analyze the influence of genetic mutations on uORFs using user-uploaded datasets. Ribo-uORF should greatly facilitate studies of uORFs and their roles in mRNA translation and posttranscriptional control of gene expression.
scAB detects multiresolution cell states with clinical significance by integrating single-cell genomics and bulk sequencing data
Authors: Zhang Qinran , Jin Suoqin , Zou Xiufen 
Published: November 2022

Abstract
Although single-cell sequencing has provided a powerful tool to deconvolute cellular heterogeneity of diseases like cancer, extrapolating clinical significance or identifying clinically-relevant cells remains challenging. Here, we propose a novel computational method scAB, which integrates single-cell genomics data with clinically annotated bulk sequencing data via a knowledge- and graph-guided matrix factorization model. Once combined, scAB provides a coarse- and fine-grain multiresolution perspective of phenotype-associated cell states and prognostic signatures previously not visible by single-cell genomics. We use scAB to enhance live cancer single-cell RNA-seq data, identifying clinically-relevant previously unrecognized cancer and stromal cell subsets whose signatures show a stronger poor-survival association. The identified fine-grain cell subsets are associated with distinct cancer hallmarks and prognosis power. Furthermore, scAB demonstrates its utility as a biomarker identification tool, with the ability to predict immunotherapy, drug responses and survival when applied to melanoma single-cell RNA-seq datasets and glioma single-cell ATAC-seq datasets. Across multiple single-cell and bulk datasets from different cancer types, we also demonstrate the superior performance of scAB in generating prognosis signatures and survival predictions over existing models. Overall, scAB provides an efficient tool for prioritizing clinically-relevant cell subsets and predictive signatures, utilizing large publicly available databases to improve prognosis and treatments.
Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA
Authors: Vermeirssen Vanessa , Deleu Jill , Morlion Annelien , Everaert Celine , De Wilde Jilke , Anckaert Jasper , Durinck Kaat , Nuytens Justine , Rishfi Muhammad , Speleman Frank , Van Droogenbroeck Hanne , Verniers Kimberly , Baietti Maria Francesca , Albersen Maarten , Leucci Eleonora , Post Edward , Best Myron G , Van Maerken Tom , De Wilde Bram , Vandesompele Jo , Decock Anneleen 
Published: November 2022

Abstract
While cell-free DNA (cfDNA) is widely being investigated, free circulating RNA (extracellular RNA, exRNA) has the potential to improve cancer therapy response monitoring and detection due to its dynamic nature. However, it remains unclear in which blood subcompartment tumour-derived exRNAs primarily reside. We developed a host-xenograft deconvolution framework, exRNAxeno, with mapping strategies to either a combined human-mouse reference genome or both species genomes in parallel, applicable to exRNA sequencing data from liquid biopsies of human xenograft mouse models. The tool enables to distinguish (human) tumoural RNA from (murine) host RNA, to specifically analyse tumour-derived exRNA. We applied the combined pipeline to total exRNA sequencing data from 95 blood-derived liquid biopsy samples from 30 mice, xenografted with 11 different tumours. Tumoural exRNA concentrations are not determined by plasma platelet levels, while host exRNA concentrations increase with platelet content. Furthermore, a large variability in exRNA abundance and transcript content across individual mice is observed. The tumoural gene detectability in plasma is largely correlated with the RNA expression levels in the tumour tissue or cell line. These findings unravel new aspects of tumour-derived exRNA biology in xenograft models and open new avenues to further investigate the role of exRNA in cancer.
Expanded roles and divergent regulation of FAMA in Brachypodium and Arabidopsis stomatal development
Authors: McKown Katelyn H , Anleu Gil M Ximena , Mair Andrea , Xu Shou-Ling , Raissig Michael T , Bergmann Dominique C 
Published: November 2022

Abstract
Stomata, cellular valves found on the surfaces of aerial plant tissues, present a paradigm for studying cell fate and patterning in plants. A highly conserved core set of related basic helix-loop-helix (bHLH) transcription factors regulates stomatal development across diverse species. We characterized BdFAMA in the temperate grass Brachypodium distachyon and found this late-acting transcription factor was necessary and sufficient for specifying stomatal guard cell fate, and unexpectedly, could also induce the recruitment of subsidiary cells in the absence of its paralogue, BdMUTE. The overlap in function is paralleled by an overlap in expression pattern and by unique regulatory relationships between BdMUTE and BdFAMA. To better appreciate the relationships among the Brachypodium stomatal bHLHs, we used in vivo proteomics in developing leaves and found evidence for multiple shared interaction partners. We reexamined the roles of these genes in Arabidopsis thaliana by testing genetic sufficiency within and across species, and found that while BdFAMA and AtFAMA can rescue stomatal production in Arabidopsis fama and mute mutants, only AtFAMA can specify Brassica-specific myrosin idioblasts. Taken together, our findings refine the current models of stomatal bHLH function and regulatory feedback among paralogues within grasses as well as across the monocot/dicot divide.
Physiological mechanisms underlying extreme longevity in mountain pine trees
Authors: Pasques Ot , Munné-Bosch Sergi 
Published: November 2022

Abstract
Ancient trees are life history longevity winners that mostly persist in remote and environmentally harsh mountainous areas. Here, we performed a multifeature analysis in a protected mature mountain pine (Pinus uncinata) forest to identify the morphological and physiological traits that make these trees unique. We compared the physiology of meristematic and somatic tissues (apical buds and needles, respectively) from juvenile, mature young, mature old, and mature ancient trees under cold stress and nonstress conditions. We successfully identified key morphological features of extreme longevity at the organism level, as well as various growth, vigor, stress, and dormancy markers underlying extreme longevity in old and ancient trees. Results indicated that evolution has exerted selective pressure on specific physiological traits that make trees become longevity winners (&lt;0.1% of the tree population were ancient trees, with an average trunk diameter &gt;100 cm and an estimated age of 700 years). Traits entailing longevity not only included apical dominance loss, epicormic growth, and modular senescence, but also an extreme plasticity in both meristematic and somatic tissues (buds and needles, respectively), as shown by various physiological markers. In conclusion, ancient trees are oddities that not only possess a unique ecological value but also show divergent physiological behaviors selected during their evolution to allow them to cope with adversities and attain long life.
Mitochondria in photosynthetic cells: Coordinating redox control and energy balance
Authors: Igamberdiev Abir U , Bykova Natalia V 
Published: November 2022

AbstractIn photosynthetic tissues in the light, the function of energy production is associated primarily with chloroplasts, while mitochondrial metabolism adjusts to balance ATP supply, regulate the reduction level of pyridine nucleotides, and optimize major metabolic fluxes. The tricarboxylic acid cycle in the light transforms into a noncyclic open structure (hemicycle) maintained primarily by the influx of malate and the export of citrate to the cytosol. The exchange of malate and citrate forms the basis of feeding redox energy from the chloroplast into the cytosolic pathways. This supports the level of NADPH in different compartments, contributes to the biosynthesis of amino acids, and drives secondary metabolism via a supply of substrates for 2-oxoglutarate-dependent dioxygenase and for cytochrome P450-catalyzed monooxygenase reactions. This results in the maintenance of redox and energy balance in photosynthetic plant cells and in the formation of numerous bioactive compounds specific to any particular plant species. The noncoupled mitochondrial respiration operates in coordination with the malate and citrate valves and supports intensive fluxes of respiration and photorespiration. The metabolic system of plants has features associated with the remarkable metabolic plasticity of mitochondria that permit the use of energy accumulated during photosynthesis in a way that all anabolic and catabolic pathways become optimized and coordinated.
Quantifying farmers’ preferences for antimicrobial use for livestock diseases in northern Tanzania
Authors: Nthambi Mary , Lembo Tiziana , Davis Alicia , Nasuwa Fortunata , Mmbaga Blandina Theophil , Matthews Louise , Hanley Nick 
Published: November 2022

Abstract
Understanding the choice behaviours of farmers around the treatment of their livestock is critical to counteracting the risks of antimicrobial resistance (AMR) emergence. Using varying disease scenarios, we measure the differences in livestock species’ treatment preferences and the effects of context variables (such as grazing patterns, herd size, travel time to agrovet shops, previous disease experience, previous vaccination experience, education level, and income) on the farmers’ treatment choices for infections across three production systems—agro-pastoral, pastoral, and rural smallholder—in northern Tanzania, where reliance on antimicrobial treatment to support the health and productivity of livestock is high. Applying a context-dependent stated choice experiment, we surveyed 1224 respondents. Mixed logit model results show that farmers have higher preferences for professional veterinary services when treating cattle, sheep, and goats, while they prefer to self-treat poultry. Antibiotics sourced from agrovet shops are the medicine of choice, independent of the health condition to treat, whether viral, bacterial, or parasitic. Nearness to agrovet shops, informal education, borrowing and home storage of medicines, and commercial poultry rearing increase the chances of self-treatment. Based on our findings, we propose interventions such as awareness and education campaigns aimed at addressing current practices that pose AMR risks, as well as vaccination and good livestock husbandry practices, capacity building, and provision of diagnostic tools.
Exosomal miR-93-5p from cancer-associated fibroblasts confers malignant phenotypes on bladder cancer cells by targeting PAFAH1B1
Authors: Lu Xiaoming , Wang Jinfeng , Dong Binbin , Wang Liping , Liu Yadong 
Published: November 2022

Background
Dysregulation of cancer-associated fibroblasts (CAFs) still greatly challenges the treatments for bladder cancer (BC), where exosomal miRNAs derived from CAFs are one of the essential effectors for tumor progression. miR-93-5p is reported to be upregulated in BC, however, it is barely investigated in BC-derived CAFs.

Method
The CAF markers were immunofluorescent-labeled and examined by western blotting assay in CAFs and normal fibroblasts (NFs). CAFs- and NFs-derived exosomes (CAFs-exo/NFs-exo) were authenticated by transmission electron microscope and nanoparticle tracking analysis. Cell viability was determined by cell counting kit-8 assay, and cell mobility was evaluated by wound healing and transwell assays. Real-time quantitative PCR was used to quantify the RNA expressions, and a western blotting assay was used for protein expression. Interaction between miR-93-5p and Platelet-Activating Factor Acetylhydrolase IB Subunit Beta (PAFAH1B1) was verified by luciferase reporter assay. HE staining assay was applied to assess the histological changes of xenografts.

Results
CAFs-exo notably enhanced cell mobility and the expression levels of miR-93-5p of BC cells compared to NFs-exo. However, inhibition of miR-93-5p in CAFs-exo exhibited attenuated pro-metastatic ability on BC cells. PAFAH1B1 was one of the predicted targets of miR-93-5p, whose mRNA level was most significantly downregulated after miR-93-5p transfection. The interaction between PAFAH1B1 and miR-93-5p was verified, and miR-93-5p negatively regulated the protein level of PAFAH1B1. Overexpression of PAFAH1B1 could efficiently reverse the effects of miR-93-5p mimic on BC cell mobility. Finally, inhibition of miR-93-5p was proved to impair the carcinogenic function of CAFs-exo in vivo.

Conclusion
Exosomal miR-93-5p derived from CAFs confers oncogenicity on BC cells via sponging PAFAH1B1, suggesting a novel therapeutic strategy for BC.
“Racing-stripe” Modification of Radial Forearm Free Flap: Technique and Experience (704 Consecutive Cases)
Authors: Melissinos Emmanuel G. , Marques Erik S. 
Published: November 2022

Background:
The radial forearm fasciocutaneous free flap (RFFF) has proven to be a versatile and reliable tool for the reconstructive microsurgeon when addressing soft-tissue defects. A significant drawback of the traditional RFFF is related to donor site morbidity and wound healing complications, especially when coverage of sizable defects is planned. The authors describe the “racing-stripe” modification of the RFFF (RS-RFFF) that involves harvesting a large segment of the deep forearm fascia with a narrow strip of skin overlying the radial vessels, thus allowing primary closure of the donor site.

Methods:
Retrospective chart review was conducted of a single surgeon’s (E.G.M.) experience of patients who underwent RS-RFFF.

Results:
Seven hundred four RS-RFFFs were performed in 698 patients over a 19-year period (2000–2019) for lower extremity reconstruction (657 flaps, 93.3%), upper extremity reconstruction (32 flaps, 4.5%), and head and neck reconstruction (15 flaps, 2.1%). Wounds secondary to trauma were the most common reason for flap reconstruction (655 wounds, 93.8%). Five hundred four RS-RFFFs were used for soft-tissue defects of the foot (129 flaps, 18.3%), ankle (309 flaps, 43.9%), and heel (66 flaps, 9.4%; 27 of which provided coverage for Achilles tendon repair or exposure). There were three flap losses (0.4%). Limb salvage rate was 100% for extremity wounds. Forearm donor site wound complications were minimal.

Conclusions:
The RS-RFFF can be consistently and safely harvested and permits low-profile, reliable coverage of small-to-medium size soft-tissue defects. Primary closure of the donor site is possible in all cases, thus minimizing wound healing complications.