bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Outcome Measurements and Impact of Simulation in Neurocritical Care Training: A Systematic Review
Authors: Yousef Khalil M. , Alananzeh Ibrahim , Beegom Shameena , Chavez Jose , Hatahet Sarah , Khalil Heba , Krom Zachary , Svetlov Olena 
Published: June 2024

ABSTRACT

AIM: The use of simulation training in neurocritical care is increasing. Yet, the pooled impact on patient and trainee outcomes remains unclear. This systematic review aims to determine the outcome measurements used after simulation training in neurocritical care and to synthesize the current evidence about the impact of simulation training on these outcomes. METHODS: A 3-step search was conducted in CINAHL, Cochrane, MEDLINE, PsychINFO, and Scopus. The inclusion criteria were composed of studies exploring simulation training in neurocritical care, published in English between 2000 and 2023. Two reviewers independently conducted screening, critical appraisal, and data extraction, using standardized Joanna Briggs Institute tools. Meta-analysis was precluded because of clinical, methodological, and statistical heterogeneity. RESULTS: Nine relevant studies were found: 1 quality improvement project and 8 quasi-experimental studies. The overall quality of the relevant studies was moderate to high (61.1%–77.8%). Three types of outcome measurements for simulation in neurocritical care were identified: knowledge and clinical performance; confidence and comfort; and teamwork, communication, and leadership skills. Simulation training was associated with a significant improvement in knowledge and clinical performance, and confidence and comfort, but not in communication and leadership skills. CONCLUSION: Significant improvement in trainees' outcomes was observed. The current literature includes significant heterogeneity in the methods of evaluating simulation outcomes, although no patient outcomes were observed. Investigating the effect of simulation in neurocritical care training on patient outcomes in future studies is warranted.
Primary leiomyosarcoma of the colon: a report of two cases and review of literature
Authors: Doan Tu Trong , Pham Duong The 
Published: June 2024

Introduction
Primary leiomyosarcoma (LMS) of the colon is a rare neoplasm and constitutes less than 0.1% of all colon malignancies. These tumors are more aggressive and have poorer prognoses than other gastrointestinal tumors, including gastrointestinal stromal tumors (GIST) or adenocarcinomas. The authors herein report two cases and review the literature to highlight the epidemiology, diagnosis, treatment and prognosis of this uncommon malignancy.

Case report
The authors reported two very rare cases of LMS of left colon, which referred to our institution with symptoms of abdominal pain. After the initial investigations, patients were diagnosed with primary colonic leiomyosarcoma that underwent laparotomy. In both cases pathological examination revealed a spindle cell tumor growing circumferentially and transmurally in the colon. Final immunohistochemistry were positive with SMA, CK and desmin without the expression of GIST markers (CD117, CD34 and DOG1) that confirmed leiomyosarcoma. One patient was diagnosed with diffused peritoneal metastasis at 6 months postoperatively and he died after 2 months of paliative care, another one is still on active surveillance.

Discussion
LMS of the colon is a really rare entity and is only presented in clinical case reports. LMS has non-specific symptoms and is commonly diagnosed when it reaches a large size. Surgery is a mainstay treatment option. Nowadays, there is no clear evidence for the effectiveness of chemotherapy and radiation therapy.

Conclusion
LMS is a rare neoplasm of colon. For the time being, there is no guidelines for treatment, but surgery still plays a fundamental role.
Comparative genomics of parasitoid lifestyle as exemplified by Mermithidae and Nematomorpha
Authors: Kirangwa Joseph , Bednarski Viktoria , Guiglielmoni Nadège , Poulin Robert , Dowle Eddy , Schiffer Philipp H. , Holovachov Oleksandr 
Published: June 2024

AbstractMermithidae and Nematomorpha are parasitoids united by the commonalities in their lifestyle – immature stages infect arthropod hosts, species from both phyla can manipulate their host to induce a similar water-seeking behaviour, and both have a final free-living non-feeding adult reproductive stage, often killing their host upon emergence. Some of these species are of great economic importance, being evaluated as biological control agents against mosquito vectors responsible for diseases like malaria, and other insect pests, but with scarce genomic resources currently available. Nematomorpha, despite being closely related to Nematoda, received insufficient attention in genomic research, leading to gaps in our understanding of their diverse genetic makeup. This study aimed to investigate the genetic features encoded in the genomes of both parasitoid taxa to identify similarities and parallels linked to their ecological lifestyles. We performed a comparative analysis of 12 genomes, comprising parasitoid, parasitic and free-living worms. The investigation revealed genomic signatures unique to parasitoid species, including expanded gene families enriched in neural transmission modulation, likely linked to the known host manipulation that both mermithids and nematomorphs exert on their hosts. The analysis also uncovered a diverse array of conserved transposable element superfamilies across both lineages. The findings from this study provide valuable insights into the potential genomic adaptations associated with parasitoidism in nematode and nematomorph worms. The identification of expanded gene families and conserved transposable element superfamilies sheds light on the molecular underpinnings of their unique biological traits. Additionally, the core set of orthologs specific to parasitoid worms offers new avenues for understanding the evolution of parasitism within these groups of organisms.
Evolutionary diversification of ancestral genes across vertebrates and insects
Authors: Mantica Federica , Irimia Manuel 
Published: June 2024

AbstractBackgroundVertebrates and insects diverged approximately 700 million years ago, and yet they retain a large core of conserved genes from their last common ancestor. These ancient genes present strong evolutionary constraints, which limit their overall sequence and expression divergence. However, these constraints can greatly vary across ancestral gene families and, in at least some cases, sequence and expression changes can have functional consequences. Importantly, overall patterns of sequence and expression divergence and their potential functional outcomes have never been explored in a genome-wide manner across large animal evolutionary distances.ResultsWe focused on approximately 7,000 highly conserved genes shared between vertebrates and insects, and we investigated global patterns of molecular diversification driven by changes in sequence and gene expression. We identified molecular features generally linked to higher or lower diversification rates, together with gene groups with similar diversification profiles in both clades. Moreover, we discovered that specific sets of genes underwent differential diversification during vertebrate and insect evolution, potentially contributing to the emergence of unique phenotypes in each clade.ConclusionsWe generated a comprehensive resource of measures of sequence and expression divergence across vertebrates and insects, which revealed a continuous spectrum of evolutionary constraints among highly conserved genes. These constraints are normally consistent between these two clades and associated with specific molecular features, but in some cases we also identified cases of lineage-specific diversification likely linked to functional evolution.
Enhanced Cell Tracking Using A GAN-based Super-Resolution Video-to-Video Time-Lapse Microscopy Generative Model
Authors: Zargari Abolfazl , Mashhadi Najmeh , Shariati S. Ali 
Published: June 2024

AbstractCells are among the most dynamic entities, constantly undergoing various processes such as growth, division, movement, and interaction with other cells as well as the environment. Time-lapse microscopy is central to capturing these dynamic behaviors, providing detailed temporal and spatial information that allows biologists to observe and analyze cellular activities in real-time. The analysis of time-lapse microscopy data relies on two fundamental tasks: cell segmentation and cell tracking. Integrating deep learning into bioimage analysis has revolutionized cell segmentation, producing models with high precision across a wide range of biological images. However, developing generalizable deep-learning models for tracking cells over time remains challenging due to the scarcity of large, diverse annotated datasets of time-lapse movies of cells. To address this bottleneck, we propose a GAN-based time-lapse microscopy generator, termed tGAN, designed to significantly enhance the quality and diversity of synthetic annotated time-lapse microscopy data. Our model features a dual-resolution architecture that adeptly synthesizes both low and high-resolution images, uniquely capturing the intricate dynamics of cellular processes essential for accurate tracking. We demonstrate the performance of tGAN in generating high-quality, realistic, annotated time-lapse videos. Our findings indicate that tGAN decreases dependency on extensive manual annotation to enhance the precision of cell tracking models for time-lapse microscopy.
Estimating population size with repeated observations of non-invasive sampling in presence of misidentification
Authors: Fraysse Rémi , Choquet Rémi , Pradel Roger 
Published: June 2024

AbstractAlthough non-invasive sampling is increasingly used in capture-recapture (CR) experiments, it carries a risk of misidentification that, if ignored, causes an overestimation of population size. Models that deal with misidentification have been proposed. However, these models assume that only one sample can be collected per individual at one occasion. This is not true for several experiments based on DNA, for example for those that extract the DNA from faecal samples. The models do not take repeated observations into account, leading to biased estimates.In this paper, we develop an approach that extends the latent multinomial model (LMM) of Link et al., 2010 using a Poisson distribution to account for simultaneous multiple sampling of the same individual. We then conduct simulations to test how our new model performs. As an illustration, we applied the new Poisson model to a collection of Eurasian otter faeces Lampa et al., 2015.Our findings indicate that repeated observations can be modelled without bias. The application on otters shows that our model is necessary to estimate properly the population size in presence of misidentification and repeated observations.
Comparative RNA profiling identifies stage-specific phasiRNAs and co-expressedArgonautegenes in Bambusoideae and Pooideae species
Authors: Bélanger Sébastien , Zhan Junpeng , Yu Yunqing , Meyers Blake C. 
Published: June 2024

ABSTRACTPhasiRNAs (phased, small interfering RNAs) play a crucial role in supporting male fertility in grasses. Earlier work in maize (Zea mays) and rice (Oryza sativa) – and subsequently many other plant species – identified premeiotic 21-nt and meiotic 24-nt phasiRNAs. More recently, a group of premeiotic 24-nt phasiRNAs were discovered in the anthers of two Pooideae species, barley (Hordeum vulgare) and bread wheat (Triticum aestivum). The conservation of premeiotic 24-nt phasiRNAs and other classes of reproductive phasiRNAs across Pooideae species remains unclear. We conducted a comparative RNA profiling of three anther stages in six Pooideae species and one Bambusoideae species. We observed complex temporal accumulation patterns of 21-nt and 24-nt phasiRNAs in Pooideae and Bambusoideae grasses. In Bambusoideae, 21-nt phasiRNAs accumulated during meiosis, whereas 24-nt phasiRNAs were present in both premeiotic and postmeiotic stages. We identified premeiotic 24-nt phasiRNAs in all seven species examined. These phasiRNAs exhibit distinct biogenesis mechanisms and potential Argonaute effectors compared to meiotic 24-nt phasiRNAs. We show that specificArgonautegenes co-expressed with stage-specific phasiRNAs are conserved across Bambusoideae and Pooideae species. Our degradome analysis identified a set of conserved miRNA target genes across species, while 21-nt phasiRNAs targets were species-specific. Cleavage of few targets was observed for 24-nt phasiRNAs.
Repeated evolution of reduced visual investment at the onset of ecological speciation in high-altitudeHeliconiusbutterflies
Authors: Rivas-Sánchez David F , Salazar Camilo , Pardo-Diaz Carolina , Merrill Richard M , Montgomery Stephen H 
Published: June 2024

AbstractColonisation of new habitats is typically followed by divergent selection acting on traits that are immediately important for fitness in the new habitat. For example, shifting sensory environments are often associated with variation in sensory traits critical for navigation and foraging. However, the extent to which the initial response to novel sensory conditions is mediated by phenotypic plasticity, and its contribution to early species divergence remains unclear. We took advantage of repeated cases of speciation inHeliconiusbutterflies with independent allopatric distributions in the west of the Colombian and Ecuadorian Andes. Using volumetric brain measurements, we analysed patterns of investment in sensory processing in brain components across different localities and habitats. We find that a higher-altitude species,H. chestertonii, differs in levels of investment in visual and olfactory brain centres compared to its lower altitude relativeH. erato venus, mainly attributable to heritable variation as inferred from comparisons between wild and common-garden reared individuals. We compared these shifts with those reported for another high-altitude species,H. himera, and its parapatric lowland counterpart,H. erato cyrbia, and demonstrate parallel reductions in the size of specific optic lobe neuropils. Conversely, for the antennal lobe, we detected disparate trait shifts inH. himeraandH. chestertoniiin respect to their lowlanderatoneighbours. Overall, our findings add weight to the adaptive potential for neuroanatomical divergence related to sensory processing during early species formation.Lay summaryRepeated associations between trait variation and environmental shifts may indicate adaptation to local sources of natural selection. For instance, in fish, the presence of certain morphological traits in specific ecological conditions across independent populations is well documented, suggesting equivalent phenotypic responses to shared sources of natural selection. We compared independent cases of ecological divergence inHeliconiusbutterflies distributed along altitude gradients from sea level to mid mountain in the west of the Colombian and Ecuadorian Andes. Shifts in altitude involve repeated, abrupt transitions from wet, large-leaved, warm forests to higher dry, open, cold scrubs. We tested hypotheses about the role of these ecological shifts in driving adaptive evolution in neuroanatomical traits during early speciation. We showed that inHeliconius, independent changes in forest-type have been accompanied by heritable parallel patterns of divergence in sensory investment in visual processing in the brain. We propose these differences likely facilitate species divergence in the face of ongoing geneflow.
Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines
Authors: Bakhtina Anna A. , Wippel Helisa H. , Chavez Juan D. , Bruce James E. 
Published: June 2024

ABSTRACTCellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitativein vivoprotein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type- specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.GRAPHICAL ABSTRACT
PFS alleviates bone destruction in collagen-induced arthritis mice associated with macrophage polarization
Authors: Sun Guangchen , Bao Chunmei , Sun Xin , Liu Yingqin 
Published: June 2024

AbstractPeriploca forrestii Schltr is a clinical traditional Chinese medicine for the treatment of Rheumatoid arthritis (RA). This study aimed to investigate effects of Periploca forrestii Schltr saponin (PFS) on bone destruction and macrophage polarization in arthritis model mice and to explore its possible mechanism. Arthritis was induced in two species, BALB/c and C57BL/6 mice, by immunization with type II chicken collagen. The arthritic mice were administered PFS for four weeks. The hindfeet, blood and spleen were harvested. Molecular expression was determined by ELISA, RT-PCR and immunoblotting. PFS treatment resulted in a significant reduction in paw swelling in both species of mice. PFS also reduced cartilage destruction and infiltration of osteoclasts in BALB/c mice. Furthermore, it decreased the levels of M1 macrophage cytokines while increasing the levels of M2 macrophage cytokines in the paw and plasma. Micro-CT results in C57BL/6 mice showed that PFS attenuated microstructural damage in bone tissue. PFS inhibited CD68 and affected the expression of M1 macrophage factors such as CCL-2, TLR4, and IL-1β in the mouse paw. In addition, PFS treatment increased the M2 macrophage factor CD206 and CD163. PFS inhibits the activation of ERK, JNK, and p38 and the expression of transcription factors, including STAT3, p65, and c-Fos. PFS may modulate pleiotropic macrophage polarization and thus play an ameliorative role in bone damage, therefore PFS may be an effective alternative drug for the treatment of RA.
Early IKKβ-dependent anabolic signature governs vascular smooth muscle cells fate and abdominal aortic aneurysm development
Authors: Doyon Priscilla , Kizilay-Mancini Ozge , Dô Florence , Huynh David , Mayer Gaétan , Lehoux Stéphanie , Ong Huy , Batardière Maelle , Quoc-Huy Vincent , Marleau Sylvie , Gravel Simon-Pierre , Servant Marc J 
Published: June 2024

ABSTRACTBackgroundAbdominal aortic aneurysm (AAA) is a detrimental disease with no effective pharmacological therapy. While inflammation is recognized as one of the key regulators of AAA, targeting inflammatory pathways once the disease is established does not impact the outcomes. However, understanding the earliest molecular indicators could shed light on the precise biological targets and prognostic markers for AAA.MethodsUsing apolipoprotein E (ApoE)-deficient mice fed with a standard diet and infused with Angiotensin II (Ang II), we conducted bulk RNA-sequencing (RNA-Seq) analysis on suprarenal (SRA) regions obtained from both unchallenged and challenged WT mice, specifically examining responses 24 hours after Ang II infusion to capture the initial phases of aortic stress response. We further created a unique model of hyperlipidemic mice in which the expression of the inhibitor of nuclear factor kappa B kinase subunit beta (IKKβ) can be conditionally (via tamoxifen injection) suppressed in vascular smooth muscle cells (VSMC). The development of AAA was evaluated using in situ examination and quantified using RT-qPCR, immunohistochemistry and fluorescence microscopy. Cultured VSMC were exposed to the selective IKKβ inhibitor MLN120b and the expression levels of phenotypic markers kruppel like factor 4 (KLF4), β-Catenin and cellular communication network factor 2 (CCN2) were addressed using cellular extracts and immunoblot analysis.ResultsRNA-Seq data support the presence of early anabolic events in SRA regions detailing activation of the mammalian target of rapamycin complex 1 (mTORC1) pathway, which paralleled cellular anabolic processes including mitochondria, ribosome and sterol biosynthesis, the Unfolded Protein Response (UPR) and fibrogenesis. Conditional deletion of theIkbkbgene in VSMC significantly reduces the incidence of SRA lesions as well as the rate of aneurysm ruptures in mice exposed to Ang II.In situanalysis further demonstrated that the protection conferred by the lack of IKKβ expression in VSMC is associated with reduced inflammatory response, the preservation of the contractile over the degradative VSMC phenotypes, and the absence of an anabolic signature.ConclusionOur results not only reinforce the major roles played by VSMC in the rapid adaptation leading to the deleterious remodeling of the vascular wall and aortic lesions but also support a paradigm aiming at repositioning the efforts focusing on anabolic rather than inflammatory events.