bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Learning Glioma Grading with the Tumor Microenvironment Analysis Protocol for A Comprehensive Learning, Discovering, and Quantifying Microenvironmental Features
Authors: Pytlarz M. , Wojnicki K. , Pilanc P. , Kaminska B. , Crimi A. 
Published: June 2023

AbstractGliomas are primary brain tumors that arise from neural stem cells or glial precursors. Diagnosis of glioma is based on histological evaluation of pathological cell features and molecular markers. Gliomas are infiltrated by myeloid cells that accumulate preferentially in malignant tumors and their abundance inversely correlates with survival, which is of interest for cancer immunotherapies. To avoid time-consuming and laborious manual examination of the images, a deep learning approach for automatic multiclass classification of tumor grades was proposed. Importantly, as an alternative way of investigating characteristics of brain tumor grades, we implemented a protocol for learning, discovering, and quantifying tumor microenvironment elements on our glioma dataset. Using only single-stained biopsies we derived characteristic differentiating tumor microenvironment phenotypic neighborhoods. A challenge of the study was given by a small sample size of human leukocyte antigen stained on glioma tissue microarrays dataset - 203 images from 5 classes - and imbalanced data distribution. This has been addressed by image augmentation of the underrepresented classes. For this glioma multiclass classification task, a residual neural network architecture has been adapted. On the validation set the average accuracy was 0.72 when the model was trained from scratch, and 0.85 with the pre-trained model. Moreover, the tumor microenvironment analysis suggested a relevant role of the myeloid cells and their accumulation to characterize glioma grades. This promising approach can be used as an additional diagnostic tool to improve assessment during intra-operative examination or sub-typing tissues for treatment selection, despite the challenges caused by the difficult dataset. We present here the distributions and visualizations of extracted tumor inter-dependencies.Graphical abstractHighlightsResearch highlight 1: We demonstrate that the ResNet-18 architecture with simple data augmentation trained in 10-fold cross-validation performs the multiclass classification relatively well even with a small imbalanced dataset with a high degree of similarities between classes.Research highlight 2: After supervised subtyping of the tumor, we investigated the usefulness of the protocol for discovery and learning tumor microenvironment elements for the same task. The protocol designed for deriving new biomarkers based on multiplex stained histological samples proved the ability to detect features characteristic of malignant tumors based only on single target stained tissue microarrays. We propose further studies on this topic can help in formulating specific criteria for improvements in diagnosis of gliomas, allowing to avoid the necessity of conducting advanced histopathological analysis or complementing genetic testing of tumor samples.
Three-dimensional anatomy of the early EoceneWhitephippus(Teleostei: Lampriformes) documents parallel conquests of the pelagic environment by multiple teleost lineages
Authors: Davesne Donald , Andrews James V. , Beckett Hermione T. , Giles Sam , Friedman Matt 
Published: June 2023

ABSTRACTThe early Eocene fossil assemblage of the London Clay (Southeastern England) is a key window to the early Paleogene diversification of teleost fishes in the open ocean. Despite their three-dimensional preservation that offers unique insight into skeletal anatomy, the London Clay fossils are still poorly described for the most part. †Whitephippus tamensisis a fossil teleost from this assemblage, known by several well-preserved specimens. Based on a complete description of the known material, including previously hidden structures (braincase, hyoid and branchial arches) revealed through 3D microtomography, we reinterpret †Whitephippusas an early member of the teleost group Lampriformes. More specifically, the anatomy of †Whitephippusindicates that it is likely a member of the so-called ‘pelagic clade’ including modern opahs and oarfishes. This redescription of †Whitephippusprovides the earliest definitive evidence of lampriforms conquering the pelagic environment, alongside numerous other teleost lineages.
Resource competition can explain simplicity in microbial community assembly
Authors: Lee Hyunseok , Bloxham Blox , Gore Jeff 
Published: June 2023

AbstractPredicting the composition and diversity of communities is a central goal in ecology. While community assembly is considered hard to predict, laboratory microcosms often follow a simple assembly rule based on the outcome of pairwise competitions. This assembly rule predicts that a species that is excluded by another species in pairwise competition cannot survive in a multispecies community with that species. Despite the empirical success of this bottom-up prediction, its mechanistic origin has remained elusive. In this study, we elucidate how this simple pattern in community assembly can emerge from resource competition. Our geometric analysis of a consumer-resource model shows that trio community assembly is always predictable from pairwise outcomes when one species grows faster than another species on every resource. We also identify all possible trio assembly outcomes under three resources and find that only two outcomes violate the assembly rule. Simulations demonstrate that pairwise competitions accurately predict trio assembly with up to 100 resources and the assembly of larger communities containing up to twelve species. We then further demonstrate accurate quantitative prediction of community composition using harmonic mean of pairwise fractions. Finally, we show that cross-feeding between species does not decrease assembly rule prediction accuracy. Our findings highlight that simple community assembly can emerge even in ecosystems with complex underlying dynamics.SignificanceMultispecies microbial communities play an essential role in the health of ecosystems ranging from the ocean to the human gut. A major challenge in microbial ecology is to understand and predict which species can coexist within a community. While a simple empirical rule utilizing only pairwise outcomes successfully predicts multispecies laboratory communities, its mechanistic origin has remained unexplained. Here, we find that the observed simplicity can emerge from competition for resources. Using a generic consumer-resource model, we demonstrate that community assembly of highly complex ecosystems is nevertheless well predicted by pairwise competitions. Our results argue that community assembly can be surprisingly simple despite the potential complexity associated with competition and crossfeeding of many different resources by many different species.
Musashi-2 (MSI2) regulation of DNA damage response in lung cancer
Authors: Bychkov Igor , Deneka Alexander , Topchu Iuliia , Pangeni Rajendra P. , Lengner Christopher , Karanicolas John , Golemis Erica A. , Makhov Petr , Boumber Yanis 
Published: June 2023

AbstractLung cancer is one of the most common types of cancers worldwide. Non-small cell lung cancer (NSCLC), typically caused byKRASandTP53driver mutations, represents the majority of all new lung cancer diagnoses. Overexpression of the RNA-binding protein (RBP) Musashi-2 (MSI2) has been associated with NSCLC progression. To investigate the role of MSI2 in NSCLC development, we compared the tumorigenesis in mice with lung-specificKras-activating mutation andTrp53deletion, with and withoutMsi2deletion (KP versus KPM2 mice). KPM2 mice showed decreased lung tumorigenesis in comparison with KP mice what supports published data. In addition, using cell lines from KP and KPM2 tumors, and human NSCLC cell lines, we found that MSI2 directly bindsATM/AtmmRNA and regulates its translation. MSI2 depletion impaired DNA damage response (DDR) signaling and sensitized human and murine NSCLC cells to treatment with PARP inhibitorsin vitroandin vivo. Taken together, we conclude that MSI2 supports lung tumorigenesis, in part, by direct positive regulation of ATM protein expression and DDR. This adds the knowledge of MSI2 function in lung cancer development. Targeting MSI2 may be a promising strategy to treat lung cancer.SignificanceThis study shows the novel role of Musashi-2 as regulator of ATM expression and DDR in lung cancer.
Polycomb sustains promoters in a deep OFF-state by limiting PIC formation to counteract transcription
Authors: Szczurek Aleksander T. , Dimitrova Emilia , Kelley Jessica R. , Klose Robert J. 
Published: June 2023

AbstractThe Polycomb system plays fundamental roles in regulating gene expression during mammalian development. However, how it controls transcription to enable gene repression has remained enigmatic. Here we employ rapid degron-based depletion coupled with live-cell transcription imaging and single-particle tracking to uncover how the Polycomb system controls transcription in single cells. We discover that the Polycomb system is not a constitutive block to transcription but instead sustains a long-lived deep promoter OFF-state which limits the frequency with which the promoter can enter into a transcribing state. We demonstrate that Polycomb sustains this deep promoter OFF-state by counteracting the binding of factors that enable early transcription pre-initiation complex formation and show that this is necessary for gene repression. Together these important discoveries provide a new rationale for how the Polycomb system controls transcription and suggests a universal mechanism that could enable the Polycomb system to constrain transcription across diverse cellular contexts.
Evaluating Minocycline as a Neuroprotective Agent in an Aged Female Rat MCAO Stroke Model
Authors: Gutierrez Liza , Tutino Vincent M. , Siddiqui Adnan H. 
Published: June 2023

AbstractThe middle cerebral artery occlusion (MCAO) suture model is widely accepted ischemic stroke model. However, researchers routinely use young male rats, ignoring that stroke risk is increased in older, post-menopausal women. To this end, we implemented (120-minute) transient- and permanent-occlusion MCAO models in female retired-breeder rats, examining the endpoint across 1-30 days to identify the optimal time course for the model. We found that in both groups the physical infarct (measured by triphenyltetrazolium chloride -TTC staining), which is present initially, was not detectable 30 days post-MCAO (even if some neurologic symptoms persist). Across shorter time-points (namely 24 hours and 7 days) we found that neurologic scores generally reach a plateau/maximum at ∽7 days, then infarct size gradually decreases over time for rats receiving a permanent MCAO. Across 3 transient occlusion times (60 minutes, 90 minutes, and 120 minutes), the longest gave the most robust result. Overall, the permeant and 120-minute transient MCAO evaluated at 7 days was optimal. Using these two models, we evaluated the neuroprotective qualities of the antibiotic, minocycline. We found that those in the treatment groups experienced a greater improvement in neurologic scores and a larger decrease in infarct size after daily treatment for seven days. This improvement was more prominent in the transiently occluded treatment group than in the permanently occluded group.
CD22L Conjugation to Insulin Attenuates Insulin-Specific B cell Activation
Authors: Apley Kyle D. , Griffith Amber S. , Downes Grant M. , Ross Patrick , Farrell Mark P. , Kendall Peggy , Berkland Cory J. 
Published: June 2023

AbstractPancreatic islet-reactive B lymphocytes promote Type 1 diabetes (T1D) by presenting antigen to islet-destructive T cells. Teplizumab, an anti-CD3 monoclonal, delays T1D onset in patients at risk, but additional therapies are needed to prevent disease entirely. Therefore, bifunctional molecules were designed to selectively inhibit T1D-promoting anti-insulin B cells by conjugating a ligand for the B cell inhibitory receptor CD22 (i.e., CD22L) to insulin, which permit these molecules to concomitantly bind to anti-insulin B cell receptors (BCRs) and CD22. Two prototypes were synthesized: 2:2 insulin-CD22L conjugate on a 4-arm PEG backbone, and 1:1 insulin-CD22L direct conjugate. Transgenic mice (125TgSD) expressing anti-insulin BCRs provided cells for in vitro testing. Cells were cultured with constructs for three days then assessed by flow cytometry. Duplicate wells with anti-CD40 simulated T cell help. Surprisingly, a 2-insulin 4-arm PEG control caused robust proliferation and activation-induced CD86 upregulation. Anti-CD40 further boosted these effects. This was unexpected, as soluble insulin alone has no effect, and may indicate that BCR-crosslinking occurs when antigens are tethered by the PEG backbone. Addition of CD22L via the 2:2 insulin-CD22L conjugate restored B cell properties to that of controls without additional beneficial effect. In contrast, the 1:1 insulin-CD22L direct conjugate significantly reduced anti-insulin B cell proliferation in the presence of anti-CD40. CD22L alone had no effect, and the constructs did not affect WT B cells. Thus, high valency constructs activate anti-insulin B cells, while low-valency antigen-CD22L conjugates co-ligate BCR and CD22, reducing B cell activation in response to simulated T cell help and reducing pathogenic B cell numbers without harming normal cells. Thus, the insulin-CD22L direct conjugate is a promising candidate for preclinical trials to prevent T1D without inducing immunodeficiency
VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution
Authors: Tian Renmao , Imanian Behzad 
Published: June 2023

AbstractBackgroundPhylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction. However, these genes have been selected based on their presence and single-copy ratio in all bacterial genomes, leaving out the gene’s ‘phylogenetic fidelity’ unexamined.ResultsFrom 30,522 complete genomes covering 11,262 species, we examined 148 bacterial core genes that have been previously used for phylogenomic analysis. In addition to the gene presence and single-copy rations, we evaluated the gene’s phylogenetic fidelity by comparing each gene’s phylogeny with its corresponding16S rRNAgene tree. Out of the 148 bacterial genes, 20 validated bacterial core genes (VBCG) were selected as the core gene set with the highest bacterial phylogenetic fidelity. Moreover, the smaller gene set resulted in a higher species presence in the tree than larger gene sets. UsingEscherichiaandSalmonellaas examples of prominent bacterial foodborne pathogens, we demonstrated that the 20 VBCG produced phylogenies with higher fidelity and resolution at species and strain levels while16S rRNAgene tree alone could not.ConclusionThe 20 validated core gene set improves the fidelity and speed of phylogenomic analysis. Among other uses, this tool improves our ability to explore the evolution, typing and tracking of bacterial strains, such as human pathogens. We have developed a Python pipeline and a desktop graphic app (available on GitHub) for users to perform phylogenomic analysis with high fidelity and resolution.
Emergence of community behaviors in the gut microbiota upon drug treatment
Authors: Garcia-Santamarina Sarela , Kuhn Michael , Devendran Saravanan , Maier Lisa , Driessen Marja , Mateus André , Mastrorilli Eleonora , Brochado Ana Rita , Savitski Mikhail M. , Patil Kiran R. , Zimmermann Michael , Bork Peer , Typas Athanasios 
Published: June 2023

SummaryPharmaceuticals can directly inhibit the growth of gut bacteria, but the degree such interactions manifest in complex community settings is an open question. Here we compared the effects of 30 drugs on a 32-species synthetic community with their effects on each community member in isolation. While most individual drug–species interactions remained the same in the community context, communal behaviors emerged in 26% of all tested cases. Cross-protection, during which drug-sensitive species became protected in community, was 6-times more frequent than cross-sensitization, the converse phenomenon. Cross-protection decreased and cross-sensitization increased at higher drug concentrations, suggesting that the resilience of microbial communities can collapse when perturbations get stronger. By metabolically profiling drug-treated communities, we showed that both drug biotransformation and bioaccumulation contribute mechanistically to communal protection. As a proof-of-principle, we molecularly dissected a prominent case: species expressing specific nitroreductases degraded niclosamide, thereby protecting both themselves and sensitive community members.
Comparative chemical genomics inBabesiaspecies identifies the alkaline phosphatase phoD as a novel determinant of resistance
Authors: Keroack Caroline D. , Elsworth Brendan , Tennessen Jacob A. , Paul Aditya S. , Hua Renee , Ramirez-Ramirez Luz , Ye Sida , Moreira Cristina M. , Meyers Marvin J. , Zarringhalam Kourosh , Duraisingh Manoj T. 
Published: June 2023

AbstractBabesiosisis an emerging zoonosis and widely distributed veterinary infection caused by 100+ species ofBabesiaparasites. The diversity ofBabesiaparasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallelin vitroevolution of resistance in independent populations of evolutionarily-relatedBabesiaspp. (B. bovisandB. divergens). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species ofBabesia,achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance inBabesiaspecies.HighlightsUse of two species forin vitroevolution identifies a high confidence locus associated with resistanceResistance mutation in phoD was validated using reverse genetics inB. divergensPerturbation of phoD using function genetics results in changes in the level of resistance to MMV019266Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatomsTogether, phoD is a novel resistance determinant in multipleBabesia spp.
The impacts of active and self-supervised learning on efficient annotation of single-cell expression data
Authors: Geuenich Michael J. , Gong Dae-won , Campbell Kieran R. 
Published: June 2023

AbstractA crucial step in the analysis of single-cell data is annotating cells to cell types and states. While a myriad of approaches have been proposed, manual labeling of cells to create training datasets remains tedious and time-consuming. In the field of machine learning, active and self-supervised learning methods have been proposed to improve the performance of a classifier while reducing both annotation time and label budget. However, the benefits of such strategies for single-cell annotation have yet to be evaluated in realistic settings. Here, we perform a comprehensive benchmarking of active and self-supervised labeling strategies across a range of single-cell technologies and cell type annotation algorithms. We quantify the benefits of active learning and self-supervised strategies in the presence of cell type imbalance and variable similarity. We introduce several heuristic procedures tailored to single-cell data — including a marker-aware adaptive reweighting cell selection procedure — that shows competitive performance with existing approaches. In addition, we demonstrate that having prior knowledge of cell type markers improves annotation accuracy. Finally, we summarize our findings into a set of recommendations for those implementing cell type annotation procedures or platforms. An R package implementing the heuristic approaches introduced in this work may be found athttps://github.com/camlab-bioml/leader.
Endocrine pancreas-specificGclcgene deletion causes a severe diabetes phenotype
Authors: Davidson Emily A. , Chen Ying , Singh Surendra , Orlicky David J. , Thompson Brian , Wang Yewei , Charkoftaki Georgia , Furnary Tristan A. , Cardone Rebecca L. , Kibbey Richard G. , Shearn Colin T. , Nebert Daniel W. , Thompson David C. , Vasiliou Vasilis 
Published: June 2023

AbstractReduced glutathione (GSH) is an abundant antioxidant that regulates intracellular redox homeostasis by scavenging reactive oxygen species (ROS). Glutamate-cysteine ligase catalytic (GCLC) subunit is the rate-limiting step in GSH biosynthesis. Using thePax6-Credriver mouse line, we deleted expression of theGclcgene in all pancreatic endocrine progenitor cells. Intriguingly,Gclcknockout (KO) mice, following weaning, exhibited an age-related, progressive diabetes phenotype, manifested as strikingly increased blood glucose and decreased plasma insulin levels. This severe diabetes trait is preceded by pathologic changes in islet of weanling mice.GclcKO weanlings showed progressive abnormalities in pancreatic morphology including: islet-specific cellular vacuolization, decreased islet-cell mass, and alterations in islet hormone expression. Islets from newly-weaned mice displayed impaired glucose-stimulated insulin secretion, decreased insulin hormone gene expression, oxidative stress, and increased markers of cellular senescence. Our results suggest that GSH biosynthesis is essential for normal development of the mouse pancreatic islet, and that protection from oxidative stress-induced cellular senescence might prevent abnormal islet-cell damage during embryogenesis.