bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modular, Vascularized Hypertrophic Cartilage Constructs for Bone Tissue Engineering Applications
Authors: Schott Nicholas G. , Kaur Gurcharan , Coleman Rhima , Stegemann Jan P. 
Published: March 2024

AbstractInsufficient vascularization is a main barrier to creating engineered bone grafts for treating large and ischemic defects. Modular tissue engineering approaches have promise in this application because of the ability to combine tissue types and to localize microenvironmental cues to drive desired cell function. In direct bone formation approaches, it is challenging to maintain sustained osteogenic activity, since vasculogenic cues can inhibit tissue mineralization. This study harnessed the physiological process of endochondral ossification to create multiphase tissues that allowed concomitant mineralization and vessel formation. Mesenchymal stromal cells in pellet culture were differentiated toward a cartilage phenotype, followed by induction to chondrocyte hypertrophy. Hypertrophic pellets exhibited increased alkaline phosphatase activity, calcium deposition, and osteogenic gene expression relative to chondrogenic pellets. In addition, hypertrophic pellets secreted and sequestered angiogenic factors, and supported new blood vessel formation by co-cultured endothelial cells and undifferentiated stromal cells. Multiphase constructs created by combining hypertrophic pellets and vascularizing microtissues and maintained in unsupplemented basal culture medium were shown to support robust vascularization and sustained tissue mineralization. These results demonstrate a newin vitrostrategy to produce multiphase engineered constructs that concomitantly support the generation of mineralize and vascularized tissue in the absence of exogenous osteogenic or vasculogenic medium supplements.Graphical Abstract
Treponema pallidumperiplasmic and membrane proteins are recognized by circulating and skin CD4+ T cells
Authors: Reid Tara B. , Godornes Charmie , Campbell Victoria L. , Laing Kerry J. , Tantalo Lauren C. , Gomez Alloysius , Pholsena Thepthara N. , Lieberman Nicole A. P. , Krause Taylor M. , Cegielski Victoria I. , Culver Lauren A. , Nguyen Nhi , Tong Denise Q. , Hawley Kelly L. , Greninger Alexander L. , Giacani Lorenzo , Cameron Caroline E. , Dombrowski Julia C. , Wald Anna , Koelle David M. 
Published: March 2024

ABSTRACTBackgroundHistologic and serologic studies suggest the induction of local and systemicTreponema pallidum(Tp)-specific CD4+ T cell responses toTpinfection. We hypothesized thatTp-specific CD4+ T cells are detectable in blood and in the skin rash of secondary syphilis and persist in both compartments after treatment.MethodsPBMC collected from 67 participants were screened by IFNγ ELISPOT response toTpsonicate.Tp-reactive T cell lines from blood and skin were probed for responses to 88 recombinantTpantigens. Peptide epitopes and HLA class II restriction were defined for selected antigens.ResultsWe detected CD4+ T cell responses toTpsonicate ex vivo. UsingTp-reactive T cell lines we observed recognition of 14 discrete proteins, 13 of which localize to bacterial membranes or the periplasmic space. After therapy,Tp-specific T cells persisted for at least 6 months in skin and 10 years in blood.ConclusionsTpinfection elicits an antigen-specific CD4+ T cell response in blood and skin.Tp-specific CD4+ T cells persist as memory in both compartments long after curative therapy. TheTpantigenic targets we identified may be high priority vaccine candidates.
Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes
Authors: Ogasawara Daisuke , Konrad David B. , Tan Zher Yin , Carey Kimberly L. , Luo Jessica , Won Sang Joon , Li Haoxin , Carter Trever , DeMeester Kristen E. , Njomen Evert , Schreiber Stuart L. , Xavier Ramnik J. , Melillo Bruno , Cravatt Benjamin F. 
Published: March 2024

SummaryChemical proteomics enables the global assessment of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, been limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically-defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these ‘photo-stereoprobes’ interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible nanoBRET assays. Integrated phenotypic analysis and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and discovering and characterizing bioactive small molecules by cell-based screening.
Non-Electrostatic Basis for an Artificial Metalloenzyme Catalysis
Authors: Mukherjee Anagh , Roy Subhendu 
Published: March 2024

ABSTRACTThe artificial metalloenzyme (referred to asIr-Q) reported by Hartwig and coworkers presented an important milestone in merging the extraordinary efficiency of biocatalyst with the versatility of small molecule chemical catalyst in catalyzing a new-to-nature carbene insertion reaction. The artificial enzyme results from formal replacement of the Fe by an Ir(Me) moiety along with four C317G, T213G, L69V, V254L mutations in a natural Cytochrome enzyme CYP119 by directed evolution method. Importantly, this is a show-stopper enzyme as it exhibits a catalytic rate enhancement similar to that of natural enzymes. Despite this remarkable discovery, there is no mechanistic understanding as to why it displays extraordinary efficiency, so far been intractable to experimental methods. In this study, we have deciphered the ‘catalytically active conformation’ ofIr-Qusing large-scale molecular dynamics simulations and rigorous quantum chemical calculations. Our study reveals how directed evolution mutations precisely position the cofactor-substrate in an unusual orientation within a reshaped active site that emerged during evolution and fostered by C−H…π interactions from more ordered mutated L69V and V254L residues. This productive conformation correctly reproduces the experimental barrier height and the catalytic effect of 2.7 kcal/mol, in excellent agreement with observed rate enhancement. Moreover, the active conformation features an unprecedented bonding interaction in a metal-carbene species that preferentially stabilizes the rate determining formation of an Iridium-Porphyrin Carbene intermediate to render the observed high catalytic rate acceleration. While the electrostatic criteria are widely established, this study suggests a new design paradigm towards realization of fully programmable protein catalysis.
How to quantify developmental synchrony in malaria parasites
Authors: Greischar Megan A. , Savill Nicholas J. , Reece Sarah E. , Mideo Nicole 
Published: March 2024

ABSTRACTMalaria infections represent an iconic example of developmental synchrony, where periodic fevers can result when the population of parasites develops synchronously within host red blood cells. The level of synchrony appears to vary across individual hosts and across parasite species and strains, variation that—once quantified—can illuminate the ecological and evolutionary drivers of synchrony. Yet current approaches for quantifying synchrony in parasites are either biased by population dynamics or unsuitable when population growth rates vary through time, features ubiquitous to parasite populationsin vitroandin vivo. Here we develop an approach to estimate synchrony that accounts for population dynamics, including changing population growth rates, and validate it with simulated time series data encompassing a range of synchrony levels in two different host-parasite systems: malaria infections of mice and human malaria parasitesin vitro. This new method accurately quantifies developmental synchrony from per capita growth rates using obtainable abundance data even with realistic sampling noise, without the need to sort parasites into developmental stages. Our approach enables variability in developmental schedules to be disentangled from even extreme variation in population dynamics, providing a comparative metric of developmental synchrony.
Increased dosage of wild-type KRAS protein drivesKRAS-mutant lung tumorigenesis and drug resistance
Authors: Ivanisevic Tonci , Magits Wout , Ma Yan , Zhao Peihua , Van Boxel Emiel , Lechat Benoit , Stites Edward , Vande Velde Greetje , Sewduth Raj , Sablina Anna 
Published: March 2024

AbstractAlmost 30% of lung adenocarcinomas are driven by activatingKRASmutations. The heterogeneous clinical behavior observed in these cancers could be due to the imbalance of wild-type and oncogenic KRAS alleles. However, the role of RAS dysregulation at the protein level needs to be further explored. A genome-wide global protein stability screen identified the CUL3 ubiquitin ligase adaptor LZTR1, as a major proteostatic regulator of wild-type but not mutant KRAS. InKRAS-mutant lung adenocarcinoma, shallow deletion ofLZTR1is observed in up to 50% of patients and is associated with hypoxic signatures and poorer progression-free disease survival. In aKras-mutant lung cancer mouse model, heterozygous loss ofLztr1promoted tumor growth, led to peritumoral vascular remodeling, and limited the response to the KRAS-G12D inhibitor MRTX1133. The vascular alteration inLZTR1-depleted lung cancer was mediated by increased wild-type KRAS protein dosage, which promoted mTOR pathway activation and a subsequent increase in VEGFA secretion. The inhibition of the PI3K/mTOR pathway using dactolisib normalized tumor vasculature, improved drug delivery, and overcame resistance to KRAS-G12D inhibitors. In summary, the dysregulation of RAS proteostasis contributes to lung tumorigenesis, and targeting wild-type KRAS signaling is crucial to overcome intrinsic resistance to inhibitors of mutant KRAS.SignificanceOur study highlights the impact of RAS proteostasis on lung cancer development and progression. Vascular normalization achieved by suppressing wild-type KRAS signaling improved the delivery and response to MRTX1133 inKRAS-mutant lung cancer with shallowLZTR1deletion.
Investigating the mechanisms of antibody binding to alpha-synuclein for the treatment of Parkinson’s Disease
Authors: Harrison Malcolm C. , Lai Pin-Kuang 
Published: March 2024

AbstractParkinson’s Disease (PD) is an idiopathic neurodegenerative disorder with the second-highest prevalence rate behind Alzheimer’s Disease. The pathophysiological hallmarks of PD are both degeneration of dopaminergic neurons in the substantia nigra pars compacta and the inclusion of misfolded alpha-synuclein (α-syn) aggregates known as Lewy bodies. Despite decades of research for potential PD treatments, none have been developed, and developing new therapeutic agents is a time-consuming and expensive process. Computational methods can be used to investigate the properties of drug candidates currently undergoing clinical trials to determine their theoretical efficiency at targeting α-syn. Monoclonal antibodies (mAbs) are biological drugs with high specificity, and Prasinezumab (PRX002) is a mAb currently in Phase II, which targets the C-terminus (AA 118-126) of α-syn. We utilized BioLuminate and PyMol for structure prediction and preparation of the fragment antigen-binding (Fab) region of PRX002 and 34 different conformations of α-syn. Protein-protein docking simulations were performed using PIPER, and 3 of the docking poses were selected based on the best fit. Molecular dynamics simulations were conducted on the docked protein structures for 1000 ns, and hydrogen bonds, electrostatic, and hydrophobic interactions were analyzed using MDAnalysis to determine which residues were interacting and how often. Hydrogen bonds were shown to form frequently between the HCDR2 region of PRX002 and α-syn. Free energy was calculated to determine binding affinity. The predicted binding affinity shows a strong antibody-antigen attraction between PRX002 and α-syn. RMSD was calculated to determine the conformational change of these regions throughout the simulation. The mAb’s developability was determined using computational screening methods. Our results demonstrate the efficiency and developability of this therapeutic agent.
Mimicking anin celluloenvironment for enzyme-free paper-based nucleic acid tests at the point of care
Authors: Beard Jeffrey W. , Hunt Samuel L. , Evans Alexander , Goenner Coleman , Miller Benjamin L. 
Published: March 2024

ABSTRACTPoint of care (PoC) nucleic acid amplification tests (NAATs) are a cornerstone of public health, providing the earliest and most accurate diagnostic method for many communicable diseases, such as HIV, in the same location the patient receives treatment. Communicable diseases disproportionately impact low-resource communities where NAATs are often unobtainable due to the resource intensive enzymes that drive the tests. Enzyme-free nucleic acid detection methods, such as hybridization chain reaction (HCR), use DNA secondary structures for self-driven amplification schemes producing large DNA nanostructures and capable of single molecule detectionin cellulo. These thermodynamically driven DNA-based tests have struggled to penetrate the PoC diagnostic field due to their inadequate limits of detection or complex workflows. Here we present a proof-of-concept NAAT that combines HCR-based amplification of a target nucleic acid sequence with paper-based nucleic acid filtration and enrichment capable of detecting sub pM levels of synthetic DNA. We reconstruct the favorable hybridization conditions of anin celluloreactionin vitroby incubating HCR in an evaporating, microvolume environment containing poly(ethylene glycol) as a crowding agent. We demonstrate that the kinetics and thermodynamics of DNA-DNA and DNA-RNA hybridization is enhanced by the dynamic evaporating environment and inclusion of crowding agents, bringing HCR closer to meeting PoC NAAT needs.
Identification of Myocardial Infarction (MI) Probability from Imbalanced Medical Survey Data: An Artificial Neural Network (ANN) with Explainable AI (XAI) Insights
Authors: Akter Simon Bin , Akter Sumya , Pias Tanmoy Sarkar , Eisenberg David , Fernandez Jorge Fresneda 
Published: March 2024

ABSTRACTIn the healthcare industry, many artificial intelligence (AI) models have attempted to overcome bias from class imbalances while also maintaining high results. Firstly, when utilizing a large number of unbalanced samples, current AI models and related research have failed to balance specificity and sensitivity – a problem that can undermine the reliability of medical research. Secondly, no reliable method for obtaining detailed interpretability has been put forth when addressing large numbers of input features. The present research addresses these two critical research gaps with a proposed lightweight Artificial Neural Network (ANN) model. Using 43 input features from the 2021 Behavioral Risk Factor Surveillance System (BRFSS) dataset, the proposed model outperforms prior models in producing balanced outcomes from markedly unbalanced large survey data. The efficacy of this proposed ANN model is attributed to its simplified design, which reduces processing demands, and its resilience in identifying the probability of myocardial infarction (MI). This is demonstrated by its 80% specificity and 77% sensitivity, and is substantiated by a Receiver Operating Characteristic Area Under the Curve (AUC) of 0.87. The outcomes across the scopes of each specified data domain were also separately represented, thus demonstrating the proposed model’s robust sensitivity. The interpretability of the model, as measured by Shapley values, reveals substantial correlations between myocardial infarction (MI) and its risk factors, including long-term medical conditions, socio-demographic factors, personal health habits, economic and social status, healthcare availability and affordability, as well as impairment statuses, providing valuable insights for improved cardiovascular risk assessment and personalized healthcare strategies.
Alcohol consumption and long-term risk of gout in men and women: a prospective study addressing potential reverse causation
Authors: Lyu Jie-Qiong , Peng Xian-Zhen , Wang Jia-Min , Miao Meng-Yuan , Tao Hao-Wei , Zhao Miao , Zhu Jie , Yang Jing , Chen Jing-Si , Qin Li-Qiang , Chen Wei , Chen Guo-Chong 
Published: March 2024

AbstractBackgroundWhile specific alcoholic beverages have been associated with gout, the influence of residual confounding and potential reverse-causation bias on these associations remains to be addressed.MethodsThe exploratory analysis included 218,740 men and 271,389 women free of gout at recruitment of the UK Biobank. Among these, 181,925 men and 223,700 women remained for the final analysis where potential reverse causation was addressed, i.e., by excluding participants who had or were likely to have reduced alcohol intake due to health issues at baseline, in addition to cases that were identified within the first 2 years of follow-up.ResultsIn the final analysis, current drinkers had a higher risk of gout than never drinkers in men (HR = 1.78, 95% CI: 1.39-2.28) but not in women (HR = 0.84, 95% CI: 0.68-1.03). Among current drinkers, higher alcohol consumption was associated a substantially higher risk of gout in men and a moderately higher risk in women. The most evident sex difference in the consumption of specific alcoholic beverages was observed for beer/cider (mean: 4.16 vs. 0.44 pints/week in men and women, respectively). Consumption of champagne/white wine, beer/cider, and spirits each was associated with a higher risk of gout in both sexes, with beer/cider showing the strongest association (HRper 1 pint/d= 1.55, 95% CI: 1.49-1.61 in men; HRper 1 pint/d= 1.71, 95% CI: 1.14-2.57 in women). In the exploratory analysis, low to moderate consumption of specific alcoholic beverages were widely associated with a lower risk of gout, whereas all these inverse associations were eliminated in the final analysis. For example, red wine intake was associated with a lower risk of gout in women in the exploratory analysis (HRper 1 glass/d= 0.79, 95% CI: 0.69-0.90), but not after adjusting for other alcoholic beverages and addressing potential reverse causation (HRper 1 glass/d= 0.91, 95% CI: 0.77-1.06).ConclusionsConsumption of total and several specific alcoholic beverages is associated with a higher risk of gout in both sexes. The sex-specific associations for total alcohol consumption may be attributable to differences in the type of alcohol consumed rather than biological differences between men and women.
Factors that influence the caste ratio in a bacterial division of labour
Authors: Domínguez Luis Alfredo Avitia , Yu Zhengzhou , Chopra Varun , Merks Roeland , van Dijk Bram , Rozen Daniel 
Published: March 2024

ABSTRACTColonies of the bacteriaStreptomyces coelicolordivide labour between cells that specialize on growth and sporulation and cells that specialize on antibiotic production. This division of labour arises due to costly chromosome deletions in the antibiotic overproducers. However, little is known about when and where these mutations occur or whether their frequency – which we liken to the caste ratio in social insects – is phenotypically plastic. To elucidate changes in the proportions of specialized cells (measured as the mutation frequency), we sampledS. coelicolorcolonies grown under different conditions. Temporally, mutation frequency increased linearly with colony age and size. Spatially, mutations accumulated disproportionately in the colony center, despite greater growth and sporulation at the periphery. Exposing colonies to sub-inhibitory concentrations of some antibiotics, a competitive cue inStreptomyces, increased mutation frequencies. Finally, direct competition with otherStreptomycesthat naturally produce antibiotics increased mutation frequencies, while also increasing spore production. Our findings provide insights into the intrinsic and environmental factors driving division of labor inStreptomyces coloniesby showing that mutation frequencies are dynamic and responsive to the competitive environment. These results show that chromosome deletions are phenotypically plastic and suggest thatStreptomycescan flexibly adjust their caste ratio.
Transposable Elements and piRNAs interaction prediction with Predictive Bi-Clustering Trees
Authors: Freire Oliveira Hiago , dos Santos Renato A. C. , Cerri Ricardo 
Published: March 2024

AbstractPIWI-interacting RNAs (piRNAs) are a class of noncoding RNAs whose actions range from regulating gene expression to silencing Transposable Elements, characterized for being from 21 to 35 nucleotides long, displaying a uracil bias at the 5’ end, and a 2’-O-methylation at the 3’ end. Transposable Elements (TEs) are genetic elements that move within host genomes. TE replication can promote harmful recombination events by generating breaks in DNA double strands, in addition to interfering with expression. Silencing of these elements by piRNAs occurs in the germ line in most animals and is essential for maintaining genome integrity. In this work, the problem of in silico interaction prediction between piRNAs and TEs was addressed by a decision tree-based algorithm, namely Predictive Bi-Clustering Trees (PBCT). In order to improve the algorithm’s performance, the piRNA-TE interaction matrix was reconstructed using a Beta-distribution-rescored Neighborhood Regularized Logistic Matrix Factorization (NRLMFβ) algorithm. PBCT was tested in 5-fold and 10-fold cross-validation configurations, both with the original interaction matrix (BICT) and the interaction matrix reconstructed by NRLMFβ (BICTR). Although not being able to predict positive interactions satisfactorily given the huge dataset imbalance, advantages could be observed when using matrix factorization. Comparatively, in the BICT method, PBCT presented higher values of AUROC and AUPRC. However, in the BICTR method, PBCT was able to correctly predict more positive interactions, which are, in fact, the primary interest of this study. Potential biological applications and ways to improve the algorithm’s performance were also discussed.Author summarypiRNAs and transposable elements are biomolecules that interact in the germ lime in most animals, such that piRNAs silence these elements to keep genome integrity. However, detecting which piRNA interacts with which TE is a laborious task with low results, given that the rules that govern these interactions still need to be fully elicited. In this paper, we addressed the interaction prediction pair piRNA-TE using a multi-label decision-tree-like algorithm called PBCT applied toin vivoknown interactions. Given that it is a Positive-Unlabeled Learning problem, since we cannot be sure of a biological negative interaction, we reconstructed the interaction matrix employing an NRLMFβ algorithm. We compared the results given the original interaction matrix and the reconstructed matrix. The results with this algorithm and parameters could have been better, even though the reconstruction has proven fruitful. Further, we addressed our problem with other multi-label learning approaches and briefly compared them. We also discussed potential biological applications and ways to improve the algorithm’s performance.