bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy
Authors: Joslyn Louis R. , Huang Weize , Miles Dale , Hosseini Iraj , Ramanujan Saroja 
Published: January 2024

AbstractDespite recent progress in adoptive T cell therapy for cancer, understanding and predicting the kinetics of infused T cells remains a challenge. Multiple factors can impact the distribution, expansion, and decay or persistence of infused T cells in patients. We have developed a novel quantitative systems pharmacology (QSP) model of TCR-transgenic T cell therapy in patients with solid tumors to describe the kinetics of endogenous T cells and multiple memory subsets of engineered T cells after infusion. These T cells undergo lymphodepletion, proliferation, trafficking, differentiation, and apoptosis in blood, lymph nodes, tumor site, and other peripheral tissues. Using the model, we generated patient-matched digital twins that recapitulate the circulating T cell kinetics reported from a clinical trial of TCR-engineered T cells targeting E7 in patients with metastatic HPV-associated epithelial cancers. Analyses of key parameters influencing cell kinetics and differences among digital twins identify stem cell-like memory T cells (Tscm) cells as an important determinant of both expansion and persistence and suggest that Tscm-related differences contribute significantly to the observed variability in cellular kinetics among patients. We simulated in silico clinical trials using digital twins and predict that Tscm enrichment in the infused product improves persistence of the engineered T cells and could enable administration of a lower dose. Finally, we verified the broader relevance of the QSP model, the digital twins, and findings on the importance of Tscm enrichment by predicting kinetics for two patients with pancreatic cancer treated with KRAS G12D targeting T cell therapy. This work offers insight into the key role of Tscm biology on T cell kinetics and provides a quantitative framework to evaluate cellular kinetics for future efforts in the development and clinical application of TCR-engineered T cell therapies.
Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis
Authors: Zerrouk Naouel , Alcraft Rachel , Hall Benjamin A. , Augé Franck , Niarakis Anna 
Published: January 2024

AbstractMacrophages play an essential role in rheumatoid arthritis. Depending on their phenotype (M1 or M2), they can play a role in the initiation or resolution of inflammation. The M1/M2 ratio in rheumatoid arthritis is higher than in healthy controls. Despite this, no treatment targeting specifically macrophages is currently used in clinics. Thus, devising strategies to selectively deplete proinflammatory macrophages and promote anti-inflammatory macrophages could be a promising therapeutic approach. State-of-the-art molecular interaction maps of M1 and M2 macrophages in rheumatoid arthritis are available and represent a dense source of knowledge; however, these maps remain limited by their static nature. Discrete dynamic modelling can be employed to study the emergent behaviours of these systems. Nevertheless, handling such large-scale models is challenging. Due to their massive size, it is computationally demanding to identify biologically relevant states in a cell- and disease-specific context. In this work, we developed an efficient computational framework that converts molecular interaction maps into Boolean models using the CaSQ tool. Next, we used a newly developed version of the BMA tool deployed to a high-performance computing cluster to identify the models’ steady states. The identified attractors are then validated using gene expression data sets and prior knowledge. We successfully applied our framework to generate and calibrate the M1 and M2 macrophage Boolean models for rheumatoid arthritis. Using KO simulations, we identified NFkB, JAK1/JAK2, and ERK1/Notch1 as potential targets that could selectively suppress proinflammatory macrophages and GSK3B as a promising target that could promote anti-inflammatory macrophages in rheumatoid arthritis.
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits
Authors: Zhao Siming , Crouse Wesley , Qian Sheng , Luo Kaixuan , Stephens Matthew , He Xin 
Published: January 2024

AbstractMany methods have been developed to leverage expression quantitative trait loci (eQTL) data to nominate candidate genes from genome-wide association studies. These methods, including colocalization, transcriptome-wide association studies (TWAS) and Mendelian randomization-based methods; however, all suffer from a key problem—when assessing the role of a gene in a trait using its eQTLs, nearby variants and genetic components of other genes’ expression may be correlated with these eQTLs and have direct effects on the trait, acting as potential confounders. Our extensive simulations showed that existing methods fail to account for these ‘genetic confounders’, resulting in severe inflation of false positives. Our new method, causal-TWAS (cTWAS), borrows ideas from statistical fine-mapping and allows us to adjust all genetic confounders. cTWAS showed calibrated false discovery rates in simulations, and its application on several common traits discovered new candidate genes. In conclusion, cTWAS provides a robust statistical framework for gene discovery.
Chromosome-level genome assemblies of Nicotiana tabacum, Nicotiana sylvestris, and Nicotiana tomentosiformis
Authors: Sierro Nicolas , Auberson Mehdi , Dulize Rémi , Ivanov Nikolai V. 
Published: January 2024

AbstractThe Solanaceae species Nicotiana tabacum, an economically important crop plant cultivated worldwide, is an allotetraploid species that appeared about 200,000 years ago as the result of the hybridization of diploid ancestors of Nicotiana sylvestris and Nicotiana tomentosiformis. The previously published genome assemblies for these three species relied primarily on short-reads, and the obtained pseudochromosomes only partially covered the genomes. In this study, we generated annotated de novo chromosome-level genomes of N. tabacum, N. sylvestris, and N. tomentosiformis, which contain 3.99 Gb, 2.32 Gb, and 1.74 Gb, respectively of sequence data, with 97.6%, 99.5%, and 95.9% aligned in chromosomes, and represent 99.2%, 98.3%, and 98.5% of the near-universal single-copy orthologs Solanaceae genes. The completion levels of these chromosome-level genomes for N. tabacum, N. sylvestris, and N. tomentosiformis are comparable to other reference Solanaceae genomes, enabling more efficient synteny-based cross-species research.
Extended-wavelength diffuse reflectance spectroscopy dataset of animal tissues for bone-related biomedical applications
Authors: Li Celina L. , Fisher Carl J. , Komolibus Katarzyna , Lu Huihui , Burke Ray , Visentin Andrea , Andersson-Engels Stefan 
Published: January 2024

AbstractDiffuse reflectance spectroscopy (DRS) has been extensively studied in both preclinical and clinical settings for multiple applications, notably as a minimally invasive diagnostic tool for tissue identification and disease delineation. In this study, extended-wavelength DRS (EWDRS) measurements of ex vivo tissues ranging from ultraviolet through visible to the short-wave infrared region (355–1919 nm) are presented in two datasets. The first dataset contains labelled EWDRS measurements collected from bone cement samples and ovine specimens including 10 tissue types commonly encountered in orthopedic surgeries for data curation purposes. The other dataset includes labelled EWDRS measurements of primarily bone structures at different depths during stepwise drilling into intact porcine skulls until plunging into the cranial cavity. The raw data with code for pre-processing and calibration is publicly available for reuse on figshare. The datasets can be utilized not only for exploratory purposes in machine learning model construction, but also for knowledge discovery in the orthopedic domain to identify important features for surgical guidance, extract physiological parameters and provide diagnostic insights.
Improving the precision of shock resuscitation by predicting fluid responsiveness with machine learning and arterial blood pressure waveform data
Authors: Gupta Chitrabhanu B. , Basu Debraj , Williams Timothy K. , Neff Lucas P. , Johnson Michael A. , Patel Nathan T. , Ganapathy Aravindh S. , Lane Magan R. , Radaei Fatemeh , Chuah Chen-Nee , Adams Jason Y. 
Published: January 2024

AbstractFluid bolus therapy (FBT) is fundamental to the management of circulatory shock in critical care but balancing the benefits and toxicities of FBT has proven challenging in individual patients. Improved predictors of the hemodynamic response to a fluid bolus, commonly referred to as a fluid challenge, are needed to limit non-beneficial fluid administration and to enable automated clinical decision support and patient-specific precision critical care management. In this study we retrospectively analyzed data from 394 fluid boluses from 58 pigs subjected to either hemorrhagic or distributive shock. All animals had continuous blood pressure and cardiac output monitored throughout the study. Using this data, we developed a machine learning (ML) model to predict the hemodynamic response to a fluid challenge using only arterial blood pressure waveform data as the input. A Random Forest binary classifier referred to as the ML fluid responsiveness algorithm (MLFRA) was trained to detect fluid responsiveness (FR), defined as a ≥ 15% change in cardiac stroke volume after a fluid challenge. We then compared its performance to pulse pressure variation, a commonly used metric of FR. Model performance was assessed using the area under the receiver operating characteristic curve (AUROC), confusion matrix metrics, and calibration curves plotting predicted probabilities against observed outcomes. Across multiple train/test splits and feature selection methods designed to assess performance in the setting of small sample size conditions typical of large animal experiments, the MLFRA achieved an average AUROC, recall (sensitivity), specificity, and precision of 0.82, 0.86, 0.62. and 0.76, respectively. In the same datasets, pulse pressure variation had an AUROC, recall, specificity, and precision of 0.73, 0.91, 0.49, and 0.71, respectively. The MLFRA was generally well-calibrated across its range of predicted probabilities and appeared to perform equally well across physiologic conditions. These results suggest that ML, using only inputs from arterial blood pressure monitoring, may substantially improve the accuracy of predicting FR compared to the use of pulse pressure variation. If generalizable, these methods may enable more effective, automated precision management of critically ill patients with circulatory shock.
Undrained shear behavior of silty sand with a constant state parameter considering initial stress anisotropy effect
Authors: Li Peipei , Zhu Chen , Pan Xiaodong , Lv Bin , Pan Kun 
Published: January 2024

AbstractField observations in sedimentation and erosion-prone areas indicate that most natural sand deposits may contain a certain amount of non-plastic fines and are often under anisotropic stress conditions. A series of triaxial compression tests were performed on clean and silty sand with fines content fc ranging from 0 to 20% at an initial mean effective stress of p0′ = 100 kPa and varying consolidation conditions to understand the impact of initial stress anisotropy on undrained shear behavior. The results indicate that the state parameter ψ is a superior predictor for characterizing the responses of sand-fines mixtures compared to the global void ratio and relative density. A comparison of the behavior of clean and silty sand with a constant ψ (= − 0.03) confirms that the sample with 10% fc exhibits the strongest dilation and greatest shear resistance, irrespective of the consolidation conditions. It is also demonstrated that the initial stress anisotropy with a comparably higher static stress ratio ηs typically diminishes the shear strength of mixtures. However, the influence of initial stress anisotropy on soil stiffness is not unilateral. The sample consolidated to a negative ηs is stiffer than that under isotropic consolidation, while the presence of a positive ηs leads to a decrease in the secant Young's modulus.
Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening
Authors: Wang Tao , Long Cha , Chang Meixia , Wu Yuan , Su Shixian , Wei Jingjiang , Jiang Suyan , Wang Xiujun , He Jianwen , Xing Dan , He Yangbo , Ran Yaoqi , Li Wei 
Published: January 2024

AbstractIn plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.
A genetic toolkit underlying the queen phenotype in termites with totipotent workers
Authors: Lin Silu , Elsner Daniel , Ams Leon , Korb Judith , Rosengaus Rebeca 
Published: January 2024

AbstractSocial insect castes (e.g., queens, workers) are prime examples of phenotypic plasticity (i.e., different phenotypes arising from the same genotype). Yet, the mechanisms that give rise to highly fertile, long-lived queens versus non-reproducing, short-lived workers are not well understood. Recently, a module of co-expressed genes has been identified that characterizes queens compared to workers of the termite Cryptotermes secundus (Kalotermitidae): the Queen Central Module (QCM). We tested whether the QCM is shared in termite species, in which queens gradually develop via early larval and late larval instars, the latter functioning as totipotent workers (linear development). Similar as in C. secundus, gene expression profiles revealed an enrichment of QCM genes in Zootermopsis angusticollis queens, a species from another termite family (Archotermopsidae). The expression of these QCM genes became gradually enriched during development from early larval instars via workers to queens. Thus, our results support the hypothesis of a conserved genetic toolkit that characterizes termite queens with gradual linear development. Our data also imply a strong caste-specific tissue specificity with the QCM signal being restricted to head-prothorax tissues in termite queens. This tissue-specific expression of key aging-related genes might have facilitated the evolution of a long lifespan in termite queens.
Towards effectiveness of cell free DNA based liquid biopsy in head and neck squamous cell carcinoma
Authors: Kowal-Wisniewska Ewelina , Jaskiewicz Katarzyna , Bartochowska Anna , Kiwerska Katarzyna , Ustaszewski Adam , Gorecki Tomasz , Giefing Maciej , Paluszczak Jaroslaw , Wierzbicka Malgorzata , Jarmuz-Szymczak Malgorzata 
Published: January 2024

AbstractLiquid biopsy is a minimally invasive procedure, that uses body fluids sampling to detect and characterize cancer fingerprints. It is of great potential in oncology, however there are challenges associated with the proper handling of liquid biopsy samples that need to be addressed to implement such analysis in patients’ care. Therefore, in this study we performed optimization of pre-analytical conditions and detailed characterization of cfDNA fraction (concentration, length, integrity score) in surgically treated HNSCC patients (n = 152) and healthy volunteers (n = 56). We observed significantly higher cfDNA concentration in patients compared to healthy controls (p < 0.0001) and a time dependent decrease of cfDNA concentration after tumor resection. Our results also revealed a significant increase of cfDNA concentration with age in both, healthy volunteers (p = 0.04) and HNSCC patients (p = 0.000002). Moreover, considering the multitude of HNSCC locations, we showed the lack of difference in cfDNA concentration depending on the anatomical location. Furthermore, we demonstrated a trend toward higher cfDNA length (range 35–10380 and 500–10380 bp) in the group of patients with recurrence during follow-up. In conclusion, our study provide a broad characterization of cfDNA fractions in HNSCC patients and healthy controls. These findings point to several aspects necessary to consider when implementing liquid biopsy in clinical practice including: (I) time required for epithelial regeneration to avoid falsely elevated levels of cfDNA not resulting from active cancer, (II) age-related accumulation of nucleic acids accompanied by less efficient elimination of cfDNA and (III) higher cfDNA length in patients with recurrence during follow-up, reflecting predominance of tumor necrosis.
Association of TyG index and central obesity with hypertension in middle-aged and elderly Chinese adults: a prospective cohort study
Authors: Chen Yang , Hu Peng , He Yangyang , Qin Hao , Hu Longlong , Yang Renqiang 
Published: January 2024

AbstractTriglyceride glucose index (TyG) and waist circumstance have been well documented to be highly correlated with hypertension. However, the joint effect of waist circumstance and TyG on the risk of hypertension is unknown in middle-aged and elderly Chinese adults. The purpose of this study was to investigate the association between TyG and the risk of new-onset hypertension in middle-aged and elderly Chinese individuals with different waist circumstances. The multicentred prospective cohort study was conducted in 28 provinces of China including a total of 5865 eligible participants aged ≥ 45 years old. Cox regression was performed to examine the relationship of TyG index and hypertension with adjustments for the pertinent variables. Besides, the relationship was explored in different groups on the basis of waist circumstance. There was no significant correlation between TyG index and new-onset hypertension after adjustment for pertinent variables (hazards ratio [HR]: 0.99; 95% confidence interval [CI]: 0.80–1.24). When the association was explored in different waist circumstance groups, multivariate cox regression analyses revealed that TyG was an independent factor positively associated with the risk of hypertension in central obesity prophase group (HR: 1.57; 95% CI 1.13–2.16). Among individuals with central obesity, relative to population with lower TyG (Q1: 4.96–8.18), people who had higher TyG (Q3: 8.52–8.95; Q4: 8.95–12.14) were associated with significantly lower HR for hypertension. There was no conspicuous correlation between TyG index with new-onset hypertension in normal waist circumstance (HR: 1.05; 95% CI 0.84–1.30). The research demonstrated the positive relationship of TyG with risk of hypertension among individuals with central obesity prophase, negative relationship of TyG with hypertension among population with central obesity and inconspicuous correlation of TyG with hypertension among individuals with normal waist. In conclusion, the study findings supported the combined effects of TyG index and waist circumference in predicting hypertension in middle-aged and elderly Chinese individuals.
Illumina reads correction: evaluation and improvements
Authors: Długosz Maciej , Deorowicz Sebastian 
Published: January 2024

AbstractThe paper focuses on the correction of Illumina WGS sequencing reads. We provide an extensive evaluation of the existing correctors. To this end, we measure an impact of the correction on variant calling (VC) as well as de novo assembly. It shows, that in selected cases read correction improves the VC results quality. We also examine the algorithms behaviour in a processing of Illumina NovaSeq reads, with different reads quality characteristics than in older sequencers. We show that most of the algorithms are ready to cope with such reads. Finally, we introduce a new version of RECKONER, our read corrector, by optimizing it and equipping with a new correction strategy. Currently, RECKONER allows to correct high-coverage human reads in less than 2.5 h, is able to cope with two types of reads errors: indels and substitutions, and utilizes a new, based on a two lengths of oligomers, correction verification technique.
Assessing the effects of foot strike patterns and shoe types on the control of leg length and orientation in running
Authors: Garofolini Alessandro , Mickle Karen J. , McLaughlin Patrick , Taylor Simon B. 
Published: January 2024

AbstractThis research investigates the stabilization of leg length and orientation during the landing phase of running, examining the effects of different footwear and foot strike patterns. Analyzing kinematic data from twenty male long-distance runners, both rearfoot and forefoot strikers, we utilized the Uncontrolled Manifold approach to assess stability. Findings reveal that both leg length and orientation are indeed stabilized during landing, challenging the hypothesis that rearfoot strikers exhibit less variance in deviations than forefoot strikers, and that increased footwear assistance would reduce these deviations. Surprisingly, footwear with a lower minimalist index enhanced post-landing stability, suggesting that cushioning contributes to both force dissipation and leg length stability. The study indicates that both foot strike patterns are capable of effectively reducing task-relevant variance, with no inherent restriction on flexibility for rearfoot strikers. However, there is an indication of potential reliance on footwear for stability. These insights advance our understanding of the biomechanics of running, highlighting the role of footwear in stabilizing leg length and orientation, which has significant implications for running efficiency and injury prevention.