bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-free chromatin particles damage genomic DNA of healthy cells via an ROS-independent mechanism
Authors: Jain Karishma , Raghuram Gorantla V. , Lopes Relestina , Khare Naveen Kumar , Shabrish Snehal , Mittra Indraneel 
Published: August 2024

AbstractSeveral hundred billion cells die daily in the human body, releasing cell-free chromatin particles (cfChPs) in the process, which then enter the blood circulation and get taken up by healthy cells. We have previously reported that, these internalized cfChPs damage genomic DNA as well cause physical damage to mitochondria, resulting in increased mitochondrial ROS production. In the current study, we evaluated the potential damaging effects of the cfChP-induced increase in ROS production on genomic DNA. NIH3T3 mouse fibroblast cells were treated with cfChPs isolated from the sera of healthy individuals (H-cfChPs) or patients with cancer (C-cfChPs) in the presence or absence of the ROS scavenger Mito-TEMPO. The pre-incubation of cfChP-treated cells with Mito-TEMPO abolished ROS production, but did not prevent genomic DNA damage induced by H-cfChPs and C-cfChPs. Our results suggest that cfChP-induced genomic DNA damage occurs in an ROS-independent manner. These findings align with emerging evidence suggesting that mitochondrial ROS may not be a direct cause of genomic DNA damage and suggest that DNA damage attributed to ROS may in-fact be induced by cfChPs. This possibility opens up new therapeutic approaches involving deactivation of cfChPs to retard ageing and other degenerative conditions traditionally attributed to oxidative stress.
Biodiversity and riparian forests are mutual biological drivers of ecosystem functions in temperate and tropical streams
Authors: Oester Rebecca , de Omena Paula M. , da Costa Larissa Corteletti , Moretti Marcelo S. , Altermatt Florian , Bruder Andreas 
Published: August 2024

AbstractFluxes of energy, matter, and organisms sustain linkages and functions within and between ecosystems. Yet, how biological drivers influence interactions and functions at the interface between aquatic and terrestrial environments (i.e., aquatic-terrestrial ecosystem functions) locally and across regions has received little attention. To test the relative importance of biological drivers on multiple aquatic-terrestrial ecosystem functions, we subsidised local terrestrial detritus in forested and non-forested stream sites in a temperate and tropical region. We also manipulated leaf litter diversity (horizontal biodiversity of resources) and macroinvertebrate access (vertical biodiversity of consumers). We measured secondary production of aquatic fungi, in-stream leaf litter nitrogen loss, and decomposition rates. The simultaneous provision of all three ecosystem functions (i.e., multifunctionality) was positively driven by vertical biodiversity and riparian forests in both regions. In both tropical and temperate streams, nitrogen loss was associated with vertical biodiversity. Decomposition rates were also enhanced by vertical biodiversity and linked to other ecosystem functions. These results reveal strong and consistent effects of biodiversity and riparian forests on aquatic-terrestrial ecosystem functions in freshwater detrital food webs in both temperate and tropical headwater streams. Thus, disentangling the drivers of ecosystem functions in these systems requires an understanding of underlying mechanisms beyond ecosystem borders.
Two distinct oscillatory auxin signals define the plasticity of lateral rooting inArabidopsis thaliana
Authors: Ren Chengzhi , Bodendorf Jule , Kleine-Vehn Jürgen 
Published: August 2024

AbstractThe so-called root clock defines lateral root pre-branch sites (PBS) but how these sites contribute to the root system architecture remains incompletely understood (1,2,3,4). Here we reveal in the model plantArabidopsis thalianathat two distinct oscillatory systems for the phytohormone auxin coordinate the spatial and temporal identity of PBS, jointly defining the lateral root density. We followed auxin signalling dynamics for days and thereby detected a systemic auxin signal oscillating in the mature primary root, which is distinct from the previously described root clock at the root tip. While the root clock spatially primes the PBS in the growing root tip, the systemic oscillatory auxin signal temporally controls the auxin-dependent identity of these PBS. Light perception in the shoot defines the strength of the systemic auxin signal and thereby controls the auxin-reliant ability of PBSs to develop into lateral roots. Moreover, PHYB and CRY1 mediate the light-dependent integration of other environmental signals, such as ambient temperature, into the control systemic auxin signalling and lateral root density. Our work reveals how two spatially distinct oscillatory auxin signals define the plasticity of plant root development in response to fluctuating conditions.
The Rab7-Epg5 and Rab39-ema modules cooperately position autophagosomes for efficient lysosomal fusions
Authors: Boda Attila , Balázs Villő , Nagy Anikó , Hargitai Dávid , Lippai Mónika , Simon-Vecsei Zsófia , Molnár Márton , Fürstenhoffer Fanni , Juhász Gábor , Lőrincz Péter 
Published: August 2024

AbstractMacroautophagy, a major self-degradation pathway in eukaryotic cells, utilizes autophagosomes to transport self-material to lysosomes for degradation. While microtubular transport is crucial for the proper function of autophagy, the exact roles of factors responsible for positioning autophagosomes remain incompletely understood. In this study, we performed a loss-of-function genetic screen targeting genes potentially involved in microtubular motility. A genetic background that blocks autophagosome-lysosome fusions was used to accurately analyze autophagosome positioning. We discovered that pre-fusion autophagosomes move towards the non-centrosomal microtubule organizing center (ncMTOC) inDrosophilafat cells, which requires a dynein-dynactin complex. This process is regulated by the small GTPases Rab7 and Rab39 together with their adaptors: Epg5 and ema, respectively. The dynein-dependent movement of vesicles toward the nucleus/ncMTOC is essential for efficient autophagosomal fusions with lysosomes and subsequent degradation. Remarkably, altering the balance of kinesin and dynein motors changes the direction of autophagosome movement, indicating a competitive relationship where normally dynein-mediated transport prevails. Since pre-fusion lysosomes were positioned similarly to autophagosomes, it indicates that pre-fusion autophagosomes and lysosomes converge at the ncMTOC, which increases the efficiency of vesicle fusions.
Development of SacB-based Counterselection for Efficient Allelic Exchange inFusobacterium nucleatum
Authors: Zhou Peng , Bibek G C , Hu Bo , Wu Chenggang 
Published: August 2024

ABSTRACTFusobacterium nucleatum, prevalent in the oral cavity, is significantly linked to overall human health. Our molecular comprehension of its role in oral biofilm formation and its interactions with the host under various pathological circumstances has seen considerable advancements in recent years, primarily due to the development of various genetic tools for DNA manipulation in this bacterium. Of these, counterselection-based unmarked in-frame mutation methods have proved notably effective. Under suitable growth conditions, cells carrying a counterselectable gene die, enabling efficient selection of rare defined allelic exchange mutants. ThesacBgene fromBacillus subtilis, encoding levansucrase, is a widely used counterselective marker partly due to the easy availability of sucrose. Yet, its potential application inF. nucleatumgenetic study remains untested. We demonstrated thatF. nucleatumcells expressingsacBin either a shuttle or suicide plasmid exhibit a lethal sensitivity to supplemental sucrose. Utilizing sucrose counterselection, we created an in-frame deletion of theF. nucleatum tonBgene, a critical gene for energy-dependent transport processes in Gram-negative bacteria, and a precise knockin of the luciferase gene immediately following the stop codon of thehslOgene, the last gene of a five-gene operon possible related to the natural competence ofF. nucleatum. Post counterselection with 5% sucrose, chromosomal plasmid loss occurred in all colonies, leading to gene alternations in half of the screened isolates. ThissacB-based counterselection technique provides a reliable method for isolating unmarked gene mutations in wild-typeF. nucleatum, enriching the toolkit for fusobacterial research.IMPORTANCEInvestigations intoFusobacterium nucleatum’s role in related diseases significantly benefit from the strategies of creating unmarked gene mutations, which hinge on using a counterselective marker. Previously, thegalk-based allelic exchange method, while effective, faced an inherent limitation – the need for a modified host. This study aims to surmount this limitation by substitutinggalKwithsacBfor gene modification inF. nucleatum. Our application of thesacB-based methodology successfully yielded atonBin-frame deletion mutant and a luciferase gene knockin at the precise chromosomal location in the wild-type background. The new method augments the existing toolkit forF. nucleatumresearch and has far-reaching implications due to the easy accessibility to the counterselection compound sucrose. We anticipate its broader adoption in further exploration, thereby reinforcing its critical role in propelling our understanding ofF. nucleatum.
Extending the IICR to multiple genomes and identification of limitations of some demographic inferential methods
Authors: Chikhi Lounès , Rodríguez Willy , Paris Cyriel , Ha-Shan Marine , Jouniaux Alexane , Arredondo Armando , Noûs Camille , Grusea Simona , Corujo Josué , Lourenço Inês , Boitard Simon , Mazet Olivier 
Published: August 2024

AbstractReconstructing the demographic history of populations and species is one of the greatest challenges facing population geneticists. [50] introduced, for a sample of sizek= 2 haploid genomes, a time- and sample-dependent parameter which they called the IICR (inverse instantaneous coalescence rate). Here we extend their work to larger sample sizes and focus onTk, the time to the first coalescence event in a haploid sample of sizekwherek≥ 2. We define the IICRkas the Inverse Instantaneous Coalescence Rate amongklineages. We show that (i) under a panmictic populationis equivalent toNe, (ii) the IICRkcan be obtained by either simulatingTkvalues or by using theQ-matrix approach of [61] and we provide the corresponding Python and R scripts. We then study the properties of theunder a limited set ofn-island and stepping-stone models. We show that (iii) in structured models theis dependent on the sample size and on the sampling scheme, even when the genomes are sampled in the same deme. For instance, we find thatplots for individuals sampled in the same deme will be shifted towards recent times with a lower plateau askincreases. We thus show that (iv) thecannot be used to represent “the demographic history” in a general sense, (v) thecan be estimated from real or simulated genomic data using the PSMC/MSMC methods [44, 65] (vi) the MSMC2 method produces smoother curves that infer something that is not the, but are close to thein the recent past when all samples are obtained from the same deme. Altogether we argue that the PSMC, MSMC and MSMC2 plots are not expected to be identical even when the genomes are sampled from the same deme, that none can be said to represent the “demographic history of populations” and that they should be interpreted with care. We suggest that the PSMC, MSMC and MSMC2 could be used together with theto identify the signature of population structure, and to develop new strategies for model choice.
Modulating Neutrophil Extracellular Trap FormationIn Vivowith Locoregional Precision using Differently Charged Self-Assembled Hydrogels
Authors: Lopez-Silva Tania L. , Anderson Caleb F. , Schneider Joel P. 
Published: August 2024

AbstractNeutrophil extracellular traps (NETs) are DNA networks released by neutrophils first described as a defense response against pathogens but have since been associated with numerous inflammatory diseases. The ability to induce NETs with locoregional specificityin vivocould facilitate studying this response in the context of disease and therapy with unprecedented control. We report the unexpected discovery that hydrogel charge predictably modulates the formation of NETs. Positively charged gels induce rapid NET release whereas negatively charged gels do not. This differential immune response to our self-assembled peptide gels enabled the development of a material platform that allows rheostat-like modulation over the degree of NET formation with anatomical and locoregional control.
Characterization and analysis of neuronal signaling using microelectrode array combined with rapid and localized cooling device for cryo-neuromodulation
Authors: Kim Jaehyun , Lee Jong Seung , Noh Soyeon , Seo Eunseok , Lee Jungchul , Kim Taesung , Cho Seung-Woo , Kim Gunho , Kim Sung Soo , Park Jungyul 
Published: August 2024

AbstractCryoanesthesia––a purely physical anesthesia treatment that freezes tissue and attenuate nerve activity––can provide fast treatment through freezing and thawing of cryo-machine and is inexpensive compared to other anesthetics. However, cryoanesthesia has not been widely adopted because securing safe and effective conditions requires quantitative measurement and analysis of neuronal signaling during freezing and recovery, for which research tools are limited. A lack of rapid and localized cooling technologies for quantitative cellular level analysis, in particular, hinders research on not only the optimal cryo-modulation of neuronal activities but also its influence to neighboring cells via cellular networks. Here, we introduce a novel cryo-neuromodulation platform, a high-speed precision probe-type cooling device (∼20°C/s at cooling) that provides localized cooling combined with a microelectrode array (MEA) system. We explored the temperature conditions for efficient silencing and recovery of neuronal activities without cell damage. We found that electrical activities of neurons were fully recovered within 1 minute of cooling duration with the maximum cooling speed, which was also confirmed with calcium imaging. The impact of silenced neurons on the neighboring neural network was explored using the localized cooling and we perceived that its influence can be transmitted if the neuronal network is well organized. Our new cryo-device provides rapid and reversible control of neural activities, which allows not just quantitative analysis of the network dynamics, but also new applications in clinical settings.
Protocol for the development and validation of machine-learning models for predicting the risk of hypertriglyceridemia in critically ill patients receiving propofol sedation using retrospective data
Authors: Deng Jiawen , Heybati Kiyan , Yadav Hemang 
Published: August 2024

ABSTRACTIntroductionPropofol is a widely used sedative-hypnotic agent for critically-ill patients requiring invasive mechanical ventilation (IMV). Despite its clinical benefits, propofol is associated with increased risks of hypertriglyceridemia. Early identification of patients at risk for propofol-associated hypertriglyceridemia is crucial for optimizing sedation strategies and preventing adverse outcomes. Machine learning (ML) models offer a promising approach for predicting individualized patient risks of propofol-associated hypertriglyceridemia.Methods and analysisWe propose the development of a ML model aimed at predicting the risk of propofol-associated hypertriglyceridemia in ICU patients receiving IMV. The study will utilize retrospective data from four Mayo Clinic sites. Nested cross-validation (CV) will be employed, with a 10-fold inner CV loop for model tuning and selection as well as an outer loop using leave-one-site-out CV for external validation. Feature selection will be conducted using Boruta and LASSO-penalized logistic regression. Data preprocessing steps include missing data imputation, feature scaling, and dimensionality reduction techniques. Six ML algorithms will be tuned and evaluated. Bayesian optimization will be used for hyperparameter selection. Global model explainability will be assessed using permutation importance, and local model explainability will be assessed using SHapley Additive exPlanations (SHAP).Ethics and disseminationThe proposed ML model aims to provide a reliable and interpretable tool for clinicians to predict the risk of propofol-associated hypertriglyceridemia in ICU patients. The final model will be deployed in a web-based clinical risk calculator. The model development process and performance measures obtained during nested cross-validation will be described in a study publication to be disseminated in a peer-reviewed journal. The proposed study has received ethics approval from the Mayo Clinic Institutional Review Board (IRB #23-007416).Strengths and limitations of this study-Robust external validation using a nested cross-validation (CV) framework will help assess the generalizability of models produced from the modeling pipeline across different hospital settings.-A diverse set of machine learning (ML) algorithms and advanced hyperparameter tuning techniques will be employed to identify the most optimal model configuration.-Integration of feature explainability will enhance the clinical applicability of the ML models by providing transparency in predictions, which can improve clinician trust and encourage adoption.-Reliance on retrospective data may introduce biases due to inconsistent or erroneous data collection, and the computational intensity of the validation approach may limit replication and future model expansion in resource-constrained settings.
Meta-analysis reveals limited reproducibility of lncRNA-related findings in hepatocellular carcinoma research
Authors: Necsulea Anamaria , Veber Philippe , Boldanova Tuyana , Ng Charlotte KY , Wieland Stefan , Heim Markus H 
Published: August 2024

AbstractBackground & AimsThe human genome comprises tens of thousands of long non-coding RNAs (lncRNAs), whose functionality is highly debated. In the field of hepatocellular carcinoma (HCC) research, as for other cancer types, lncRNAs are increasingly reported to act as oncogenes or tumor suppressors and are put forward as useful diagnostic or prognostic biomarkers. Here, we investigate the reliability of these claims by performing a meta-analysis of the associations between HCC and lncRNAs reported in the scientific literature, and by assessing lncRNA expression patterns in two HCC patient cohorts.Approach & ResultsWhile nowadays up to 6% of all HCC-related publications cite lncRNAs, we show that most reported associations between HCC and lncRNAs have not been reproduced. In general, lncRNAs are less often differentially expressed between HCC tissues and controls compared to protein-coding genes. However, HCC-associated lncRNAs are frequently up-regulated in tumor samples, consistent with the fact that they are often selected based on transcriptome-wide comparative analyses. We perform a detailed examination of the 25 lncRNAs that are most frequently cited in association with HCC. For 10 out of these 25 lncRNAs, including well known lncRNAs such asMALAT1,NEAT1,H19andXIST, we identify important conflicts between the biological roles and expression patterns previously reported for them in HCC and the expression patterns that we observe here. Finally, we observe that HCC-associated publications that cite lncRNAs are retracted three times more often than publications that cite protein-coding genes.ConclusionsOur results thus highlight the poor reproducibility of lncRNA-related claims in association with HCC, which is problematic in a context where new biomarkers and molecular targets for therapy are greatly needed.
Chromosome breakage-replication/fusion enables rapid DNA amplification
Authors: Zhang Cheng-Zhong , Pellman David 
Published: August 2024

AbstractDNA rearrangements are thought to arise from two classes of processes. The first class involves DNA breakage and fusion (“cut-and-paste”) without net DNA gain or loss. The second class involves aberrant DNA replication (“copy-and-paste”) and can produce either net DNA gain or loss. We previously demonstrated that the partitioning of chromosomes into aberrant structures of the nucleus, micronuclei or chromosome bridges, can generate cut-and-paste rearrangements by chromosome fragmentation and ligation. Surprisingly, in the progeny clones of single cells that have undergone chromosome bridge breakage, we identified large segmental duplications and short sequence insertions that are commonly attributed to copy-and-paste processes. Here, we demonstrate that both large duplications and short insertions are inherent outcomes of the replication and fusion of unligated DNA ends, a process we term breakage-replication/fusion (B-R/F). We propose that B-R/F provides a unifying explanation for complex rearrangement patterns including chromothripsis and chromoanasynthesis and enables rapid DNA amplification after chromosome fragmentation.
Reading; through the eyes of a university student: A double-masked randomised placebo-controlled cross-over protocol investigating coloured spectacle lens efficacy in adults with visual stress.
Authors: Harkin Darragh Liam , Little Julie-Anne , McCullough Sara J. 
Published: August 2024

Background: Visual stress is a reading disorder characterised by perceptual distortions, asthenopia and headache whilst reading, alongside increased sensitivity to repeated striped patterns (‘pattern glare’), in the absence of underlying ocular pathology. Coloured filters including tinted spectacle lenses and coloured overlays/acetates have been reported to ameliorate visual stress symptoms. However, evidence on coloured spectacle lenses efficacy at managing symptoms of visual stress, particularly in adults, is lacking, with two recent systematic reviews advocating the need for large-scale randomised control trials. Methods: This is a double-masked randomised placebo-controlled trial. University students identified with symptoms of visual stress, through use of a reading symptom questionnaire and mid-spatial frequency pattern glare test, will be recruited. Sample size for power of 90% at 5% significance, accounting for 10% dropout will be 65. Participants will be randomly assigned experimental and control coloured spectacle lenses to wear for six weeks followed by a two week washout period, prior to wear of the alternate lenses for a further six weeks with a two week washout period. Participants will compare both sets of spectacle lenses in a ‘head-to-head’ comparison after the secondary washout period, prior to choosing the preferred lenses for voluntary future wear. Long-term adherence to the preferred lenses will be assessed three months post-comparison. Researchers and participants will be masked to spectacle lenses worn throughout the duration of the trial. Reading performance will be assessed with both sets of lenses at various time points within the trial. A range of reading tests, reading symptoms and pattern glare evaluation will be used to monitor change in reading performance and visual stress symptoms during the trial. Discussion: The study will evaluate the hypothesis that coloured spectacle lenses increase reading speed and reduce severity and frequency of reading symptoms in adults with visual stress. Trial Registration: The trial is registered at clinicaltrials.gov:NCT04318106