bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interictal epileptic network hubs as a biomarker for automatic localization of the epileptogenic zone: a connectivity and machine learning based analysis of stereo-EEG
Authors: Susi G. , Gozzo F. , Di Giacomo R. , Panzica F. , Duran D. , Spreafico R. , Tassi L. , Varotto G. 
Published: January 2024

ABSTRACTObjectiveThe study was aimed at developing an automatic system, based on complex network analysis and machine learning, to identify interictal network-based biomarkers in patients with drug-resistant focal epilepsy and no visible anatomical lesions candidate for surgery, able to support the localization of the Epileptogenic Zone (EZ) and to further disclose properties of the interictal epileptogenic network.Methods3 min of interictal SEEG signals, recorded in 18 patients with drug-resistant epilepsy, different EZ localization, negative MRI, were analysed. Patients were divided into seizure-free (SF) and non-seizure free (NSF) groups, according to their post-surgical outcome. After a first step of effective connectivity estimation, hubs were defined through the combination of nine graph theory-based indices of centrality. The values of centrality indices related to these hubs were used as input of an ensemble subspace discriminant classifier.ResultsThe proposed procedure was able to automatically localise the EZ with 98% sensitivity and 59% specificity for SF patients. Moreover, our results showed a clear difference between SF and NSF patients, mainly in terms of false positive rate (i.e., the percentage of NEZ leads classified as EZ), which resulted significantly higher in NSF patients. Lastly, the centrality indexes confirmed a different role of the Propagation Zone in NSF and SF groups.SignificanceResults pointed out that network centrality plays a key role in interictal epileptogenic network, even in case of the absence of anatomical alterations and SEEG epileptic abnormalities, and that the combination of connectivity, graph theory, and machine learning analysis can efficiently support interictal EZ localization. These findings also suggest that poorer post-surgical prognosis can be associated with larger connectivity alteration, with wider “hubs”, and with a different involvement of the PZ, thus making this approach a promising biomarker for surgical outcome.Impact statementThe correct localization of the epileptogenic zone is still an unsolved question, mainly based on visual and subjective analysis of electrophysiological recordings, and highly time-consuming due to the needing of ictal recording. This issue is even more critical in patients with negative MRI and extra-temporal EZ localization. The approach proposed in this study represents an innovative and effective tool to reveal interictal epileptogenic network abnormalities, able to support and improve the EZ presurgical identification and to capture differences between poor and good post-surgical outcome
Multifaceted Roles of Histone Lysine Lactylation in Meiotic Gene Dynamics and Recombination
Authors: Zhang Xiaoyu , Liu Yan , Wang Ning 
Published: January 2024

AbstractMale germ cells, which are responsible for producing millions of genetically diverse sperm through meiosis in the testis, rely on lactate as their central energy metabolite. Recent study has revealed that lactate induces epigenetic modification in cells through histone lactylation, a post-translational modification involving the addition of lactyl groups to lysine residues on histones. Here we report dynamic histone lactylation at histone H4-lysine 5 (K5), -K8, and -K12 during meiosis prophase I in mouse spermatogenesis. By profiling genome-wide occupancy of histone H4-K8 lactylation (H4K8la), which peaks at zygotene, our data show that H4K8la mark is observed at the promoters of genes exhibiting active expression with Gene Ontology (GO) functions enriched for meiosis. Notably, our data also demonstrate that H4K8la is closely associated with recombination hotspots, where machinery involved in the processing DNA double-stranded breaks (DSBs), such as SPO11, DMC1, RAD51, and RPA2, is engaged. In addition, H4K8la was also detected at the meiosis-specific cohesion sites (marked by RAD21L and REC8) flanking the recombination hotspots. Collectively, our findings suggest that histone lactylation serves as a novel mechanism through which lactate regulates germ cell meiosis.
Improving Nitrofurantoin Resistance Prediction inEscherichia colifrom Whole Genome Sequence by Integrating NfsA/B Enzyme Assays
Authors: Dulyayangkul Punyawee , Sealey Jordan E , Lee Winnie WY , Satapoomin Naphat , Reding Carlos , Heesom Kate J. , Williams Philip B , Avison Matthew B 
Published: January 2024

AbstractNitrofurantoin resistance inEscherichia coliis primarily caused by mutations damaging two enzymes, NfsA and NfsB. Studies based on small isolate collections with defined nitrofurantoin MICs have found significant random genetic drift innfsAandnfsBmaking it extremely difficult to predict nitrofurantoin resistance from whole genome sequence (WGS) where both genes are not obviously disrupted by nonsense or frameshift mutations or insertional inactivation. Here we report a WGS survey of 200E. colifrom community urine samples, of which 34 were nitrofurantoin resistant. We characterised individual non-synonymous mutations seen innfsAandnfsBamong this collection using complementation cloning and assays of NfsA/B enzyme activity in cell extracts. We definitively identified R203C, H11Y, W212R, A112E, A112T and A122T in NfsA and R121C, Q142H, F84S, P163H, W46R, K57E and V191G in NfsB as amino acid substitutions that reduce enzyme activity sufficiently to cause resistance. In contrast, E58D, I117T, K141E, L157F, A172S, G187D and A188V in NfsA and G66D, M75I, V93A and A174E in NfsB, are functionally silent in this context. We identified that 9/166 (5.4%) of nitrofurantoin susceptible isolates were “pre-resistant”, defined as having loss of function mutations innfsAornfsB. Finally, using NfsA/B enzyme activity assay and proteomics we demonstrated that 9/34 (26.5%) of nitrofurantoin resistant isolates carried functionally wild-typenfsBornfsB/nfsA. In these cases, enzyme activity was reduced through downregulated gene expression. Our biological understanding of nitrofurantoin resistance is greatly improved by this analysis, but is still insufficient to allow its reliable prediction from WGS data.
Resolution of ribosomal stalling by ABCF ATPases YfmR and YkpA/YbiT
Authors: Takada Hiraku , Fujiwara Keigo , Atkinson Gemma C. , Shinobu Chiba , Hauryliuk Vasili 
Published: January 2024

ABSTRACTEfficiency of protein synthesis on the ribosome is strongly affected by the amino acid composition of the assembled amino acid chain. Challenging sequences include proline-rich motifs as well as highly positively and negatively charged amino acid stretches. Members of the F subfamily of ABC ATPases (ABCFs) have been long hypothesised to promote translation of such problematic motifs. In this study we have applied genetics and reporter-based assays to characterise the four housekeeping ABCF ATPases ofBacillus subtilis: YdiF, YfmM, YfmR/Uup and YkpA/YbiT. We show that YfmR cooperates with the translation factor EF-P that promotes translation of Pro-rich motifs. Simultaneous loss of both YfmR and EF-P results in a dramatic growth defect. Surprisingly, this growth defect can be largely suppressed though overexpression of an EF-P variant lacking the otherwise crucial 5-amino-pentanolylated residue K32. Usingin vivoreporter assays, we show that overexpression of YfmR can alleviate ribosomal stalling on Asp-Pro motifs. Finally, we demonstrate that YkpA/YbiT promotes translation of positively and negatively charged motifs but is inactive in resolving ribosomal stalls on proline-rich stretches. Collectively, our results provide insights into the function of ABCF translation factors in modulating protein synthesis inB. subtilis.
Apnea, Intermittent Hypoxemia, and Bradycardia Events Predict Late-Onset Sepsis in Extremely Preterm Infants
Authors: Kausch Sherry L. , Lake Douglas E. , Di Fiore Juliann M. , Weese-Mayer Debra E. , Claure Nelson , Ambalavanan Namasivayam , Vesoulis Zachary A. , Fairchild Karen D. , Dennery Phyllis A. , Hibbs Anna Maria , Martin Richard J. , Indic Premananda , Travers Colm P. , Bancalari Eduardo , Hamvas Aaron , Kemp James S. , Carroll John L. , Moorman J. Randall , Sullivan Brynne A. ,   The Prematurity-Related Ventilatory Control (Pre-Vent) Investigators
Published: January 2024

AbstractObjectivesDetection of changes in cardiorespiratory events, including apnea, periodic breathing, intermittent hypoxemia (IH), and bradycardia, may facilitate earlier detection of sepsis. Our objective was to examine the association of cardiorespiratory events with late-onset sepsis for extremely preterm infants (<29 weeks’ gestational age (GA)) on versus off invasive mechanical ventilation.Study DesignRetrospective analysis of data from infants enrolled in Pre-Vent (ClinicalTrials.govidentifierNCT03174301), an observational study in five level IV neonatal intensive care units. Clinical data were analyzed for 737 infants (mean GA 26.4w, SD 1.71). Monitoring data were available and analyzed for 719 infants (47,512 patient-days), of whom 109 had 123 sepsis events. Using continuous monitoring data, we quantified apnea, periodic breathing, bradycardia, and IH. We analyzed the relationships between these daily measures and late-onset sepsis (positive blood culture >72h after birth and ≥ 5d antibiotics).ResultsFor infants not on a ventilator, apnea, periodic breathing, and bradycardia increased before sepsis diagnosis. During times on a ventilator, increased sepsis risk was associated with longer IH80 events and more bradycardia events before sepsis. IH events were associated with higher sepsis risk, but did not dynamically increase before sepsis, regardless of ventilator status. A multivariable model predicted sepsis with an AUC of 0.783.ConclusionWe identified cardiorespiratory signatures of late-onset sepsis. Longer IH events were associated with increased sepsis risk but did not change temporally near diagnosis. Increases in bradycardia, apnea, and periodic breathing preceded the clinical diagnosis of sepsis.
A prognostic molecular signature of hepatic steatosis is spatially heterogeneous and dynamic in human liver
Authors: Perry Andrew S. , Hadad Niran , Chatterjee Emeli , Ramos Maria Jimenez , Farber-Eger Eric , Roshani Rashedeh , Stolze Lindsay K. , Zhao Shilin , Martens Liesbet , Kendall Timothy J. , Thone Tinne , Amancherla Kaushik , Bailin Samuel , Gabriel Curtis L. , Koethe John , Carr J. Jeffrey , Terry James Greg , Freedman Jane , Tanriverdi Kahraman , Alsop Eric , Keuren-Jensen Kendall Van , Sauld John F.K. , Mahajan Gautam , Khan Sadiya , Colangelo Laura , Nayor Matthew , Fisher-Hoch Susan , McCormick Joseph , North Kari E. , Below Jennifer , Wells Quinn , Abel Dale , Kalhan Ravi , Scott Charlotte , Guilliams Martin , Fallowfield Jonathan A. , Banovich Nicholas E. , Das Saumya , Shah Ravi 
Published: January 2024

SUMMARYMetabolic dysfunction-associated steatotic liver disease (MASLD) prevalence is increasing in parallel with an obesity pandemic, calling for novel strategies for prevention and treatment. We defined a circulating proteome of human MASLD across ≈7000 proteins in ≈5000 individuals from diverse, at-risk populations across the metabolic health spectrum, demonstrating reproducible diagnostic performance and specifying both known and novel metabolic pathways relevant to MASLD (central carbon and amino acid metabolism, hepatocyte regeneration, inflammation, fibrosis, insulin sensitivity). A parsimonious proteomic signature of MASLD was associated with a protection from MASLD and its related multi-system metabolic consequences in >26000 free-living individuals, with an additive effect to polygenic risk. The MASLD proteome was encoded by genes that demonstrated transcriptional enrichment in liver, with spatial transcriptional activity in areas of steatosis in human liver biopsy and dynamicity for select targets in human liver across stages of steatosis. We replicated several top relations from proteomics and spatial tissue transcriptomics in a humanized “liver-on-a-chip” model of MASLD, highlighting the power of a full translational approach to discovery in MASLD. Collectively, these results underscore utility of blood-based proteomics as a dynamic “liquid biopsy” of human liver relevant to clinical biomarker and mechanistic applications.
Prognostic value of echocardiographic velocity time integral ratio post transcatheter edge-to-edge mitral valve repair
Authors: Scalia Isabel G. , Farina Juan M. , Wraith Rachel , Brown Lisa , Abbas Mohammed Tiseer , Pereyra Milagros , Allam Mohamed , Mahmoud Ahmed K. , Kamel Moaz A. , Barry Timothy , Fortuin F. David , Lester Steven J. , Sweeney John , Sell-Dottin Kristen A. , Alkhouli Mohamad , Holmes David R. , Chao Chieh-Ju , Alsidawi Said , Ayoub Chadi , Arsanjani Reza 
Published: January 2024

AbstractObjectiveResidual mitral regurgitation (MR) is frequent after transcatheter edge-to-edge repair (TEER). There is controversy regarding the clinical impact of residual MR and its quantitative assessment by transthoracic echocardiography (TTE), which is often challenging with multiple eccentric jets and artifact from the clip. The utility of the velocity time integral (VTI) ratio between the mitral valve (MV) and left ventricular outflow tract (LVOT), (VTIMV/LVOT), a simple Doppler measurement that increases with MR, has not been assessed post TEER.MethodsBaseline characteristics, clinical outcomes, and TTE data from patients who underwent TEER between 2014 and 2021 across three academic centers were analyzed. Post-procedure TTEs were evaluated for VTIMV/LVOTin the first three months after TEER. One-year outcomes including all-cause and cardiac mortality, major adverse cardiac events, and MV reintervention were compared between patients with high VTIMV/LVOT(≥ 2.5) and low (< 2.5).ResultsIn total, 372 patients were included (mean age 78.7 ± 8.8 years, 68% male, mean pre-TEER ejection fraction of 50.5 ± 14.7%). Follow up TTEs were performed at a median of 37.5 (IQR 30 - 48) days post-procedure. Patients with high VTIMV/LVOThad significantly higher all-cause mortality (HR 2.10, p = 0.003), cardiac mortality (HR 3.03, p = 0.004) and heart failure admissions (HR 2.28, p < 0.001) at one-year post-procedure. There was no association between raised VTIMV/LVOTand subsequent MV reintervention.ConclusionHigh VTIMV/LVOThas clinically significant prognostic value at one year post TEER. This tool could be used to select patients for consideration of repeat intervention.What is already known on this topicResidual mitral valve dysfunction after transcatheter edge-to-edge repair (TEER) is common and associated with poorer clinical outcomes. Quantification and subsequent prognostication are complex and challenging.What this study addsThe ratio of velocity time integral of the mitral valve to left ventricular outflow tract on echocardiography (VTIMV/LVOT) independently predicts risk of all-cause and cardiac mortality and heart failure admissions at one year following TEER.How this study might affect research, practice or policyThese findings may allow for early identification of a high-risk cohort post TEER that may benefit from closer surveillance and more aggressive intervention.
New insights into the domain of unknown function DUF of EccC5, the pivotal ATPase providing the secretion driving force to the ESX5 secretion system
Authors: Ceballos-Zúñiga Fernando , Menéndez Margarita , Pérez-Dorado Inmaculada 
Published: January 2024

SummaryType VII secretion (T7S) systems, also referred to as ESAT6 secretion (ESX) systems, are molecular machines that have gained great attention due to their implication in cell homeostasis and host pathogen interactions in mycobacteria. The latter include important human pathogens such asMycobacterium tuberculosis(Mtb), the etiological cause of human tuberculosis and a pandemic accounting for more than 1 million deaths every year. The ESX5 system is exclusively found in slow-growing pathogenic mycobacteria, where it mediates the secretion of a large family of virulence factors, the PE and PPE proteins. The secretion driving force is provided by EccC5, a multidomain ATPase operating through four globular cytosolic domains, an N-terminal domain of unknown function (EccCDUF) and three FtsK/SpoIIIE ATPase domains. Recent structural and functional studies of ESX3 and ESX5 systems have revealed EccCDUFas an ATPase-like fold domain with potential ATPase activity, and whose functionality is essential for secretion. Here we report the crystal structure ofMtbEccC5DUFdomain at 2.05 Å resolution, which unveils a nucleotide-free structure with degeneratedcis-acting andtrans-acting elements involved in ATP-binding and hydrolysis. Our crystallographic study, together with a biophysical assessment ofMtbEccC5DUFinteraction with ATP/Mg2+, supports the absence of ATPase activity proposed for this domain. We show that this degeneration is also present in DUF domains of other ESX and ESX-like systems, which are likely to exhibit poor or null ATPase activity. Moreover, and based on anin-silicomodel ofMtbEccC5N-terminal region, we propose thatMtbEccC5DUFis a degenerated ATPase domain that may have retained the ability to hexamerise. Observations that call the attention on DUF domains as structural elements with potential implications in the opening and closure of the membrane pore during the secretion process.
Fragmented micro-growth habitats present opportunities for alternative competitive outcomes
Authors: Batsch Maxime , Guex Isaline , Todorov Helena , Heiman Clara M. , Vacheron Jordan , Vorholt Julia A. , Keel Christoph , van der Meer Jan Roelof 
Published: January 2024

AbstractBacteria in nature often proliferate in highly patchy environments, such as soil pores, particles, plant roots or leaves. The resulting spatial fragmentation leads to cells being constrained to smaller habitats, shared with potentially fewer other species. The effects of microhabitats on the emergence of bacterial interspecific interactions are poorly understood, but potentially important for the maintenance of diversity at a larger scale. To study this more in-depth, we contrasted paired species-growth in picoliter droplets at low population census with that in large (macro) population liquid suspended cultures. Four interaction scenarios were imposed by using different bacterial strain combinations and media: substrate competition, substrate independence, growth inhibition, and cell killing by tailocins. In contrast to macro-level culturing, we observed that fragmented growth in picoliter droplets in all cases yielded more variable outcomes, and even reversing the macro-level assumed interaction type in a small proportion of droplet habitats. Timelapse imaging and mathematical simulations indicated that the variable and alternative interaction outcomes are a consequence of founder cell phenotypic variation and small founder population sizes. Simulations further suggested that increased growth kinetic variation may be a crucial selectable property for slower-growing bacterial species to survive competition. Our results thus demonstrate how microhabitat fragmentation enables the proliferation of alternative interaction trajectories and contributes to the maintenance of higher species diversity under substrate competition.
DIB-BOT: An open-source hardware approach for high throughput droplet interface bilayer deposition
Authors: Mason Alexander F , Wickham Shelley FJ , Baker Matthew AB 
Published: January 2024

AbstractDroplet interface bilayers (DIBs) provide a controlled lipid environment for the single-molecule investigation of a range of biologically relevant membrane-bound processes and have garnered attention for their potential applications in bottom-up artificial cells, biosensing, and biophysics. However, the fabrication of DIBs is currently hindered by time-consuming processes and specialized equipment. These fabrication limitations prevent the scale-up of DIB assays, making it difficult to generate the large data sets required to achieve statistically significant conclusions in single-molecule biological assays where heterogeneous behaviour is often observed. This research describes an open-source solution, dubbed “DIB-BOT,” constructed by coupling a nanoinjector with an entry-level 3D printer. We present DIB-BOT as a platform to achieve rapid, reproducible, and reliable fabrication of large numbers of DIBs, addressing the limitations of manual methods. Leveraging commercially available off-the-shelf components, DIB-BOT exhibits high spatial reproducibility, minimal user input, and the ability to scale experiments rapidly. Here we demonstrate the utility of the system by integrating pairwise droplet assembly with a fluorescence plate-reader to execute a biologically relevant assay. When compared with manual DIB fabrication, the DIB-BOT had a tenfold reduction in droplet volume error, a threefold reduction in positional error, and 100% droplet yield. Overall, this method has potential to reduce entry barriers to the use of DIB methods, broadening the applications of DIB research, and generating higher quality data sets.
Usutu virus and West Nile virus use a transcellular route of neuroinvasion across anin vitromodel of the human blood-brain barrier
Authors: Marshall Eleanor M. , Koopmans Marion , Rockx Barry 
Published: January 2024

ABSTRACTWest Nile virus (WNV) leads to thousands of cases of severe neurological disease in humans each year. Usutu virus (USUV) is closely related to WNV, but rarely induces disease in humans. We hypothesised that USUV is less able to cross the blood-brain barrier, and is therefore less likely to infect the brain. Therefore, we developed anin vitroBBB model consisting of primary human brain microvascular endothelial cells (BMECs), pericytes and astrocytes. Both USUV and WNV invaded across thein vitroBBB via a transcellular mechanism in absence of barrier disruption. USUV replicated to lower titres than WNV but induced a comparable cytokine and chemokine response, with modulation of key factors associated with barrier function and immune-cell migration. In conclusion, USUV appears attenuated in its ability to replicate at this interface compared with WNV, but further work must to done to identify key determinants underlying the differing clinical presentations.
mTORC3 activity is regulated by GSK3β through the activation of PKCδ that phosphorylates and activates STAT1
Authors: Zhan Jun , Harwood Frank C. , Cardone Monica , Grosveld Gerard C. 
Published: January 2024

AbstractThe mechanistic target of rapamycin serine/threonine kinase (mTOR), a critical regulator of cell proliferation, is implicated in many human diseases, including cancer. Our laboratory recently discovered a new mTOR complex, called mTORC3, distinct from the two canonical mTOR complexes, mTORC1, and mTORC2, which causes accelerated proliferation and increased malignancy of cancer cells. Understanding how mTORC3 is controlled is an important approach to designing cancer therapies targeting mTORC3. Having investigated how mTORC3 activity was affected by glycogen synthase kinase-3β (GSK3β), a known regulator of mTOR activity, we found that cells do not assemble mTORC3 upon GSK3β knockout, due to extinguished expression of ETV7, an essential component of the mTORC3 complex. We discovered that the lack of ETV7 expression resulted from reduced phosphorylation of serine 727 (S727) of the Signal Transducer and Activator of Transcription 1 (STAT1), which is required for transcriptional activation of ETV7. Finally, we identified that GSK3β through PKCδ phosphorylates STAT1-S727. Together, we identified a novel GSK3β/PKCδ/ STAT1 pathway in Karpas cells that regulates ETV7 transcription, thus positively regulating mTORC3 activity. The identification of this signaling pathway could benefit the therapeutic design for numerous diseases including cancer.