bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noninvasive assessment of intracranial pressure using subharmonic-aided pressure estimation: An experimental study in canines
Authors: Zheng Shuai , Zhang Yanfen , Cheng Linggang , Wang Hongbin , Li Rui , Chen Zhiguang , Zhang Yukang , He Wen , Zhang Wei 
Published: June 2022

BACKGROUND
Intracranial hypertension is a common clinicopathological syndrome in neurosurgery, and a timely understanding of the intracranial pressure (ICP) may help guide clinical treatment. We aimed to investigate the correlation between subharmonic contrast-enhanced ultrasound (SHCEUS) parameters and ICP in experimental canines.

METHODS
A dynamic model of ICP change from 11 mm Hg to 50 mm Hg was established in experimental canines by placing a latex balloon into the epidural space and injecting saline into the balloon. In addition, a pressure sensor was placed in the brain parenchyma to record the changes in ICP. When the ICP stabilized after each increase, subharmonic-aided pressure estimation (SHAPE) technology was performed to obtain the SHCEUS parameters, including the basal venous and adjacent intracranial arterial subharmonic amplitude and SHAPE gradient (subharmonic amplitude in the intracranial artery minus that in the basal vein). The correlation between these parameters and ICP was analyzed.

RESULTS
The subharmonic amplitude of the basal vein was negatively correlated with the ICP (r = −0.798), and the SHAPE gradient was positively correlated with the ICP (r = 0.628). According to the guidelines for ICP monitoring in patients with traumatic brain injury, we defined 20 mm Hg, 25 mm Hg, and 30 mm Hg as the cutoff ICP levels. The area under the receiver operating characteristic curve of the basal venous subharmonic amplitude for diagnosing intracranial hypertension ≥20 mm Hg, ≥25 mm Hg, and ≥30 mm Hg was 0.867 (95% confidence interval [CI], 0.750–0.943), 0.884 (95% CI, 0.770–0.954), and 0.875 (95% CI, 0.759–0.948), respectively. The area under the receiver operating characteristic curve of the SHAPE gradient for diagnosing intracranial hypertension ≥20 mm Hg, ≥25 mm Hg, and ≥30 mm Hg was 0.839 (95% CI, 0.716–0.924), 0.842 (95% CI, 0.720–0.926), and 0.794 (95% CI, 0.665–0.890), respectively.

CONCLUSION
SHCEUS parameters are correlated with ICP. The SHAPE technique can assist in evaluating ICP changes in canines, which provides a new idea and method for evaluating ICP.
Plasma-based assays distinguish hyperfibrinolysis and shutdown subgroups in trauma-induced coagulopathy
Authors: Lawson Michael A. , Holle Lori A. , Dow Nathan E. , Hennig Grant , de Laat Bas , Moore Hunter B. , Moore Ernest E. , Cohen Mitchell J. , Bouchard Beth A. , Freeman Kalev , Wolberg Alisa S. 
Published: June 2022

BACKGROUND
Trauma patients with abnormal fibrinolysis have increased morbidity and mortality. Knowledge of mechanisms differentiating fibrinolytic phenotypes is important to optimize treatment. We hypothesized that subjects with abnormal fibrinolysis identified by whole blood viscoelastometry can also be distinguished by plasma thrombin generation, clot structure, fibrin formation, and plasmin generation measurements.

METHODS
Platelet-poor plasma (PPP) from an observational cross-sectional trauma cohort with fibrinolysis shutdown (% lysis at 30 minutes [LY30] < 0.9, n = 11) or hyperfibrinolysis (LY30 > 3%, n = 9) defined by whole blood thromboelastography were studied. Noninjured control subjects provided comparative samples. Thrombin generation, fibrin structure and formation, and plasmin generation were measured by fluorescence, confocal microscopy, turbidity, and a fluorescence-calibrated plasmin assay, respectively, in the absence/presence of tissue factor or tissue plasminogen activator (tPA).

RESULTS
Whereas spontaneous thrombin generation was not detected in PPP from control subjects, PPP from hyperfibrinolysis or shutdown patients demonstrated spontaneous thrombin generation, and the lag time was shorter in hyperfibrinolysis versus shutdown. Addition of tissue factor masked this difference but revealed increased thrombin generation in hyperfibrinolysis samples. Compared with shutdown, hyperfibrinolysis PPP formed denser fibrin networks. In the absence of tPA, the fibrin formation rate was faster in shutdown than hyperfibrinolysis, but hyperfibrinolysis clots lysed spontaneously; these differences were masked by addition of tPA. Tissue plasminogen activator–stimulated plasmin generation was similar in hyperfibrinolysis and shutdown samples. Differences in LY30, fibrin structure, and lysis correlated with pH.

CONCLUSION
This exploratory study using PPP-based assays identified differences in thrombin generation, fibrin formation and structure, and lysis in hyperfibrinolysis and shutdown subgroups. These groups did not differ in their ability to promote tPA-triggered plasmin generation. The ability to characterize these activities in PPP facilitates studies to identify mechanisms that promote adverse outcomes in trauma.

LEVEL OF EVIDENCE
Prognostic/Epidemiological; Level III.
Experimental Models of Ischemic Lung Damage for the Study of Therapeutic Reconditioning During Ex Vivo Lung Perfusion
Authors: Parapanov Roumen , Wang Xingyu , Wang Yabo , Debonneville Anne , Lugrin Jérôme , Liaudet Lucas , Krueger Thorsten 
Published: June 2022

Background.
Ex vivo lung perfusion (EVLP) may allow therapeutic reconditioning of damaged lung grafts before transplantation. This study aimed to develop relevant rat models of lung damage to study EVLP therapeutic reconditioning for possible translational applications.

Methods.
Lungs from 31 rats were exposed to cold ischemia (CI) or warm ischemia (WI), inflated at various oxygen fractions (FiO2), followed by 3 h EVLP. Five groups were studied as follow: (1) C21 (control): 3 h CI (FiO2 0.21); (2) C50: 3 h CI (FiO2 0.5); (3) W21: 1 h WI, followed by 2 h CI (FiO2 0.21); (4) W50: 1 h WI, followed by 2 h CI (FiO2 0.5); and (5) W2h: 2 h WI, followed by 1 h CI (FiO2 0.21). Following 3 h EVLP, we measured static pulmonary compliance (SPC), pulmonary vascular resistance, lung weight gain (edema), oxygenation capacity (differential partial pressure of oxygen), and protein carbonyls in lung tissue (oxidative stress), as well as lactate dehydrogenase (LDH, lung injury), nitrotyrosine (nitro-oxidative stress), interleukin-6 (IL-6, inflammation), and proteins (permeability edema) in bronchoalveolar lavage (BAL). Perivascular edema was quantified by histology.

Results.
No significant alterations were noted in C21 and C50 groups. W21 and W50 groups had reduced SPC and disclosed increased weight gain, BAL proteins, nitrotyrosine, and LDH. These changes were more severe in the W50 group, which also displayed greater oxidative stress. In contrast, both W21 and W50 showed comparable perivascular edema and BAL IL-6. In comparison with the other WI groups, W2h showed major weight gain, perivascular edema, SPC reduction, drop of differential partial pressure of oxygen, and massive increases of BAL LDH and proteins but comparable increase of IL-6 and biomarkers of oxidative stress.

Conclusions.
These models of lung damage of increasing severity might be helpful to evaluate new strategies for EVLP therapeutic reconditioning. A model combining 1 h WI and inflation at FiO2 of 0.5 seems best suited for this purpose by reproducing major alterations of clinical lung ischemia-reperfusion injury.
MELD-GRAIL and MELD-GRAIL-Na Are Not Superior to MELD or MELD-Na in Predicting Liver Transplant Waiting List Mortality at a Single-center Level
Authors: Chetwood John D. , Wells Mark V. , Tsoutsman Tatiana , Pulitano Carlo , Crawford Michael D. , Liu Ken , Strasser Simone I. , McCaughan Geoffrey W. , Majumdar Avik 
Published: June 2022

Background.
Controversy exists regarding the best predictive model of liver transplant waiting list (WL) mortality. Models for end-stage liver disease–glomerular filtration rate assessment in liver disease (MELD-GRAIL) and MELD-GRAIL-Na were recently described to provide better prognostication, particularly in females. We evaluated the performance of these scores compared to MELD and MELD-Na.

Methods.
Consecutive patients with cirrhosis waitlisted for liver transplant from 1998 to 2017 were examined in this single-center study. The primary outcome was 90-d WL mortality. MELD, MELD-Na, MELD-GRAIL, and MELD-GRAIL-Na at the time of WL registration were compared. Model discrimination was assessed with area under the receiver operating characteristic curves and Harrell’s C-index after fitting Cox models. Model calibration was examined with Grønnesby and Borgan’s modification of the Hosmer-Lemeshow formula and by comparing predicted/observed outcomes across model strata.

Results.
The study population comprised 1108 patients with a median age of 53.5 (interquartile range 48–59) y and male predominance (74.9%). All models had excellent areas under the receiver operating characteristic curves for the primary outcome (MELD 0.89, MELD-Na 0.91, MELD-GRAIL 0.89, MELD-GRAIL-Na 0.89; all comparisons P > 0.05). Youden index cutoffs for 90-d mortality were as follows: MELD, 19; MELD-Na, 22; MELD-GRAIL, 18; and MELD-GRAIL-Na, 17. Variables associated with 90-d mortality on multivariable Cox regression were sodium, bilirubin, creatinine, and international normalized ratio. There were no differences in model discrimination using Harrell’s C-index. All models were well calibrated; however, divergence between observed and predicted mortality was noted with scores ≥25.

Conclusion.
There were no demonstrable differences in discrimination or calibration of GRAIL-based models compared with MELD or MELD-Na in our cohort. This suggests that GRAIL-based models may not have meaningful improvements in discriminatory ability when applied to other settings.
Conserved reduction of m6A marks during aging and neurodegeneration is linked to altered translation of synaptic transcripts
Authors: Castro-Hernández Ricardo , Berulava Tea , Metelova Maria , Epple Robert , Centeno Tonatiuh Peña , Sakib M Sadman , Burkhart Susanne , Ninov Momchil , Bohnsack Katherine E. , Bohnsack Markus T. , Delalle Ivana , Fischer Andre 
Published: June 2022

AbstractN6-methyladenosine (m6A) plays diverse roles in the regulation of mRNA metabolism. In the mammalian brain it has been linked to developmental processes and memory function. However, the precise role of m6A in the context synaptic plasticity and especially during impaired cognition are not fully understood. Here, we describe the mouse and human brain m6A epi-transcriptome in a tissue-specific manner. We furthermore show that m6A levels undergo a massive decrease across mouse brain regions as a consequence of aging. In addition, Alzheimer's disease in humans correlates with decreased N6-methylation in a similar population of transcripts that are linked to synaptic function and localized to synapses, such as the calcium/calmodulin-dependent kinase II (CaMKII). We furthermore show that reduced m6A levels impair synaptic protein-synthesis of CAMKII. Our results suggest that m6A-RNA-methylation is an important mechanism to control synaptic protein synthesis which is affected early in cognitive diseases.Significance statementThe addition of N6-methyladenosine (m6A) to RNA plays a role in various cellular processes and its de-regulation has been linked to several devastating diseases. The precise role of m6A RNA-methylation in the adult brain is, however, not well understood. In our study, we describe the genome-wide m6A epi-transcriptome in the healthy and diseased brains of mice and humans. Our data demonstrate that a substantial amount of m6A transcripts are conserved. These transcripts are linked to the regulation of synaptic processes and are localized to synapses. In the diseases brain we detect RNA hypomethylation across multiple transcripts in all investigated brain regions and across species. At the mechanistic level we find that reduced m6A levels specifically impairs synaptic protein-synthesis.
Analysis of task-related MEG functional brain networks using dynamic mode decomposition
Authors: Partamian Hmayag , Tabbal Judie , Hassan Mahmoud , Karameh Fadi 
Published: June 2022

AbstractObjectiveFunctional connectivity networks explain the different brain states during diverse motor, cognitive, and sensory functions. Extracting spatial network configurations and their temporal evolution is crucial for understanding the brain function during diverse behavioral tasks.ApproachIn this study, we introduce the use of dynamic mode decomposition (DMD) to extract the dynamics of brain networks. We compared DMD with principal component analysis (PCA) using real magnetoencephalography (MEG) data during motor and memory tasks.Main ResultsThe framework generates dominant spatial brain networks and their time dynamics during simple tasks, such as button press and left-hand movement, as well as more complex tasks, such as picture naming and memory tasks. Our findings show that the DMD-based approach provides a better temporal resolution than the PCA-based approach.SignificanceWe believe that DMD has a very high potential for deciphering the spatiotemporal dynamics of electrophysiological brain network states during tasks.
Exploiting the mediating role of the metabolome to unravel transcript-to-phenotype associations
Authors: Auwerx Chiara , Sadler Marie C. , Reymond Alexandre , Kutalik Zoltán , Porcu Eleonora 
Published: June 2022

AbstractDespite the success of genome-wide association studies (GWASs) in identifying genetic variants associated with complex traits, understanding the mechanisms behind these statistical associations remains challenging. Several methods that integrate methylation, gene expression, and protein quantitative trait loci (QTLs) with GWAS data to determine their causal role in the path from genotype to phenotype have been proposed. Here, we developed and applied a multi-omics Mendelian randomization (MR) framework to study how metabolites mediate the effect of gene expression on complex traits. We identified 206 transcript-metabolite-trait causal triplets for 28 medically relevant phenotypes. Sixty-seven of these associations were missed by classical transcriptome-wide MR, which only uses gene expression and GWAS data. Among these, we identify biologically relevant pathways, such as betweenANKHand calcium levels mediated by citrate andSLC6A12and serum creatinine through modulation of the levels of the renal osmolyte betaine. We show that the signals missed by transcriptome-wide MR are found thanks to the gain in power allowed by integrating multiple omics-layer. Simulation analyses show that with larger molecular QTL studies and in case of mediated effects, our multi-omics MR framework outperforms classical MR approaches designed to detect causal relationships between single molecular traits and complex phenotypes.
Human pericytes degrade α-synuclein aggregates in a strain-dependent manner
Authors: Dieriks Birger Victor , Highet Blake , Alik Ania , Bellande Tracy , Stevenson Taylor J. , Low Victoria , Park Thomas I-H , Correia Jason , Schweder Patrick , Faull Richard L. M. , Melki Ronald , Curtis Maurice A. , Dragunow Mike 
Published: June 2022

ABSTRACTParkinson’s disease (PD) is a progressive, neurodegenerative disorder characterised by the abnormal accumulation of α-synuclein (α-syn) aggregates. Central to disease progression is the gradual spread of pathological α-syn. α-syn aggregation is closely linked to progressive neuron loss. As such, clearance of α-syn aggregates may slow the progression of PD and lead to less severe symptoms. Evidence that non-neuronal cells play a role in PD and other synucleinopathies such as Lewy body dementia and multiple system atrophy are increasing. Our previous work has shown that pericytes — vascular mural cells that regulate the blood-brain barrier — contain α-syn aggregates in human PD brains. Here, we demonstrate that pericytes efficiently internalise fibrillar α-syn irrespective of being in a monoculture or mixed neuronal cell culture. Pericytes efficiently break down α-syn aggregates in vitro, with clear differences in the number of α-syn aggregates/cell and average aggregate size when comparing five pure α-syn strains (Fibrils, Ribbons, fibrils65, fibrils91 and fibrils110). Furthermore, pericytes derived from PD brains have a less uniform response than those derived from control brains. Our results highlight the vital role brain vasculature may play in reducing α-syn burden in PD.
Convergent approaches to delineate the metabolic regulation of tumor invasion by hyaluronic acid biosynthesis
Authors: Shimpi Adrian A. , Tan Matthew L. , Vilkhovoy Michael , Dai David , Roberts L. Monet , Kuo Joe , Huang Lingting , Varner Jeffrey D. , Paszek Matthew , Fischbach Claudia 
Published: June 2022

AbstractMetastasis is the leading cause of breast cancer-related deaths and often driven by invasion and cancer-stem like cells (CSCs). Both the CSC phenotype and invasion have been associated with increased hyaluronic acid (HA) production. How these independent observations are connected, and which role metabolism plays in this process remains unclear due in part to the lack of convergent approaches that integrate engineered model systems, computational tools, and cancer biology. Using microfluidic invasion models, metabolomics, computational flux balance analysis (FBA), and bioinformatic analysis of patient data we investigated the functional links between the stem-like, invasive, and metabolic phenotype of breast cancer cells as a function of HA biosynthesis. Our results suggest that CSCs are more invasive than non-CSCs and that broad metabolic changes caused by overproduction of HA play a role in this process. Accordingly, overexpression of hyaluronic acid synthases (HAS) 2 or 3 induced a metabolic phenotype that promoted breast cancer cell stemness and invasion in vitro and upregulated a transcriptomic signature that was predictive of increased invasion and worse survival in patients. Collectively, this study suggests that HA overproduction leads to metabolic adaptations that help satisfy the energy demands necessary for 3D invasion of breast cancer stem cells further highlighting the importance of engineered model systems and multidisciplinary approaches in cancer research.
Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP
Authors: Lorenz Daniel A. , Shen Kylie A. , Her Hsuan-Lin , Rothamel Katie , Hutt Kasey R. , Nojadera Allan C. , Bruns Stephanie C. , Manakov Sergei A. , Chapman Karen B. , Yeo Gene W. 
Published: June 2022

AbstractUV cross-linking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the current enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the ability to process many RBPs in parallel. We present a new method termed antibody-barcode eCLIP (ABC) that utilizes DNA-barcoded antibodies and proximity ligation of the DNA oligonucleotides to RBP-protected RNA fragments to interrogate multiple RBPs simultaneously. We observe performance comparable to eCLIP with the advantage of a reduced hands-on time of 2 days and dramatically increased scaling while minimizing sample-to-sample variation and maintaining the same material requirement of a single eCLIP experiment.
Metallo-Supramolecular Branched Polymer Protects Particles from Air-water Interface in Single-Particle Cryo-Electron Microscopy
Authors: Xu Yixin , Qin Yuqi , Wang Lang , Zhang Yingyi , Wang Yufeng , Dang Shangyu 
Published: June 2022

AbstractRecent technological breakthroughs in single-particle cryo-electron microscopy (cryo-EM) enabled rapid atomic structure determination of biological macromolecules. A major bottleneck in the current single particle cryo-EM pipeline is the preparation of good quality frozen cryo-EM grids, which is mostly a trial-and-error process. Among many issues, preferred particle orientation and sample damage by air-water interface (AWI) are common practical problems. Here we reported a method of applying metallo-supramolecular branched polymer (MSBP) in the cryo-sample preparation for high-resolution single-particle cryo-EM. Our data shows that MSBP keeps a majority of particles away from air-water interface and mitigates preferred orientation as verified by the analyses of apoferritin, hemagglutinin (HA) trimer and various sample proteins. The use of MSBP is a simple method to improve particle distribution for high-resolution structure determination in single-particle cryo-EM.
Rotavirus spike protein VP4 mediates viroplasm assembly by association to actin filaments
Authors: Vetter Janine , Papa Guido , Seyffert Michael , Gunasekera Kapila , Lorenzo Giuditta De , Wiesendanger Mahesa , Reymond Jean-Louis , Fraefel Cornel , Burrone Oscar R. , Eichwald Catherine 
Published: June 2022

AbstractThe formation of viroplasms is a well-conserved step in the rotavirus (RV) life cycle. In these structures, both virus genome replication and progeny assembly take place. A stabilized microtubule cytoskeleton and lipid droplets are required for the viroplasm formation, which involves several virus proteins. The viral spike protein VP4 has not previously been shown to have a direct role in viroplasm formation. However, it is involved with virus-cell attachment, endocytic internalization, and virion morphogenesis. Moreover, VP4 interacts with actin cytoskeleton components, mainly in processes involving virus entrance and egress, and thereby may have an indirect role in viroplasm formation. In this study, we used reverse genetics to construct a recombinant RV, rRV/VP4-BAP, which contains a biotin acceptor peptide (BAP) in the K145-G150 loop of the VP4 lectin domain, permitting live monitoring. The recombinant virus was replication competent but showed a reduced fitness. We demonstrate that rRV/VP4-BAP infection, as opposed to rRV/wt infection, did not lead to a reorganized actin cytoskeleton as viroplasms formed were insensitive to drugs that depolymerize actin and inhibit myosin. Moreover, wt VP4, but not VP4-BAP, appeared to associate with actin filaments. Similarly, VP4 in co-expression with NSP5 and NSP2 induced a significant increase in the number of viroplasm-like structures. Interestingly, a small peptide mimicking loop K145-G150 rescued the phenotype of rRV/VP4-BAP by increasing its ability to form viroplasms and hence, improve virus progeny formation. Collectively, these results provide a direct link between VP4 and the actin cytoskeleton to catalyze viroplasm assembly.IMPORTANCEThe spike protein VP4 participates in diverse steps of the rotavirus (RV) life cycle, including virus-cell attachment, internalization, modulation of endocytosis, virion morphogenesis, and virus egress. Using reverse genetics, we constructed for the first time a recombinant RV, rRV/VP4-BAP, harboring a heterologous peptide in the lectin domain (loop K145-G150) of VP4. The rRV/VP4-BAP was replication-competent but with reduced fitness due to a defect in the ability to reorganize the actin cytoskeleton, which affected the efficiency of viroplasm assembly. This defect was rescued by adding a permeable small-peptide mimicking the wild-type VP4 loop K145-G150. In addition to revealing a new role of VP4, our findings suggest that rRV harboring an engineered VP4 could be used as a new dual vaccination platform providing immunity against RV and additional heterologous antigens.