bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stiffness pulsation of the human brain detected by non-invasive time-harmonic elastography
Authors: Meyer Tom , Kreft Bernhard , Bergs Judith , Antes Erik , Anders Matthias S. , Wellge Brunhilde , Braun Jürgen , Doyley Marvin , Tzschätzsch Heiko , Sack Ingolf 
Published: August 2023

Introduction: Cerebral pulsation is a vital aspect of cerebral hemodynamics. Changes in arterial pressure in response to cardiac pulsation cause cerebral pulsation, which is related to cerebrovascular compliance and cerebral blood perfusion. Cerebrovascular compliance and blood perfusion influence the mechanical properties of the brain, causing pulsation-induced changes in cerebral stiffness. However, there is currently no imaging technique available that can directly quantify the pulsation of brain stiffness in real time.Methods: Therefore, we developed non-invasive ultrasound time-harmonic elastography (THE) technique for the real-time detection of brain stiffness pulsation. We used state-of-the-art plane-wave imaging for interleaved acquisitions of shear waves at a frequency of 60 Hz to measure stiffness and color flow imaging to measure cerebral blood flow within the middle cerebral artery. In the second experiment, we used cost-effective lineby-line B-mode imaging to measure the same mechanical parameters without flow imaging to facilitate future translation to the clinic.Results: In 10 healthy volunteers, stiffness increased during the passage of the arterial pulse wave from 4.8% ± 1.8% in the temporal parenchyma to 11% ± 5% in the basal cisterns and 13% ± 9% in the brain stem. Brain stiffness peaked in synchrony with cerebral blood flow at approximately 180 ± 30 ms after the cardiac R-wave. Line-by-line THE provided the same stiffness values with similar time resolution as high-end plane-wave THE, demonstrating the robustness of brain stiffness pulsation as an imaging marker.Discussion: Overall, this study sets the background and provides reference values for time-resolved THE in the human brain as a cost-efficient and easy-touse mechanical biomarker associated with cerebrovascular compliance.
Improving mass change estimation in Panama with the GRACE/GFO gravity field using the variational mode decomposition
Authors: Jian Guangyu , Xu Chuang , Yao Chaolong 
Published: August 2023

In this study, we aim to estimate the mass changes in Panama using the Gravity Recovery and Climate Experiment level-2 products, which are formed as spherical harmonic coefficients and limited by stripe noise. The empirical de-striping method and the temporal filter achieved by empirical mode decomposition can be used to reveal the signals but are still limited in signal reservation and noise reduction. To this end, we put forward a novel efficient strategy that uses the variational mode decomposition algorithm to filter the time series of each SHC separately. Based on the two reliable mascon products and in situ short-term groundwater observations, various comparisons in spatial, spectral, and temporal domains are implemented. In addition, the SNR (signal-to-noise ratio) index and the three-cornered hat method are adopted for assessment. The main results and conclusions are as follows: 1) Our filter outperforms the two previous methods with the best SNR (2.14) and the lowest Panama regional uncertainty (70 mm) for all available months. 2) Our estimate of the basin groundwater storage is closest to one of the groundwater observations with the maximum correlation coefficient (0.72, p&lt;0.05). This result suggests that our method seems to detect small-scale mass signals that are undetectable in the two mascon products. Our work provides a reference for studying the mass change of small-scale basins in low latitudes.
Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features
Authors: Shcherbinin Dmitrii S. , Karnaukhov Vadim K. , Zvyagin Ivan V. , Chudakov Dmitriy M. , Shugay Mikhail 
Published: August 2023

IntroductionT-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens. While a large number of TCR sequences specific to different antigenic peptides are known to date, the structural data describing the conformation and contacting residues for TCR-peptide-MHC complexes is relatively limited. In the present study we aim to extend and analyze the set of available structures by performing highly accurate template-based modeling of these complexes using TCR sequences with known specificity. MethodsIdentification of CDR3 sequences and their further clustering, based on available spatial structures, V- and J-genes of corresponding T-cell receptors, and epitopes, was performed using the VDJdb database. Modeling of the selected CDR3 loops was conducted using a stepwise introduction of single amino acid substitutions to the template PDB structures, followed by optimization of the TCR-peptide-MHC contacting interface using the Rosetta package applications. Statistical analysis and recursive feature elimination procedures were carried out on computed energy values and properties of contacting amino acid residues between CDR3 loops and peptides, using R.ResultsUsing the set of 29 complex templates (including a template with SARS-CoV-2 antigen) and 732 specificity records, we built a database of 1585 model structures carrying substitutions in either TCRα or TCRβ chains with some models representing the result of different mutation pathways for the same final structure. This database allowed us to analyze features of amino acid contacts in TCR - peptide interfaces that govern antigen recognition preferences and interpret these interactions in terms of physicochemical properties of interacting residues.ConclusionOur results provide a methodology for creating high-quality TCR-peptide-MHC models for antigens of interest that can be utilized to predict TCR specificity.
Inflammatory biomarkers and delirium: a Mendelian randomization study
Authors: Yu Miao , Li Yuxuan , Li Baohua , Ge Qinggang 
Published: August 2023

BackgroundThe association between inflammatory biomarkers and individual delirium symptoms remains controversial in observational studies. We investigated the relationship between inflammatory biomarkers and the risk of developing delirium.MethodsA bidirectional two-sample Mendelian randomization (MR) was performed. Genetic instruments associated with peripheral tumor necrosis factor-a (TNF-a) C-reactive protein (CRP), interleukin (IL)-1α, IL-1β, IL-2, IL-8, IL-6, soluble IL-6 receptor alpha (sIL-6Rα), and soluble gp130 were identified in three different large summary genome-wide association studies (GWAS) conducted in the European population. Summary-level statistics for delirium not induced by alcohol and other psychoactive substances were obtained from the FinnGen consortium (2,612 cases and 325,306 controls). The estimated causal effects were performed using instruments' variants at the genome-wide significant level (P &lt; 5e-8 and P &lt; 5e-6), applying a linkage disequilibrium clumping approach with a threshold of r2 &lt; 0.001 for each of the exposures. Reverse causation was also performed. The inverse-variance weighted method (IVW), MR-Egger method, weighted median method, MR-Egger regression, and MR Pleiotropy RESidual Sum were used for MR analyses.ResultsAt the genome-wide significant level (P &lt; 5e-8, r2 &lt; 0.001), genetically predicted sIL-6Rα was significantly associated with a decreased risk of delirium with less than three single-nucleotide polymorphisms (SNPs) in all three GWAS data sources (ORWaldratio = 0.89, 95% CI: 0.79–0.96, PWaldratio = 0.0016; ORIVW = 0.88, 95% CI: 0.79–0.97, PIVW = 0.008; ORIVW = 0.88, 95% CI: 0.80–0.96, PIVW = 0.004). The causal relationship between sIL-6Rα and delirium became non-significant when a more liberal threshold of P of &lt; 5e-6 was applied (all PIVW &gt; 0.05). At the two genome-wide significance levels (P &lt; 5e-8 and P &lt; 5e-6), we found no evidence for the causal effects of peripheral TNF-α, CRP, IL-1α, IL-1β, IL-2, IL-6, IL-8, and soluble gp130 on delirium (all P &gt; 0.05). The MR-Egger intercept and MR-PRESSO results indicated that no SNP had possible pleiotropy (all P &gt; 0.05). Regarding the reverse, no evidence for an effect of delirium on these inflammatory biomarkers could be found (all P &gt; 0.05).ConclusionThe results of this MR analysis did not support that peripheral TNF-α, CRP, IL-1α, IL-1β, IL-2, IL-6, sIL-6Rα, soluble gp130, and IL-8 were causally associated with delirium. More research is needed to explore the role of inflammatory factors in the pathogenesis of delirium.
Quantitative analysis of the optogenetic excitability of CA1 neurons
Authors: Schoeters Ruben , Tarnaud Thomas , Weyn Laila , Joseph Wout , Raedt Robrecht , Tanghe Emmeric 
Published: August 2023

IntroductionOptogenetics has emerged as a promising technique for modulating neuronal activity and holds potential for the treatment of neurological disorders such as temporal lobe epilepsy (TLE). However, clinical translation still faces many challenges. This in-silico study aims to enhance the understanding of optogenetic excitability in CA1 cells and to identify strategies for improving stimulation protocols.MethodsEmploying state-of-the-art computational models coupled with Monte Carlo simulated light propagation, the optogenetic excitability of four CA1 cells, two pyramidal and two interneurons, expressing ChR2(H134R) is investigated.Results and discussionThe results demonstrate that confining the opsin to specific neuronal membrane compartments significantly improves excitability. An improvement is also achieved by focusing the light beam on the most excitable cell region. Moreover, the perpendicular orientation of the optical fiber relative to the somato-dendritic axis yields superior results. Inter-cell variability is observed, highlighting the importance of considering neuron degeneracy when designing optogenetic tools. Opsin confinement to the basal dendrites of the pyramidal cells renders the neuron the most excitable. A global sensitivity analysis identified opsin location and expression level as having the greatest impact on simulation outcomes. The error reduction of simulation outcome due to coupling of neuron modeling with light propagation is shown. The results promote spatial confinement and increased opsin expression levels as important improvement strategies. On the other hand, uncertainties in these parameters limit precise determination of the irradiance thresholds. This study provides valuable insights on optogenetic excitability of CA1 cells useful for the development of improved optogenetic stimulation protocols for, for instance, TLE treatment.
A weighted cranial diffusion-weighted imaging scale for Wilson’s disease
Authors: Wang Shi-jing , Geng Hao , Cheng Si-rui , Xu Chen-chen , Zhang Rui-qi , Wang Yu , Wu Tong , Li Bo , Wang Tao , Han Yong-sheng , Ding Zeng-hui , Sun Yi-ning , Wang Xun , Han Yong-zhu , Cheng Nan 
Published: August 2023

ObjectivesCranial magnetic resonance imaging (MRI) could be a crucial tool for the assessment for neurological symptoms in patients with Wilson’s disease (WD). Diffusion-weighted imaging (DWI) hyperintensity reflects the acute brain injuries, which mainly occur in specific brain regions. Therefore, this study aimed to develop a weighted cranial DWI scale for patients with WD, with special focus on specific brain regions.Materials and methodsIn total, 123 patients with WD were enrolled, 118 of whom underwent 1.5 T-MRI on admission. The imaging score was calculated as described previously and depended on the following sequences: one point was acquired when abnormal intensity occurred in the T1, T2, and fluid-attenuation inversion recovery sequences, and two points were acquired when DWI hyperintensity were found. Consensus weighting was conducted based on the symptoms and response to treatment.ResultsIntra-rater agreement were good (r = 0.855 [0.798–0.897], p &lt; 0.0001). DWI hyperintensity in the putamen was a high-risk factor for deterioration during de-copper therapy (OR = 8.656, p &lt; 0.05). The high-risk factors for readmission for intravenous de-copper therapies were DWI hyperintensity in the midbrain (OR = 3.818, p &lt; 0.05) and the corpus callosum (OR = 2.654, p &lt; 0.05). Both scoring systems had positive correlation with UWDRS scale (original semi-quantitative scoring system, r = 0.35, p &lt; 0.001; consensus semi-quantitative scoring system, r = 0.351, p &lt; 0.001.). Compared to the original scoring system, the consensus scoring system had higher correlations with the occurrence of deterioration (OR = 1.052, 95%CI [1.003, 1.0103], p &lt; 0.05) and readmission for intravenous de-copper therapy (OR = 1.043, 95%CI [1.001, 1.086], p &lt; 0.05).ConclusionThe predictive performance of the consensus semi-quantitative scoring system for cranial MRI was improved to guide medication, healthcare management, and prognosis prediction in patients with WD. For every point increase in the neuroimaging score, the risk of exacerbations during treatment increased by 5.2%, and the risk of readmission to the hospital within 6 months increased by 4.3%.
Self-regulation learning as active inference: dynamic causal modeling of an fMRI neurofeedback task
Authors: Vargas Gabriela , Araya David , Sepulveda Pradyumna , Rodriguez-Fernandez Maria , Friston Karl J. , Sitaram Ranganatha , El-Deredy Wael 
Published: August 2023

IntroductionLearning to self-regulate brain activity by neurofeedback has been shown to lead to changes in the brain and behavior, with beneficial clinical and non-clinical outcomes. Neurofeedback uses a brain-computer interface to guide participants to change some feature of their brain activity. However, the neural mechanism of self-regulation learning remains unclear, with only 50% of the participants succeeding in achieving it. To bridge this knowledge gap, our study delves into the neural mechanisms of self-regulation learning via neurofeedback and investigates the brain processes associated with successful brain self-regulation.MethodsWe study the neural underpinnings of self-regulation learning by employing dynamical causal modeling (DCM) in conjunction with real-time functional MRI data. The study involved a cohort of 18 participants undergoing neurofeedback training targeting the supplementary motor area. A critical focus was the comparison between top-down hierarchical connectivity models proposed by Active Inference and alternative bottom-up connectivity models like reinforcement learning.ResultsOur analysis revealed a crucial distinction in brain connectivity patterns between successful and non-successful learners. Particularly, successful learners evinced a significantly stronger top-down effective connectivity towards the target area implicated in self-regulation. This heightened top-down network engagement closely resembles the patterns observed in goal-oriented and cognitive control studies, shedding light on the intricate cognitive processes intertwined with self-regulation learning.DiscussionThe findings from our investigation underscore the significance of cognitive mechanisms in the process of self-regulation learning through neurofeedback. The observed stronger top-down effective connectivity in successful learners indicates the involvement of hierarchical cognitive control, which aligns with the tenets of Active Inference. This study contributes to a deeper understanding of the neural dynamics behind successful self-regulation learning and provides insights into the potential cognitive architecture underpinning this process.
The nucleus accumbens functional connectivity in patients with insomnia using resting-state fMRI
Authors: Li Fangjie , Liu Chengyong , Qin Shan , Wang Xiaoqiu , Wan Qingyun , Li Zhuoyuan , Wang Luyao , Yang Huayuan , Jiang Jiehui , Wu Wenzhong 
Published: August 2023

BackgroundThe aim of this study was to investigate the functional abnormalities between the nucleus accumbens (NAc) and the whole brain in individuals with Insomnia Disorder (ID) using resting-state functional magnetic resonance imaging (fMRI). Additionally, the study aimed to explore the underlying neural mechanisms of ID.MethodsWe enrolled 18 participants with ID and 16 normal controls (NC). Resting-state functional connectivity (FC) between the NAc and the whole brain voxels was calculated and compared between the two groups to identify differential brain region. Receiver operating characteristic (ROC) curve analysis was employed to assess the ability of differential features to distinguish between groups. Furthermore, Pearson correlation analysis was performed to examine the relationship between neurocognitive scores and differential features.ResultsThe ID group exhibited significantly reduced FC values in several brain regions, including the right supplementary motor area, the bilateral middle frontal gyrus, the bilateral median cingulate and paracingulate gyri and the left precuneus. The area under the curve (AUC) of the classification model based on FC in these brain regions was 83.3%. Additionally, the abnormal functional changes observed in ID patients were positively correlated with the Fatigue Severity Scale (R = 0.650, p = 0.004).ConclusionThese findings suggest that the NAc may play a crucial role in the diagnosis of ID and could serve as a potential imaging biomarker, providing insights into the underlying neural mechanisms of the disorder.
Postnatal development of extracellular matrix and vascular function in small arteries of the rat
Authors: Nourian Zahra , Hong Kwangseok , Li Min , Castorena-Gonzalez Jorge A. , Martinez-Lemus Luis A. , Clifford Philip S. , Meininger Gerald A. , Hill Michael A. 
Published: August 2023

Introduction: Vascular extracellular matrix (ECM) is dominated by elastic fibers (elastin with fibrillin-rich microfibrils) and collagens. Current understanding of ECM protein development largely comes from studies of conduit vessels (e.g., aorta) while resistance vessel data are sparse. With an emphasis on elastin, we examined whether changes in postnatal expression of arteriolar wall ECM would correlate with development of local vasoregulatory mechanisms such as the myogenic response and endothelium-dependent dilation.Methods: Rat cerebral and mesenteric arteries were isolated at ages 3, 7, 11, 14, 19 days, 2 months, and 2 years. Using qPCR mRNA expression patterns were examined for elastin, collagen types I, II, III, IV, fibrillin-1, and -2, lysyl oxidase (LOX), and transglutaminase 2.Results: Elastin, LOX and fibrillar collagens I and III mRNA peaked at day 11–14 in both vasculatures before declining at later time-points. 3D confocal imaging for elastin showed continuous remodeling in the adventitia and the internal elastic lamina for both cerebral and mesenteric vessels. Myogenic responsiveness in cannulated cerebral arteries was detectable at day 3 with constriction shifted to higher intraluminal pressures by day 19. Myogenic responsiveness of mesenteric vessels appeared fully developed by day 3. Functional studies were performed to investigate developmental changes in endothelial-dependent dilation. Endothelial-dependent dilation to acetylcholine was less at day 3 compared to day 19 and at day 3 lacked an endothelial-derived hyperpolarizing factor component that was evident at day 19.Conclusion: Collectively, in the rat small artery structural remodeling and aspects of functional control continue to develop in the immediate postnatal period.
Heavy metal induced resistance to herbivore of invasive plant: implications from inter- and intraspecific comparisons
Authors: Zhou Yue , Chen Chao , Xiong Yuntao , Xiao Feng , Wang Yi 
Published: August 2023

IntroductionHeavy metals can affect the content of secondary metabolites in plants, which are one of the important defenses of plants against herbivores. However, studies on the effects of heavy metals on secondary metabolites of invasive plants are scarce. Phytolacca americana is an invasive plant in China, which can hyperaccumulate the heavy metal Mn.MethodsThis study used two Mn treatments (control and treatment group) and four species from Phytolacca (including the native and introduced populations of P. americana, its native and exotic congeners in China) to investigate the impact of heavy metal Mn on the invasive ability of P. americana.ResultsThe results show that heavy metal Mn can enhance the inhibitory effect of the introduced populations of P. americana on the growth of herbivore (the weight of herbivore has decreased by 66%), and altered the feeding preferences of herbivore. We also found that heavy metal Mn can significantly increase the content of quantitative resistance in the leaves of the introduced populations of P. americana and is higher than its native populations, native and exotic congeners. In addition, heavy metal Mn caused the quantitative resistance of the exotic congener significantly higher than that of the native congeners.DiscussionIn summary, the heavy metal Mn can increase the content of secondary metabolites in leaves to enhance the interspecific competitive advantage of P. americana and promote its invasion, and also increase the invasion risk of exotic species.
Cryo-attenuated properties of Tilia miqueliana pericarps and seeds
Authors: Wu Yu , Sun Xiao Rui , Peng Chen Yin , Shen Yong Bao , Visscher Anne M. , Pritchard Hugh W. , Wang Ming Zhu , Deng Zhi Yun 
Published: August 2023

IntroductionCryo treatment of dry seeds is known to attenuate the structure of fruit and seed coats, but little is known about the microstructural impacts of such treatment. The seeds of Tilia miqueliana are dispersed within a hard pericarp, the manual removal (hulling) of which is time-consuming and inefficient. Rapid hulling technology is urgently needed for sustainable production and convenience of edible nuts.MethodsWe explored the mechanistic basis of liquid nitrogen (N)-treatment weakening of the pericarp of T. miqueliana fruits using a range of microscopical, biophysical and chemical approaches.ResultsLiquid N treatment (40 s) resulted in lower pericarp contents of cellulose and hemicellulose, and increased amounts of lignin. Profound changes in cell structure and mechanical properties included the emergence of large holes and gaps between the mesocarp and endocarp cells. Also, the toughness of the pericarp decreased, whilst the hardness and brittleness increased, thereby changing the fracture type from ductile to brittle. Liquid N treatment of dry fruits followed by tapping with a hammer, reduced the number of damaged seeds three-fold and pericarp peeling time four-fold compared with manual hulling, whilst seed viability was not negatively affected.DiscussionComparable findings for the efficient and economical removal of hard covering structures from dispersal units of five more species from three other families following liquid N treatment indicates the potential application of our findings to large-scale production of seeds and seedlings for breeding, forestry and conservation/restoration purposes. Furthermore, it introduces a novel concept for postharvest treatment and pre-treatment of deep processing in nuts.