bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations of stress and stress-related psychiatric disorders with GrimAge acceleration: review and suggestions for future work
Authors: Protsenko Ekaterina , Wolkowitz Owen M. , Yaffe Kristine 
Published: May 2023

AbstractThe notion of “biological aging” as distinct from chronological aging has been of increasing interest in psychiatry, and many studies have explored associations of stress and psychiatric illness with accelerated biological aging. The “epigenetic clocks” are one avenue of this research, wherein “biological age” is estimated using DNA methylation data from specific CpG dinucleotide sites within the human genome. Many iterations of the epigenetic clocks have been developed, but the GrimAge clock continues to stand out for its ability to predict morbidity and mortality. Several studies have now explored associations of stress, PTSD, and MDD with GrimAge acceleration (GrimAA). While stress, PTSD, and MDD are distinct psychiatric entities, they may share common mechanisms underlying accelerated biological aging. Yet, no one has offered a review of the evidence on associations of stress and stress-related psychopathology with GrimAA. In this review, we identify nine publications on associations of stress, PTSD, and MDD with GrimAA. We find that results are mixed both within and across each of these exposures. However, we also find that analytic methods — and specifically, the choice of covariates — vary widely between studies. To address this, we draw upon popular methods from the field of clinical epidemiology to offer (1) a systematic framework for covariate selection, and (2) an approach to results reporting that facilitates analytic consensus. Although covariate selection will differ by the research question, we encourage researchers to consider adjustment for tobacco, alcohol use, physical activity, race, sex, adult socioeconomic status, medical comorbidity, and blood cell composition.
Metabolism-based targeting of MYC via MPC-SOD2 axis-mediated oxidation promotes cellular differentiation in group 3 medulloblastoma
Authors: Martell Emma , Kuzmychova Helgi , Kaul Esha , Senthil Harshal , Chowdhury Subir Roy , Morrison Ludivine Coudière , Fresnoza Agnes , Zagozewski Jamie , Venugopal Chitra , Anderson Chris M. , Singh Sheila K. , Banerji Versha , Werbowetski-Ogilvie Tamra E. , Sharif Tanveer 
Published: May 2023

AbstractGroup 3 medulloblastoma (G3 MB) carries the worst prognosis of all MB subgroups. MYC oncoprotein is elevated in G3 MB tumors; however, the mechanisms that support MYC abundance remain unclear. Using metabolic and mechanistic profiling, we pinpoint a role for mitochondrial metabolism in regulating MYC. Complex-I inhibition decreases MYC abundance in G3 MB, attenuates the expression of MYC-downstream targets, induces differentiation, and prolongs male animal survival. Mechanistically, complex-I inhibition increases inactivating acetylation of antioxidant enzyme SOD2 at K68 and K122, triggering the accumulation of mitochondrial reactive oxygen species that promotes MYC oxidation and degradation in a mitochondrial pyruvate carrier (MPC)-dependent manner. MPC inhibition blocks the acetylation of SOD2 and oxidation of MYC, restoring MYC abundance and self-renewal capacity in G3 MB cells following complex-I inhibition. Identification of this MPC-SOD2 signaling axis reveals a role for metabolism in regulating MYC protein abundance that has clinical implications for treating G3 MB.
Dynamic evolution of the active center driven by hemilabile coordination in Cu/CeO2 single-atom catalyst
Authors: Chen Zheng , Liu Zhangyun , Xu Xin 
Published: May 2023

AbstractHemilability is an important concept in homogeneous catalysis where both the reactant activation and the product formation can occur simultaneously through a reversible opening and closing of the metal-ligand coordination sphere. However, this effect has rarely been discussed in heterogeneous catalysis. Here, by employing a theoretical study on CO oxidation over substituted Cu1/CeO2 single atom catalysts, we show that dynamic evolution of metal-support coordination can significantly change the electronic structure of the active center. The evolution of the active center is shown to either strengthen or weaken the metal-adsorbate bonding as the reaction proceeds from reactants, through intermediates, to products. As a result, the activity of the catalyst can be increased. We explain our observations by extending hemilability effects to single atom heterogenous catalysts and anticipate that introducing this concept can offer a new insight into the important role active site dynamics have in catalysis toward the rational design of more sophisticated single atom catalyst materials.
From individual elements to macroscopic materials: in search of new superconductors via machine learning
Authors: Pereti Claudio , Bernot Kevin , Guizouarn Thierry , Laufek František , Vymazalová Anna , Bindi Luca , Sessoli Roberta , Fanelli Duccio 
Published: May 2023

AbstractAn approach to supervised classification and regression of superconductive materials is proposed which builds on the DeepSet technology. This enables us to provide the chemical constituents of the examined compounds as an input to the algorithm, while avoiding artefacts that could originate from the chosen ordering in the list. The performance of the method are successfully challenged for both classification (tag a given material as superconducting) and regression (quantifying the associated critical temperature). We then searched through the International Mineralogical Association list with the trained neural network. Among the obtained superconducting candidates, three materials were selected to undergo a thorough experimental characterization. Superconductivity has been indeed confirmed for the synthetic analogue of michenerite, PdBiTe, and observed for the first time in monchetundraite, Pd2NiTe2, at critical temperatures in good agreement with the theory predictions. This latter is the first certified superconducting material to be identified by artificial intelligence methodologies.
Macrophages maintain mammary stem cell activity and mammary homeostasis via TNF-α-PI3K-Cdk1/Cyclin B1 axis
Authors: Zhou Yu , Ye Zi , Wei Wei , Zhang Mengna , Huang Fujing , Li Jinpeng , Cai Cheguo 
Published: May 2023

AbstractAdult stem cell niche is a special environment composed of a variety stromal cells and signals, which cooperatively regulate tissue development and homeostasis. It is of great interest to study the role of immune cells in niche. Here, we show that mammary resident macrophages regulate mammary epithelium cell division and mammary development through TNF-α-Cdk1/Cyclin B1 axis. In vivo, depletion of macrophages reduces the number of mammary basal cells and mammary stem cells (MaSCs), while increases mammary luminal cells. In vitro, we establish a three-dimensional culture system in which mammary basal cells are co-cultured with macrophages, and interestingly, macrophage co-culture promotes the formation of branched functional mammary organoids. Moreover, TNF-α produced by macrophages activates the intracellular PI3K/Cdk1/Cyclin B1 signaling in mammary cells, thereby maintaining the activity of MaSCs and the formation of mammary organoids. Together, these findings reveal the functional significance of macrophageal niche and intracellular PI3K/Cdk1/Cyclin B1 axis for maintaining MaSC activity and mammary homeostasis.
Inter-brain coupling reflects disciplinary differences in real-world classroom learning
Authors: Chen Jingjing , Qian Penghao , Gao Xinqiao , Li Baosong , Zhang Yu , Zhang Dan 
Published: May 2023

AbstractThe classroom is the primary site for learning. A vital feature of classroom learning is the division of educational content into various disciplines. While disciplinary differences could substantially influence the learning process toward success, little is known about the neural mechanism underlying successful disciplinary learning. In the present study, wearable EEG devices were used to record a group of high school students during their classes of a soft (Chinese) and a hard (Math) discipline throughout one semester. Inter-brain coupling analysis was conducted to characterize students’ classroom learning process. The students with higher scores in the Math final exam were found to have stronger inter-brain couplings to the class (i.e., all the other classmates), whereas the students with higher scores in Chinese were found to have stronger inter-brain couplings to the top students in the class. These differences in inter-brain couplings were also reflected in distinct dominant frequencies for the two disciplines. Our results illustrate disciplinary differences in the classroom learning from an inter-brain perspective, suggesting that an individual’s inter-brain coupling to the class and to the top students could serve as potential neural correlates for successful learning in hard and soft disciplines correspondingly.
Fatigue database of additively manufactured alloys
Authors: Zhang Zian , Xu Zhiping 
Published: May 2023

AbstractFatigue is a process of mechanical degradation that is usually assessed based on empirical rules and experimental data obtained from standardized tests. Fatigue data of engineering materials are commonly reported in S-N (the stress-life relation), ε-N (the strain-life relation), and da/dN-ΔK (the relation between the fatigue crack growth rate and the stress intensity factor range) data. Fatigue and static mechanical properties of additively manufactured (AM) alloys, as well as the types of materials, parameters of AM, processing, and testing are collected from thousands of scientific articles till the end of 2022 using natural language processing, machine learning, and computer vision techniques. The results show that the performance of AM alloys could reach that of conventional alloys although data dispersion and system deviation are present. The database (FatigueData-AM2022) is formatted in compact structures, hosted in an open repository, and analyzed to show their patterns and statistics. The quality of data collected from the literature is measured by defining rating scores for datasets reported in individual studies and through the fill rates of data entries across all the datasets. The database also serves as a high-quality training set for data processing using machine learning models. The procedures of data extraction and analysis are outlined and the tools are publicly released. A unified language of fatigue data is suggested to regulate data reporting for the fatigue performance of materials to facilitate data sharing and the development of open science.
Modeling the antidepressant treatment response to transcranial magnetic stimulation using an exponential decay function
Authors: Berlow Yosef A. , Zandvakili Amin , Brennan McKenna C. , Williams Leanne M. , Price Lawrence H. , Philip Noah S. 
Published: May 2023

AbstractRecovery from depression often demonstrates a nonlinear pattern of treatment response, where the largest reduction in symptoms is observed early followed by smaller improvements. This study investigated whether this exponential pattern could model the antidepressant response to repetitive transcranial magnetic stimulation (TMS). Symptom ratings from 97 patients treated with TMS for depression were collected at baseline and after every five sessions. A nonlinear mixed-effects model was constructed using an exponential decay function. This model was also applied to group-level data from several published clinical trials of TMS for treatment-resistant depression. These nonlinear models were compared to corresponding linear models. In our clinical sample, response to TMS was well modeled with the exponential decay function, yielding significant estimates for all parameters and demonstrating superior fit compared to a linear model. Similarly, when applied to multiple studies comparing TMS modalities as well as to previously identified treatment response trajectories, the exponential decay models yielded consistently better fits compared to linear models. These results demonstrate that the antidepressant response to TMS follows a nonlinear pattern of improvement that is well modeled with an exponential decay function. This modeling offers a simple and useful framework to inform clinical decisions and future studies.
Dreams share phenomenological similarities with task-unrelated thoughts and relate to variation in trait rumination and COVID-19 concern
Authors: Raffaelli Quentin , Andrews Eric S. , Cegavske Caitlin C. , Abraham Freya F. , Edgin Jamie O. , Andrews-Hanna Jessica R. 
Published: May 2023

AbstractWhile recent neurocognitive theories have proposed links between dreams and waking life, it remains unclear what kinds of waking thoughts are most similar in their phenomenological characteristics to those of dreams. To investigate this question and examine relevance of dreams to significant personal concerns and dispositional mental health traits, we employed ecological momentary assessment and trait questionnaires across 719 young adults who completed the study during the COVID-19 pandemic, a time marked by considerable societal concern. Across the group and at the level of individual differences, dreams showed the highest correspondence with task-unrelated thoughts. Participants who self-reported greater COVID-19 concern rated their dreams as more negative and unconstructive, a relationship which was moderated by trait rumination. Furthermore, dreams perceived as more negative unconstructive and immersive in nature associated with increased trait rumination beyond variation in rumination explained by waking task-unrelated thoughts alone. Together, these results point to similarities between perceived characteristics of dreams and task-unrelated thoughts, and support a relationship between dreams, current concerns, and mental health.
Functional characterization of the phosphotransferase system in Parageobacillus thermoglucosidasius
Authors: Bidart Gonzalo N. , Gharabli Hani , Welner Ditte Hededam 
Published: May 2023

AbstractParageobacillus thermoglucosidasius is a thermophilic bacterium characterized by rapid growth, low nutrient requirements, and amenability to genetic manipulation. These characteristics along with its ability to ferment a broad range of carbohydrates make P. thermoglucosidasius a potential workhorse in whole-cell biocatalysis. The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates and sugar derivatives in bacteria, making it important for their physiological characterization. In this study, the role of PTS elements on the catabolism of PTS and non-PTS substrates was investigated for P. thermoglucosidasius DSM 2542. Knockout of the common enzyme I, part of all PTSs, showed that arbutin, cellobiose, fructose, glucose, glycerol, mannitol, mannose, N-acetylglucosamine, N-acetylmuramic acid, sorbitol, salicin, sucrose, and trehalose were PTS-dependent on translocation and coupled to phosphorylation. The role of each putative PTS was investigated and six PTS-deletion variants could not grow on arbutin, mannitol, N-acetylglucosamine, sorbitol, and trehalose as the main carbon source, or showed diminished growth on N-acetylmuramic acid. We concluded that PTS is a pivotal factor in the sugar metabolism of P. thermoglucosidasius and established six PTS variants important for the translocation of specific carbohydrates. This study lays the groundwork for engineering efforts with P. thermoglucosidasius towards efficient utilization of diverse carbon substrates for whole-cell biocatalysis.
Plant extracts have dual mechanism on the protection against dentine erosion: action on the dentine substrate and modification of the salivary pellicle
Authors: Niemeyer Samira Helena , Baumann Tommy , Lussi Adrian , Scaramucci Tais , Carvalho Thiago Saads 
Published: May 2023

AbstractTo investigate the effect of some polyphenol-rich plant extracts on the protection of dentine against demineralization, both acting on the dentine and on the salivary pellicle. Dentine specimens (n = 180) were randomly distributed into 6 experimental groups (n = 30/group): Control (deionized water), Açaí extract, Blueberry extract, Green tea extract, Grape seed extract, and Sn2+/F− (mouthrinse containing stannous and fluoride). Each group was further divided into two subgroups (n = 15), according to the site of action of the substance: on the dentine surface (D) or on the salivary pellicle (P). The specimens were submitted to 10 cycles: 30 min incubation in human saliva (P) or only in humid chamber (D), 2 min immersion in experimental substances, 60 min of incubation in saliva (P) or not (D), and 1 min erosive challenge. Dentine surface loss (DSL), amount of degraded collagen (dColl) and total calcium release were analyzed. Green tea, Grape seed and Sn2+/F− showed significant protection, with least DSL and dColl. The Sn2+/F− showed better protection on D than on P, whereas Green tea and Grape seed showed a dual mode of action, with good results on D, and even better on P. Sn2+/F− showed the lowest values of calcium release, not differing only from Grape seed. Sn2+/F− is more effective when acting directly on the dentine surface, while Green tea and Grape seed have a dual mode of action: with a positive effect on the dentine surface itself, but an improved efficacy in the presence of the salivary pellicle. We further elucidate the mechanism of action of different active ingredients on dentine erosion, where Sn2+/F− acts better on the dentine surface, but plant extracts have a dual mode of action, acting on the dentine itself as well as on the salivary pellicle, improving the protection against acid demineralization.
Changes in body perception following virtual object manipulation are accompanied by changes of the internal reference scale
Authors: Kirsch Wladimir , Kunde Wilfried 
Published: May 2023

AbstractChanges in body perception often arise when observers are confronted with related yet discrepant multisensory signals. Some of these effects are interpreted as outcomes of sensory integration of various signals, whereas related biases are ascribed to learning-dependent recalibration of coding individual signals. The present study explored whether the same sensorimotor experience entails changes in body perception that are indicative of multisensory integration and those that indicate recalibration. Participants enclosed visual objects by a pair of visual cursors controlled by finger movements. Then either they judged their perceived finger posture (indicating multisensory integration) or they produced a certain finger posture (indicating recalibration). An experimental variation of the size of the visual object resulted in systematic and opposite biases of the perceived and produced finger distances. This pattern of results is consistent with the assumption that multisensory integration and recalibration had a common origin in the task we used.
Comparison of ozonesonde measurements in the upper troposphere and lower Stratosphere in Northern India with reanalysis and chemistry-climate-model data
Authors: Fadnavis Suvarna , Sagalgile Archana , Sonbawne Sunil , Vogel Bärbel , Peter Thomas , Wienhold Frank G. , Dirksen Ruud , Oelsner Peter , Naja Manish , Müller Rolf 
Published: May 2023

AbstractThe variability and trend of ozone (O3) in the Upper troposphere and Lower Stratosphere (UTLS) over the Asian region needs to be accurately quantified. Ozone in the UTLS radiatively heats this region and cools the upper parts of the stratosphere. This results in an impact on relative humidity, static stability in the UTLS region and tropical tropopause temperature. A major challenge for understanding ozone chemistry in the UTLS is sparse observations and thus the representation of precursor gases in model emission inventories. Here, we evaluate ozonesonde measurements during August 2016 at Nainital, in the Himalayas, against ozone from multiple reanalyses and the ECHAM6-HAMMOZ model. We find that compared to measurements both reanalyses and ECHAM6-HAMMOZ control simulation overestimate ozone mixing ratios in the troposphere (20 ppb) and in the UTLS (55 ppb). We performed sensitivity simulations using the ECHAM6-HAMMOZ model for a 50% reduction in the emission of (1) NOx and (2) VOCs. The model simulations with NOXreduction agree better with the ozonesonde observations in the lower troposphere and in the UTLS. Thus, neither reanalyses nor ECHAM6-HAMMOZ results can reproduce observed O3over the South Asian region. For a better representation of O3in the ECHAM6-HAMMOZ model, NOXemission should be reduced by 50% in the emission inventory. A larger number of observations of ozone and precursor gases over the South Asian region would improve the assessment of ozone chemistry in models.
Charge-density wave associated with higher-order Fermi-surface nesting in monolayer VS2
Authors: Kawakami Tappei , Sugawara Katsuaki , Oka Hirofumi , Nakayama Kosuke , Yaegashi Ken , Souma Seigo , Takahashi Takashi , Fukumura Tomoteru , Sato Takafumi 
Published: May 2023

AbstractFermi-surface (FS) nesting originating from Peierls’ idea of electronic instabilities in one-dimensional materials is a key concept to stabilize charge-density wave (CDW), whereas its applicability to two-dimensional (2D) materials is under intensive debate. Here we report unusual CDW associated with the higher-order FS nesting in monolayer 2D VS2. Angle-resolved photoemission spectroscopy and scanning tunneling microscopy uncovered stripe CDW with $$\sqrt {21} R10.9^\circ \times \sqrt 3 R30^\circ$$

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periodicity together with an energy-gap opening on the entire FS. We suggest that this CDW involves the higher-order FS-nesting vector 2q twice larger than that of the normal one (q), as supported by the anomalies in the calculated phonon dispersion and electronic susceptibility. The present results suggest that the cooperation of q and 2q nesting leads to the fully gapped CDW state unlike the case of conventional single q nesting which produces a partial gap, pointing to an intriguing mechanism of CDW transition.
Adaptive mechanisms facilitate robust performance in noise and in reverberation in an auditory categorization model
Authors: Parida Satyabrata , Liu Shi Tong , Sadagopan Srivatsun 
Published: May 2023

AbstractFor robust vocalization perception, the auditory system must generalize over variability in vocalization production as well as variability arising from the listening environment (e.g., noise and reverberation). We previously demonstrated using guinea pig and marmoset vocalizations that a hierarchical model generalized over production variability by detecting sparse intermediate-complexity features that are maximally informative about vocalization category from a dense spectrotemporal input representation. Here, we explore three biologically feasible model extensions to generalize over environmental variability: (1) training in degraded conditions, (2) adaptation to sound statistics in the spectrotemporal stage and (3) sensitivity adjustment at the feature detection stage. All mechanisms improved vocalization categorization performance, but improvement trends varied across degradation type and vocalization type. One or more adaptive mechanisms were required for model performance to approach the behavioral performance of guinea pigs on a vocalization categorization task. These results highlight the contributions of adaptive mechanisms at multiple auditory processing stages to achieve robust auditory categorization.