bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial genome diversity across the subphylum Saccharomycotina
Authors: Wolters John F. , LaBella Abigail L. , Opulente Dana A. , Rokas Antonis , Hittinger Chris Todd
Published: November 2023

Introduction

Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.

Methods

By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades.

Results

Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements.

Discussion

As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
Streptomyces tamarix sp. nov.: antagonism against Alternaria gaisen producing streptochlorin, isolated from Tamarix root soil
Authors: Chen Yi-huang , Wu Yi Zheng , Liu Qin , Xia Zhanfeng , Wang JianMing , Luo Xiao-Xia
Published: November 2023

By the end of 2021, the pear yield in Xinjiang reached 1,795,900 tons, accounting for 1/9 of the country. Pear black spot, caused by Alternaria gaisen disease, has had a significant impact on the pear industry. A. gaisen can infect nearly all pear plants, resulting in black spots on the fruit that negatively affect both yield and quality. This study focused on the TRM76323 strain of Streptomyces, which was isolated from the soil of Tamarix chinensis in Xinjiang Province. Through a multiphase classification and identification method, the genetic classification status of the antagonistic strains was determined. The study also identified the antibacterial active components of streptochlorin using modern isolation and purification techniques. The antagonistic activity of Streptomyces against Alternaria was analyzed through in vitro and in vivo experiments. This research not only expanded the resource bank of antagonistic microorganisms in extreme environments in Xinjiang, but also identified active components that could contribute to the development of new drug lead compounds. Additionally, this study presents a novel approach for the prevention and control of pear black spot disease.
Research progress on GlnR-mediated regulation in Actinomycetes
Authors: Gao Bo , Li Guoqiang , Gu Dayong , Wang Jin
Published: November 2023

This review constitutes a summary of current knowledge on GlnR, a global regulator, that assumes a critical function in the regulation of nitrogen metabolism of Actinomycetes. In cross-regulation with other regulators, GlnR was also shown to play a role in the regulation of carbon and phosphate metabolisms as well as of secondary metabolism. A description of the structure of the GlnR protein and of its binding sites in various genes promoters regions is also provided. This review thus provides a global understanding of the critical function played by GlnR in the regulation of primary and secondary metabolism in Actinomycetes.
Insights into lignocellulose degradation: comparative genomics of anaerobic and cellulolytic Ruminiclostridium-type species
Authors: You Mengcheng , Zhao Qiuyun , Liu Yuansheng , Zhang Wenhao , Shen Zhewei , Ren Zhenxing , Xu Chenggang
Published: November 2023

Mesophilic, anaerobic, and cellulolytic Ruminiclostridium-type bacterial species can secrete an extracellular, multi-enzyme machinery cellulosome, which efficiently degrades cellulose. In this study, we first reported the complete genome of Ruminiclostridium papyrosolvens DSM2782, a single circular 5,027,861-bp chromosome with 37.1% G + C content, and compared it with other Ruminiclostridium-type species. Pan-genome analysis showed that Ruminiclostridium-type species share a large number of core genes to conserve basic functions, although they have a high level of intraspecific genetic diversity. Especially, KEGG mapping revealed that Ruminiclostridium-type species mainly use ABC transporters regulated by two-component systems (TCSs) to absorb extracellular sugars but not phosphotransferase systems (PTSs) that are employed by solventogenic clostridia, such as Clostridium acetobutylicum. Furthermore, we performed comparative analyses of the species-specific repertoire of CAZymes for each of the Ruminiclostridium-type species. The high similarity of their cohesins suggests a common ancestor and potential cross-species recognition. Additionally, both differences between the C-terminal cohesins and other cohesins of scaffoldins and between the dockerins linking with cellulases and other catalytic domains indicate a preference for the location of cellulosomal catalytic subunits at scaffoldins. The information gained in this study may be utilized directly or developed further by genetic engineering and optimizing enzyme systems or cell factories for enhanced biotechnological biomass deconstruction and biofuel production.
Casein hydrolysate's effects on the fermentation properties, texture, and chemical characteristics and the bacterial microbiota of fermented glutinous rice dough
Authors: Guo Ling , Liu Biqi , Jiang Yujun , Zhang Wei , Han Jing , Qu Wenxuan , Han Yuxi , Zhao Xinhuai , Yang Xinyan
Published: November 2023

To investigate how casein hydrolysate affected the physicochemical properties and microbiological diversity of the glutinous rice dough (natural fermentation and yeast fermentation), we analyzed its fermentation properties, carbohydrate, protein degradation, texture, and bacterial composition. According to the findings, casein hydrolysate increased the total LAB number, as well as organic acid content, in naturally fermented and yeast fermented glutinous rice dough by 3.59 and 8.19%, respectively, and reduced the fermentation time by at least 2 h. Meanwhile, casein hydrolysate enhanced the content of reducing sugars by 4.46 and 13.53% and increased protease activity by 29.9 and 27.7%. In addition, casein hydrolysate accelerated protein breakdown and regulated the hardness of the dough to improve the texture. Casein hydrolysate enriched the bacterial richness and diversity of dough. After adding casein hydrolysate, it promoted the growth of Pediococcus, Enterococcus, Lactobacillus, and Streptococcus. According to the Spearman correlation analysis, environmental factors (pH, lactic acid, acetic acid, reducing sugar content, and protease activity) exhibited the major driver for the abundance of bacterial species (Spearman correlation coefficient: −0.71 to 0.78). As a potential food additive, casein hydrolysate can improve the fermentation and quality of glutinous rice dough, increase consumer acceptance of cereal foods, and give consumers healthier options.
Carotenoids synthesis affects the salt tolerance mechanism of Rhodopseudomonas palustris
Authors: Li Meijie , Zhu Tongtong , Yang Rumeng , Wang Zhaobao , Liu Min , Yang Jianming
Published: November 2023

Rhodopseudomonas palustris CGA009 is a Gram-negative, purple non-sulfur, metabolically diverse bacterium with wide-ranging habitats. The extraordinary ability of R. palustris to decompose a variety of raw materials and convert them into high-value products makes it an attractive host for biotechnology and industrial applications. However, being a freshwater bacterium R. palustris has limited application in highly-saline environments. Therefore, it is of great significance to obtain the salt-tolerant strain of R. palustris and understand its tolerance mechanism. In this study, R. palustris CGA009 was successfully evolved into eight salt-tolerant strains using an adaptive laboratory evolution technique. RPAS-11 (R. palustris anti-salt strain 11) was selected as the best salt-tolerant strain and was used in further studies to explore the salt-tolerance mechanism. The expression of most genes associated with the carotenoid synthesis in RPAS-11 increased significantly under high concentration of salt stress, suggesting that carotenoid synthesis is one of the reasons for the salt tolerance of RPAS-11. Gene overexpression and knockout experiments were performed to get clear about the role of carotenoids in salt stress tolerance. RPAS-11-IDI, the mutant with overexpression of IDI (Isopentenyl diphosphate isomerase) exhibited enhanced salt tolerance, whereas the knockout mutant CGA009-∆crtI showed a decline in salt tolerance. In addition, the results indicated that rhodopin, a carotenoid compound, was the key pigment responsible for the salt tolerance in R. palustris. Furthermore, the production of lycopene, a widely-used carotenoid, was also increased. Taken together, our research helps to deepen the understanding of the salt tolerance mechanism of R. palustris and also widens the application of R. palustris in highly-saline environments.
The causal relationship between gut microbiota and leukemia: a two-sample Mendelian randomization study
Authors: Chen Guanjun , Kuang Zheshu , Li Fan , Li Jianchang
Published: November 2023

Background

The association between gut microbiota and leukemia has been established, but the causal relationship between the two remains unclear.

Methods

A bidirectional two-sample Mendelian randomization (MR) was used to analyze the causal relationship between gut microbiota and leukemia. Microbiome data (n = 14,306) and leukemia (n = 1,145) data were both sourced from European populations. Single nucleotide polymorphisms (SNPs) were selected as instrumental variables based on several criteria. We employed various MR methods, such as the inverse variance weighted (IVW) method, to evaluate the causal effect between exposure and outcomes and conducted sensitivity analyses to validate the heterogeneity and pleiotropy of the instrumental variables.

Results

5,742 qualified instrumental variables were included. In the primary MR results, a total of 10 gut microbial taxa were associated with leukemia risk. Genus Blautia and genus Lactococcus are risk factors for acute lymphoblastic leukemia [genus Blautia odds ratio (OR): 1.643, 95% confidence interval (CI): 1.592 ~ 1.695, Adjusted p < 0.001; genus Lactococcus OR: 2.152, 95% CI: 1.447 ~ 3.199, Adjusted p = 0.011]. Genus Rikenellaceae RC9 gut group, genus Anaerostipes, genus Slackia, and genus Lachnospiraceae ND3007 group are risk factors for acute myeloid leukemia [genus Rikenellaceae RC9 gut group OR: 1.964, 95% CI: 1.573 ~ 2.453, Adjusted p < 0.001; genus Anaerostipes OR: 2.515, 95% CI: 1.503 ~ 4.209, Adjusted p = 0.017; genus Slackia OR: 2.553, 95% CI: 1.481 ~ 4.401, Adjusted p = 0.022; genus Lachnospiraceae ND3007 group OR: 3.417, 95% CI: 1.960 ~ 5.959, Adjusted p = 0.001]. Genus Ruminococcaceae UCG011 and genus Ruminococcaceae UCG014 were risk factors for chronic myeloid leukemia (genus Ruminococcaceae UCG011 OR: 2.010, 95% CI: 1.363 ~ 2.963, Adjusted p = 0.044; genus Ruminococcaceae UCG014 OR: 3.101, 95% CI: 1.626 ~ 5.915, Adjusted p = 0.044). Genus Slackia was a protective factor for acute lymphoblastic leukemia (genus Slackia OR: 0.166, 95% CI: 0.062 ~ 0.443, Adjusted p = 0.017). Family Acidaminococcaceae was a protective factor for acute myeloid leukemia (family Acidaminococcaceae OR: 0.208, 95% CI: 0.120 ~ 0.361, Adjusted p < 0.001). Genus Desulfovibrio was a protective factor for chronic lymphoblastic leukemia (genus Desulfovibrio OR: 0.581, 95% CI: 0.440 ~ 0.768, Adjusted p = 0.020). Sensitivity analysis revealed no heterogeneity or pleiotropy between SNPs.

Conclusion

This study revealed the causal relationship between the gut microbiota and leukemia, and identified potential pathogenic bacteria and probiotic taxa associated with the onset of leukemia. This research may aid in the early detection of various types of leukemia and offer a new direction for the prevention and treatment of leukemia.
Alterations of gut microbiota and short-chain fatty acids induced by Balantidium polyvacuolum in the hindgut of Xenocyprinae fishes providing new insights into the relationship among protozoa, gut microbiota and host
Authors: Bu Xialian , Li Zhongyang , Zhao Weishan , Zeng Qingwen , Chen Yushun , Li Wenxiang , Zou Hong , Li Ming , Wang Guitang
Published: November 2023

Introduction

Parasitic ciliates are protozoans with a global distribution. Along with the gut microbiota, they have formed a micro-ecosystem that affects the host’s nutrition, metabolism, and immunity. The interactions and relationships among the three components of this microecosystem (protozoa, gut microbiota, and host) remain only partially understood. Xenocypris fish and the unique ciliate Balantidium polyvacuolum in its hindgut are good materials to study the interplay.

Methods

In this study, 16S rRNA gene amplicon sequencing and short-chain fatty acids (SCFAs) identification were used. Network was also constructed to understand their relationships.

Results

We found that the gut microbiota of B. polyvacuolum-infected X. davidi and X. argentea had higher diversity, richness, and evenness than uninfected ones. B. polyvacuolum could lead to an increase of Fusobacterium and Chloroflexi in both X. davidi and X. argentea, while significantly increase the abundance of genera Romboutsia and Clostridium in X. argentea. Besides, B. polyvacuolum could significantly increase the content of total SCFAs and acetic acid in X. davidi and increase the concentrations of propionic, isobutyric and butanoic acids in X. argentea. Furthermore, correlation analyses showed that B. polyvacuolum may alter SCFAs by affecting key SCFAs-producing bacteria such as Clostridium and Cetobacterium.

Discussion

This study greatly expands our understanding of relationships among B. polyvacuolum, gut microbiota and host Xenocypris fish, which sheds new insights into the mechanism of interaction among protozoa, gut microbiota and host.
Genotype and environment factors driven licorice growth and rhizospheric soil fungal community changes
Authors: Han Tingting , Li Xianen , Luo Dan , Ji Changhao , Chen Caixia , He Chao
Published: November 2023

Introduction

Licorice (Glycyrrhiza uralensis Fisch.) is a widely recognized significant form of medicine in China, with a long-standing history and extensive usage. It is considered the oldest and most prevalent herbal medicine in China. Currently, the licorice market is confronted with the primary challenges of mixed genotypes, inconsistent quality, and inadequate glycyrrhizic acid content.

Methods

We conducted field experiments to investigate the impact of various cultivation locations on the growth characteristics, active ingredients, rhizospheric soil physicochemical properties and fungal communities of licorice that ten different genotypes.

Results

The findings indicated significant variations in these parameters across ten different genotypes of licorice originating from two distinct production regions. The growth characteristics of licorice were primarily influenced by genotype, whereas the active ingredients of licorice were mainly influenced by environmental factors and soil physicochemical properties. Furthermore, the rhizospheric soil physicochemical properties of licorice plants were more influenced by environmental factors than genotypes. Additionally, the distribution of rhizospheric soil fungi in licorice plants of the same genotype exhibited significant variations across different cultivation areas. The utilization of structural equation model synthesis reveals variations in the quantity and strength of pathways that influence the growth characteristics, active ingredients, and rhizospheric soil microbial community of licorice across different cultivation regions.

Discussion

Based on the main results, according to its growth characteristics and active ingredients, Z009 proved to be the most suitable genotype for cultivation in Jingtai. From a perspective centered on the active ingredient, Z010 proved to be the most optimal genotype for licorice cultivation in both production areas. Our study aims to enhance the understanding of the ecological adaptability of various genotypes of licorice resources and to identify appropriate licorice genotypes for specific cultivation regions. This research holds significant practical implications for enhancing the yield and quality of licorice, thereby improving its overall development.
CsrA selectively modulates sRNA-mRNA regulator outcomes
Authors: Rojano-Nisimura Alejandra Matsuri , Simmons Trevor R. , Leistra Abigail N. , Mihailovic Mia K. , Buchser Ryan , Ekdahl Alyssa M. , Joseph Isabella , Curtis Nicholas C. , Contreras Lydia M.
Published: November 2023

Post-transcriptional regulation, by small RNAs (sRNAs) as well as the global Carbon Storage Regulator A (CsrA) protein, play critical roles in bacterial metabolic control and stress responses. The CsrA protein affects selective sRNA-mRNA networks, in addition to regulating transcription factors and sigma factors, providing additional avenues of cross talk between other stress-response regulators. Here, we expand the known set of sRNA-CsrA interactions and study their regulatory effects. In vitro binding assays confirm novel CsrA interactions with ten sRNAs, many of which are previously recognized as key regulatory nodes. Of those 10 sRNA, we identify that McaS, FnrS, SgrS, MicL, and Spot42 interact directly with CsrA in vivo. We find that the presence of CsrA impacts the downstream regulation of mRNA targets of the respective sRNA. In vivo evidence supports enhanced CsrA McaS-csgD mRNA repression and showcases CsrA-dependent repression of the fucP mRNA via the Spot42 sRNA. We additionally identify SgrS and FnrS as potential new sRNA sponges of CsrA. Overall, our results further support the expanding impact of the Csr system on cellular physiology via CsrA impact on the regulatory roles of these sRNAs.
Identification of cuproptosis-related biomarkers and analysis of immune infiltration in allograft lung ischemia-reperfusion injury
Authors: Qin Jianying , Xiao Xiaoyue , Li Silin , Wen Ning , Qin Ke , Li Haibin , Wu Jihua , Lu Bing , Li Minghu , Sun Xuyong
Published: November 2023

Background: Allograft lung ischemia-reperfusion injury (ALIRI) is a major cause of early primary graft dysfunction and poor long-term survival after lung transplantation (LTx); however, its pathogenesis has not been fully elucidated. Cell death is a mechanism underlying ALIRI. Cuproptosis is a recently discovered form of programmed cell death. To date, no studies have been conducted on the mechanisms by which cuproptosis-related genes (CRGs) regulate ALIRI. Therefore, we explored the potential biomarkers related to cuproptosis to provide new insights into the treatment of ALIRI.

Materials and methods: Datasets containing pre- and post-LTx lung biopsy samples and CRGs were obtained from the GEO database and previous studies. We identified differentially expressed CRGs (DE-CRGs) and performed functional analyses. Biomarker genes were selected using three machine learning algorithms. The ROC curve and logistic regression model (LRM) of these biomarkers were constructed. CIBERSORT was used to calculate the number of infiltrating immune cells pre- and post-LTx, and the correlation between these biomarkers and immune cells was analyzed. A competing endogenous RNA network was constructed using these biomarkers. Finally, the biomarkers were verified in a validation set and a rat LTx model using qRT-PCR and Western blotting.

Results: Fifteen DE-CRGs were identified. GO analysis revealed that DE-CRGs were significantly enriched in the mitochondrial acetyl-CoA biosynthetic process from pyruvate, protein lipoylation, the tricarboxylic acid (TCA) cycle, and copper-transporting ATPase activity. KEGG enrichment analysis showed that the DE-CRGs were mainly enriched in metabolic pathways, carbon metabolism, and the TCA cycle. NFE2L2, NLRP3, LIPT1, and MTF1 were identified as potential biomarker genes. The AUC of the ROC curve for each biomarker was greater than 0.8, and the LRM provided an excellent classifier with an AUC of 0.96. These biomarkers were validated in another dataset and a rat LTx model, which exhibited good performance. In the CIBERSORT analysis, differentially expressed immune cells were identified, and the biomarkers were associated with the immune cells.

Conclusion:NFE2L2, NLRP3, LIPT1, and MTF1 may serve as predictors of cuproptosis and play an important role in the pathogenesis of cuproptosis in ALIRI.
Ten questions to AI regarding the present and future of proteomics
Authors: Stransky Stephanie , Sun Yan , Shi Xuyan , Sidoli Simone
Published: November 2023

The role of a scientist is at first not so different from a philosopher. They both need to question common thinking and evaluate whether reality is not as we always thought. Based on this, we need to design hypotheses, experiments, and analyses to prove our alternative vision. Artificial Intelligence (AI) is rapidly moving from an “assistant” into a proper “colleague” for literature mining, data analysis and interpretation, and literally having (almost) real scientific conversations. However, being AI based on existing information, if we rely on it excessively will we still be able to question the status quo? In this article, we are particularly interested in discussing the future of proteomics and mass spectrometry with our new electronic collaborator. We leave to the reader the judgement whether the answers we received are satisfactory or superficial. What we were mostly interested in was laying down what we think are critical questions that the proteomics community should occasionally ask to itself. Proteomics has been around for more than 30 years, but it is still missing a few critical steps to fully address its promises as being the new genomics for clinical diagnostics and fundamental science, while becoming a user-friendly tool for every lab. Will we get there with the help of AI? And will these answers change in a short period, as AI continues to advance?
Impaired night-time mobility in patients with Parkinson’s disease: a systematic review
Authors: Li Shengyiwen , Lin Qingyang , Bao Yannan , Feng Yichen , Li Dianyou , Zhang Chencheng
Published: November 2023

Impaired bed mobility (IBM) is a symptom characteristic of patients having difficulty intentionally moving their bodies during nighttime sleep. IBM is one of the most common nocturnal symptoms of Parkinson’s disease (PD) and may lead to extreme pain and even death; it also increases the burden on the patients’ caregivers. In this systematic review, we included 19 studies involving a total of 1,407 patients with PD to observe the causes, assessment methods, and treatment options for IBM. We conclude that the extent of IBM is positively correlated with the severity of symptoms such as disease duration, dyskinesia and decreased sleep quality in patients with PD, and the evidence implies that IBM may be able to serve as a prodromal feature in the development of PD. IBM probably results from low nocturnal dopamine concentrations, reduced function of the spinal tract, torque problems in the muscles, and aging. Therefore, treatment is mostly based on continuously increasing the patient’s nocturnal dopamine concentration, while deep brain stimulation (DBS) also has a mitigating effect on IBM. Both scales and sensors are commonly used to measure the severity of IBM, the wearable device monitoring and scales being updated makes measurements easier and more accurate. The future of the advancement in this field lies in the use of more family-oriented devices (such as smart phones or watches and bracelets, etc.) to monitor IBM’s symptoms and select the appropriate therapeutic treatment according to the severity of the symptoms to relieve patients’ suffering.
Associations of sarcopenia, sarcopenia parameters and motoric cognitive risk syndrome in Chinese older adults
Authors: Jiang Dian , Chen Xi , Huang Jundan , Wu Lina , Chen Yifei , Feng Hui , Hu Mingyue
Published: November 2023

Background

Motoric cognitive risk syndrome (MCR) is a pre-dementia symptom strongly predicting cognitive decline and dementia. Although advancements in elucidating the epidemiology of MCR, the evidence about the association between sarcopenia, sarcopenia parameters, and MCR remains scarce.

Objectives

The purpose of this study was to determine the associations between sarcopenia, sarcopenia parameters, and MCR among community-dwelling Chinese older adults.

Methods

A total of 4,184 community-dwelling older adults from the China Health and Retirement Longitudinal Study (CHARLS) in the 2011 waves were included. Sarcopenia was diagnosed according to the Asian Working Group for Sarcopenia criteria. Sarcopenia parameters included handgrip strength (HGS), height-adjusted appendicular skeletal muscle mass (ASM/Ht2), and five-times sit-to-stand test time (FTSSTT). MCR was defined as subjective cognitive complaints and slow gait speed without dementia or impaired mobility. The associations between sarcopenia, sarcopenia parameters, and MCR were conducted using the logistic regression model. The restricted cubic spline with four knots were performed to determine the nonlinear and linear relationships between HGS, ASM/Ht2, FTSSTT, and MCR.

Results

The prevalence of MCR in wave 2011 of CHARLS was 11.2%. After adjustment for potential confounders, we found sarcopenia [odd ratio (OR) (95% CI): 1.70 (1.13 ~ 2.54), p = 0.011], lower HGS [0.97 (0.96 ~ 0.99), p = 0.001], and more FTSSTT [1.12 (1.10 ~ 1.15), p < 0.001] were significantly associated with a higher risk of MCR. There was an inverse linear dose–response between HGS and MCR (p for overall = 0.008, p for nonlinearity =0.776). The nonlinear relationship between FTSSTT and MCR was found (p for overall <0.001, p for nonlinearity = 0.025) with FTSSTT ≥29 s being associated with a higher risk of MCR. A dose–response relationship was not found between ASM/Ht2 and MCR (p for overall =0.589).

Conclusion

Sarcopenia, lower HGS, and higher FTSSTT are associated with MCR among older adults in China, while the latter two exhibit a dose–response relationship with MCR. It is suggested that timely identification and management of sarcopenia and its parameters may help delay the progression of cognitive impairment and promote healthy aging.
Interface-enhanced conductivities in surfactant-mediated, solution-grown ionic crystalline complexes
Authors: Chen Jihua , Keum Jong , Wang Yangyang , Wang Hanyu , Lokitz Bradley , Yang Guang , Yuan Yue , Kumar Rajeev , Advincula Rigoberto
Published: November 2023

Renewable energy is increasingly relying on optimized electrolytes and interfaces. In this work, Tween 20 and sodium chloride are selected as a model system to reveal the effects of surfactants on salt crystallization in the context of ionic conductivity and interface optimization. At a varied crystallization speed and mix ratio, it is demonstrated that the resultant solution-grown ionic crystalline complexes can achieve a highly tunable ion transport with a controllable crystalline interface. X-ray diffraction results rule out the possibility of polymorphism in the NaCl/Tween 20 systems, which further supports the importance of an optimized crystalline network for optimizing permittivity or ionic conductivity. Raman mapping and machine learning techniques are used to perform semantic segmentation on highly heterogeneous NaCl/Tween 20 complexes. Furthermore, FTIR measurements demonstrate that inter- and intra-molecular interactions play critical roles in the formation of these crystals. This work lays a foundation toward future optimization of such complex ion systems for a specific salt or crystallization modifier in energy storage or ion transport applications.
Cellular computation and cognition
Authors: Fitch W. Tecumseh
Published: November 2023

Contemporary neural network models often overlook a central biological fact about neural processing: that single neurons are themselves complex, semi-autonomous computing systems. Both the information processing and information storage abilities of actual biological neurons vastly exceed the simple weighted sum of synaptic inputs computed by the “units” in standard neural network models. Neurons are eukaryotic cells that store information not only in synapses, but also in their dendritic structure and connectivity, as well as genetic “marking” in the epigenome of each individual cell. Each neuron computes a complex nonlinear function of its inputs, roughly equivalent in processing capacity to an entire 1990s-era neural network model. Furthermore, individual cells provide the biological interface between gene expression, ongoing neural processing, and stored long-term memory traces. Neurons in all organisms have these properties, which are thus relevant to all of neuroscience and cognitive biology. Single-cell computation may also play a particular role in explaining some unusual features of human cognition. The recognition of the centrality of cellular computation to “natural computation” in brains, and of the constraints it imposes upon brain evolution, thus has important implications for the evolution of cognition, and how we study it.
Brain entropy changes in classical trigeminal neuralgia
Authors: Liu Xiang , Ge Xiuhong , Tang Xue , Ye Haiqi , Pan Lei , Zhu Xiaofen , Hu Hanjun , Ding Zhongxiang , Wang Luoyu
Published: November 2023

Background

Classical trigeminal neuralgia (CTN) is a common and severe chronic neuropathic facial pain disorder. The pathological mechanisms of CTN are not fully understood. Recent studies have shown that resting-state functional magnetic resonance imaging (rs-fMRI) could provide insights into the functional changes of CTN patients and the complexity of neural processes. However, the precise spatial pattern of complexity changes in CTN patients is still unclear. This study is designed to explore the spatial distribution of complexity alterations in CTN patients using brain entropy (BEN).

Methods

A total of 85 CTN patients and 79 age- and sex-matched healthy controls (HCs) were enrolled in this study. All participants underwent rs-fMRI and neuropsychological evaluations. BEN changes were analyzed to observe the spatial distribution of CTN patient complexity, as well as the relationship between these changes and clinical variables. Sixteen different machine learning methods were employed to classify the CTN patients from the HCs, and the best-performing method was selected.

Results

Compared with HCs, CTN patients exhibited increased BEN in the thalamus and brainstem, and decreased BEN in the inferior semilunar lobule. Further analyses revealed a low positive correlation between the average BEN values of the thalamus and neuropsychological assessments. Among the 16 machine learning methods, the Conditional Mutual Information Maximization-Random Forest (CMIM-RF) method yielded the highest area under the curve (AUC) of 0.801.

Conclusions

Our study demonstrated that BEN changes in the thalamus and pons and inferior semilunar lobule were associated with CTN and machine learning methods could effectively classify CTN patients and HCs based on BEN changes. Our findings may provide new insights into the neuropathological mechanisms of CTN and have implications for the diagnosis and treatment of CTN.
The impact of thrombus surface morphology of the basilar artery on the successful rate of mechanical thrombectomy
Authors: Jiang Xinzhao , Yu Shufeng , Wang David , Dong YI , Wang Peng
Published: November 2023

Objective

The present study aimed to investigate the impact of angiographic thrombus surface morphology on the angiographic and clinical outcomes of basilar artery occlusion (BAO).

Methods

This retrospective study included 141 patients with acute BAO who underwent mechanical thrombectomy (MT). We categorized thrombus surface phenotypes as either regular (smooth and straight, either convex or concave) or irregular. Patients with BAO were grouped based on the presence of a regular or irregular phenotype, and we compared their angiographic and clinical outcomes.

Results

In total, 52.5% (74/141) of acute BAO patients exhibited a regular thrombus morphology. These patients had a higher rate of first-pass effect (28.4% vs. 4.5%, p = 0.0002) and fewer retrieval attempts (2 vs. 2; p = 0.0198) compared to those with irregular morphology. Among patients treated with contact aspiration (CA), the regular thrombus morphology showed a higher first-pass success rate (45.7% vs. 12.8%; p = 0.0017), a shorter procedural duration (46 vs. 50 min; p = 0.0159), and fewer retrieval attempts (1 vs. 2; p = 0.0338) compared to stent retriever (SR) thrombectomy. Both the regular thrombus morphology (OR 7.72, 95% CI 2.02–29.52; p = 0.003) and using CA as the first-line treatment (OR 3.37, 95% CI 1.12–10.13; p = 0.031) independently predicted first-pass success.

Conclusion

For BAO patients treated with CA as the primary strategy, the presence of a regular thrombus surface might predict higher first-pass success and shorter procedural duration. A diligent assessment of thrombus morphology within the MT workflow could improve the feasibility of procedural techniques.
Evaluation of vestibulo-ocular reflex with functional head impulse test in healthy individuals: normative values
Authors: Cengiz Deniz Uğur , Erbek Hatice Seyra , Çolak Sanem Can , Kurtcu Büşra , Demirel Birişik Sümeyye , Karababa Ercan , Kuşman Buşra , Özdemir Emre Akgün , Işık Mehmet , Demir İsmail
Published: November 2023

Objectives

This study aimed to determine the normative values of the functional head impulse test (fHIT) test in healthy young adults.

Materials and methods

The study included 100 individuals, 58 females and 42 males, aged 20–25 years. Beon Solution Zero Branco (TV) fHIT test was applied to all participants. FHIT results were analyzed in terms of lateral-posterior–anterior semicircular canals (SSCs), gender, and right–left ear.

Results

In the fHIT test, for the lateral SSC the mean percent correct answer (%CA) values for 4,000–6,000°/s2 and 1,000–7,000°/s2 were 88.52 ± 9.04 and 89.91 ± 6.95, respectively; for the posterior SSC, the mean %CA values for SSC 3000–6,000°/s2 and 1,000–7,000°/s2 were 90.63 ± 8.69 and 91.16 ± 7.42, respectively; for the anterior SSC, the mean %CA values for 3,000–6,000°/s2 and 1,000–7,000°/s2 were 91.21 ± 7.96 and 91.49 ± 7.13, respectively. There was no statistically significant difference between the right and left ear in %CA values at all accelerations in all SSCs (p > 0.05). There was a statistically significant difference between genders in the mean %CA values for 6,000–7,000°/s2, 4,000–6,000°/s2, and 1,000–7,000°/s2 in the lateral SSC and 3,000–6,000°/s2 in the anterior SSC (p < 0.05).

Conclusion

The FHIT is a noninvasive test battery that functionally evaluates the VOR of the six semicircular canals. In clinical use, the determination of normative values at all accelerations (1,000–7,000 degrees/s2) constitutes an important database for future studies to distinguish pathologic results.
Using machine learning to explore the characteristics of eye movement patterns and relationship with cognition ability of Chinese children aged 1–6 years
Authors: Zhou Shuqing , Hou Li , Wang Na , Liu Fulin , Wei Ning , Chi Xia , Yu Dongchuan , Zhang Xin , Tong Meiling
Published: November 2023

Researchers have begun to investigate the relationship between eye movement characteristics of gaze patterns and cognitive abilities, and have attempted to use eye-tracking technology as a new method to evaluate cognitive abilities. Traditional eye movement analysis methods typically separate spatial and temporal information of eye movements, mostly analyze averaged data, and consider individual differences as noise. In addition, current eye movement studies on gaze patterns mostly involve adults, while research on infants and toddlers is limited with small sample sizes and narrow age ranges. It is still unknown whether the conclusions drawn from adult-based research can be applied to children. Consequently, eye movement research on gaze patterns in children is necessary. To address the concerns stated above, this study used the Hidden Markov machine learning method to model gaze patterns of 330 children aged 1–6 years while observing faces freely, and analyzed characteristics of eye movement gaze patterns. Additionally, we analyzed the correlation between gaze patterns of 31 toddlers aged 1–3 years and 37 preschoolers aged 4–6 years, and the different dimensions of cognitive abilities. The findings indicated that children exhibited holistic and analytic gaze patterns while observing different faces freely. More children adopted a holistic gaze pattern, and there were age-specific gaze pattern characteristics and regularities. Gaze patterns of toddlers may be correlated with their adaptive abilities and gaze patterns of preschoolers may be correlated with their visual space abilities. Specifically, toddlers aged 1–3 years showed a moderate negative correlation between the H-A scale and the adaptive dimension, while preschoolers aged 4–6 years showed a low negative correlation between the H-A scale and the visual space dimension. This study may provide new insights into the characteristics of children’s eye-movement gaze patterns during face observation, and potentially offer objective evidence for future research aimed at promoting the use of eye-tracking technology in the assessment of toddlers’ adaptive abilities and preschoolers’ visual space abilities in the field of face perception.
Case report: Two case reports of cryptogenic brain abscess caused by Fusobacterium nucleatum and literature review
Authors: Zhang Zuoxin , Liu Jing , Su Linxi , Huang Weiwei , Pei Yuchun , Huang Guohao , Yang Lin , Lv Shengqing , Yin Jinbo , Liu Guolong
Published: November 2023

Brain abscess originates from a localized cerebritis area of brain parenchyma, remaining a refractory infectious disease in the central nervous system. Causative pathogens can be wide-ranging, including bacteria, fungi, or parasites; thus, precise pathogen identification and individualized antimicrobial therapy determine patients’ outcomes. Here, we report two cases where both patients only presented with limb dysfunction, but without symptoms, signs, or biological evidence of infection. Samples were obtained through brain stereoscopic surgeries and microbial identifications were performed to confirm the infection of Fusobacterium nucleatum. Further appropriate treatments were given, and the patients recovered well. Patient 1 was a 73-year-old male with a 20-day history of left-sided limbs weakness. A brain MRI showed a space-occupying lesion with a heterogeneously ring-enhancement character in the right frontal lobe. This patient underwent puncture biopsy of the lesion with robot-assisted guidance to confirm a brain abscess. Empirical antibiotic therapy was immediately given until the pathogen was identified as Fusobacterium nucleatum; thus, he received specific antibiotic therapy with metronidazole and recovered well after treatment. Patient 2 was a 22-year-old female with heart disease history who complained of right-sided limb weakness for nine days. A brain MRI showed a circular enhanced lesion with a thin capsule wall and surrounding edema in the left frontal lobe. This patient underwent puncture drainage of the lesion with robot-assisted guidance and a brain abscess was confirmed. Empirical antibiotic therapy was given until the pathogen was identified as Fusobacterium nucleatum and then she also received metronidazole treatment. Her symptoms recovered and the lesion disappeared after 1 month. Hence, we reviewed the diagnosis and treatment of cryptogenic brain abscess caused by Fusobacterium nucleatum and highlight that precise neurosurgical interventions and identification of causative pathogens are crucial for the management of brain abscess.
Local field potentials and single unit dynamics in motor cortex of unconstrained macaques during different behavioral states
Authors: Yun Richy , Rembado Irene , Perlmutter Steve I. , Rao Rajesh P. N. , Fetz Eberhard E.
Published: November 2023

Different sleep stages have been shown to be vital for a variety of brain functions, including learning, memory, and skill consolidation. However, our understanding of neural dynamics during sleep and the role of prominent LFP frequency bands remain incomplete. To elucidate such dynamics and differences between behavioral states we collected multichannel LFP and spike data in primary motor cortex of unconstrained macaques for up to 24 h using a head-fixed brain-computer interface (Neurochip3). Each 8-s bin of time was classified into awake-moving (Move), awake-resting (Rest), REM sleep (REM), or non-REM sleep (NREM) by using dimensionality reduction and clustering on the average spectral density and the acceleration of the head. LFP power showed high delta during NREM, high theta during REM, and high beta when the animal was awake. Cross-frequency phase-amplitude coupling typically showed higher coupling during NREM between all pairs of frequency bands. Two notable exceptions were high delta-high gamma and theta-high gamma coupling during Move, and high theta-beta coupling during REM. Single units showed decreased firing rate during NREM, though with increased short ISIs compared to other states. Spike-LFP synchrony showed high delta synchrony during Move, and higher coupling with all other frequency bands during NREM. These results altogether reveal potential roles and functions of different LFP bands that have previously been unexplored.
Causes of microcephaly in human—theoretical considerations
Authors: Heide Michael , Huttner Wieland B.
Published: November 2023

As is evident from the theme of the Research Topic “Small Size, Big Problem: Understanding the Molecular Orchestra of Brain Development from Microcephaly,” the pathomechanisms leading to mirocephaly in human are at best partially understood. As molecular cell biologists and developmental neurobiologists, we present here a treatise with theoretical considerations that systematically dissect possible causes of microcephaly, which we believe is timely. Our considerations address the cell types affected in microcephaly, that is, the cortical stem and progenitor cells as well as the neurons and macroglial cell generated therefrom. We discuss issues such as progenitor cell types, cell lineages, modes of cell division, cell proliferation and cell survival. We support our theoretical considerations by discussing selected examples of factual cases of microcephaly, in order to point out that there is a much larger range of possible pathomechanisms leading to microcephaly in human than currently known.
Characterization of a de novo GABBR2 variant linked to autism spectrum disorder
Authors: Bielopolski Noa , Stawarski Michal , Roitman Ilana , Fridman Karen , Wald-Altman Shane , Früh Simon , Bettler Bernhard , Nissenkorn Andreea
Published: November 2023

GABAB receptors (GABABRs) are G protein-coupled receptors for γ-aminobutyric acid (GABA), the major inhibitory neurotransmitter in the central nervous system. Pathogenic variants in the GABBR1 and GABBR2 genes, which encode the GB1 and GB2 subunits of GABABRs, are implicated in several neurological and developmental disorders, including epilepsy and autism. Here we present a 7-year-old boy with Level 3 Autism Spectrum Disorder who carries a de novo heterozygous missense GABBR2 p.Arg212Gln variant. This variant was identified through whole exome sequencing and classified as variant of unknown significance (VUS). Treatment with the GABABR agonist baclofen showed no clinical improvement, raising the question whether this VUS is responsible for the patient’s phenotype. We conducted a study to investigate the impact of the GABBR2 p.Arg212Gln and the previously reported GABBR2 p.Arg212Trp variants on protein structure and receptor activity. This study utilized a combination of molecular dynamics (MD) simulations, and in vitro experiments. Our simulations demonstrate that both amino acid substitutions locally alter amino acid interactions in the extracellular domain of GB2. Most importantly, the substitutions influence the positioning of transmembrane helices, shifting the conformation towards an active state with GABBR2 p.Arg212Gln and an inactive state with GABBR2 p.Arg212Trp. Functional assays confirmed the MD predictions, as evidenced by increased constitutive activity and enhanced potency of GABA for GABBR2 p.Arg212Gln, and a decreased constitutive activity with a loss of GABA potency for GABBR2 p.Arg212Trp. Our findings demonstrate the utility of MD simulations in predicting the functional consequences of VUS. Clarifying the pathogenic mechanisms associated with gene variants will aid in the identification of personalized treatment approaches.