bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulating the effect of climate change on soil microbial community in an Abies georgei var. smithii forest
Authors: Fu Fangwei , Li Jiangrong , Li Yueyao , Chen Wensheng , Ding Huihui , Xiao Siying
Published: June 2023

Qinghai–Tibet Plateau is considered a region vulnerable to the effects of climate change. Studying the effects of climate change on the structure and function of soil microbial communities will provide insight into the carbon cycle under climate change. However, to date, changes in the successional dynamics and stability of microbial communities under the combined effects of climate change (warming or cooling) remain unknown, which limits our ability to predict the consequences of future climate change. In this study, in situ soil columns of an Abies georgei var. smithii forest at 4,300 and 3,500 m elevation in the Sygera Mountains were incubated in pairs for 1 year using the PVC tube method to simulate climate warming and cooling, corresponding to a temperature change of ±4.7°C. Illumina HiSeq sequencing was applied to study alterations in soil bacterial and fungal communities of different soil layers. Results showed that warming did not significantly affect the fungal and bacterial diversity of the 0–10 cm soil layer, but the fungal and bacterial diversity of the 20–30 cm soil layer increased significantly after warming. Warming changed the structure of fungal and bacterial communities in all soil layers (0–10 cm, 10–20 cm, and 20–30 cm), and the effect increased with the increase of soil layers. Cooling had almost no significant effect on fungal and bacterial diversity in all soil layers. Cooling changed the structure of fungal communities in all soil layers, but it showed no significant effect on the structure of bacterial communities in all soil layers because fungi are more adapted than bacteria to environments with high soil water content (SWC) and low temperatures. Redundancy analysis (RDA) and hierarchical analysis showed that changes in soil bacterial community structure were primarily related to soil physical and chemical properties, whereas changes in soil fungal community structure primarily affected SWC and soil temperature (Soil Temp). The specialization ratio of fungi and bacteria increased with soil depth, and fungi were significantly higher than bacteria, indicating that climate change has a greater impact on microorganisms in deeper soil layers, and fungi are more sensitive to climate change. Furthermore, a warmer climate could create more ecological niches for microbial species to coexist and increase the strength of microbial interactions, whereas a cooler climate could have the opposite effect. However, we found differences in the intensity of microbial interactions in response to climate change in different soil layers. This study provides new insights to understand and predict future effects of climate change on soil microbes in alpine forest ecosystems.
Low avidity circulating SARS-CoV-2 reactive CD8+ T cells with proinflammatory TEMRA phenotype are associated with post-acute sequelae of COVID-19
Authors: Paniskaki Krystallenia , Konik Margarethe J. , Anft Moritz , Heidecke Harald , Meister Toni L. , Pfaender Stephanie , Krawczyk Adalbert , Zettler Markus , Jäger Jasmin , Gaeckler Anja , Dolff Sebastian , Westhoff Timm H. , Rohn Hana , Stervbo Ulrik , Scheibenbogen Carmen , Witzke Oliver , Babel Nina
Published: June 2023

The role of adaptive SARS-CoV-2 specific immunity in post-acute sequelae of COVID-19 (PASC) is not well explored, although a growing population of convalescent COVID-19 patients with manifestation of PASC is observed. We analyzed the SARS-CoV-2-specific immune response, via pseudovirus neutralizing assay and multiparametric flow cytometry in 40 post-acute sequelae of COVID-19 patients with non-specific PASC manifestation and 15 COVID-19 convalescent healthy donors. Although frequencies of SARS-CoV-2-reactive CD4+ T cells were similar between the studied cohorts, a stronger SARS-CoV-2 reactive CD8+ T cell response, characterized by IFNγ production and predominant TEMRA phenotype but low functional TCR avidity was detected in PASC patients compared to controls. Of interest, high avidity SARS-CoV-2-reactive CD4+ and CD8+ T cells were comparable between the groups demonstrating sufficient cellular antiviral response in PASC. In line with the cellular immunity, neutralizing capacity in PASC patients was not inferior compared to controls. In conclusion, our data suggest that PASC may be driven by an inflammatory response triggered by an expanded population of low avidity SARS-CoV-2 reactive pro-inflammatory CD8+ T cells. These pro-inflammatory T cells with TEMRA phenotype are known to be activated by a low or even without TCR stimulation and lead to a tissue damage. Further studies including animal models are required for a better understanding of underlying immunopathogensis. Summary: A CD8+ driven persistent inflammatory response triggered by SARS-CoV-2 may be responsible for the observed sequelae in PASC patients.
Effect of Trichoderma viride on rhizosphere microbial communities and biocontrol of soybean root rot
Authors: Gao Peixin , Qi Kai , Han Yujuan , Ma Liguo , Zhang Bo , Zhang Yueli , Guan Xiumin , Qi Junshan
Published: June 2023

Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.
CCL4 participates in the reprogramming of glucose metabolism induced by ALV-J infection in chicken macrophages
Authors: Wu Huixian , Zaib Gul , Luo Huan , Guo Wang , Wu Ting , Zhu Shutong , Wang Chenjun , Chai Wenxian , Xu Qi , Cui Hengmi , Hu Xuming
Published: June 2023

Interferon and chemokine-mediated immune responses are two general antiviral programs of the innate immune system in response to viral infections and have recently emerged as important players in systemic metabolism. This study found that the chemokine CCL4 is negatively regulated by glucose metabolism and avian leukosis virus subgroup J (ALV-J) infection in chicken macrophages. Low expression levels of CCL4 define this immune response to high glucose treatment or ALV-J infection. Moreover, the ALV-J envelope protein is responsible for CCL4 inhibition. We confirmed that CCL4 could inhibit glucose metabolism and ALV-J replication in chicken macrophages. The present study provides novel insights into the antiviral defense mechanism and metabolic regulation of the chemokine CCL4 in chicken macrophages.
ST-YOLOA: a Swin-transformer-based YOLO model with an attention mechanism for SAR ship detection under complex background
Authors: Zhao Kai , Lu Ruitao , Wang Siyu , Yang Xiaogang , Li Qingge , Fan Jiwei
Published: June 2023

A synthetic aperture radar (SAR) image is crucial for ship detection in computer vision. Due to the background clutter, pose variations, and scale changes, it is a challenge to construct a SAR ship detection model with low false-alarm rates and high accuracy. Therefore, this paper proposes a novel SAR ship detection model called ST-YOLOA. First, the Swin Transformer network architecture and coordinate attention (CA) model are embedded in the STCNet backbone network to enhance the feature extraction performance and capture global information. Second, we used the PANet path aggregation network with a residual structure to construct the feature pyramid to increase global feature extraction capability. Next, to cope with the local interference and semantic information loss problems, a novel up/down-sampling method is proposed. Finally, the decoupled detection head is used to achieve the predicted output of the target position and the boundary box to improve convergence speed and detection accuracy. To demonstrate the efficiency of the proposed method, we have constructed three SAR ship detection datasets: a norm test set (NTS), a complex test set (CTS), and a merged test set (MTS). The experimental results show that our ST-YOLOA achieved an accuracy of 97.37%, 75.69%, and 88.50% on the three datasets, respectively, superior to the effects of other state-of-the-art methods. Our ST-YOLOA performs favorably in complex scenarios, and the accuracy is 4.83% higher than YOLOX on the CTS. Moreover, ST-YOLOA achieves real-time detection with a speed of 21.4 FPS.
Bimodal modulation of L1 interneuron activity in anterior cingulate cortex during fear conditioning
Authors: Fossati Giuliana , Kiss-Bodolay Daniel , Prados Julien , Chéreau Ronan , Husi Elodie , Cadilhac Christelle , Gomez Lucia , Silva Bianca A. , Dayer Alexandre , Holtmaat Anthony
Published: June 2023

The anterior cingulate cortex (ACC) plays a crucial role in encoding, consolidating and retrieving memories related to emotionally salient experiences, such as aversive and rewarding events. Various studies have highlighted its importance for fear memory processing, but its circuit mechanisms are still poorly understood. Cortical layer 1 (L1) of the ACC might be a particularly important site of signal integration, since it is a major entry point for long-range inputs, which is tightly controlled by local inhibition. Many L1 interneurons express the ionotropic serotonin receptor 3a (5HT3aR), which has been implicated in post-traumatic stress disorder and in models of anxiety. Hence, unraveling the response dynamics of L1 interneurons and subtypes thereof during fear memory processing may provide important insights into the microcircuit organization regulating this process. Here, using 2-photon laser scanning microscopy of genetically encoded calcium indicators through microprisms in awake mice, we longitudinally monitored over days the activity of L1 interneurons in the ACC in a tone-cued fear conditioning paradigm. We observed that tones elicited responses in a substantial fraction of the imaged neurons, which were significantly modulated in a bidirectional manner after the tone was associated to an aversive stimulus. A subpopulation of these neurons, the neurogliaform cells (NGCs), displayed a net increase in tone-evoked responses following fear conditioning. Together, these results suggest that different subpopulations of L1 interneurons may exert distinct functions in the ACC circuitry regulating fear learning and memory.
Predicting SARS-CoV-2 infection among hemodialysis patients using multimodal data
Authors: Duan Juntao , Li Hanmo , Ma Xiaoran , Zhang Hanjie , Lasky Rachel , Monaghan Caitlin K. , Chaudhuri Sheetal , Usvyat Len A. , Gu Mengyang , Guo Wensheng , Kotanko Peter , Wang Yuedong
Published: June 2023

Background

The coronavirus disease 2019 (COVID-19) pandemic has created more devastation among dialysis patients than among the general population. Patient-level prediction models for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are crucial for the early identification of patients to prevent and mitigate outbreaks within dialysis clinics. As the COVID-19 pandemic evolves, it is unclear whether or not previously built prediction models are still sufficiently effective.

Methods

We developed a machine learning (XGBoost) model to predict during the incubation period a SARS-CoV-2 infection that is subsequently diagnosed after 3 or more days. We used data from multiple sources, including demographic, clinical, treatment, laboratory, and vaccination information from a national network of hemodialysis clinics, socioeconomic information from the Census Bureau, and county-level COVID-19 infection and mortality information from state and local health agencies. We created prediction models and evaluated their performances on a rolling basis to investigate the evolution of prediction power and risk factors.

Result

From April 2020 to August 2020, our machine learning model achieved an area under the receiver operating characteristic curve (AUROC) of 0.75, an improvement of over 0.07 from a previously developed machine learning model published by Kidney360 in 2021. As the pandemic evolved, the prediction performance deteriorated and fluctuated more, with the lowest AUROC of 0.6 in December 2021 and January 2022. Over the whole study period, that is, from April 2020 to February 2022, fixing the false-positive rate at 20%, our model was able to detect 40% of the positive patients. We found that features derived from local infection information reported by the Centers for Disease Control and Prevention (CDC) were the most important predictors, and vaccination status was a useful predictor as well. Whether or not a patient lives in a nursing home was an effective predictor before vaccination, but became less predictive after vaccination.

Conclusion

As found in our study, the dynamics of the prediction model are frequently changing as the pandemic evolves. County-level infection information and vaccination information are crucial for the success of early COVID-19 prediction models. Our results show that the proposed model can effectively identify SARS-CoV-2 infections during the incubation period. Prospective studies are warranted to explore the application of such prediction models in daily clinical practice.
Diagnostic accuracy of telestroke consultation: a Louisiana based tele-network experience
Authors: Poongkunran Mugilan , Ulep Robin D. , Stuntz Gage A. , Mitchell Sara , Gaines Kenneth J. , Vidal Gabriel , Chehebar Daniel , Iwuchukwu Ifeanyi O. , McGrade Harold , Mohammed Alaa E. , Zweifler Richard M.
Published: June 2023

Background and purpose

Telestroke has grown significantly since its implementation. Despite growing utilization, there is a paucity of data regarding the diagnostic accuracy of telestroke to distinguish between stroke and its mimics. We aimed to evaluate diagnostic accuracy of telestroke consultations and explore the characteristics of misdiagnosed patients with a focus on stroke mimics.

Methods

We conducted a retrospective study of all the consultations in our Ochsner Health’s TeleStroke program seen between April 2015 and April 2016. Consultations were classified into one of three diagnostic categories: stroke/transient ischemic attack, mimic, and uncertain. Initial telestroke diagnosis was compared with the final diagnosis post review of all emergency department and hospital data. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (LR+) and negative likelihood ratio (LR−) for diagnosis of stroke/TIA versus mimic were calculated. Area under receiver-operating characteristic curve (AUC) analysis to predict true stroke was performed. Bivariate analysis based on the diagnostic categories examined association with sex, age, NIHSS, stroke risk factors, tPA given, bleeding after tPA, symptom onset to last known normal, symptom onset to consult, timing in the day, and consult duration. Logistic regression was performed as indicated by bivariate analysis.

Results

Eight hundred and seventy-four telestroke evaluations were included in our analysis. Accurate diagnosis through teleneurological consultation was seen in 85% of which 532 were strokes (true positives) and 170 were mimics (true negatives). Sensitivity, specificity, PPV, NPV were 97.8, 82.5, 93.7 and 93.4%, respectively. LR+ and LR− were 5.6 and 0.03. AUC (95% CI) was 0.9016 (0.8749–0.9283). Stroke mimics were more common with younger age and female gender and in those with less vascular risk factors. LR revealed OR (95% CI) of misdiagnosis for female gender of 1.9 (1.3–2.9). Lower age and lower NIHSS score were other predictors of misdiagnosis.

Conclusion

We report high diagnostic accuracy of the Ochsner Telestroke Program in discriminating stroke/TIA and stroke mimics, with slight tendency towards over diagnosis of stroke. Female gender, younger age and lower NIHSS score were associated with misdiagnosis.
Impact of sex and APOE-ε4 genotype on patterns of regional brain atrophy in Alzheimer's disease and healthy aging
Authors: Sauty Benoît , Durrleman Stanley
Published: June 2023

Alzheimer's Disease (AD) is a heterogeneous disease that disproportionately affects women and people with the APOE-ε4 susceptibility gene. We aim to describe the not-well-understood influence of both risk factors on the dynamics of brain atrophy in AD and healthy aging. Regional cortical thinning and brain atrophy were modeled over time using non-linear mixed-effect models and the FreeSurfer software with t1-MRI scans from the Alzheimer's Disease Neuroimaging Initiative (N= 1,502 subjects, 6,728 images in total). Covariance analysis was used to disentangle the effect of sex and APOE genotype on the regional onset age and pace of atrophy, while correcting for educational level. A map of the regions mostly affected by neurodegeneration is provided. Results were confirmed on gray matter density data from the SPM software. Women experience faster atrophic rates in the temporal, frontal, parietal lobes and limbic system and earlier onset in the amygdalas, but slightly later onset in the postcentral and cingulate gyri as well as all regions of the basal ganglia and thalamus. APOE-ε4 genotypes leads to earlier and faster atrophy in the temporal, frontal, parietal lobes, and limbic system in AD patients, but not in healthy patients. Higher education was found to slightly delay atrophy in healthy patients, but not for AD patients. A cohort of amyloid positive patients with MCI showed a similar impact of sex as in the healthy cohort, while APOE-ε4 showed similar associations as in the AD cohort. Female sex is as strong a risk factor for AD as APOE−ε4 genotype regarding neurodegeneration. Women experience a sharper atrophy in the later stages of the disease, although not a significantly earlier onset. These findings may have important implications for the development of targeted intervention.
Olfactory memory in mild cognitive impairment and Alzheimer’s disease
Authors: Audronyte Egle , Sutnikiene Vaiva , Pakulaite-Kazliene Gyte , Kaubrys Gintaras
Published: June 2023

Introduction

Olfaction is impaired in Alzheimer’s disease (AD). However, olfactory memory has rarely been examined. As the pathogenesis of AD remains largely unknown, collecting more data regarding the occurrence and progression of its symptoms would help gain more insight into the disease.

Objective

To investigate olfactory memory and its relationship with verbal memory and other clinical features in patients with early-stage AD.

Methods

Three groups of participants were enrolled in this study: patients with mild dementia due to AD (MD-AD, N = 30), patients with mild cognitive impairment due to AD (MCI-AD, N = 30), and cognitively normal older participants (CN, N = 30). All participants underwent cognitive evaluation (Clinical Dementia Rating scale, Mini Mental State Examination, Alzheimer’s Disease Assessment Scale–Cognitive Subscale, delayed verbal recall, and verbal fluency tests) and assessment of olfactory immediate and delayed recognition memory.

Results

Olfactory immediate and delayed recognition memory scores were significantly lower in the MD-AD group than in the MCI-AD and CN groups. The MCI-AD and CN groups did not differ significantly [in both cases, Kruskal–Wallis test, p < 0.05; post hoc analysis revealed significant differences between the MD-AD and MCI-AD groups and between the MD-AD and CN groups (p < 0.05), and no significant difference between the MCI-AD and CN groups (p > 0.05)]. Verbal immediate recall, delayed recall after 5 min, and delayed recall after 30 min scores were significantly worse in the MD-AD and MCI-AD groups than in the CN group. MD-AD and MCI-AD groups did not differ significantly [in all cases Kruskal–Wallis test, p < 0.05; post hoc analysis revealed significant differences between MD-AD and CN groups, and MCI-AD and CN groups (p < 0.05) and no significant difference between MD-AD and MCI-AD groups (p > 0.05)]. Duration of AD symptoms was a strong predictor of both immediate and delayed olfactory recognition memory scores.

Conclusion

Olfactory memory impairment was observed in patients with AD. The changes progress during the course of the disease. However, unlike verbal memory, olfactory memory is not significantly impaired in the prodromal stage of AD.
Comparison of revascularization and conservative treatment for hemorrhagic moyamoya disease in East Asian Countries: a single-center case series and a systematic review with meta-analysis
Authors: Zhang Xiang-Hua , He Jun-Hua , Zhang Xiang-Sheng , Zhang Jing , Wang Cheng-jun , Dong Yi-Peng , Tao Wu
Published: June 2023

Objective

The optimal treatment approach for hemorrhagic moyamoya disease (HMMD) remains a topic of debate, particularly regarding the comparative efficacy of revascularization versus conservative treatment. Our study, which included a single-center case series and a systematic review with meta-analysis, aimed to determine whether surgical revascularization is associated with a significant reduction in postoperative rebleeding, ischemic events, and mortality compared to conservative treatment among East Asian HMMD patients.

Methods

We conducted a systematic literature review by searching PubMed, Google Scholar, Wanfang Med Online (WMO), and the China National Knowledge Infrastructure (CNKI). The outcomes of surgical revascularization and conservative treatment, including rebleeding, ischemic events and mortality, were compared. The authors' institutional series of 24 patients were also included and reviewed in the analysis.

Results

A total of 19 East Asian studies involving 1,571 patients as well as our institution's retrospective study of 24 patients were included in the study. In the adult patients-only studies, those who underwent revascularization had significantly lower rates of rebleeding, ischemic events, and mortality compared to those who received conservative treatment (13.1% (46/352) vs. 32.4% (82/253), P < 0.00001; 4.0% (5/124) vs. 14.9% (18/121), P = 0.007; and 3.3% (5/153) vs. 12.6% (12/95), P = 0.01, respectively). In the adult/pediatric patients' studies, similar statistical results of rebleeding, ischemic events, and mortality have been obtained (70/588 (11.9%) vs. 103/402 (25.6%), P = 0.003 or <0.0001 in a random or fixed-effects model, respectively; 14/296 (4.7%) vs. 26/183 (14.2%), P = 0.001; and 4.6% (15/328) vs. 18.7% (23/123), P = 0.0001, respectively).

Conclusion

The current single-center case series and systematic review with meta-analysis of studies demonstrated that surgical revascularization, including direct, indirect, and a combination of both, significantly reduces rebleeding, ischemic events, and mortality in HMMD patients in the East Asia region. More well-designed studies are warranted to further confirm these findings.
Differentially expressed miRNA profiles of serum-derived exosomes in patients with sudden sensorineural hearing loss
Authors: Zhang Juhong , Ma Haizhu , Yang Guijun , Ke Jing , Sun Wenfang , Yang Li , Kuang Shaojing , Li Hai , Yuan Wei
Published: June 2023

Objectives

This study aimed to compare the expressed microRNA (miRNA) profiles of serum-derived exosomes of patients with sudden sensorineural hearing loss (SSNHL) and normal hearing controls to identify exosomal miRNAs that may be associated with SSNHL or serve as biomarkers for SSNHL.

Methods

Peripheral venous blood of patients with SSNHL and healthy controls was collected to isolate exosomes. Nanoparticle tracking analysis, transmission electron microscopy, and Western blotting were used to identify the isolated exosomes, after which total RNA was extracted and used for miRNA transcriptome sequencing. Differentially expressed miRNAs (DE-miRNAs) were identified based on the thresholds of P < 0.05 and |log2fold change| > 1 and subjected to functional analyses. Finally, four exosomal DE-miRNAs, including PC-5p-38556_39, PC-5p-29163_54, PC-5p-31742_49, and hsa-miR-93-3p_R+1, were chosen for validation using quantitative real-time polymerase chain reaction (RT-qPCR).

Results

Exosomes were isolated from serum and identified based on particle size, morphological examination, and expression of exosome-marker proteins. A total of 18 exosomal DE-miRNAs, including three upregulated and 15 downregulated miRNAs, were found in SSNHL cases. Gene ontology (GO) functional annotation analysis revealed that target genes in the top 20 terms were mainly related to “protein binding,” “metal ion binding,” “ATP binding,” and “intracellular signal transduction.” Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these target genes were functionally enriched in the “Ras,” “Hippo,” “cGMP-PKG,” and “AMPK signaling pathways.” The expression levels of PC-5p-38556_39 and PC-5p-29163_54 were significantly downregulated and that of miR-93-3p_R+1 was highly upregulated in SSNHL. Consequently, the consistency rate between sequencing and RT-qPCR was 75% and sequencing results were highly reliable.

Conclusion

This study identified 18 exosomal DE-miRNAs, including PC-5p-38556_39, PC-5p-29163_54, and miR-93-3p, which may be closely related to SSNHL pathogenesis or serve as biomarkers for SSNHL.
Heart rate variability during auricular acupressure at the left sympathetic point on healthy volunteers: a pilot study
Authors: Trinh Dieu-Thuong Thi , Le Hoang-Linh Thi , Bui Minh-Man Pham , Thai Khac-Minh
Published: June 2023

Introduction

This research is a pilot, single-blinded study investigating heart rate variability (HRV) during auricular acupressure at the left sympathetic point (AH7) in healthy volunteers.

Methods

There were 120 healthy volunteers with hemodynamic indexes (heart rate, blood pressure) within normal ranges, randomly divided into two groups AG and SG (in each group having a gender ratio 1:1, aged 20−29), to receive either auricular acupressure using ear seed (AG) or sham method using adhesive patches without seed (SG) at the left sympathetic point while lying in a supine position. Acupressure intervention lasted 25 min, and HRV was recorded by a photoplethysmography device–namely, Kyto HRM-2511B and Elite appliance.

Results

Auricular acupressure at the left Sympathetic point (AG) led to a significant reduction in heart rate (HR) (p < 0.05) and a considerable increase in HRV parameters demonstrated by HF (High-frequency power) (p < 0.05), compared to sham auricular acupressure (SG). However, no significant changes in LF (Low-frequency power) and RR (Respiratory rate) (p > 0.05) were observed in both groups during the process.

Conclusion

These findings suggest that auricular acupressure at the left sympathetic point may activate the parasympathetic nervous system while a healthy person is lying relaxed.
An integrated convolutional neural network for classifying small pulmonary solid nodules
Authors: Mei Mengqing , Ye Zhiwei , Zha Yunfei
Published: June 2023

Achieving accurate classification of benign and malignant pulmonary nodules is essential for treating some diseases. However, traditional typing methods have difficulty obtaining satisfactory results on small pulmonary solid nodules, mainly caused by two aspects: (1) noise interference from other tissue information; (2) missing features of small nodules caused by downsampling in traditional convolutional neural networks. To solve these problems, this paper proposes a new typing method to improve the diagnosis rate of small pulmonary solid nodules in CT images. Specifically, first, we introduce the Otsu thresholding algorithm to preprocess the data and filter the interference information. Then, to acquire more small nodule features, we add parallel radiomics to the 3D convolutional neural network. Radiomics can extract a large number of quantitative features from medical images. Finally, the classifier generated more accurate results by the visual and radiomic features. In the experiments, we tested the proposed method on multiple data sets, and the proposed method outperformed other methods in the small pulmonary solid nodule classification task. In addition, various groups of ablation experiments demonstrated that the Otsu thresholding algorithm and radiomics are helpful for the judgment of small nodules and proved that the Otsu thresholding algorithm is more flexible than the manual thresholding algorithm.
Arcuate fasciculus and pre-reading language development in children with prenatal alcohol exposure
Authors: Ostertag Curtis , Reynolds Jess E. , Kar Preeti , Dewey Deborah , Gibbard W. Ben , Tortorelli Christina , Lebel Catherine
Published: June 2023

Introduction

Prenatal alcohol exposure (PAE) contributes to widespread neurodevelopmental challenges, including reading, and has been associated with altered white matter. Here, we aimed to investigate whether arcuate fasciculus (AF) development is associated with pre-reading language skills in young children with PAE.

Methods

A total of 51 children with confirmed PAE (25 males; 5.6 ± 1.1 years) and 116 unexposed controls (57 males; 4.6 ± 1.2 years) underwent longitudinal diffusion tensor imaging (DTI), for a total of 111 scans from participants with PAE and 381 scans in the unexposed control group. We delineated the left and right AF and extracted mean fractional anisotropy (FA) and mean diffusivity (MD). Pre-reading language ability was assessed using age-standardized phonological processing (PP) and speeded naming (SN) scores of the NEPSY-II. Linear mixed effects models were run to determine the relationship between diffusion metrics and age, group, sex, and age-by-group interactions, with subject modeled as a random factor. A secondary mixed effect model analysis assessed the influence of white matter microstructure and PAE on pre-reading language ability using diffusion metric-by-age-by-group interactions, with 51 age- and sex-matched unexposed controls.

Results

Phonological processing (PP) and SN scores were significantly lower in the PAE group (p< 0.001). In the right AF, there were significant age-by-group interactions for FA (p< 0.001) and MD (p= 0.0173). In the left AF, there was a nominally significant age-by-group interaction for MD that failed to survive correction (p= 0.0418). For the pre-reading analysis, a significant diffusion-by-age-by-group interaction was found for left FA (p= 0.0029) in predicting SN scores, and for the right FA (p= 0.00691) in predicting PP scores.

Discussion

Children with PAE showed altered developmental trajectories for the AF, compared with unexposed controls. Children with PAE, regardless of age, showed altered brain-language relationships that resembled those seen in younger typically developing children. Our findings support the contention that altered developmental trajectories in the AF may be associated with functional outcomes in young children with PAE.
Vitis Vinifera Leaf Extract Protects Against Glutamate-Induced Oxidative Toxicity in HT22 Hippocampal Neuronal Cells and Increases Stress Resistance Properties in Caenorhabditis Elegans
Authors: Duangjan Chatrawee , Rangsinth Panthakarn , Zhang Shaoxiong , Gu Xiaojie , Wink Michael , Tencomnao Tewin
Published: June 2023

Vitis vinifea has been used for traditional medicines, food, beverages, and dietary antioxidant supplements. The chemical compositions and biological activities of the fruits and seeds have been extensively investigated. However, the biological effects of the leaves are limited, and its anti-neurodegeneration or antiaging activities are little known. The current work aims to study the beneficial effects of V. vinifera leaf extract on neuroprotective effects in HT22 cells, antiaging, and oxidative stress resistance properties in the Caenorhabditis elegans model. The ethanol extract was characterized by phytochemical composition using gas/liquid chromatography–mass spectrometry and reversed-phase high-performance liquid chromatography. The beneficial effects of V. vinifera ethanol (VVE) extract on antioxidant properties, neuroprotective effects, and the underlying mechanisms were studied by in vitro and in vivo studies. In HT22 cells, we found that VVE has a protective effect against glutamate-mediated oxidative stress-induced cell death. The gene expression of cellular antioxidant enzymes such as CAT, SODs, GSTs, and GPx was upregulated by VVE treatment. Moreover, VVE was also shown to alleviate oxidative stress and attenuate reactive oxygen species accumulation in C. elegans. We demonstrated that VVE could upregulate the expression of stress-response genes gst-4 and sod-3 and downregulate the expression of hsp-16.2. Our results suggest that the oxidative stress resistance properties of VVE are possibly involved in DAF-16/FoxO transcription factors. VVE reduced age-related markers (lipofuscin) while did not extend the life span of C. elegans under normal conditions. This study reports the neuroprotective effect and antioxidant activity of V. vinifera leaf extract and suggests its potential as a dietary or alternative supplement to defend against oxidative stress and age-related diseases.
Circular RNAs in ferroptosis: regulation mechanism and potential clinical application in disease
Authors: Li Fei , Li Pei-Feng , Hao Xiao-Dan
Published: June 2023

Ferroptosis, an iron-dependent non-apoptotic form of cell death, is reportedly involved in the pathogenesis of various diseases, particularly tumors, organ injury, and degenerative pathologies. Several signaling molecules and pathways have been found to be involved in the regulation of ferroptosis, including polyunsaturated fatty acid peroxidation, glutathione/glutathione peroxidase 4, the cysteine/glutamate antiporter system Xc-, ferroptosis suppressor protein 1/ubiquinone, and iron metabolism. An increasing amount of evidence suggests that circular RNAs (circRNAs), which have a stable circular structure, play important regulatory roles in the ferroptosis pathways that contribute to disease progression. Hence, ferroptosis-inhibiting and ferroptosis-stimulating circRNAs have potential as novel diagnostic markers or therapeutic targets for cancers, infarctions, organ injuries, and diabetes complications linked to ferroptosis. In this review, we summarize the roles that circRNAs play in the molecular mechanisms and regulatory networks of ferroptosis and their potential clinical applications in ferroptosis-related diseases. This review furthers our understanding of the roles of ferroptosis-related circRNAs and provides new perspectives on ferroptosis regulation and new directions for the diagnosis, treatment, and prognosis of ferroptosis-related diseases.
Comprehensive analysis on the magnetic field error of a K–Rb–21Ne comagnetometer with low-frequency bias magnetic field sensitivity
Authors: Wu Zhihong , Liu Feng , Wang Zhuo , Fan Wenfeng , Pang Haoying , Quan Wei
Published: June 2023

The spin-exchange relaxation-free comagnetometer (SERFC) is of important research value compared to existing high-precision gyroscopes because of its extremely high theoretical limit sensitivity and long-term stability, in which one significant limiting factor is the magnetic field error. First, the relationship between the magnetic field gradient and the nuclear spin relaxation mechanism is introduced into the frequency response and steady-state response models of SERFC. Then, a novel method for suppression of the low-frequency magnetic field error based on the modified bias magnetic field sensitivity model is proposed. Finally, the effectiveness of the proposed suppression methods is demonstrated by optimizing the cell temperature, pump light power, and compensation magnetic field gradient to increase the suppression factor by 72.19%, 20.24%, and 69.86%, and the corresponding bias instability increased by 55.41%, 20.84%, and 27.63%, respectively. This study contributes to improving the long-term zero bias stability of the SERFC.
A mechanistic pharmacokinetic model for intrathecal administration of antisense oligonucleotides
Authors: Linninger Andreas A. , Barua Dipak , Hang Yaming , Iadevaia Sergio , Vakilynejad Majid
Published: June 2023

Intrathecal administration is an important mode for delivering biological agents targeting central nervous system (CNS) diseases. However, current clinical practices lack a sound theorical basis for a quantitative understanding of the variables and conditions that govern the delivery efficiency and specific tissue targeting especially in the brain. This work presents a distributed mechanistic pharmacokinetic model (DMPK) for predictive analysis of intrathecal drug delivery to CNS. The proposed DMPK model captures the spatiotemporal dispersion of antisense oligonucleotides (ASO) along the neuraxis over clinically relevant time scales of days and weeks as a function of infusion, physiological and molecular properties. We demonstrate its prediction capability using biodistribution data of antisense oligonucleotide (ASO) administration in non-human primates. The results are in close agreement with the observed ASO pharmacokinetics in all key compartments of the central nervous system. The model enables determination of optimal injection parameters such as intrathecal infusion volume and duration for maximum ASO delivery to the brain. Our quantitative model-guided analysis is suitable for identifying optimal parameter settings to target specific brain regions with therapeutic drugs such as ASOs.
Tree seedling growth allocation of Castanopsis kawakamii is determined by seed-relative positions
Authors: Zhu Jing , Jiang Lan , Chen Lyuyi , Jin Xing , Xing Cong , Liu Jinfu , Yang Yongchuan , He Zhongsheng
Published: June 2023

Plants allocate growth to different organs as a strategy to obtain limiting resources in different environments. Tree seeds that fall from a mother tree settle on, within, or below the forest floor and litter layer, and their relative positions can determine seedling biomass and nutrient allocation and ultimately affect survival to the sapling stage. However, how emerged seedling biomass and nutrients of each organ are affected by seeds in different positions is not yet completely understood in subtropical forests. Therefore, an experiment was conducted with seeds positioned above the litter layers of different thicknesses, on the forest floor, and beneath the litter layer, and the influences of seed position on biomass allocation and nutrient use efficiency of emerged seedlings ofCastanopsis kawakamiiwas examined. The aim of the study was to determine the optimal seed position to promote regeneration. Allocation strategies were well coordinated in the emerged seedlings from different seed positions. Seedlings from seeds positioned above litter layers of different thicknesses (~40 and 80 g of litter) allocated growth to leaf tissue at the expense of root tissue (lower root mass fraction) and increased nitrogen (N) and phosphorus (P) accumulation and nutrient use efficiency. Seedlings from seeds positioned beneath a deep litter layer allocated most growth to roots (high root: shoot ratio, root mass fraction) to capture available resources at the expense of leaf growth. Seedlings from seeds positioned on the forest floor allocated most growth to roots to obtain limiting resources. Further, we also found that these traits were clustered into three groups based on trait similarity, and the cumulative interpretation rate was 74.2%. Thus, seed relative positions significantly affected seedling growth by altering the allocation of resources to different organs. The different strategies indicated that root N:P ratios (entropy weight vector was 0.078) and P nutrient use efficiency were essential factors affecting seedling growth in the subtropical forest. Of the seed positions analyzed, beneath a moderate litter layer (~40 g of litter) was the most suitable position for the growth and survival ofCastanopsisseedlings. In future studies, field and lab experiments will be combined to reveal the mechanisms underlying forest regeneration.
Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. pelargonii strain 305 and novel type III effectors identified in Xanthomonas
Authors: Wagner Naama , Ben-Meir Daniella , Teper Doron , Pupko Tal
Published: June 2023

Xanthomonas hortorum pv. pelargonii is the causative agent of bacterial blight in geranium ornamental plants, the most threatening bacterial disease of this plant worldwide. Xanthomonas fragariae is the causative agent of angular leaf spot in strawberries, where it poses a significant threat to the strawberry industry. Both pathogens rely on the type III secretion system and the translocation of effector proteins into the plant cells for their pathogenicity. Effectidor is a freely available web server we have previously developed for the prediction of type III effectors in bacterial genomes. Following a complete genome sequencing and assembly of an Israeli isolate of Xanthomonas hortorum pv. pelargonii - strain 305, we used Effectidor to predict effector encoding genes both in this newly sequenced genome, and in X. fragariae strain Fap21, and validated its predictions experimentally. Four and two genes in X. hortorum and X. fragariae, respectively, contained an active translocation signal that allowed the translocation of the reporter AvrBs2 that induced the hypersensitive response in pepper leaves, and are thus considered validated novel effectors. These newly validated effectors are XopBB, XopBC, XopBD, XopBE, XopBF, and XopBG.
Clonal integration promotes the growth of Phragmites australis populations in saline wetlands of the Yellow River Delta
Authors: Guan Bo , Yu Junbao , Wu Mengdi , Liu Xiaoling , Wang Xuehong , Yang Jisong , Zhou Di , Zhang Xiaolong
Published: June 2023

Estuarine wetlands are highly heterogeneous due to strong interactions between freshwater input and seawater intrusion. However, little is known about how clonal plant populations adapt to heterogeneous salinity in soil environments. In the present study, the effects of clonal integration on Phragmites australis populations under salinity heterogeneity were studied using field experiments with 10 treatments in the Yellow River Delta. Clonal integration significantly increased plant height, aboveground biomass, underground biomass, root–shoot ratio, intercellular CO2 concentration, net photosynthetic rate, stomatal conductance, transpiration rate, and stem Na+ content under homogeneous treatment. Under the heterogeneous salt treatment, clonal integration significantly affected total aboveground and underground biomass, photosynthetic traits, and stem Na+ content under different salt gradients. The increase in salt concentration inhibited the physiological activity and growth of P. australis to varying degrees. Compared with the heterogeneous saline environment, clonal integration was more beneficial to P. australis populations in the homogeneous saline habitat. The results of the present study suggest that P. australis prefers homogeneous saline habitats; however, plants can adapt to heterogeneous salinity conditions via clonal integration.
Transcriptome analysis showed that tomato-rootstock enhanced salt tolerance of grafted seedlings was accompanied by multiple metabolic processes and gene differences
Authors: Wu Xiaolei , Yuan Ding , Bian Xinyu , Huo Ruixiao , Lü Guiyun , Gong Binbin , Li Jingrui , Liu Sichao , Gao Hongbo
Published: June 2023

Introduction

Grafting is a commonly used cultural practice to counteract salt stress and is especially important for vegetable production. However, it is not clear which metabolic processes and genes are involved in the response of tomato rootstocks to salt stress.

Methods

To elucidate the regulatory mechanism through which grafting enhances salt tolerance, we first evaluated the salt damage index, electrolyte permeability and Na+ accumulation in tomato (Solanum lycopersicum L.) leaves of grafted seedlings (GSs) and nongrafted seedlings (NGSs) subjected to 175 mmol·L− 1 NaCl for 0-96 h, covering the front, middle and rear ranges.

Results

Compared with the NGS, the GSs were more salt tolerant, and the Na+ content in the leaves decreased significantly. Through transcriptome sequencing data analysis of 36 samples, we found that GSs exhibited more stable gene expression patterns, with a lower number of DEGs. WRKY and PosF21 transcription factors were significantly upregulated in the GSs compared to the NGSs. Moreover, the GSs presented more amino acids, a higher photosynthetic index and a higher content of growth-promoting hormones. The main differences between GSs and NGSs were in the expression levels of genes involved in the BR signaling pathway, with significant upregulation of XTHs. The above results show that the metabolic pathways of “photosynthetic antenna protein”, “amino acid biosynthesis” and “plant hormone signal transduction” participate in the salt tolerance response of grafted seedlings at different stages of salt stress, maintaining the stability of the photosynthetic system and increasing the contents of amino acids and growth-promoting hormones (especially BRs). In this process, the transcription factors WRKYs, PosF21 and XTHs might play an important role at the molecular level.

Discussion

The results of this study demonstrates that grafting on salt tolerant rootstocks can bring different metabolic processes and transcription levels changes to scion leaves, thereby the scion leaves show stronger salt tolerance. This information provides new insight into the mechanism underlying tolerance to salt stress regulation and provides useful molecular biological basis for improving plant salt resistance.