bluuebunny/crossref_metadata_2025 huggingface dataset:
Divergent assembly of soil microbial necromass from microbial and organic fertilizers in Chimonobambusa hejiangensis forest
Authors: Cai Xue , Long Zhijian , Li Yongyang , Cao Ying , Wang Boya , Zhao Bo , Ren Peng , Zhao Xin , Huang Yan , Lu Xueqin , Hu Shanglian , Xu Gang
Published: June 2024

Introduction

Variability in microbial residues within soil aggregates are becoming progressively essential to the nutritive and sustainability of soils, and are therefore broadly regarded as an indispensable part of soil organic matter. It is unexplored how the widespread implementation of microbial fertilisers in agricultural production impacts soil organic nutrients, in particular the microbial residue fraction.

Methods

We performed a three-year field experiment to verify the distinct impacts of microbial and organic fertilizers on carbon accumulation in soil microbial leftovers among aggregate fractions.

Results

Microbial residual carbon was shown to decrease insignificantly during the application of microbial fertilizer and to rise marginally afterwards with the utilization of organic fertilizer. However, the combined effects of the two fertilizers had substantial impacts on the accumulation of microbial residual carbon. Changes in the structure of the fungi and bacteria shown in this study have implications for the short-term potential of microbial fertilizer shortages to permanent soil carbon sequestration. Additionally, our findings revealed variations in microbial residue accumulation across the microbial fertilizers, with Azotobacter chroococcum fertilizer being preferable to Bacillus mucilaginosus fertilizer due to its higher efficiency. In this scenario of nutrient addition, fungal residues may serve as the primary binding component or focal point for the production of new microaggregates, since the quantity of SOC provided by fungal residues increased while that supplied by bacterial residues decreased.

Discussion

Our findings collectively suggested that the mechanisms behind the observed bacterial and fungal MRC (microbial residue carbon) responses to microbial fertilizer or organic fertilizer in bamboo forest soils are likely to be distinct. The application of microbial fertilizers for a limited duration led to a decline soil stable carbon pool, potentially influencing the regulation of soil nutrients in such hilly bamboo forests.
Prevalence of multidrug-resistant Escherichia coli isolates and virulence gene expression in poultry farms in Jos, Nigeria
Authors: Agusi Ebere Roseann , Kabantiyok Dennis , Mkpuma Nicodemus , Atai Rebecca Bitiyong , Okongwu-Ejike Chidinma , Bakare Ebun Lydia , Budaye James , Sule Kabiru Garba , Rindaps Rindah Joy , James Gyallak Kingsley , Audu Benshak John , Agada Godwin Ojonugwa , Adegboye Oyelola , Meseko Clement Adebajo
Published: June 2024

Introduction

Antimicrobial resistance is increasingly becoming a global health concern. This study aimed to investigate and report MDR Escherichia coli (E. coli) prevalence, resistance, and virulence genes from poultry in Jos, Plateau State, Nigeria.

Methods

The samples were analyzed using microbiological standard methods and polymerase chain reactions (PCRs).

Results

A total of 179 cloacal swabs were collected from bothlocal and exotic poultry breeds, of which 99.4% (178/179) tested positive for E. coli. Among these culturally identified samples, 99.4% (177/178) were furtherconfirmed Escherichia coli with a molecular weight of 401 bp. Multidrugresistance of 45% (80/178) was observed from the confirmed isolates. PCR assays were conducted to detect genes associated with resistance to antibiotics, specifically, tetracycline (tetA gene), sulfonamide (sul1 gene), ampicillin (ampC gene), and quinolone (gyrA gene). Antimicrobial susceptibility test (AST) results revealed substantial antibiotic resistance, with 81.9% (145/177) of the isolates being resistant to tetracycline, 80.2% (142/177) to quinolone, 69.5% (123/177) to sulfonamide, and 66.1% (117/177) to ampicillin. Further analysis on 18 isolates that showed resistance to up to four different antibiotics was carried out using multiplex PCR to detect eae, hlyA, rfbE, fliC, and fstx virulence genes. The study found that 44.4% (15/18) of the isolates were positive for the eae gene, 27.7% (5/18) for stx, 22.2% (4/18) for rfbe gene, and 5.5% (1) for hlya gene, and none tested positive for fliC gene.

Conclusion

These results showed high antibiotic resistance, virulent genes, and significant levels of MDR in E. coli from poultry. This study highlights the urgent need for antimicrobial stewardship practices within the poultry industry due to their profound implications for food safety and public health. This issue is particularly critical in Nigeria, where poultry farming constitutes a significant portion of smallholder farming practices.
Temporal heterogeneity of the root microbiome in Panax ginseng soils across ecological compartments under mild soil disturbance
Authors: Shi Zhenting , Yang Limin , Yang Meiling , Li Kexin , Yang Li , Han Mei
Published: June 2024

Introduction

Knowledge on spatiotemporal heterogeneity of plant root microbiomes is lacking. The diversity of the root microbiome must be revealed for understanding plant–microbe interactions and the regulation of functionally crucial microbial taxa.

Methods

We here investigated the dynamics of microbial group characteristics within each soil ecological compartment [rhizoplane (B), rhizosphere (J), and bulk soil (T)] across different cultivation years (year 4: F4 and year 5: F5) by using high-throughput sequencing (16S and ITS).

Results

According to the species diversity, microbiome diversity and the ASV (amplified sequence variant) number in the rhizoplane ecotone increased significantly with an increase in the planting years. By contrast, the microbiome diversity of the rhizosphere soil remained relatively stable. PCoA and PERMANOVA analyses revealed that microbial taxa among different planting years and ecological compartments varied significantly. Planting years exerted the least effect on the rhizosphere microbiome, but their impact on fungi in the rhizoplane and bacteria in the bulk soil was the most significant.

Discussion

Planting years influenced the microbial community composition in various ecological compartments of ginseng root soil. Potentially harmful fungi such as Cryptococcus (2.83%), Neonectria (0.89%), llyonectria (0.56%), Gibberella (0.41%), Piloderma (4.44%), and Plectosphaerella (3.88%) were enriched in F5B with an increase in planting years, whereas the abundance of potentially beneficial Mortierella increased. Correlation analysis indicated associations between bacterial taxa and soil pH/S-CAT, and between fungal taxa and soil moisture content/total potassium. Our study highlights the significance of changes in rhizoplane fungi and the stability of the rhizosphere microbial community in comprehending plant ecological sustainability.
Bacillus licheniformis-based intensive fermentation of Tibetan tea improved its bioactive compounds and reinforced the intestinal barrier in mice
Authors: Zhu Hui , Zhou Xiaoli , Shen Caihong , Ao Zonghua , Cao Xiaonian , Song Chuan , Mehmood Muhammad Aamer , Wu Tao , Mei Jie , He Manli , Ma Yi , Wang Ning
Published: June 2024

Tibetan tea changes during microorganism fermentation. Research on microorganisms in Tibetan tea has focused on their identification, while studies on the influence of specific microorganisms on the components and health functions of Tibetan tea are lacking. Bacillus licheniformis was inoculated into Tibetan tea for intensive fermentation, and the components of B. licheniformis-fermented tea (BLT) were detected by liquid chromatography with tandem mass spectrometry (UHPLC-TOF-MS), and then the effects of BLT on intestinal probiotic functions were investigated by experiments on mice. The results revealed the metabolites of BLT include polyphenols, alkaloids, terpenoids, amino acids, and lipids. Intensified fermentation also improved the antioxidant capacity in vivo and the protective effect on the intestinal barrier of Tibetan tea. In addition, the enhanced fermentation of Tibetan tea exerted intestinal probiotic effects by modulating the relative abundance of short-chain fatty acid-producing bacteria in the intestinal flora. Therefore, intensive fermentation with B. licheniformis can improve the health benefits of Tibetan tea.
Insights into the biodegradation of pentachlorobiphenyl by Microbacterium paraoxydans: proteomic and metabolomic studies
Authors: Ji Lei , Chang Xiaoyu , Wang Leilei , Fu Xiaowen , Lai Wenkai , Zheng Liwen , Li Qi , Xing Yingna , Yang Zhongfeng , Guan Yuyao , Yang Fenglong
Published: June 2024

Bacterial degradation mechanism for high chlorinated pentachlorobiphenyl (PentaCB) with worse biodegradability has not been fully elucidated, which could limit the full remediation of environments afflicted by the complex pollution of polychlorinated biphenyls (PCBs). In this research, a new PentaCB-degrading bacterium Microbacterium paraoxydans that has not been reported was obtained using enzymatic screening method. The characteristics of its intracellular enzymes, proteome and metabolome variation during PentaCB degradation were investigated systematically compared to non-PentaCB conditions. The findings indicate that the degradation rate of PentaCB (1 mg/L) could reach 23.9% within 4 hours and achieve complete degradation within 12 hours, with the mixture of intracellular enzymes being most effective at a pH of 6.0. During the biodegradation of PentaCB, the 12 up-regulated proteins characterized included ABC transporter PentaCB-binding protein, translocase protein TatA, and signal peptidase I (SPase I), indicating the presence of functional proteins for PentaCB degradation in both the cytoplasm and the outer surface of the cytoplasmic membrane. Furthermore, five differentially enriched metabolites were strongly associated with the aforementioned proteins, especially the up-regulated 1, 2, 4-benzenetriol which feeds into multiple degradation pathways of benzoate, chlorocyclohexane, chlorobenzene and aminobenzoate. These relevant results help to understand and speculate the complex mechanisms regarding PentaCB degradation by M. paraoxydans, which have both theoretical and practical implications for PCB bioremediation.
Genetics of resistance to trimethoprim in cotrimoxazole resistant uropathogenic Escherichia coli: integrons, transposons, and single gene cassettes
Authors: Poey María Eloísa , de los Santos Eliana , Aznarez Diego , García-Laviña César X. , Laviña Magela
Published: June 2024

Cotrimoxazole, the combined formulation of sulfamethoxazole and trimethoprim, is one of the treatments of choice for several infectious diseases, particularly urinary tract infections. Both components of cotrimoxazole are synthetic antimicrobial drugs, and their combination was introduced into medical therapeutics about half a century ago. In Gram-negative bacteria, resistance to cotrimoxazole is widespread, being based on the acquisition of genes from the auxiliary genome that confer resistance to each of its antibacterial components. Starting from previous knowledge on the genotype of resistance to sulfamethoxazole in a collection of cotrimoxazole resistant uropathogenic Escherichia coli strains, this work focused on the identification of the genetic bases of the trimethoprim resistance of these same strains. Molecular techniques employed included PCR and Sanger sequencing of specific amplicons, conjugation experiments and NGS sequencing of the transferred plasmids. Mobile genetic elements conferring the trimethoprim resistance phenotype were identified and included integrons, transposons and single gene cassettes. Therefore, strains exhibited several ways to jointly resist both antibiotics, implying different levels of genetic linkage between genes conferring resistance to sulfamethoxazole (sul) and trimethoprim (dfrA). Two structures were particularly interesting because they represented a highly cohesive arrangements ensuring cotrimoxazole resistance. They both carried a single gene cassette, dfrA14 or dfrA1, integrated in two different points of a conserved cluster sul2-strA-strB, carried on transferable plasmids. The results suggest that the pressure exerted by cotrimoxazole on bacteria of our environment is still promoting the evolution toward increasingly compact gene arrangements, carried by mobile genetic elements that move them in the genome and also transfer them horizontally among bacteria.
Variation in soil bacterial community characteristics inside and outside the West Ordos National Nature Reserve, northern China
Authors: Guo Pu , Li Shuai , Zhu Jinlei , Lu Qi
Published: June 2024

Nature reserves are crucial for protecting biological habitats and maintaining biodiversity. Soil bacterial community plays an irreplaceable role in the structure and function of ecosystem. However, the impact of nature reserves on soil bacterial communities is still unclear. To explore the effects of desert grassland nature reserve management on soil microbial communities, we compared the differences in soil bacterial community composition, α-diversity and community structure inside and outside a desert grassland nature reserve, and explored the correlation between soil bacterial communities and plant biomass and soil chemical index. We found that (1) the relative abundance of Acidobacteriota is highest in the soil both inside and outside the nature reserve in shrub grassland; (2) the Chao1 index of soil bacterial communities in the core protected zone and general control zone of the reserve was significantly higher than that outside the reserve (p < 0.05) in the shrub grassland. Similarly, in the herbaceous grassland, the Shannon index of soil bacterial communities was significantly higher in the core protected zone of the reserve than that outside the reserve (p < 0.05). (3) While we found no significant difference in soil bacterial community structure between inside and outside the reserve in the shrub grassland, we found that the soil bacterial community structure in the core protected zone was significantly different from that outside the reserve in the herbaceous grassland (p < 0.05); (4) we also found that higher plant productivity and soil nutrients promoted most soil dominant bacterial phyla, while higher soil pH and salinity inhibited most soil dominant bacterial phyla. Our findings thus help better understand the influencing factors of and the mechanisms behind variation in soil bacterial communities inside and outside desert grassland nature reserves.
Enhancing pathogen description and antibiotic regimen selection in community-acquired pneumonia through RT-qPCR assays
Authors: Zhao Na , Ren Hongyu , Zhang Yingmiao , Jiang Yan , Deng Jianping , Jiang Luxi , Lu Zhongxin , Qin Tian
Published: June 2024

Background

Adults with community-acquired pneumonia (CAP) in China suffer high morbidity. CAP is caused by a multitude of pathogens; however, pathogen-directed clinical symptoms are often lacking. Therefore, patients lacking an accurate microbiological diagnosis are administered with empirical antimicrobials.

Methods

We collected bronchoalveolar lavage fluid, as well as clinical and laboratory data from 650 adult patients with CAP admitted to three hospitals in Hubei, Sichuan, and Zhejiang provinces in China. Specimens were cultured and tested using real-time reverse transcription qPCR (RT-qPCR) assays for the presence of 42 respiratory bacteria and viruses. CAP was investigated with respect to regions, genders, and age and patterns of infections or co-infections. Employing clinical guidelines adapted for diagnosis, we assessed retrospectively the appropriate pathogen-directed therapy and compared it with the initial empirical therapies.

Results

Our study identified that 21.38% (139/650) of the patients were classified as having Severe CAP (S-CAP), with a higher prevalence among males, older adults, and during the warm season. Bacterial pathogens were detected in 35.53% (231/650) of cases. K. pneumoniae, H. influenzae, and S. aureus were the most prevalent bacteria across different demographics and regions. Viral pathogens were found in 48.76% (317/650) of patients Epstein-Barr, Human rhinovirus, and Cytomegalovirus were the most common viruses. Co-infections were present in 24.31% (158/650) of cases, with viral-bacterial co-infections being the most frequent. The RT-qPCR demonstrated significantly higher detection rates for key pathogens compared to standard culture methods. It showed potential in optimizing antimicrobial prescriptions by allowing for de-escalation in 18.30% (95/518) of patients, among which reducing the number of excessive antibiotics mainly comprised decreasing the use of 2nd or 3rd generation cephalosporins (5.79%, 30/518) and β-lactamase inhibitor combinations.

Conclusion

The study highlights the significant burden of S-CAP, particularly among specific demographics and seasons. The prevalence of bacterial and viral pathogens, along with the high rate of co-infections, emphasizes the need for comprehensive diagnostic approaches. The RT-qPCR assays emerge as a superior diagnostic tool, offering enhanced pathogen detection capabilities and facilitating more precise antimicrobial therapy. This could lead to improved patient outcomes and contribute to the rational use of antimicrobials, addressing the growing concern of antibiotic resistance.
Less spatial exploration is associated with poorer spatial memory in midlife adults
Authors: Puthusseryppady Vaisakh , Cossio Daniela , Yu Shuying , Rezwana Farnaz , Hegarty Mary , Jacobs Emily G. , Chrastil Elizabeth R.
Published: June 2024

Introduction

Despite its importance for navigation, very little is known about how the normal aging process affects spatial exploration behavior. We aimed to investigate: (1) how spatial exploration behavior may be altered early in the aging process, (2) the relationship between exploration behavior and subsequent spatial memory, and (3) whether exploration behavior can classify participants according to age.

Methods

Fifty healthy young (aged 18–28) and 87 healthy midlife adults (aged 43–61) freely explored a desktop virtual maze, learning the locations of nine target objects. Various exploration behaviors (object visits, distance traveled, turns made, etc.) were measured. In the test phase, participants navigated from one target object to another without feedback, and their wayfinding success (% correct trials) was measured.

Results

In the exploration phase, midlife adults exhibited less exploration overall compared to young adults, and prioritized learning target object locations over maze layout. In the test phase, midlife adults exhibited less wayfinding success when compared to the young adults. Furthermore, following principal components analysis (PCA), regression analyses indicated that both exploration quantity and quality components were associated with wayfinding success in the midlife group, but not the young adults. Finally, we could classify participants according to age with similar accuracy using either their exploration behavior or wayfinding success scores.

Discussion

Our results aid in the understanding of how aging impacts spatial exploration, and encourages future investigations into how pathological aging may affect spatial exploration behavior.
Investigating the effects of chiropractic care on resting-state EEG of MCI patients
Authors: Ziloochi Fahimeh , Niazi Imran Khan , Amjad Imran , Cade Alice , Duehr Jenna , Ghani Usman , Holt Kelly , Haavik Heidi , Shalchyan Vahid
Published: June 2024

Introduction

Mild cognitive impairment (MCI) is a stage between health and dementia, with various symptoms including memory, language, and visuospatial impairment. Chiropractic, a manual therapy that seeks to improve the function of the body and spine, has been shown to affect sensorimotor processing, multimodal sensory processing, and mental processing tasks.

Methods

In this paper, the effect of chiropractic intervention on Electroencephalogram (EEG) signals in patients with mild cognitive impairment was investigated. EEG signals from two groups of patients with mild cognitive impairment (n = 13 people in each group) were recorded pre- and post-control and chiropractic intervention. A comparison of relative power was done with the support vector machine (SVM) method and non-parametric cluster-based permutation test showing the two groups could be separately identified with high accuracy.

Results

The highest accuracy was obtained in beta2 (25–35 Hz) and theta (4–8 Hz) bands. A comparison of different brain areas with the SVM method showed that the intervention had a greater effect on frontal areas. Also, interhemispheric coherence in all regions increased significantly after the intervention. The results of the Wilcoxon test showed that intrahemispheric coherence changes in frontal-occipital, frontal-temporal and right temporal-occipital regions were significantly different in two groups.

Discussion

Comparison of the results obtained from chiropractic intervention and previous studies shows that chiropractic intervention can have a positive effect on MCI disease and using this method may slow down the progression of mild cognitive impairment to Alzheimer’s disease.
Human cerebral organoids: cellular composition and subcellular morphological features
Authors: Mateos-Martínez Patricia , Coronel Raquel , Sachse Martin , González-Sastre Rosa , Maeso Laura , Rodriguez Maria Josefa , Terrón María C. , López-Alonso Victoria , Liste Isabel
Published: June 2024

Introduction

Human cerebral organoids (hCOs) derived from pluripotent stem cells are very promising for the study of neurodevelopment and the investigation of the healthy or diseased brain. To help establish hCOs as a powerful research model, it is essential to perform the morphological characterization of their cellular components in depth.

Methods

In this study, we analyzed the cell types consisting of hCOs after culturing for 45 days using immunofluorescence and reverse transcriptase qualitative polymerase chain reaction (RT-qPCR) assays. We also analyzed their subcellular morphological characteristics by transmission electron microscopy (TEM).

Results

Our results show the development of proliferative zones to be remarkably similar to those found in human brain development with cells having a polarized structure surrounding a central cavity with tight junctions and cilia. In addition, we describe the presence of immature and mature migrating neurons, astrocytes, oligodendrocyte precursor cells, and microglia-like cells.

Discussion

The ultrastructural characterization presented in this study provides valuable information on the structural development and morphology of the hCO, and this information is of general interest for future research on the mechanisms that alter the cell structure or function of hCOs.
Machine learning-based nomogram: integrating MRI radiomics and clinical indicators for prognostic assessment in acute ischemic stroke
Authors: Guo Kun , Zhu Bo , Li Rong , Xi Jing , Wang Qi , Chen KongBo , Shao Yuan , Liu Jiaqi , Cao Weili , Liu Zhiqin , Di Zhengli , Gu Naibing
Published: June 2024

Background

Acute Ischemic Stroke (AIS) remains a leading cause of mortality and disability worldwide. Rapid and precise prognostication of AIS is crucial for optimizing treatment strategies and improving patient outcomes. This study explores the integration of machine learning-derived radiomics signatures from multi-parametric MRI with clinical factors to forecast AIS prognosis.

Objective

To develop and validate a nomogram that combines a multi-MRI radiomics signature with clinical factors for predicting the prognosis of AIS.

Methods

This retrospective study involved 506 AIS patients from two centers, divided into training (n = 277) and validation (n = 229) cohorts. 4,682 radiomic features were extracted from T1-weighted, T2-weighted, and diffusion-weighted imaging. Logistic regression analysis identified significant clinical risk factors, which, alongside radiomics features, were used to construct a predictive clinical-radiomics nomogram. The model’s predictive accuracy was evaluated using calibration and ROC curves, focusing on distinguishing between favorable (mRS ≤ 2) and unfavorable (mRS > 2) outcomes.

Results

Key findings highlight coronary heart disease, platelet-to-lymphocyte ratio, uric acid, glucose levels, homocysteine, and radiomics features as independent predictors of AIS outcomes. The clinical-radiomics model achieved a ROC-AUC of 0.940 (95% CI: 0.912–0.969) in the training set and 0.854 (95% CI: 0.781–0.926) in the validation set, underscoring its predictive reliability and clinical utility.

Conclusion

The study underscores the efficacy of the clinical-radiomics model in forecasting AIS prognosis, showcasing the pivotal role of artificial intelligence in fostering personalized treatment plans and enhancing patient care. This innovative approach promises to revolutionize AIS management, offering a significant leap toward more individualized and effective healthcare solutions.
BrainCDNet: a concatenated deep neural network for the detection of brain tumors from MRI images
Authors: Reddy K. Rasool , Rajesh Kandala N. V. P. S. , Dhuli Ravindra , Kumar Vuddagiri Ravi
Published: June 2024

Introduction

Brain cancer is a frequently occurring disease around the globe and mostly developed due to the presence of tumors in/around the brain. Generally, the prevalence and incidence of brain cancer are much lower than that of other cancer types (breast, skin, lung, etc.). However, brain cancers are associated with high mortality rates, especially in adults, due to the false identification of tumor types, and delay in the diagnosis. Therefore, the minimization of false detection of brain tumor types and early diagnosis plays a crucial role in the improvement of patient survival rate. To achieve this, many researchers have recently developed deep learning (DL)-based approaches since they showed a remarkable performance, particularly in the classification task.

Methods

This article proposes a novel DL architecture named BrainCDNet. This model was made by concatenating the pooling layers and dealing with the overfitting issues by initializing the weights into layers using ‘He Normal’ initialization along with the batch norm and global average pooling (GAP). Initially, we sharpen the input images using a Nimble filter, which results in maintaining the edges and fine details. After that, we employed the suggested BrainCDNet for the extraction of relevant features and classification. In this work, two different forms of magnetic resonance imaging (MRI) databases such as binary (healthy vs. pathological) and multiclass (glioma vs. meningioma vs. pituitary) are utilized to perform all these experiments.

Results and discussion

Empirical evidence suggests that the presented model attained a significant accuracy on both datasets compared to the state-of-the-art approaches, with 99.45% (binary) and 96.78% (multiclass), respectively. Hence, the proposed model can be used as a decision-supportive tool for radiologists during the diagnosis of brain cancer patients.
A protocol to quantify cross-sectional and longitudinal differences in duction patterns
Authors: Willeford Kevin T. , Copel Victoria , Rong Hua
Published: June 2024

Currently, there is no established system for quantifying patterns of ocular ductions. This poses challenges in tracking the onset and evolution of ocular motility disorders, as current clinical methodologies rely on subjective observations of individual movements. We propose a protocol that integrates image processing, a statistical framework of summary indices, and criteria for evaluating both cross-sectional and longitudinal differences in ductions to address this methodological gap. We demonstrate that our protocol reliably transforms objective estimates of ocular rotations into normative patterns of total movement area and movement symmetry. This is a critical step towards clinical application in which our protocol could first diagnose and then track the progression and resolution of ocular motility disorders over time.
A single fast Hebbian-like process enabling one-shot class addition in deep neural networks without backbone modification
Authors: Hosoda Kazufumi , Nishida Keigo , Seno Shigeto , Mashita Tomohiro , Kashioka Hideki , Ohzawa Izumi
Published: June 2024

One-shot learning, the ability to learn a new concept from a single instance, is a distinctive brain function that has garnered substantial interest in machine learning. While modeling physiological mechanisms poses challenges, advancements in artificial neural networks have led to performances in specific tasks that rival human capabilities. Proposing one-shot learning methods with these advancements, especially those involving simple mechanisms, not only enhance technological development but also contribute to neuroscience by proposing functionally valid hypotheses. Among the simplest methods for one-shot class addition with deep learning image classifiers is “weight imprinting,” which uses neural activity from a new class image data as the corresponding new synaptic weights. Despite its simplicity, its relevance to neuroscience is ambiguous, and it often interferes with original image classification, which is a significant drawback in practical applications. This study introduces a novel interpretation where a part of the weight imprinting process aligns with the Hebbian rule. We show that a single Hebbian-like process enables pre-trained deep learning image classifiers to perform one-shot class addition without any modification to the original classifier's backbone. Using non-parametric normalization to mimic brain's fast Hebbian plasticity significantly reduces the interference observed in previous methods. Our method is one of the simplest and most practical for one-shot class addition tasks, and its reliance on a single fast Hebbian-like process contributes valuable insights to neuroscience hypotheses.
Secular trends and determinants of ad libitum energy intake measured in a research setting from 1999-2020
Authors: Ahern Mary M. , Stinson Emma J. , Piaggi Paolo , Krakoff Jonathan , Votruba Susanne B.
Published: June 2024

Introduction

Historically, secular and seasonal trend analyses have been examined using self-report measures of intake. Rarely are objective measures and known determinants of dietary intake used in these analyses. Our objective was to quantify the seasonal and secular differences in an objective ad libitum intake paradigm while considering the contribution of determinants, such as fat-free mass (FFM) index and spontaneous physical activity (SPA) limited to the restricted space of a whole-room calorimeter.

Methods

For this study, recruitment of N = 292 healthy, diabetes free, adults occurred from 1999 to 2020. Assessment during their 10-day stay included body composition (by DXA), SPA (by an approximately 24-h stay in whole-room calorimetry), and ad libitum intake (by a vending machine for 3 days). This secondary analysis used general linear models (GLM) to investigate secular and seasonal differences while adjusting for sex, age, FFM index, FM (fat mass) index, SPA, and race/ethnicity.

Results

FFM index and SPA were positively associated with all intake measures (p < 0.05). In all adjusted seasonal models, season did not affect intake. Adjusted secular trends models (kcals/year) demonstrated a decrease in total kcals (β = −55), intake as percent weight maintaining energy needs (β = −2), protein kcals (β = −10), fat kcals (β = −27), and carbohydrates kcals (β = −22) (all p < 0.05). After further adjustment for SPA, significance remained in all intake measures (p < 0.05). Secular trends in body composition revealed no changes in weight, BMI, and percent body fat (all p > 0.20).

Discussion

Our results indicate that over time, ad libitum intake decreased in this controlled research setting and remained significant even after accounting for positive determinants of intake. A significant ad libitum decrease, coupled with no change in body composition, may highlight a participant bias toward calorie restriction in a controlled setting over time and deserves further investigation.
A semi-automatic deep learning model based on biparametric MRI scanning strategy to predict bone metastases in newly diagnosed prostate cancer patients
Authors: Xinyang Song , Tianci Shen , Xiangyu Hu , Shuang Zhang , Yangyang Wang , Mengying Du , Tonghui Xu , Jingran Zhou , Feng Yang
Published: June 2024

Objective

To develop a semi-automatic model integrating radiomics, deep learning, and clinical features for Bone Metastasis (BM) prediction in prostate cancer (PCa) patients using Biparametric MRI (bpMRI) images.

Methods

A retrospective study included 414 PCa patients (BM, n=136; NO-BM, n=278) from two institutions (Center 1, n=318; Center 2, n=96) between January 2016 and December 2022. MRI scans were confirmed with BM status via PET-CT or ECT pre-treatment. Tumor areas on bpMRI images were delineated as tumor’s region of interest (ROI) using auto-delineation tumor models, evaluated with Dice similarity coefficient (DSC). Samples were auto-sketched, refined, and used to train the ResNet BM prediction model. Clinical, radiomics, and deep learning data were synthesized into the ResNet-C model, evaluated using receiver operating characteristic (ROC).

Results

The auto-segmentation model achieved a DSC of 0.607. Clinical BM prediction’s internal validation had an accuracy (ACC) of 0.650 and area under the curve (AUC) of 0.713; external cohort had an ACC of 0.668 and AUC of 0.757. The deep learning model yielded an ACC of 0.875 and AUC of 0.907 for the internal, and ACC of 0.833 and AUC of 0.862 for the external cohort. The Radiomics model registered an ACC of 0.819 and AUC of 0.852 internally, and ACC of 0.885 and AUC of 0.903 externally. ResNet-C demonstrated the highest ACC of 0.902 and AUC of 0.934 for the internal, and ACC of 0.885 and AUC of 0.903 for the external cohort.

Conclusion

The ResNet-C model, utilizing bpMRI scanning strategy, accurately assesses bone metastasis (BM) status in newly diagnosed prostate cancer (PCa) patients, facilitating precise treatment planning and improving patient prognoses.
Odontogenic cystic lesion segmentation on cone-beam CT using an auto-adapting multi-scaled UNet
Authors: Huang Zimo , Li Bo , Cheng Yong , Kim Jinman
Published: June 2024

Objectives

Precise segmentation of Odontogenic Cystic Lesions (OCLs) from dental Cone-Beam Computed Tomography (CBCT) is critical for effective dental diagnosis. Although supervised learning methods have shown practical diagnostic results in segmenting various diseases, their ability to segment OCLs covering different sub-class varieties has not been extensively investigated.

Methods

In this study, we propose a new supervised learning method termed OCL-Net that combines a Multi-Scaled U-Net model, along with an Auto-Adapting mechanism trained with a combined supervised loss. Anonymous CBCT images were collected retrospectively from one hospital. To assess the ability of our model to improve the diagnostic efficiency of maxillofacial surgeons, we conducted a diagnostic assessment where 7 clinicians were included to perform the diagnostic process with and without the assistance of auto-segmentation masks.

Results

We collected 300 anonymous CBCT images which were manually annotated for segmentation masks. Extensive experiments demonstrate the effectiveness of our OCL-Net for CBCT OCLs segmentation, achieving an overall Dice score of 88.84%, an IoU score of 81.23%, and an AUC score of 92.37%. Through our diagnostic assessment, we found that when clinicians were assisted with segmentation labels from OCL-Net, their average diagnostic accuracy increased from 53.21% to 55.71%, while the average time spent significantly decreased from 101s to 47s (P<0.05).

Conclusion

The findings demonstrate the potential of our approach as a robust auto-segmentation system on OCLs in CBCT images, while the segmented masks can be used to further improve OCLs dental diagnostic efficiency.
Case report: Endoscopic full-thickness resection of gastric metastatic tumor from renal cell carcinoma
Authors: Yan Xiaochen , Liu Lina , Wang Wenhao , Liu Chunyan , Cui Zhenqin
Published: June 2024

Renal cell carcinoma (RCC) is a common malignant kidney tumor; however, gastric metastasis is rare. We report the case of an 82-year-old male patient who developed gastric metastasis 12 years after an initial diagnosis of RCC. The patient underwent endoscopic full-thickness resection (EFTR), and the gastric metastatic focus was successfully removed. Postoperative pathology and immunohistochemistry showed that the gastric metastasis originated from RCC. Although gastric metastasis of RCC is rare, it should be suspected in patients with a history of RCC or gastrointestinal symptoms. EFTR is associated with reduced trauma and greater retention of gastric tissue and function. It is a more appropriate choice than surgical resection; however, it requires more endoscopists.
Geriatric nutritional risk index and mortality from all-cause, cancer, and non-cancer in US cancer survivors: NHANES 2001–2018
Authors: Qiu Xiuxiu , Wu Qidong , Zhang Yiyi , Zhu Yingjie , Yang Ming , Tao Li
Published: June 2024

Background

Malnutrition is strongly correlated with worsened treatment outcomes, reduced standard of living, and heightened mortality rates among individuals with cancer. Our research explores how the Geriatric Nutritional Risk Index (GNRI), a measure of nutritional status, relates to all-cause mortality, cancer-specific, and non-cancer mortality among middle-aged and older adult cancer patients.

Methods

We enrolled 3,253 participants aged 40 and above who were diagnosed with cancer. The data was obtained from the National Health and Nutrition Examination Survey (NHANES) dataset covering the period from 2001 to 2018, with a median follow-up duration of 83 months. According to the GNRI levels, patients in the study were classified into two distinct groups: the group with a low GNRI (<98) and the group with a high GNRI (≥ 98). We conducted a Kaplan-Meier survival analysis to assess how survival rates vary with different nutritional conditions. Multivariable Cox regression analyses were performed to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for all-cause mortality, as well as cancer-specific and non-cancer-related mortality. Restricted cubic spline (RCS) analyses and subgroup evaluations were performed to augment the robustness and validity of our findings.

Results

A total of 1,171 deaths were documented, with 383 attributed to cancer, and 788 from other causes. After adjusting for potential confounders, the analysis demonstrated that, within a specified range, an elevation in the GNRI is inversely associated with mortality from all causes, cancer-specific, and non-cancer causes. Moreover, Kaplan-Meier survival curves for all-cause, cancer-specific, and non-cancer mortality distinctly showed a more pronounced decrease in survival rates among individuals in the low GNRI group (<98). Notably, the restricted cubic spline regression model (RCS) revealed statistically significant non-linear associations between GNRI scores and mortality rates. The P-values were ≤0.001 for both all-cause and non-cancer mortality, and 0.024 for cancer-specific mortality.

Conclusion

Our study conclusively demonstrated a robust correlation between GNRI scores and mortality rates among cancer patients, encompassing all-cause mortality as well as specific mortality related to both cancerous and non-cancerous causes. The GNRI may be a valuable prognostic tool for predicting cancer mortality outcomes, offering insights that may inform nutritional management and influence the clinical treatment strategies for cancer survivors.
Revealing tumor cells and tissues with high selectivity through folic acid-targeted nanofluorescence probes responsive to acidic microenvironments
Authors: Li Jing , He Hongyi , Liu Shuyan , Li Xining , Wu Fengfeng
Published: June 2024

Tumor-specific fluorescent probes must fulfill the dual requirements of targeted accumulation within tumors and high-resolution imaging capabilities. To achieve both tumor-targeted accumulation and high-resolution imaging performance, we developed a composite comprising an acid-responsive bodipy conjugated to amphiphilic PEG-b-PLA polymer, along with folic acid (FA)-modified PEG-b-PLA as a targeting moiety for active tumor-specific accumulation. Finally, a novel assembly of hybrid fluorescent nanoparticles was successfully synthesized by integrating these two components, demonstrating exceptional responsiveness to acidic conditions for fluorescence excitation and remarkable tumor-targeted accumulation capabilities. We conducted comprehensive in vitro and in vivo investigations employing techniques such as analysis of physicochemical properties, fluorescence-based probes detection at varying pH levels, assessment of in vitro cytotoxicity, evaluation of cellular uptake capacity, analysis of lysosomal co-localization imaging, examination of tumor fluorescence images in vivo, and investigation of biological distribution patterns. The results demonstrated that the acid-responsive nanofluorescence probe we designed and synthesized possesses desirable physical and chemical characteristics, including a small particle size and low cytotoxicity. Moreover, it exhibits rapid real-time response to acidic environments and displays enhanced fluorescence intensity, enabling the real-time tracking of probe entry into tumor cells as well as intracellular lysozyme accumulation. We achieved highly specific in vivo tumor visualization by combining nanoprobes targeting folate receptor. Through imaging cervical tumor mice, we demonstrated the precise imaging performance and high targeted accumulation of FA-targeted nanofluorescence probes in tumor tissue. Furthermore, we confirmed the in vivo safety of the FA-targeted nanofluorescence probe through biological distribution analysis. These findings highlight the potential widespread application of FA-targeted acid-responsive nanofluorescence probes for selective imaging of tumor cells and tissues.
MUC21: a new target for tumor treatment
Authors: Li Miao , Li Hui , Yuan Ting , Liu Zhi , Li Yukun , Tan Yingzheng , Long Yunzhu
Published: June 2024

MUC21, also known as Epiglycanin, is a high-molecular-weight glycoprotein with transmembrane mucin properties. It consists of a tandem repeat domain, a stem domain, a transmembrane domain and a cytoplasmic tail. MUC21 is expressed is observed in normal tissues in organs like the thymus, testes, lungs, and large intestine. Research has shown that MUC21 is expressed in esophageal squamous cell carcinoma, lung adenocarcinoma, glioblastoma, thyroid cancer, melanoma, and various other malignant tumors in distinctive manner. Additionally, tumor invasion, metastasis, and poor prognosis are linked to it. Some researchers believe that MUC21 has the potential to become a new target in cancer treatment. This review aims to deliver a comprehensive overview of the glycosylation, function, and research progress of MUC21 in multiple types of cancer and infectious diseases.
Comparative adaptability assessment of bread wheat and synthetic hexaploid genotypes under saline conditions using physiological, biochemical, and genetic indices
Authors: Alghabari Fahad , Shah Zahid Hussain
Published: June 2024

The tolerance to salinity stress is an intricate phenomenon at cellular and whole plant level that requires the knowledge of contributing physiological and biochemical processes and the genetic control of participating traits. In this context, present study was conducted with objective to evaluate the physiological, biochemical, and genetic responses of different wheat genotypes including bread wheat (BW) and synthetic hexaploids (SHs) under saline and control environment. The experiment was conducted in two factorial arrangement in randomized complete block design (RCBD), with genotypes as one factor and treatments as another factor. A significant decline in physiological traits (chlorophyll, photosynthesis, stomatal conductance, transpiration, and cell membrane stability) was observed in all genotypes due to salt stress; however, this decline was higher in BW genotypes as compared to four SH genotypes. In addition, the biochemical traits including enzymes [superoxide dismutase, catalase, and peroxidase (POD)] activity, proline, and glycine betaine (GB) illustrated significant increase along with increase in the expression of corresponding genes (TaCAT1, TaSOD, TaPRX2A, TaP5CS, and TaBADH-A1) due to salt stress in SHs as compared to BW. Correspondingly, highly overexpressed genes, TaHKT1;4, TaNHX1, and TaAKT1 caused a significant decline in Na+/K+ in SH as compared to BW genotypes under salt stress. Moreover, correlation analysis, principal component analysis (PCA), and heatmap analysis have further confirmed that the association and expression of physiological and biochemical traits varied significantly with salinity stress and type of genotype. Overall, the physiological, biochemical, and genetic evaluation proved SHs as the most useful stock for transferring salinity tolerance to other superior BW cultivars via the right breeding program.
Genomics and resequencing of Fagopyrum dibotrys from different geographic regions reveals species evolution and genetic diversity
Authors: Zheng Si-hao , Diao Yong-chao , Du Jie , Li Jin-tong , Zhao Sha , Liu Mei-juan , Lin Hui-cai , Zeng Yan , Wang Ji-yong
Published: June 2024

Fagopyrum dibotrys, belonging to the family Polygonaceae and genus Fagopyrum, is used in traditional Chinese medicine and is rich in beneficial components, such as flavonoids. As its abundant medicinal value has become increasingly recognized, its excessive development poses a considerable challenge to wild germplasm resources, necessitating artificial cultivation and domestication. Considering these factors, a high-quality genome of F. dibotrys was assembled and the evolutionary relationships within Caryophyllales were compared, based on which 58 individual samples of F. dibotrys were re-sequenced. We found that the samples could be categorized into three purebred populations and regions distributed at distinct elevations. Our varieties were cultivated from the parental populations of the subpopulation in central Yunnan. F. dibotrys is speculated to have originated in the high-altitude Tibetan Plateau region, and that its combination with flavonoids can protect plants against ultraviolet radiation; this infers a subpopulation with a high accumulation of flavonoids. This study assembled a high-quality genome and provided a theoretical foundation for the future introduction, domestication, and development of cultivated varieties of F. dibotrys.