bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiology of extended-spectrum β-lactamases in Enterobacterales in Taiwan for over two decades
Authors: Chao Chien-Ming , Lai Chih-Cheng , Yu Wen-Liang
Published: January 2023

The emergence of antimicrobial resistance among microorganisms is a serious public health concern, and extended-spectrum β-lactamases (ESBL)-producingEnterobacteralesis one of the major concerns among antibiotic-resistant bacteria. Although the prevalence of ESBL inEnterobacteraleshas been increasing with time, the prevalence of ESBL could differ according to the species, hospital allocation, sources of infections, nosocomial or community acquisitions, and geographic regions. Therefore, we conducted a comprehensive review of the epidemiology of ESBL-producingEnterobacteralesin Taiwan. Overall, the rates of ESBL producers are higher in northern regions than in other parts of Taiwan. In addition, the genotypes of ESBL vary according to differentEnterobacterales. SHV-type ESBLs (SHV-5 and SHV-12) were the major types ofEnterobacter cloacaecomplex, butSerratia marcescens, Proteus mirabilis, Escherichia coli,andKlebsiella pneumoniaewere more likely to possess CTX-M-type ESBLs (CTX-M-3 and CTX-M-14). Moreover, a clonal sequence type of O25b-ST131 has been emerging among urinary or bloodstreamE. coliisolates in the community in Taiwan, and this clone was potentially associated with virulence, ESBL (CTX-M-15) production, ciprofloxacin resistance, and mortality. Finally, the evolution of the genetic traits of the ESBL-producingEnterobacteralesisolates helps us confirm the interhospital and intrahospital clonal dissemination in several regions of Taiwan. In conclusion, continuous surveillance in the investigation of ESBL production amongEnterobacteralesis needed to establish its long-term epidemiology.
Genome-centered metagenomics illuminates adaptations of core members to a partial Nitritation–Anammox bioreactor under periodic microaeration
Authors: Shao Yung-Hsien , Wu Yu-Wei , Naufal Muhammad , Wu Jer-Horng
Published: January 2023

The partial nitritation-anaerobic ammonium oxidation (anammox; PN-A) process has been considered a sustainable method for wastewater ammonium removal, with recent attempts to treat low-strength wastewater. However, how microbes adapt to the alternate microaerobic-anoxic operation of the process when treating low ammonium concentrations remains poorly understood. In this study, we applied a metagenomic approach to determine the genomic contents of core members in a PN-A reactor treating inorganic ammonium wastewater at loading as low as 0.0192 kg-N/m3/day. The metabolic traits of metagenome-assembled genomes from 18 core species were analyzed. Taxonomically diverse ammonia oxidizers, including two Nitrosomonas species, a comammox Nitrospira species, a novel Chloroflexota-related species, and two anammox bacteria, Ca. Brocadia and Ca. Jettenia, accounted for the PN-A reactions. The characteristics of a series of genes encoding class II ribonucleotide reductase, high-affinity bd-type terminal oxidase, and diverse antioxidant enzymes revealed that comammox Nitrospira has a superior adaptation ability over the competitors, which may confer the privileged partnership with anammox bacteria in the PN-A reactor. This finding is supported by the long-term monitoring experiment, showing the predominance of the comammox Nitrospira in the ammonia-oxidizing community. Metagenomic analysis of seven heterotrophs suggested that nitrate reduction is a common capability in potentially using endogenous carbohydrates and peptides to enhance nitrogen removals. The prevalence of class II ribonucleotide reductase and antioxidant enzymes genes may grant the adaptation to cyclically microaerobic/anoxic environments. The predominant heterotroph is affiliated with Chloroflexota; its genome encodes complete pathways for synthesizing vitamin B6 and methionine. By contrast, other than the two growth factors, Nitrospira and anammox bacteria are complementary to produce various vitamins and amino acids. Besides, the novel Chloroflexota-related ammonia oxidizer lacks corresponding genes for detoxifying the reactive oxygen species and thus requires the aid of co-existing members to alleviate oxidative stress. The analysis results forecast the exchanges of substrates and nutrients as well as the collective alleviation of oxidative stress among the core populations. The new findings of the genomic features and predicted microbial interplay shed light on microbial adaptation to intermittent microaeration specific to the PN-A reactor, which may aid in improving its application to low-strength ammonium wastewater.
The biogeography of colonial volvocine algae in the Yangtze River basin
Authors: Hu Yuxin , Zhang Jing , Huang Jie , Zhou Mingchun , Hu Sheng
Published: January 2023

Colonial Volvocine Algae (CVA) are of great significance for biological evolution study, but little is presently known about their biogeographic distribution. Meanwhile, with the impact of climate change and human activities, their effects on the distribution and structures of CVA communities also remain largely unknown. Herein, the biogeography of CVA was investigated in the Yangtze River basin, 172 sampling sites were set up within a catchment area of 1,800,000  km2, and the distribution and community composition of CVA were studied using single-molecule real-time sequencing and metabarcoding technology based on the full-length 18S sequence. In 76 sampling sites, CVA was discovered in two families, eight genera, and nine species. Eudorina and Colemanosphaera were the main dominant genus. Based on the result of the random forest model and Eta-squared value, the distribution of CVA was significantly influenced by water temperature, altitude, and TP. CVA could be suitably distributed at an average water temperature of 22°C, an average TP concentration of 0.06 mg/L, and an altitude lower than 3,920  m. To assess the effects of anthropogenic pollution on the structures and co-occurrence patterns of CVA communities, we used a stress index calculated by 10 environmental factors to divide the CVA community into low and high pollution group. Network analysis showed that greater pollution levels would have a negative impact on the co-occurrence patterns and diversity of the CVA community. Finally, to study the scientific distribution of CVA under current and future climate change scenarios, we analyzed the climate suitability regionalization of CVA with the maximum entropy model based on 19 climatic factors and four climate scenarios from 2021 to 2040 published by CMIP6. Our results reveal the suitable areas of CVA, and temperature is an important environmental factor affecting the distribution of CVA. With the change of climate in the future, the Three Gorges Reservoir Area, Chaohu Lake, and Taihu Lake are still highly suitable areas for CVA, but the habitat of CVA may be fragmented, and more thorough temporal surveys and sampling of the sediment or mud are needed to investigate the fragmentation of CVA.
A Maverick-like cluster in the genome of a pathogenic, moderately virulent strain of Gallibacterium anatis, ESV200, a transient biofilm producer
Authors: Sanchez-Alonso Patricia , Cobos-Justo Elena , Avalos-Rangel Miguel Angel , López-Reyes Lucía , Paniagua-Contreras Gloria Luz , Vaca-Paniagua Felipe , Anastacio-Marcelino Estela , López-Ochoa Ana Jaqueline , Pérez Marquez Victor M. , Negrete-Abascal Erasmo , Vázquez-Cruz Candelario
Published: January 2023

Introduction

Gallibacterium anatis causes gallibacteriosis in birds. These bacteria produce biofilms and secrete several fimbrial appendages as tools to cause disease in animals. G. anatis strains contain up to three types of fimbriae. Complete genome sequencing is the strategy currently used to determine variations in the gene content of G. anatis, although today only the completely circularized genome of G. anatis UMN179 is available.

Methods

The appearance of growth of various strains of G. anatis in liquid culture medium was studied. Biofilm production and how the amount of biofilm was affected by DNase, Proteinase K, and Pronase E enzymes were analyzed. Fimbrial gene expression was performed by protein analysis and qRT-PCR. In an avian model, the pathogenesis generated by the strains G. anatis ESV200 and 12656-12 was investigated. Using bioinformatic tools, the complete genome of G. anatis ESV200 was comparatively studied to search for virulence factors that would help explain the pathogenic behavior of this strain.

Results and Discussion

G. anatis ESV200 strain differs from the 12656-12 strain because it produces a biofilm at 20%. G. anatis ESV200 strain express fimbrial genes and produces biofilm but with a different structure than that observed for strain 12656-12. ESV200 and 12656-12 strains are pathogenic for chickens, although the latter is the most virulent. Here, we show that the complete genome of the ESV200 strain is similar to that of the UNM179 strain. However, these strains have evolved with many structural rearrangements; the most striking chromosomal arrangement is a Maverick-like element present in the ESV200 strain.
Effect of β − hydroxy − γ -aminophosphonate (β − HPC) on the hydrolytic activity of Nocardia brasiliensis as determined by FT−IR spectrometry
Authors: Martínez-Robles Sandra , González-Ballesteros Erik , Reyes-Esparza Jorge , Trejo-Teniente Isaí , Jaramillo-Loranca Blanca Estela , Téllez-Jurado Alejandro , Vázquez-Valadez Víctor H. , Angeles Enrique , Vargas Hernández Genaro
Published: January 2023

The use of immunomodulatory and metabolic modulating drugs has been considered a better strategy to improve the efficacy of conventional treatments against pathogens and metabolic diseases. L-carnitine is relevant in fatty acid metabolism and energy production by β-oxidation, but it also has a beneficial therapeutic immunomodulatory effect. The β-hydroxy-γ-aminophosphonate (β-HPC) was developed, synthesized and studied in different pathologies as a more soluble and stable analog than L-carnitine, which has been studied in bacterial physiology and metabolism; therefore, we set out to investigate the direct effect of β-HPC on the metabolism of N. brasiliensis, which causes actinomycetoma in Mexico and is underdiagnosed. To analyze the effect of β-HPC on the metabolic capacity of the bacterium for the hydrolysis of substrate casein, L-tyrosine, egg yolk, and tween 80, Fourier transform infrared spectroscopy (FT-IR) was employed. It was found that β-HPC increases the metabolic activity of N. brasiliensis associated with increased growth and increased hydrolysis of the substrates tested. By the effect of β-HPC, it was observed that, in the hydrolysis of L-tyrosine, the aromatic ring and functional groups were degraded. At 1515 cm–1, any distinctive signal or peak for this amino acid was missing, almost disappearing at 839, 720, 647, and 550 cm–1. In casein, hydrolysis is enhanced in the substrate, which is evident by the presence of NH, OH, amide, and CO. In casein, hydrolysis is enhanced in the substrate, which is evident by the presence of NH, OH, amide, COO, and P = O signals, characteristic of amino acids, in addition to the increase of the amide I and II bands. In Tween 80 the H-C = and C = C signals disappear and the ether signals are concentrated, it was distinguished by the intense band at 1100 cm–1. Egg yolk showed a large accumulation of phosphate groups at 1071 cm–1, where phosvitin is located. FT-IR has served to demonstrate that β-HPC is a hydrolysis enhancer. Furthermore, by obtaining the spectrum of N. brasiliensis, we intend to use it as a quick comparison tool with other spectra related to actinobacteria. Eventually, FT-IR may serve as a species identification option.
Testing the passive sampling hypothesis: The role of dispersal in shaping microbial species-area relationship
Authors: Deng Wei , Yu Guo-Bin , Yang Xiao-Yan , Xiao Wen
Published: January 2023

Dispersal is one of the key processes determining biodiversity. The passive sampling hypothesis, which emphasizes dispersal processes, suggests that larger habitats receive more species from the species pool as the main mechanism leading to more species in larger habitats than in smaller habitats (i.e., species-area relationships). However, the specific mechanisms by which dispersion shapes biodiversity still need to be discovered due to the difficulties of quantifying dispersal and the influence of multiple factors. Solving the above problem with a designed experiment is necessary to test the passive sampling hypothesis. This study designed a passive sampling experiment using sterile filter paper to quantify the microbial diffusion process, excluding the effects of pure sampling effects, habitat heterogeneity, and extinction processes. The results of high-throughput sequencing showed that a larger filter paper could receive more colonists, and the passive sampling hypothesis of SAR was confirmed. Dispersal shaped SAR by increasing species richness, especially rare species, and increasing the species replacement rate between habitats. These two processes are the mechanisms by which dispersal shapes biodiversity patterns. Compared with the results of this study, the commonly used mathematical model of passive sampling was able to predict the richness of non-rare species accurately but underestimated the richness of rare species. Underestimating rare species by mathematical models of passive sampling is more severe in small habitats. These findings provide new insights into the study of dispersal processes and the mechanism of species-area relationships.
Changyanning regulates gut microbiota and metabolism to ameliorate intestinal injury induced by ETEC K88
Authors: Guo Pei , Wang Zongke , Lv Xiaojing , Wang Xin , Yu Jiaying , Tian Xuelei , Shan Hu , Qin Zhihua
Published: January 2023

Enterotoxigenic Escherichia coli (ETEC) is a common pathogen of swine colibacillosis, which can causing a variety of diseases initiate serious economic losses to the animal husbandry industry. The traditional Chinese medicine Changyanning (CYN) often used for diarrhea caused by the accumulation of damp heat in the gastrointestinal tract, has anti-bacterial, anti-inflammatory and anti-oxidation effects. This study investigated the effect of CYN on gut microbiota and metabolism in mice infected with ETEC K88. A total of 60 Kunming mices were divided into Control group, ETEC K88 group, CYN.L group (2.5 g/kg), CYN.M group (5 g/kg), CYN.H group (10 g/kg) and BTW group (10 g/kg), determined clinical symptoms, intestinal morphology, inflammatory responses, gut microbiota as well as serum metabolites. CYN administration elevated ETEC K88-induced body weight loss, ameliorated duodenum, ilem, colon pathological injury, and reduced the increase of spleen index caused by ETEC. CYN also reduced the levels of pro-inflammatory cytokines (IL-6, TNE-α) in the serum. 16s rRNA gene sequencing results showed that CYN increased the abundance of beneficial bacteria Lactobacillus but decreased the abundance of pathogenic bacteria Escherichia in the feces of mice. Moreover, CYN participates in amino acid biosynthesis and metabolism in the process of serum metabolism to regulates ameliorate intestinal injury induced by ETEC K88. In conclusion, CYN regulates gut microbiota and metabolism to ameliorate intestinal injury induced by ETEC K88.
A closer look into the microbiome of microalgal cultures
Authors: Steinrücken Pia , Jackson Steve , Müller Oliver , Puntervoll Pål , Kleinegris Dorinde M. M.
Published: January 2023

Although bacteria are commonly co-occurring in microalgal cultivation and production systems, little is known about their community structure and how it might be affected by specific microalgal groups or growth conditions. A better understanding about the underlying factors that determine the growth of specific bacterial populations is not only important for optimizing microalgal production processes, but also in the context of product quality when the algal biomass is to be used for future food or feed. We analyzed the bacterial community composition associated with nine microalgal strains in stock culture, maintained in two different growth media, to explore how specific taxonomic microalgal groups, microalgal origin, or the growth medium affect the bacterial community composition. Furthermore, we monitored the bacterial community composition for three Phaeodactylum strains during batch cultivation in bubble columns to examine if the bacterial composition alters during cultivation. Our results reveal that different microalgal genera, kept at the same cultivation conditions over many years, displayed separate and unique bacterial communities, and that different strains of the same genus had very similar bacterial community compositions, despite originating from different habitats. However, when maintained in a different growth medium, the bacterial composition changed for some. During batch cultivation, the bacterial community structure remained relatively stable for each Phaeodactylum strain. This indicates that microalgae seem to impact the development of the associated bacterial communities and that different microalgal genera could create distinct conditions that select for dominance of specific bacteria. However, other factors such as the composition of growth medium also affect the formation of the bacterial community structure.
Myeloid masquerade: Microglial transcriptional signatures in retinal development and disease
Authors: Pitts Kristen M. , Margeta Milica A.
Published: January 2023

Microglia are dynamic guardians of neural tissue and the resident immune cells of the central nervous system (CNS). The disease-associated microglial signature (DAM), also known as the microglial neurodegenerative phenotype (MGnD), has gained significant attention in recent years as a fundamental microglial response common to various neurodegenerative disease pathologies. Interestingly, this signature shares many features in common with developmental microglia, suggesting the existence of recycled gene programs which play a role both in early neural circuit formation as well as in response to aging and disease. In addition, recent advances in single cell RNA sequencing have revealed significant heterogeneity within the original DAM signature, with contributions from both yolk sac-derived microglia as well as bone marrow-derived macrophages. In this review, we examine the role of the DAM signature in retinal development and disease, highlighting crosstalk between resident microglia and infiltrating monocytes which may critically contribute to the underlying mechanisms of age-related neurodegeneration.
Deep learning on lateral flow immunoassay for the analysis of detection data
Authors: Liu Xinquan , Du Kang , Lin Si , Wang Yan
Published: January 2023

Lateral flow immunoassay (LFIA) is an important detection method in vitro diagnosis, which has been widely used in medical industry. It is difficult to analyze all peak shapes through classical methods due to the complexity of LFIA. Classical methods are generally some peak-finding methods, which cannot distinguish the difference between normal peak and interference or noise peak, and it is also difficult for them to find the weak peak. Here, a novel method based on deep learning was proposed, which can effectively solve these problems. The method had two steps. The first was to classify the data by a classification model and screen out double-peaks data, and second was to realize segmentation of the integral regions through an improved U-Net segmentation model. After training, the accuracy of the classification model for validation set was 99.59%, and using combined loss function (WBCE + DSC), intersection over union (IoU) value of segmentation model for validation set was 0.9680. This method was used in a hand-held fluorescence immunochromatography analyzer designed independently by our team. A Ferritin standard curve was created, and the T/C value correlated well with standard concentrations in the range of 0–500 ng/ml (R2 = 0.9986). The coefficients of variation (CVs) were ≤ 1.37%. The recovery rate ranged from 96.37 to 105.07%. Interference or noise peaks are the biggest obstacle in the use of hand-held instruments, and often lead to peak-finding errors. Due to the changeable and flexible use environment of hand-held devices, it is not convenient to provide any technical support. This method greatly reduced the failure rate of peak finding, which can reduce the customer’s need for instrument technical support. This study provided a new direction for the data-processing of point-of-care testing (POCT) instruments based on LFIA.
Dynamic changes in the glycocalyx and clinical outcomes in patients undergoing endovascular treatments for large vessel occlusion
Authors: Liang Dan , Zeng Xiuli , Yao Mingzheng , Li Fei , Lin Jiaxing , Zhang Liang , Liu Jialin , Huang Li'an
Published: January 2023

Purpose

We aimed to verify the prognostic value of the glycocalyx as a marker of blood–brain barrier damage in patients with acute ischemic stroke undergoing endovascular therapy.

Methods

We recruited patients with large vessel occlusion who were undergoing recanalization and tested their glycocalyx at multiple time points. On the basis of the 90-day follow-up data, the patients were divided into a survivor group and a nonsurvivor group. In addition, neurological function was tracked, and patients were divided into a neurological deterioration group and a group without neurological deterioration. Associations between outcomes and dynamic changes in the glycocalyx were determined using a linear mixed model, and significant factors were used as covariates.

Results

Nonsurvivors and patients with neurological deterioration had significantly higher syndecan-1 concentrations than survivors and patients without neurological deterioration, and syndecan-1 tended to decline after endovascular therapy (p < 0.05). The increased level of syndecan-1 at 36 h after endovascular treatment was positively correlated with the National Institute of Health Stroke Scale score for neurological deterioration (r = 0.702, p = 0.005). However, there was no significant difference in the level of hyaluronic acid or heparan sulfate in the plasma of patients with different clinical outcomes.

Conclusion

Pre-reperfusion syndecan-1 levels in patients with large vessel occlusion stroke are associated with 90-day mortality and the re-degradation of syndecan-1 is positively associated with neurological deterioration.
Attitudes of people with multiple sclerosis toward brain donation
Authors: Marrie Ruth Ann , Kosowan Leanne , Cutter Gary R. , Fox Robert J. , Salter Amber
Published: January 2023

Objective

Research directly examining brain tissue has played an important role in understanding the pathology and pathogenesis of multiple sclerosis (MS) and other diseases of the central nervous system. Such research relies heavily on donations of post-mortem brain tissue yet little is known about the attitudes of people with multiple sclerosis (MS) about brain donation. We aimed to assess the attitudes of people with MS toward brain donation, their preferences related to discussions of brain donation, and factors associated with attitudes toward brain donation including sociodemographic and clinical characteristics, health literacy and religiosity.

Methods

In a cross-sectional study, we surveyed participants in the North American Research Committee on Multiple Sclerosis (NARCOMS) Registry regarding their attitudes toward brain donation, reasons for participating or not participating in brain donation, and related communication preferences. We used multivariable logistic regression analyses to test factors associated with attitudes regarding brain donation.

Results

Most of the 4,520 participants were women (80.8%), self-identified as white (88.1%), with a post-secondary education, functional health literacy and moderate-severe disability. Sixty-two percent of participants would consider brain donation. Factors associated with considering brain donation included female gender, having a post-secondary education, being physically active, having moderate-severe disability and more comorbidities, and alcohol intake. Seventy-five percent of participants indicated that they preferred to receive information regarding brain donations from physicians.

Conclusion

Two-thirds of people with MS would consider brain donation. People with MS desire to hear about brain donation from their health care providers rather than other sources.
Brain-derived neurotrophic factor Val66Met polymorphism modulates the effects of circadian desynchronization on activity and sleep in male mice
Authors: Phillips Derrick J. , Blaine Scott , Wallace Naomi K. , Karatsoreos Ilia N.
Published: January 2023

Introduction

Understanding how environmental interact challenges with genetic predispositions modulate health and wellbeing is an important area of biomedical research. Circadian rhythms play an important role in coordinating the multitude of cellular and tissue processes that organisms use to predict and adapt to regular changes in the environment, and robust circadian rhythms contribute to optimal physiological and behavioral responses to challenge. However, artificial lighting and modern round-the-clock lifestyles can disrupt the circadian system, leading to desynchronization of clocks throughout the brain and body. When coupled with genetic predispositions, circadian desynchronization may compound negative outcomes. Polymorphisms in the brain-derived neurotrophic (BDNF) gene contribute to variations in neurobehavioral responses in humans, including impacts on sleep, with the common Val66Met polymorphism linked to several negative outcomes.

Methods

We explored how the Val66Met polymorphism modulates the response to environmental circadian desynchronization (ECD) in a mouse model. ECD was induced by housing adult male mice in a 20 h light-dark cycle (LD10:10; 10 h light, 10 h dark). Sleep and circadian activity were recorded in homozygous (Met) mice and their wild-type (Val) littermates in a standard 24 h LD cycle (LD12:12), then again after 20, 40, and 60 days of ECD.

Results

We found ECD significantly affected the sleep/wake timing in Val mice, however, Met mice maintained appropriate sleep timing after 20 days ECD, but not after 40 and 60 days of ECD. In addition, the rise in delta power at lights on was absent in Val mice but was maintained in Met mice. To elucidate the circadian and homeostatic contribution to disrupted sleep, mice were sleep deprived by gentle handling in LD12:12 and after 20 days in ECD. Following 6 h of sleep deprivation delta power was increased for both Val and Met mice in LD12:12 and ECD conditions. However, the time constant was significantly longer in the Val mice during ECD compared to LD12:12, suggesting a functioning but altered sleep homeostat.

Discussion

These data suggest the Val66Met mutation is associated with an ability to resist the effects of LD10:10, which may result in carriers suffering fewer negative impacts of ECD.
Assessing MR-compatibility of somatosensory stimulation devices: A systematic review on testing methodologies
Authors: Travassos Carolina , Sayal Alexandre , Direito Bruno , Pereira João , Sousa Teresa , Castelo-Branco Miguel
Published: January 2023

Functional magnetic resonance imaging (fMRI) has been extensively used as a tool to map the brain processes related to somatosensory stimulation. This mapping includes the localization of task-related brain activation and the characterization of brain activity dynamics and neural circuitries related to the processing of somatosensory information. However, the magnetic resonance (MR) environment presents unique challenges regarding participant and equipment safety and compatibility. This study aims to systematically review and analyze the state-of-the-art methodologies to assess the safety and compatibility of somatosensory stimulation devices in the MR environment. A literature search, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines, was performed in PubMed, Scopus, and Web of Science to find original research on the development and testing of devices for somatosensory stimulation in the MR environment. Nineteen records that complied with the inclusion and eligibility criteria were considered. The findings are discussed in the context of the existing international standards available for the safety and compatibility assessment of devices intended to be used in the MR environment. In sum, the results provided evidence for a lack of uniformity in the applied testing methodologies, as well as an in-depth presentation of the testing methodologies and results. Lastly, we suggest an assessment methodology (safety, compatibility, performance, and user acceptability) that can be applied to devices intended to be used in the MR environment.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier CRD42021257838.
Novel diagnostic biomarkers related to immune infiltration in Parkinson’s disease by bioinformatics analysis
Authors: Zhang Pengfei , Zhao Liwen , Li Hongbin , Shen Jie , Li Hui , Xing Yongguo
Published: January 2023

Background

Parkinson’s disease (PD) is Pengfei Zhang Liwen Zhao Pengfei Zhang Liwen Zhao a common neurological disorder involving a complex relationship with immune infiltration. Therefore, we aimed to explore PD immune infiltration patterns and identify novel immune-related diagnostic biomarkers.

Materials and methods

Three substantia nigra expression microarray datasets were integrated with elimination of batch effects. Differentially expressed genes (DEGs) were screened using the “limma” package, and functional enrichment was analyzed. Weighted gene co-expression network analysis (WGCNA) was performed to explore the key module most significantly associated with PD; the intersection of DEGs and the key module in WGCNA were considered common genes (CGs). The CG protein–protein interaction (PPI) network was constructed to identify candidate hub genes by cytoscape. Candidate hub genes were verified by another two datasets. Receiver operating characteristic curve analysis was used to evaluate the hub gene diagnostic ability, with further gene set enrichment analysis (GSEA). The immune infiltration level was evaluated by ssGSEA and CIBERSORT methods. Spearman correlation analysis was used to evaluate the hub genes association with immune cells. Finally, a nomogram model and microRNA-TF-mRNA network were constructed based on immune-related biomarkers.

Results

A total of 263 CGs were identified by the intersection of 319 DEGs and 1539 genes in the key turquoise module. Eleven candidate hub genes were screened by the R package “UpSet.” We verified the candidate hub genes based on two validation sets and identified six (SYT1, NEFM, NEFL, SNAP25, GAP43, and GRIA1) that distinguish the PD group from healthy controls. Both CIBERSORT and ssGSEA revealed a significantly increased proportion of neutrophils in the PD group. Correlation between immune cells and hub genes showed SYT1, NEFM, GAP43, and GRIA1 to be significantly related to immune cells. Moreover, the microRNA-TFs-mRNA network revealed that the microRNA-92a family targets all four immune-related genes in PD pathogenesis. Finally, a nomogram exhibited a reliable capability of predicting PD based on the four immune-related genes (AUC = 0.905).

Conclusion

By affecting immune infiltration, SYT1, NEFM, GAP43, and GRIA1, which are regulated by the microRNA-92a family, were identified as diagnostic biomarkers of PD. The correlation of these four genes with neutrophils and the microRNA-92a family in PD needs further investigation.
Machine-learning prediction of BMI change among doctors and nurses in North China during the COVID-19 pandemic
Authors: Wang Qihe , Chu Haiyun , Qu Pengfeng , Fang Haiqin , Liang Dong , Liu Sana , Li Jinliang , Liu Aidong
Published: January 2023

Objective

The COVID-19 pandemic has become a major public health concern over the past 3 years, leading to adverse effects on front-line healthcare workers. This study aimed to develop a Body Mass Index (BMI) change prediction model among doctors and nurses in North China during the COVID-19 pandemic, and further identified the predicting effects of lifestyles, sleep quality, work-related conditions, and personality traits on BMI change.

Methods

The present study was a cross-sectional study conducted in North China, during May-August 2022. A total of 5,400 doctors and nurses were randomly recruited from 39 COVID-19 designated hospitals and 5,271 participants provided valid responses. Participants’ data related to social-demographics, dietary behavior, lifestyle, sleep, personality, and work-related conflicts were collected with questionnaires. Deep Neural Network (DNN) was applied to develop a BMI change prediction model among doctors and nurses during the COVID-19 pandemic.

Results

Of participants, only 2,216 (42.0%) individuals kept a stable BMI. Results showed that personality traits, dietary behaviors, lifestyles, sleep quality, burnout, and work-related conditions had effects on the BMI change among doctors and nurses. The prediction model for BMI change was developed with a 33-26-20-1 network framework. The DNN model achieved high prediction efficacy, and values of R2, MAE, MSE, and RMSE for the model were 0.940, 0.027, 0.002, and 0.038, respectively. Among doctors and nurses, the top five predictors in the BMI change prediction model were unbalanced nutritional diet, poor sleep quality, work-family conflict, lack of exercise, and soft drinks consumption.

Conclusion

During the COVID-19 pandemic, BMI change was highly prevalent among doctors and nurses in North China. Machine learning models can provide an automated identification mechanism for the prediction of BMI change. Personality traits, dietary behaviors, lifestyles, sleep quality, burnout, and work-related conditions have contributed to the BMI change prediction. Integrated treatment measures should be taken in the management of weight and BMI by policymakers, hospital administrators, and healthcare workers.
Adequate vitamin D level associated with reduced risk of sporadic colorectal cancer
Authors: Ma Yanhui , Deng Lin , Huangfu Yuchan , Zhou Yunlan , Wang Ping , Shen Lisong
Published: January 2023

Purpose

The effect of vitamin D level pertinent to colorectal cancer incidence, progression, or mortality risk is complicated, and study findings are mixed. Therefore, we evaluated whether serum vitamin D [25-hydroxyvitamin D, 25(OH)D] is associated with the incidence of sporadic colorectal cancer (CRC).

Methods

This study is a retrospective analysis of the relationship between serum 25(OH)D level and the risk of CRC. Age, sex, body mass index, history of polyp, disease conditions (i.e., diabetes), medications, and other eight vitamins were used as confounding factors. A total of 389 participants were enrolled in this study, including comprising 83 CRC patients without a family history and 306 healthy controls, between January 2020 and March 2021 at the Department of Colorectal Surgery and Endoscope Center at the Xinhua Hospital, Shanghai Jiao Tong University School of Medicine. Adjusted smoothing spline plots, subgroup analysis, and multivariate logistic regression analysis were conducted to estimate the relative risk between serum 25(OH)D and sporadic CRC risk.

Results

After fully adjusting the confounding factors, it was found that circulating 25(OH)D played a protective role in patients with CRC (OR = 0.76 [0.63, 0.92], p = 0.004) and that an adequate vitamin D level was significantly associated with a reduced CRC risk compared to vitamin D deficiency or sufficiency (OR = 0.31 [0.11, 0.9], p = 0.03). According to this study, statins did not affect the potential protective effects of vitamin D (OR = 1.02 [0.97, 1.08], p = 0.44) and may account for the inverse association between serum 25(OH)D and colorectal cancer.

Conclusion

An adequate level of serum 25(OH)D was associated with a reduced CRC risk, especially for the elderly. The finding on the absence of protective effect of vitamin D in the statin use subgroup, suggests it may be one of the substantial contributing confounders, and warrants further investigation.
Association between dietary vitamin C and telomere length: A cross-sectional study
Authors: Cai Yuan , Zhong Yu-di , Zhang Hao , Lu Pei-lin , Liang Yong-yi , Hu Biao , Wu Hui
Published: January 2023

Background

Currently, telomere length is known to reflect the replication potential and longevity of cells, and many studies have reported that telomere length is associated with age-related diseases and biological aging. Studies have also shown that vitamin C acts as an oxidant and free radical scavenger to protect cells from oxidative stress and telomere wear, thus achieving anti-aging effects. At present, there are few and incomplete studies on the relationship between vitamin C and telomere length, so this study aims to explore the relationship between vitamin C and telomere length.

Methods

This study used cross-sectional data from the National Health and Nutrition Examination Surveys (NHANES) database from 1999 to 2002, a total of 7,094 participants were selected from all races in the United States. Male participants accounted for 48.2% and female participants accounted for 51.8%. The correlation between vitamin C and telomere length was assessed using a multiple linear regression model, and the effect of dietary vitamin C on telomere length was obtained after adjusting for confounding factors such as age, gender, race, body mass index (BMI), and poverty income ratio (PIR).

Results

This cross-sectional study showed that vitamin C was positively correlated with telomere length, with greater dietary vitamin C intake associated with longer telomeres (β = 0.03, 95% CI: 0.01–0.05, P = 0.003).

Conclusion

This study shows that vitamin C intake is positively correlated with human telomere length, which is of guiding significance for our clinical guidance on people’s health care, but our study need to be confirmed by more in-depth and comprehensive other research results.
Novel nutritional indicator as predictors among subtypes of lung cancer in diagnosis
Authors: Li Haiyang , Cheng Zhangkai J. , Liang Zhiman , Liu Mingtao , Liu Li , Song Zhenfeng , Xie Chuanbo , Liu Junling , Sun Baoqing
Published: January 2023

Introduction

Lung cancer is a serious global health concern, and its subtypes are closely linked to lifestyle and dietary habits. Recent research has suggested that malnutrition, over-nutrition, electrolytes, and granulocytes have an effect on the development of cancer. This study investigated the impact of combining patient nutritional indicators, electrolytes, and granulocytes as comprehensive predictors for lung cancer treatment outcomes, and applied a machine learning algorithm to predict lung cancer.

Methods

6,336 blood samples were collected from lung cancer patients classified as lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LUAD), and small cell lung cancer (SCLC). 2,191 healthy individuals were used as controls to compare the differences in nutritional indicators, electrolytes and granulocytes among different subtypes of lung cancer, respectively.

Results

Our results demonstrated significant differences between men and women in healthy people and NSCLC, but no significant difference between men and women in SCLC patients. The relationship between indicators is basically that the range of indicators for cancer patients is wider, including healthy population indicators. In the process of predicting lung cancer through nutritional indicators by machine learning, the AUC of the random forest model was as high as 93.5%, with a sensitivity of 75.9% and specificity of 96.5%.

Discussion

This study supports the feasibility and accuracy of nutritional indicators in predicting lung cancer through the random forest model. The successful implementation of this novel prediction method could guide clinicians in providing both effective diagnostics and treatment of lung cancers.
Can cereal-legume intercrop systems contribute to household nutrition in semi-arid environments: A systematic review and meta-analysis
Authors: Chimonyo Vimbayi Grace Petrova , Govender Laurencia , Nyathi Melvin , Scheelbeek Pauline Franka Denise , Choruma Dennis Junior , Mustafa Maysoun , Massawe Festo , Slotow Rob , Modi Albert Thembinkosi , Mabhaudhi Tafadzwanashe
Published: January 2023

Introduction

Intercropping cereals with legumes can intensify rainfed cereal monocropping for improved household food and nutritional security. However, there is scant literature confirming the associated nutritional benefits.

Methodology

A systematic review and meta-analysis of nutritional water productivity (NWP) and nutrient contribution (NC) of selected cereal-legume intercrop systems was conducted through literature searches in Scopus, Web of Science and ScienceDirect databases. After the assessment, only nine articles written in English that were field experiments comprising grain cereal and legume intercrop systems were retained. Using the R statistical software (version 3.6.0), paired t-tests were used to determine if differences existed between the intercrop system and the corresponding cereal monocrop for yield (Y), water productivity (WP), NC, and NWP.

Results

The intercropped cereal or legume yield was 10 to 35% lower than that for the corresponding monocrop system. In most instances, intercropping cereals with legumes improved NY, NWP, and NC due to their added nutrients. Substantial improvements were observed for calcium (Ca), where NY, NWP, and NC improved by 658, 82, and 256%, respectively.

Discussion

Results showed that cereal-legume intercrop systems could improve nutrient yield in water-limited environments. Promoting cereal- legume intercrops that feature nutrient-dense legume component crops could contribute toward addressing the SDGs of Zero Hunger (SDG 3), Good Health and Well-3 (SDG 2) and Responsible consumption and production (SDG 12).
Prognostic impact of sarcopenia in patients with locally advanced adenocarcinoma of the esophagogastric junction treated with neoadjuvant chemoradiotherapy
Authors: Ming Jiao , Du Rongxu , Geng Jianhao , Li Shuai , Liu Zhiyan , Cai Yong , Zhu Xianggao , Zhang Yangzi , Wang Hongzhi , Wang Zhilong , Tang Lei , Zhang Xiaotian , Peng Zhi , Wu Aiwen , Bu Zhaode , Peng Yifan , Yan Yan , Li Zhongwu , Li Yongheng , Li Ziyu , Wang Weihu
Published: January 2023

Background

Few studies have evaluated the significance of sarcopenia in predicting the outcomes of patients with adenocarcinoma of the esophagogastric junction (AEG), especially those who received neoadjuvant chemoradiotherapy (NCRT). We aimed to identify the sarcopenic status and its impact on the outcomes of patients with locally advanced AEG who received NCRT followed by radical surgery or systemic therapy.

Materials and methods

Patients with T3-4N+M0 AEG with accessible abdominal computed tomography (CT) before and after NCRT were retrospectively analyzed. Body composition parameters, particularly the skeletal muscle index (SMI), were assessed using a CT-based method, and sarcopenia was defined using a predetermined SMI cutoff value. Survival analysis was conducted using the Kaplan–Meier method. A Cox proportional hazards regression model was used to identify independent prognostic factors. Receiver operating characteristic curve analysis was carried out, and the area under the curve (AUC) was calculated to test the prognostic accuracy of different factors.

Results

A total of 63 patients were enrolled, 65.1 and 79.4% of whom developed pre- and post-NCRT sarcopenia, respectively. Patients with pre-NCRT sarcopenia had lower radical surgery rates (70.7 vs. 95.5%, p = 0.047) than those without sarcopenia; however, sarcopenic status did not affect other short-term outcomes, including treatment-related toxicity and efficacy. Pre-NCRT sarcopenia was identified as an independent predictive factor for poor overall survival (OS) [adjusted hazard ratio (HR), 6.053; p = 0.002] and progression-free survival (PFS) (adjusted HR, 2.873; p = 0.031). Compared with nutritional indices such as the Nutritional Risk Screening 2002, weight loss during NCRT, and post-NCRT sarcopenia, pre-NCRT sarcopenia was regarded as the best predictive index for the 5-year OS (AUC = 0.735) and PFS rates (AUC = 0.770).

Conclusion

Pre-NCRT sarcopenia may be an independent predictive factor for OS and PFS rates in patients with locally advanced AEG receiving multimodal treatment.
Case Report: A rare case of primary paraganglioma of the gallbladder with a literature review
Authors: Xia Yijun , Wang Shi , Wang Xidong , Du Jiya , Zhang Lei , Xia Long
Published: January 2023

Introduction

Paragangliomas of the gallbladder are exceptionally rare. To date, only a few cases of this disease have been reported globally, and the majority were found incidentally during surgery. Although complete resection can achieve a curative effect, specific targeted drugs may have survival benefits for patients with potential recurrence and metastasis risks.

Case presentation

A 48-year-old woman was scheduled for anatomical central hepatectomy due to the discovery of a liver mass. Surprisingly, a gallbladder tumor accompanied by intrahepatic invasion was found rather than primary liver lesions during the operation. Postoperatively, the lesion was confirmed to be a paraganglioma originating from the gallbladder with intrahepatic invasion detectable on histopathology. After surgery, the patient was treated with a new targeted drug, surufatinib {200 mg, q.d. [quaque die (every day)]}, and no recurrence was observed during the regular follow-up.

Discussion

Gallbladder paraganglioma is rare and occult, and surgeons do not know it well, so it is easily misdiagnosed before surgery. Postoperative pathological examination is the gold standard for diagnosis.

Conclusion

Given that the tumor contained abundant blood sinuses, the early and continuous enhancement of dynamic enhanced CT scanning was its characteristic manifestation. We presented a case in which a primary gallbladder paraganglioma was identified accidentally in a patient who was misdiagnosed with a liver lesion before surgery. Based on our experience in this work, the en bloc resection technique in combination with surufatinib might have a survival benefit to patients at risk of potential recurrence or metastasis; however, further follow-up observations are needed.