bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of parallel metabolomics and transcriptomics reveals metabolic patterns in porcine oocytes during maturation
Authors: Gao Ming , Chen Minjian , Chen Qiuzhen , Zhu Shuai , Wang Hengjie , Yang Weizheng , Wang Xi , Wang Qiang , Gu Ling
Published: February 2023

Well-controlled metabolism is the prerequisite for optimal oocyte development. To date, numerous studies have focused mainly on the utilization of exogenous substrates by oocytes, whereas the underlying mechanism of intrinsic regulation during meiotic maturation is less characterized. Herein, we performed an integrated analysis of parallel metabolomics and transcriptomics by isolating porcine oocytes at three time points, cooperatively depicting the global picture of the metabolic patterns during maturation. In particular, we identified the novel metabolic features during porcine oocyte meiosis, such as the fall in bile acids, the active one-carbon metabolism and a progressive decline in nucleotide metabolism. Collectively, the current study not only provides a comprehensive multiple omics data resource, but also may facilitate the discovery of molecular biomarkers that could be used to predict and improve oocyte quality.
Individual species and site dynamics are the main drivers of spatial scaling of stability in aquatic communities
Authors: Hodapp Dorothee , Armonies Werner , Dannheim Jennifer , Downing John A. , Filstrup Christopher T. , Hillebrand Helmut
Published: February 2023

Introduction

Any measure of ecological stability scales with the spatial and temporal extent of the data on which it is based. The magnitude of stabilization effects at increasing spatial scale is determined by the degree of synchrony between local and regional species populations.

Methods

We applied two recently developed approaches to quantify these stabilizing effects to time series records from three aquatic monitoring data sets differing in environmental context and organism type.

Results and Discussion

We found that the amount and general patterns of stabilization with increasing spatial scale only varied slightly across the investigated species groups and systems. In all three data sets, the relative contribution of stabilizing effects via asynchronous dynamics across space was higher than compensatory dynamics due to differences in biomass fluctuations across species and populations. When relating the stabilizing effects of individual species and sites to species and site-specific characteristics as well as community composition and aspects of spatial biomass distribution patterns, however, we found that the effects of single species and sites showed large differences and were highly context dependent, i.e., dominant species can but did not necessarily have highly stabilizing or destabilizing effects on overall community biomass. The sign and magnitude of individual contributions depended on community structure and the spatial distribution of biomass and species in space. Our study therefore provides new insights into the mechanistic understanding of ecological stability patterns across scales in natural species communities.
Identification of the core genes in Randall’s plaque of kidney stone and immune infiltration with WGCNA network
Authors: Yu Lingyun , Li Gefei , Jin Shiyao , Su Jiahong , Li Shoulin
Published: February 2023

Background: Randall’s plaque is regarded as the precursor lesion of lithiasis. However, traditional bioinformatic analysis is limited and ignores the relationship with immune response. To investigate the underlying calculi formation mechanism, we introduced innovative algorithms to expand our understanding of kidney stone disease.

Methods: We downloaded the GSE73680 series matrix from the Gene Expression Omnibus (GEO) related to CaOx formation and excluded one patient, GSE116860. In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package. Furthermore, high-correlated gene co-expression modules were confirmed by the WGCNA package to establish a protein–protein interaction (PPI) network. Finally, the CaOx samples were processed by the CIBERSORT algorithm to anchor the key immune cells group and verified in the validation series matrix GSE117518.

Results: The study identified 840 upregulated and 1065 downregulated genes. The GO/KEGG results revealed fiber-related or adhesion-related terms and several pathways in addition to various diseases identified from the DO analysis. Moreover, WGCNA selected highly correlated modules to construct a PPI network. Finally, 16 types of immune cells are thought to participate in urolithiasis pathology and are related to hub genes in the PPI network that are proven significant in the validation series matrix GSE117518.

Conclusion: Randall’s plaque may relate to genes DCN, LUM, and P4HA2 and M2 macrophages and resting mast immune cells. These findings could serve as potential biomarkers and provide new research directions.
COVID-19 in children and the influence on the employment activity of their female caregivers: A cross sectional gender perspective study
Authors: Jaime Trujillo Catalina , Herrera Olano Natalia , Rico Gutiérrez Kevin , Medellín Daniela , Sánchez Paola , Mesa-Rubio María Lucía , Naranjo Melisa Sofía , Moreno Sergio Mauricio , Bonilla Carolina , Barrera Pedro , Restrepo-Gualteros Sonia M. , Mejia Luz Marina , Baquero Olga Lucía , Piñeros Juan Gabriel , Ramírez Varela Andrea
Published: February 2023

Introduction

During the COVID-19 pandemic, women disproportionately assume more unpaid activities, affecting their employment.

Objective

Describe the influence of COVID-19 on the employment of caregivers of children and adolescents from a gender perspective.

Methods

Cross-sectional study in three high-complexity hospitals in Bogotá, Colombia from April 2020 to June 2021. A subsample of the FARA cohort was taken, including those patients with a positive test for SARS-COV2. We took as our analysis category children older than 8 years and younger than 18 years who had a positive SARS-COV2 test, as well as, caregivers of all children with a positive SARS-COV2 test. This subsample was drawn from the FARA cohort. A survey was applied to them. We carried out a descriptive and stratified analysis by age group, educational, and socioeconomic level.

Results

We included 60 surveys of caregivers and 10 surveys of children. The main caregiver in 94.8% of the cases was a female. At the beginning of the pandemic, 63.3% of the caregivers were employed, and 78.9% of those lost their employment. The vast majority of these caregiver were women (96.6%, n = 29). A predominance of loss of work activity was documented in caregivers of children in early childhood 66.6% (n = 20), with lower education 66.6% (n = 20), and from lower strata 56.6% (n = 17).

Conclusion

Caregivers of children with COVID-19 with low educational levels and lower socioeconomic conditions, as well as those with children under 5 years showed greater likelihood of employment loss between the interviewed subsample.
Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines
Authors: Francisco Junior Ronaldo da Silva , Temerozo Jairo R. , Ferreira Cristina dos Santos , Martins Yasmmin , Souza Thiago Moreno L. , Medina-Acosta Enrique , Vasconcelos Ana Tereza Ribeiro de
Published: February 2023

Introduction

Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with the disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs.

Methods

We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments.

Results

We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes.

Discussion

Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.
Switch to ocrelizumab in MS patients treated with natalizumab in extended interval dosing at high risk of PML: A 96-week follow-up pilot study
Authors: Santiago-Setien Pilar , Barquín-Rego Cristina , Hernández-Martínez Paula , Ezquerra-Marigomez María , Torres-Barquin Marta , Menéndez-Garcia Cristina , Uriarte Fernando , Jiménez-López Yésica , Misiego Mercedes , Sánchez de la Torre Jose Ramón , Setien Sonia , Delgado-Alvarado Manuel , Riancho Javier
Published: February 2023

We aimed to assess the long-term safety and effectiveness of ocrelizumab in a cohort of patients with multiple sclerosis (MS) at high risk of progressive multifocal leukoencephalopathy (PML), previously treated with natalizumab in extending interval dosing (EID), who switched to ocrelizumab and to compare them with patients who continued EID-natalizumab. Thirty MS patients previously treated with natalizumab in EID (every 8 weeks) were included in this observational retrospective cohort study. Among them, 17 patients were switched to ocrelizumab and 13 continued with EID-natalizumab. Except for the John Cunningham virus (JCV) index, no significant differences were detected between both groups. Main outcome measures included: annualized relapse rate (ARR), radiological activity, disability progression, and the NEDA-3 index. Patients were followed for 96 weeks. The median washout period in ocrelizumab-switchers was 6 weeks. Among them, AAR and radiological activity during follow-up were 0.03, without significant differences in comparison with the previous period on natalizumab-EID. The comparison between ocrelizumab-switchers and patients continuing on EID-natalizumab showed no significant differences in AAR, radiological activity, or disability progression. However, the proportion of patients maintaining a NEDA-3 status in week 96 was slightly superior among ocrelizumab-switchers (94 vs 69%). No serious adverse events were observed in any group. In conclusion, switching from EID-natalizumab to ocrelizumab can be considered as a therapeutic option, particularly in patients with MS at high risk of PML, to mitigate the risks of both PML and disease reactivation.
Chronological changes of viral shedding in adult inpatients with Omicron infection in Shanghai, China
Authors: Zhou Xinru , Huang Xiaochun , Sun Tingting , Jin Xiaolan , Tian Zhaofeng , Xue Miao , Kang Jinsong , Gao Bai , Xu Aijing , Chen Yi , Jia Yin , Liu Shanrong
Published: February 2023

Background

Coronavirus disease 2019 (COVID-19) caused by the Omicron variant occurred in Shanghai, China, but its clinical characteristics and virology have not been comprehensively described.

Methods

This retrospective cohort study included adult inpatients (≥18 years) diagnosed with COVID-19 at Changhai Hospital. Laboratory and clinical data were obtained from electronic medical records to investigate the clinical characteristics of COVID-19 and the variations in the patients’ laboratory indexes were examined.

Results

The symptoms of COVID-19 caused by the Omicron variant were relatively mild. Upper respiratory tract specimens yielded higher positive detection rates than lower respiratory tract and intestinal specimens. Peak COVID-19 viral load was reached at the time of admission; quantification cycle (Cq) values increased to approximately 35 after 8.54 days. In vivo viral shedding duration correlated with age and disease severity (p<0.05). The older the patient and the more severe the disease, the longer the duration of viral shedding was. Portion parameters of blood routine, coagulative function, clinical chemistry, and inflammatory factor showed a certain correlation with the SARS-CoV-2 viral load.

Conclusions

Virus replication and shedding are rapid in Omicron-positive patients; COVID-19 in these patients is characterized by acute onset, mild symptoms, and fast recovery. Older patients and those with more severe disease demonstrate prolonged virus shedding. Routine hematological indexes can reveal disease severity and help clinically evaluate the patient’s condition.
Deciphering the sequential changes of monocytes/macrophages in the progression of IDD with longitudinal approach using single-cell transcriptome
Authors: Li Weihang , Zhao Yingjing , Wang Yongchun , He Zhijian , Zhang Linyuan , Yuan Bin , Li Chengfei , Luo Zhuojing , Gao Bo , Yan Ming
Published: February 2023

Intervertebral disk degeneration (IDD) is a chronic inflammatory disease with intricate connections between immune infiltration and oxidative stress (OS). Complex cell niches exist in degenerative intervertebral disk (IVD) and interact with each other and regulate the disk homeostasis together. However, few studies have used longitudinal approach to describe the immune response of IDD progression. Here, we conducted conjoint analysis of bulk-RNA sequencing and single-cell sequencing, together with a series of techniques like weighted gene co-expression network analysis (WGCNA), immune infiltration analysis, and differential analysis, to systematically decipher the difference in OS-related functions of different cell populations within degenerative IVD tissues, and further depicted the longitudinal alterations of immune cells, especially monocytes/macrophages in the progression of IDD. The OS-related genes CYP1A1, MMP1, CCND1, and NQO1 are highly expressed and might be diagnostic biomarkers for the progression of IDD. Further landscape of IVD microenvironment showed distinct changes in cell proportions and characteristics at late degeneration compared to early degeneration of IDD. Monocytes/macrophages were classified into five distinct subpopulations with different roles. The trajectory lineage analysis revealed transcriptome alterations from effector monocytes/macrophages and regulatory macrophages to other subtypes during the evolution process and identified monocytes/macrophage subpopulations that had rapidly experienced the activation of inflammatory or anti-inflammatory responses. This study further proposed that personalized therapeutic strategies are needed to be formulated based on specific monocyte/macrophage subtypes and degenerative stages of IDD.
TRPV6 deficiency attenuates stress and corticosterone-mediated exacerbation of alcohol-induced gut barrier dysfunction and systemic inflammation
Authors: Meena Avtar S. , Shukla Pradeep K. , Rao Rupa , Canelas Cherie , Pierre Joseph F. , Rao RadhaKrishna
Published: February 2023

Introduction

Chronic stress is co-morbid with alcohol use disorder that feedback on one another, thus impeding recovery from both disorders. Stress and the stress hormone corticosterone aggravate alcohol-induced intestinal permeability and liver damage. However, the mechanisms involved in compounding tissue injury by stress/corticosterone and alcohol are poorly defined. Here we explored the involvement of the TRPV6 channel in stress (or corticosterone) 3and alcohol-induced intestinal epithelial permeability, microbiota dysbiosis, and systemic inflammation.

Methods

Chronic alcohol feeding was performed on adult wild-type and Trpv6-/- mice with or without corticosterone treatment or chronic restraint stress (CRS). The barrier function was determined by evaluating inulin permeability in vivo and assessing tight junction (TJ) and adherens junction (AJ) integrity by immunofluorescence microscopy. The gut microbiota composition was evaluated by 16S rRNA sequencing and metagenomic analyses. Systemic responses were assessed by evaluating endotoxemia, systemic inflammation, and liver damage.

Results

Corticosterone and CRS disrupted TJ and AJ, increased intestinal mucosal permeability, and caused endotoxemia, systemic inflammation, and liver damage in wild-type but not Trpv6-/- mice. Corticosterone and CRS synergistically potentiated the alcohol-induced breakdown of intestinal epithelial junctions, mucosal barrier impairment, endotoxemia, systemic inflammation, and liver damage in wild-type but not Trpv6-/- mice. TRPV6 deficiency also blocked the effects of CRS and CRS-mediated potentiation of alcohol-induced dysbiosis of gut microbiota.

Conclusions

These findings indicate an essential role of TRPV6 in stress, corticosterone, and alcohol-induced intestinal permeability, microbiota dysbiosis, endotoxemia, systemic inflammation, and liver injury. This study identifies TRPV6 as a potential therapeutic target for developing treatment strategies for stress and alcohol-associated comorbidity.
USFP: An unbalanced severe typhoon formation prediction framework based on transfer learning
Authors: Pan Xiaotian , Wang Xiang , Zhao Chengwu , Wu Jianping , Wang Huizan , Wang Senzhang , Chen Sihao
Published: February 2023

Introduction

Severe typhoons, as extreme weather events, can cause a large number of casualties and property damage in coastal areas. There are mainly three kinds of methods for the prediction of severe typhoon formation, which are the numerical-based methods, the statistical-based methods, and the machine learning-based methods. However, existing methods do not consider the unbalance between the number of ordinary typhoon samples and severe typhoon samples, which makes the accuracies of existing methods in the prediction of severe typhoons much lower than that of ordinary typhoons.

Methods

In this paper, we propose an unbalanced severe typhoon formation prediction (USFP) framework based on transfer learning. We first propose a severe typhoon pre-learning model which is used to learn prior knowledge from a constructed balanced dataset. Then, we propose an unbalanced severe typhoon re-learning model which utilizes the prior knowledge learning from the pre-learning model. Our USFP framework fuses three different variables, which are atmospheric variables, sea surface variables, and ocean hydrographic variables.

Results

Extensive experiments based on datasets of three different regions show that our USFP framework outperforms the numerical model IFS of ECMWF and existing machine learning methods.
Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption
Authors: Yang Jian , Liu Minhai , Zhou Tingting , Li Qi , Lin Zhihua
Published: February 2023

DNA methylation is a critical epigenetic modification that dynamically regulates gene expression in organisms facing abiotic stress. However, few studies have comprehensively examined the role of DNA methylation in marine fish during environmental adaptation. Therefore, this study explored the methylome dynamics and DNA methylation regulation mechanisms in large yellow croaker (Larimichthys crocea) during low-salinity adaption. The methylation level in the gills was notably raised in the S-group (5‰ salinity) compared to C-group (25‰ salinity). A total of 109 differentially methylated promoter target genes and 581 differentially expressed genes were identified via whole-genome bisulfite sequencing (WGBS) and RNA-seq of gills in the two salinity groups, respectively. Moreover, 23 hypo-methylated/up-regulated differentially methylated genes (DMGs) and 28 hyper-methylated/down-regulated DMGs were identified through integrative analysis, which were mainly enriched in signal transduction, ion exchange, energy metabolism, and cytoskeleton system and other biological processes. Collectively, our findings suggested that low-salinity stress can induce adaptive genome-wide DNA methylation changes, which can in turn affect the transcription of genes in large yellow croaker during low-salinity adaptation. Therefore, our findings provide new insights into the regulatory mechanisms of marine fish in response to rapid environmental changes.
Effects of spatial bottom friction parameterization scheme on the tidal dynamics in the macrotidal East China Seas
Authors: Qian Suhui , Du Yunfei , Wei Zilu , Zhang Jicai , Cheng Jun , Wang Daosheng , Wang Ya Ping
Published: February 2023

In this study, the effects of different bottom friction coefficient (BFC) parameterization schemes on the modelling of four principal tidal constituents (M2, S2, K1, O1 tides) in the macrotidal East China Seas were investigated by using a high-resolution model based on FVCOM (Finite Volume Community Ocean Model). The applied BFC schemes include: the empirical constant (EC-BFC), sediment-dependent form (SD-BFC), and spatial varying BFC obtained from adjoint data assimilation (SV-BFC). The comparisons between the simulated results and the observations from satellite altimeters and tidal gauge stations indicated that the SV-BFC scheme is superior to others. The locations of amphidromic points calculated with EC-BFC and SD-BFC were in the northwest of those from SV-BFC. The variations in tidal dynamics between different BFC schemes were closely related to the spatial distributions of BFCs, especially in high-valued BFC areas, e.g., the West Korea Bay, the South Yellow Sea, and the eastern coasts of Jiangsu, Zhejiang and Fujian provinces. The tidal energy flux transporting into Bohai and Yellow Seas increased under the SV-BFC scheme, while smaller tidal energy flux transporting from the Korea Strait was generated by SV-BFC as compared to those from EC-BFC and SD-BFC. The high-valued BFC areas in the SV-BFC scheme dissipated larger amounts of tidal energy, and the average values of Simpson-Hunter numbers were lower than those with the other two schemes. However, the values of Simpson-Hunter numbers increased in the West Korea Bay and Jianghua Bay with high-valued BFCs because of the decreasing current velocity under the headland-shaped topography.
Resource environment load prediction method for metal material machining based on process condition similarity matching
Authors: Xing Zhipeng , Dai Haicong , Xiong Jiaji , Zhang Jiong , Li Yufeng
Published: February 2023

Introduction: Resource environment load data are important for analyzing and improving the environmental performance, which are affected by the process condition of metal material machining processes. However, the environmental performance assessment in previous research focused on the results under the specific process conditions. The resource environment load data need to be re-collected when the process conditions are changed for a credible assessment, which is time- consuming and tedious.

Methods: This paper proposed a process condition- oriented prediction method of resource environment load data with limited samples. The significance of process condition elements on the resource environment load data was analyzed, and then the resource environment load was predicted according to the similarity between the process condition to be predicted and the existing process conditions.

Results and Dicussion: The results show that the average prediction accuracy of this method exceeds 90%, and further the accuracy for predicting the environmental performances using the predicted data is more than 93% which would help process designers to choose the better process condition for machining the metal materials.
Low prevalence of hepatitis delta infection in Cuban HBsAg carriers: Prospect for elimination
Authors: de los Ángeles Rodríguez Lay Licel , Tan Zexi , Villalba Maria Caridad Montalvo , Suárez Marcia Samada , Corredor Marité Bello , Hernández Dayesi López , Sánchez Barbara Marrero , Alonso Lidunka Valdés , Sausy Aurélie , Hübschen Judith M.
Published: February 2023

Introduction

Infection with hepatitis delta virus (HDV) is one of the most severe hepatitis B virus (HBV) complications, with a more rapid progression to cirrhosis and an increased risk of hepatic decompensation and death. Data on HDV infection in Cuba are limited. The aims of our study were to determine the HDV prevalence in HBsAg carriers and to characterize the HDV strains circulating. The data were used to assess the possibility of HDV elimination in the Cuban HBV epidemiological setting.

Methods

Five hundred and two serum samples from the same number of HBsAg carriers collected in the period 2006–2019 from all over the country were tested for anti-HDV total antibodies. If positive, the samples were analyzed for HDV-RNA using Real-Time RT-PCR targeting the ribozyme and HD antigen domains followed by genotyping based on phylogenetic analysis.

Results

Two samples were anti-HDV positive [0.39% (95% CI 0.11–1.44)]. One of them was also HDV-RNA positive. Clinically, the patient with active HDV infection had compensated liver cirrhosis. Phylogenetic analysis showed that the virus belonged to genotype 1 and thus clustered with contemporary strains from North America, Europe, Middle East, and Asia.

Discussion

This is the first HDV study, including molecular detection and virus characterization, done after the introduction of the universal childhood anti-hepatitis B vaccination. The very low prevalence of HDV infection in HBsAg carriers combined with the high HBV vaccination coverage of all newborn children, of previously identified risk groups, and of the general population currently under 40 years of age suggests that HDV elimination is feasible in Cuba if the success in HBV control is maintained.
Insights from comparison of the clinical presentation and outcomes of patients hospitalized with COVID-19 in an Italian internal medicine ward during first and third wave
Authors: Ticinesi Andrea , Parise Alberto , Nouvenne Antonio , Cerundolo Nicoletta , Prati Beatrice , Guerra Angela , Tuttolomondo Domenico , Gaibazzi Nicola , Meschi Tiziana
Published: February 2023

Background

The reasons of variability of clinical presentation of coronavirus disease-19 (COVID-19) across different pandemic waves are not fully understood, and may include individual risk profile, SARS-CoV-2 lineage and seasonal variations of viral spread. The objective of this retrospective study was to compare the characteristics and outcomes of patients admitted with confirmed coronavirus disease-19 (COVID-19) in the same season during the first (March 2020) and the third pandemic wave (March 2021, dominance of SARS-CoV-2 B.1.1.7 lineage) in an internal medicine ward of a large teaching hospital in Italy.

Materials and methods

Data of 769 unvaccinated patients (399 from the first and 370 from the third wave) were collected from clinical records, including symptom type and duration, extension of lung abnormalities on chest computed tomography (CT) and PaO2/FiO2 ratio on admission arterial blood gas analysis.

Results

Third wave patients were in average younger (median 65, interquartile range [IQR] 55–75, vs. 72, IQR 61–81 years old, p < 0.001), with less comorbidities and better pulmonary (CT visual score median 25, IQR 15–40, vs. 30, IQR 15–50, age- and sex-adjusted p = 0.017) and respiratory involvement (PaO2/FiO2 median 288, IQR 237–338, vs. 233, IQR 121–326 mmHg, age- and sex-adjusted p < 0.001) than first wave patients. Hospital mortality was lower (19% vs. 36%, p < 0.001), but not for subjects over 75 years old (46 vs. 49%). Age, number of chronic illnesses, PCT levels, CT visual score [Odds Ratio (OR) 1.022, 95% confidence interval (CI) 1.009–1.036, p < 0.001] and PaO2/FiO2 (OR 0.991, 95% CI 0.988–0.994, p < 0.001), but not the pandemic wave, were associated with mortality on stepwise multivariate logistic regression analysis.

Conclusion

Despite the higher virulence of B.1.1.7 lineage, we detected milder clinical presentation and improved mortality in patients hospitalized during the third COVID-19 wave, with involvement of younger subjects. The reasons of this discrepancy are unclear, but could involve the population effect of vaccination campaigns, that were being conducted primarily in older frail subjects during the third wave.
Gut microbiota variation between climatic zones and due to migration strategy in passerine birds
Authors: Schmiedová Lucie , Kreisinger Jakub , Kubovčiak Jan , Těšický Martin , Martin Jean-Francois , Tomášek Oldřich , Kauzálová Tereza , Sedláček Ondřej , Albrecht Tomáš
Published: February 2023

Introduction

Decreasing biotic diversity with increasing latitude is an almost universal macroecological pattern documented for a broad range of taxa, however, there have been few studies focused on changes in gut microbiota (GM) across climatic zones.

Methods

Using 16S rRNA amplicon profiling, we analyzed GM variation between temperate (Czechia) and tropical (Cameroon) populations of 99 passerine bird species and assessed GM similarity of temperate species migrating to tropical regions with that of residents/short-distance migrants and tropical residents. Our study also considered the possible influence of diet on GM.

Results

We observed no consistent GM diversity differences between tropical and temperate species. In the tropics, GM composition varied substantially between dry and rainy seasons and only a few taxa exhibited consistent differential abundance between tropical and temperate zones, irrespective of migration behavior and seasonal GM changes. During the breeding season, trans-Saharan migrant GM diverged little from species not overwintering in the tropics and did not show higher similarity to tropical passerines than temperate residents/short-distance migrants. Interestingly, GM of two temperate-breeding trans-Saharan migrants sampled in the tropical zone matched that of tropical residents and converged with other temperate species during the breeding season. Diet had a slight effect on GM composition of tropical species, but no effect on GM of temperate hosts.

Discussion

Consequently, our results demonstrate extensive passerine GM plasticity, the dominant role of environmental factors in its composition and limited effect of diet.
Artificial Intelligence in microbiomes analysis: A review of applications in dermatology
Authors: Sun Te , Niu Xueli , He Qing , Chen Fujun , Qi Rui-Qun
Published: February 2023

Microorganisms are closely related to skin diseases, and microbiological imbalances or invasions of exogenous pathogens can be a source of various skin diseases. The development and prognosis of such skin diseases are also closely related to the type and composition ratio of microorganisms present. Therefore, through detection of the characteristics and changes in microorganisms, the possibility for diagnosis and prediction of skin diseases can be markedly improved. The abundance of microorganisms and an understanding of the vast amount of biological information associated with these microorganisms has been a formidable task. However, with advances in large-scale sequencing, artificial intelligence (AI)-related machine learning can serve as a means to analyze large-scales of data related to microorganisms along with determinations regarding the type and status of diseases. In this review, we describe some uses of this exciting, new emerging field. In specific, we described the recognition of fungi with convolutional neural networks (CNN), the combined application of microbial genome sequencing and machine learning and applications of AI in the diagnosis of skin diseases as related to the gut-skin axis.
Secondary metabolites from the Endophytic fungi Fusarium decemcellulare F25 and their antifungal activities
Authors: Song Ziwei , Sun Yan Jun , Xu Shuangyu , Li Gang , Yuan Chunmao , Zhou Kang
Published: February 2023

Seven new compounds, including three isocoumarins (1–3), three pyrrolidinone derivatives (8–10), and one pentaene diacid (15), together with 13 known compounds, were isolated from the rice culture of the endophytic fungus Fusarium decemcellulare F25. Their structures and stereochemistry were established using HRESIMS, NMR, electronic circular dichroism (ECD) calculations, and single-crystal X-ray diffraction. The possible biosynthetic pathways for compounds 1–3 and 8–10 were proposed. The antifungal efficacies of compounds 1 ̶ 20 were evaluated against Colletotrichum musae, and compounds 13, 14, and 17 exhibited inhibitory activities against C. musae with MIC values of 256, 64 and 128 μg/mL, respectively.
Neural correlates of subjective cognitive decline in adults at high risk for Alzheimer’s disease
Authors: Ben-Ami Liat , Ravona-Springer Ramit , Tsarfaty Galia , Raizman Reut , Shumacher Aleeza , Sharvit-Ginon Inbal , Greenbaum Lior , Bendlin Barbara B. , Okun Eitan , Heymann Anthony , Schnaider Beeri Michal , Livny Abigail
Published: February 2023

Introduction

Recently, interest has emerged in subjective cognitive decline (SCD) as a potential precursor to Alzheimer’s disease (AD) dementia. Whether individuals with SCD harbor brain alterations in midlife, when AD-related pathology begins, is yet to be elucidated. Furthermore, the role of apolipoprotein ε4 (APOE ε4) allele, a robust AD risk factor, in the relationship between SCD and brain alterations is unknown. We examined whether APOE genotype modulates the association of SCD with brain measures in individuals at high AD risk.

Methods

Middle-aged adults with parental history of AD dementia underwent magnetic resonance imaging (MRI) and the Memory Functioning Questionnaire. Regression analysis tested the extent to which SCD was associated with activation during an functional MRI (fMRI) working-memory task, and white-matter microstructure. APOE ε4 genotype was tested as a moderator.

Results

Among APOE ε4 carriers, but not among non-carriers, SCD was associated with higher activation in the anterior cingulate (p = 0.003), inferior, middle, and superior frontal cortices (p = 0.041, p = 0.048, p = 0.037, respectively); and with lower fractional anisotropy in the uncinate fasciculus (p = 0.002), adjusting for age, sex, and education.

Conclusion

In middle aged, cognitively normal individuals at high AD risk, higher SCD was associated with greater brain alterations possibly reflecting incipient AD pathology. When accompanied by a family history of AD and an APOE ε4 allele, SCD may have important clinical value, allowing a window for early intervention and for participants’ stratification in AD prevention clinical trials.
Octogenarians with chronic kidney disease in the nephrology clinic: Progressors vs. non-progressors
Authors: Frías Aida , Vargas Francisco , Sandino Justo , Berzal Raquel , Rivero Marta , Cordero Lucía , Cavero Teresa , Segura Julián , García Florencio , Hernández Eduardo , Gutiérrez Eduardo , Auñón Pilar , Zamanillo Irene , Pascual Julio , Morales Enrique
Published: February 2023

Background

The current definition of chronic kidney disease applied to patients over the age of 80 has increased the number of referrals to Nephrology. However not all of these patients may benefit from its assessment. This study aims to analyze the evolution of ≥80 years old patients referred to Nephrology.

Methods

Single-center study including patients ≥80 years old with eGFR <60 mL/min/1,73m2 who were referred to Nephrology consultation for the first time. Clinical and analytical parameters were collected retrospectively 12 months before the visit, and prospectively at baseline, and 12 and 24 months after the initial visit. We divided patients into two groups based on annual eGFR loss: progressors (>5 mL/min/1.73m2) and non-progressors (≤5 mL/min/1,73m2).

Results

A total of 318 patients were included, mean age was 84,9 ± 4 (80-97) years. Baseline serum creatinine was 1,65 ± 0,62 mg/dL, eGRF 35 (28-42) mL/min/1,73, and albumin/creatinine ratio 36 (7-229) mg/g. 55,7% of the patients met the definition of progressor at baseline (initial-progressors), 26,3% were progressors after a 12-month follow-up and 13,4% after 24 months. 21,2% and 11,4% of initial-progressors met this definition at 12 and 24 month follow up. The main risk factor for progression was albuminuria. No relationship was found between the nephrologist intervention and the evolution of renal function among initial non-progressors.

Conclusion

Elderly patients who have stable renal function at the time of referral will continue to have stable renal function over the subsequent 24 months and thus may not need to be referred to a nephrologist.
Effects of intensive vs. standard blood pressure control on cognitive function: Post-hoc analysis of the STEP randomized controlled trial
Authors: Fan Jiali , Bai Jingjing , Liu Wei , Cai Jun
Published: February 2023

Background

The STEP (Strategy of Blood Pressure Intervention in the older Hypertensive Patients) trial showed that intensive systolic blood pressure (SBP) control resulted in a lower incidence of cardiovascular events than standard treatment. This study analyzed the effects of intensive SBP lowering on cognitive function.

Methods

STEP was a multicenter, randomized controlled trial of hypertensive patients aged 60–80 years. Participants were randomly assigned (1:1) to SBP goals of 110–130 mmHg (intensive treatment) or 130–150 mmHg (standard treatment). Each individual was asked to complete a cognitive function test (Mini-Mental State Examination; MMSE) at baseline and during follow-up. The primary outcome for this study was the annual change in MMSE score. Subjects with a score less than education-specific cutoff point were categorized as cognitive decline.

Results

The analysis enrolled 6,501 participants (3,270 participants in the intensive-treatment and 3,231 participants in the standard-treatment groups). Median follow-up was 3.34 years. There was a minor change in MMSE score, with an annual change of −0.001 [95% confidence interval [CI] −0.020, 0.018] and 0.030 (95% CI 0.011, 0.049) in the intensive- and standard-treatment groups, respectively (p = 0.052). Cognitive decline occurred in 46/3,270 patients (1.4%) in the intensive-treatment group and 42/3,231 (1.3%) in the standard-treatment group (hazard ratio 0.005, 95% CI 0.654, 1.543, p = 0.983).

Conclusions

Compared with standard treatment, intensive SBP treatment did not result in a significant change in cognitive function test score. The impact of intensive blood pressure lowering was not evident using this global cognitive function test.

Trial registration

ClinicalTrials.gov. Unique identifier: NCT03015311.
Elucidation of the mechanism underlying impaired sensorimotor gating in patients with primary blepharospasm using prepulse inhibition
Authors: Hao Xinqing , Huang Xiaofeng , Yin Xiaoxue , Wang Hai-Yang , Lu Ren , Liang Zhanhua , Song Chunli
Published: February 2023

Objective

We aimed to analyze prepulse inhibition (PPI) impairment of the blink reflex in patients with primary blepharospasm (BSP).

Methods

We recruited 30 BSP patients and 20 gender- and age-matched healthy controls (HCs). Weak electrical stimulation was applied to the right index finger at interstimulus intervals (ISIs) of 120, 200, and 300 ms before the supraorbital nerve stimulation to investigate PPI size [PPI size = (1 – R2 area at prepulse trials/R2 area at baseline trials) × 100%].

Results

The prepulse stimulus significantly inhibited the R2 component at the three ISIs in both groups, but less inhibition was shown in the BSP group (p < 0.05). In HCs, the prepulse stimulus induced prolonged R2 and R2c latencies at the three ISIs and increased the R1 amplitude at ISIs of 120 ms; these changes were absent in BSP patients. In the BSP group, patients with sensory tricks showed better PPI than patients without sensory tricks. Disease duration and motor symptom severity showed no significant correlation with PPI size.

Conclusion

In BSP patients, PPI was impaired while R1 facilitation was absent. PPI size did not correlate with the motor symptom severity and disease duration. Patients with sensory tricks showed better PPI than those without sensory tricks.
Genetic polymorphisms of PRKAA1 (AMPKα1) and postherpetic pain susceptibility: Multicenter, randomized control, and haplotype analysis study
Authors: Mei Yang , Chen Qi , Li Yu-Ping , Chen Yao-hua , Xia Juan , Zeng Jie , Yu Le-hua , Li Wei , Cui Jian
Published: February 2023

Adenosine 5′-monophosphate (AMP)-activated protein kinase (AMPK) is a pivotal regulatory protein in energy metabolism. In a pilot study, we found that AMPK-associated energy metabolism imbalance in neurons contributes to the occurrence and maintenance of neuropathic pain (NeP). This study aimed to explore the relationship between genetic polymorphisms of AMPK gene (Rs13361707, rs3792822, and rs10074991) in PRKAA1 and postherpetic neuralgia (PHN) in Chinese individuals. Hundred and thirty two patients with PHN and 118 control individuals were enrolled in this study. All blood samples were shuffled and blinded to the person performing the haplotype analysis. Rs13361707, rs3792822, and rs10074991 PRKAA1 genotypes were identified in all participants. Dominant and recessive models were used for evaluating the association between these nucleotide polymorphisms and PHN susceptibility. A haplotype analysis of PHN patients and healthy controls was performed. Clinical characteristics between the two groups were not significantly different (p > 0.05) except that the ages in control subjects were younger than the PHN patients (p < 0.05). Genotypes and allele frequencies are significantly different between the PHN patients and control subjects for the rs13361707 and rs10074991 polymorphisms (p < 0.05), but not for rs3792822 (p > 0.05). In addition, the CCG haplotype of rs13361707-rs3792822-rs10074991 correlated negatively with PHN occurrence, but TCA was positively correlated with PHN (p < 0.05). Our results indicate that PRKAA1 gene polymorphisms rs13361707 and rs10074991 were associated with a risk of PHN, and that the CCG haplotype of rs13361707-rs3792822-rs10074991 correlated negatively with PHN occurrence in haplotype analysis. TCA was positively associated with PHN in Chinese individuals.
Evaluation of corrective effect of 6 degree of freedom couch on setup errors in intensity modulated radiotherapy for postoperative rectal cancer patients
Authors: Xu Hui , Zhang Zunhao , Tian Bo , Li Xiongfei , Bian Yunfei , Liang Xianwei , Bo Changwen
Published: February 2023

Objective

To explore the corrective effect of 6 degree of freedom couch on rotation errors in intensity modulated radiotherapy (IMRT) for postoperative rectal cancer patients, further to probe into the clinical application value of 6 degree of freedom couch in radiotherapy.

Methods

From January 1, 2020 to December 1, 2020, 30 patients with rectal cancer receiving postoperative intensity modulated radiotherapy in The First Hospital of Hebei Medical University were included in this retrospective study. The setup error values in all direction of patients before and after 6 degree of freedom correction were collected during each radiotherapy session.

Results

In this study, a total of 382 data before and after the correction of 6 degree of freedom couch were collected. It was found that the setup errors in the Y direction gradually increased, was maximal in the third week, and then became smaller, and the setup errors in the other directions increased with the extension of radiotherapy time and reached the maximum at the 5th week. In the translation direction, the setup errors value in Z direction occurred more frequently than that in X and Y directions between the range of 0.21-0.80 cm. In the rotation direction, the setup errors value in rotation X direction occurred more frequently than that in rotation Y and Z directions between the range of 0.21°-2.99°. In addition, after the correction of the 6 degree of freedom couch in real time, the setup errors in patients were significantly reduced in all directions (P < 0.05).

Conclusion

In summary, it was recommended to clinically use 6 degree of freedom couch combined with IMRT for real-time correction of placement errors in patients with rectal cancer undergoing radiotherapy. At the same time, it was necessary to observe the tumor size and body weight changes of patients on the 5th week. If necessary, radiotherapy positioning and planning should be performed in time.
Analysis of prognostic factors and construction of prognostic models for triple-positive breast cancer
Authors: Geng Anqi , Xiao Jingjing , Dong Bingyao , Yuan Shifang
Published: February 2023

Objective

By identifying the clinicopathological characteristics and prognostic influences of patients with triple-positive breast cancer (TPBC) at Xijing Hospital in China compared with those in the United States, this study aims to construct a nomogram model to forecast the overall survival rate (OS) of TPBC patients.

Method

The Surveillance, Epidemiology, and End Results (SEER) database was used to screen 5769 patients as the training cohort, and 191 patients from Xijing Hospital were used as the validation cohort. Cox risk-proportional model was applied to select variables and the nomogram model was constructed based on the training cohort. The performance of the model was evaluated by calculating the C-index and generating calibration plots in the training and validation cohorts.

Results

Cox multifactorial analysis showed that age, chemotherapy, radiotherapy, M-stage, T-stage, N-stage, and the mode of surgery were all independent risk factors for the prognosis of TPBC patients (all P<0.05). With this premise, the nomogram model was constructed and evaluated. The C-index value of the nomogram model was 0.830 in the training group and 0.914 in the validation group. Moreover, both the calibration and ROC curves for the proposed model exhibited reliable performance, and the clinical decision curve analysis showed that the proposed model can bring clinical benefits.

Conclusions

The constructed nomogram can accurately predict individual survival probabilities and may serve as a clinical decision support tool for clinicians to optimize treatment in individuals.
A huge verrucous carcinoma of the lower lip reconstructed by double Abbe flap: A case report and literature review
Authors: Chai Ke , Liu Jinbing , Xiao Rong , Zhang Guiying , Zhan Yi
Published: February 2023

Lip verrucous carcinoma is a rare low-grade neoplasm, with an unsightly appearance and locally aggressive nature. Treatment of verrucous carcinoma is as yet challenging, no well-defined guidelines for effective and safe management of this disease are available. A case of a patient with a huge verrucous carcinoma of the lower lip successfully treated by surgical excision and double Abbe flap reconstruction technique is presented, and striking features of lip locations of this tumor as well as their management are discussed.