bluuebunny/crossref_metadata_2025 huggingface dataset:
The use of multiple datasets to identify autophagy-related molecular mechanisms in intracerebral hemorrhage
Authors: Xiao Yinggang , Zhang Yang , Wang Cunjin , Ge Yali , Gao Ju , Huang Tianfeng
Published: April 2023

Background: Intracerebral hemorrhage (ICH) is a stroke syndrome with high mortality and disability rates, but autophagy’s mechanism in ICH is still unclear. We identified key autophagy genes in ICH by bioinformatics methods and explored their mechanisms.

Methods: We downloaded ICH patient chip data from the Gene Expression Omnibus (GEO) database. Based on the GENE database, differentially expressed genes (DEGs) for autophagy were identified. We identified key genes through protein–protein interaction (PPI) network analysis and analyzed their associated pathways in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene-motif rankings, miRWalk and ENCORI databases were used to analyze the key gene transcription factor (TF) regulatory network and ceRNA network. Finally, relevant target pathways were obtained by gene set enrichment analysis (GSEA).

Results: Eleven autophagy-related DEGs in ICH were obtained, and IL-1B, STAT3, NLRP3 and NOD2 were identified as key genes with clinical predictive value by PPI and receiver operating characteristic (ROC) curve analysis. The candidate gene expression level was significantly correlated with the immune infiltration level, and most of the key genes were positively correlated with the immune cell infiltration level. The key genes are mainly related to cytokine and receptor interactions, immune responses and other pathways. The ceRNA network predicted 8,654 interaction pairs (24 miRNAs and 2,952 lncRNAs).

Conclusion: We used multiple bioinformatics datasets to identify IL-1B, STAT3, NLRP3 and NOD2 as key genes that contribute to the development of ICH.
A look under the hood of genomic-estimated breed compositions for brangus cattle: What have we learned?
Authors: Li Zhi , He Jun , Yang Fang , Yin Shishu , Gao Zhendong , Chen Wenwu , Sun Chuanyu , Tait Richard G. , Bauck Stewart , Guo Wei , Wu Xiao-Lin
Published: April 2023

The Brangus cattle were developed to utilize the superior traits of Angus and Brahman cattle. Their genetic compositions are expected to be stabilized at 3/8 Brahman and 5/8 Angus. Previous studies have shown more than expected Angus lineage with Brangus cattle, and the reasons are yet to be investigated. In this study, we revisited the breed compositions for 3,605 Brangus cattle from three perspectives: genome-wise (GBC), per chromosomes (CBC), and per chromosome segments (SBC). The former (GBC) depicted an overall picture of the “mosaic” genome of the Brangus attributable to their ancestors, whereas the latter two criteria (CBC and SBC) corresponded to local ancestral contributions. The average GBC for the 3,605 Brangus cattle were 70.2% Angus and 29.8% Brahman. The K-means clustering supported the postulation of the mixture of 1/2 Ultrablack (UB) animals in Brangus. For the non-UB Brangus animals, the average GBC were estimated to be 67.4% Angus and 32.6% Brahman. The 95% confidence intervals of their overall GBC were 60.4%–73.5% Angus and 26.5%–39.6% Brahman. Possibly, genetic selection and drifting have resulted in an approximately 5% average deviation toward Angus lineage. The estimated ancestral contributions by chromosomes were heavily distributed toward Angus, with 27 chromosomes having an average Angus CBC greater than 62.5% but only two chromosomes (5 and 20) having Brahman CBC greater than 37.5%. The chromosomal regions with high Angus breed proportions were prevalent, tending to form larger blocks on most chromosomes. In contrast, chromosome segments with high Brahman breed proportion were relatively few and isolated, presenting only on seven chromosomes. Hence, genomic hitchhiking effects were strong where Angus favorable alleles resided but weak where Brahman favorable alleles were present. The functions of genes identified in the chromosomal regions with high (≥75%) Angus compositions were diverse yet may were related to growth and body development. In contrast, the genes identified in the regions with high (≥37.5%) Brahman compositions were primarily responsible for disease resistance. In conclusion, we have addressed the questions concerning the Brangus genetic make-ups. The results can help form a dynamic picture of the Brangus breed formation and the genomic reshaping.
The EDA/EDAR/NF-κB pathway in non-syndromic tooth agenesis: A genetic perspective
Authors: Gao Yanzi , Jiang Xiaohui , Wei Zhi , Long Hu , Lai Wenli
Published: April 2023

Non-syndromic tooth agenesis (NSTA) is one of the most common dental developmental malformations affected by genetic factors predominantly. Among all 36 candidate genes reported in NSTA individuals, EDA, EDAR, and EDARADD play essential roles in ectodermal organ development. As members of the EDA/EDAR/NF-κB signaling pathway, mutations in these genes have been implicated in the pathogenesis of NSTA, as well as hypohidrotic ectodermal dysplasia (HED), a rare genetic disorder that affects multiple ectodermal structures, including teeth. This review provides an overview of the current knowledge on the genetic basis of NSTA, with a focus on the pathogenic effects of the EDA/EDAR/NF-κB signaling pathway and the role of EDA, EDAR, and EDARADD mutations in developmental tooth defects. We also discuss the phenotypic overlap and genetic differences between NSTA and HED. Ultimately, this review highlights the importance of genetic analysis in diagnosing and managing NSTA and related ectodermal disorders, and the need for ongoing research to improve our understanding of these conditions.
Integrated analysis of multi-omics data reveals T cell exhaustion in sepsis
Authors: Li Qiaoke , Sun Mingze , Zhou Qi , Li Yulong , Xu Jinmei , Fan Hong
Published: April 2023

Background

Sepsis is a heterogeneous disease, therefore the single-gene-based biomarker is not sufficient to fully understand the disease. Higher-level biomarkers need to be explored to identify important pathways related to sepsis and evaluate their clinical significance.

Methods

Gene Set Enrichment Analysis (GSEA) was used to analyze the sepsis transcriptome to obtain the pathway-level expression. Limma was used to identify differentially expressed pathways. Tumor IMmune Estimation Resource (TIMER) was applied to estimate immune cell abundance. The Spearman correlation coefficient was used to find the relationships between pathways and immune cell abundance. Methylation and single-cell transcriptome data were also employed to identify important pathway genes. Log-rank test was performed to test the prognostic significance of pathways for patient survival probability. DSigDB was used to mine candidate drugs based on pathways. PyMol was used for 3-D structure visualization. LigPlot was used to plot the 2-D pose view for receptor-ligand interaction.

Results

Eighty-four KEGG pathways were differentially expressed in sepsis patients compared to healthy controls. Of those, 10 pathways were associated with 28-day survival. Some pathways were significantly correlated with immune cell abundance and five pathways could be used to distinguish between systemic inflammatory response syndrome (SIRS), bacterial sepsis, and viral sepsis with Area Under the Curve (AUC) above 0.80. Seven related drugs were screened using survival-related pathways.

Conclusion

Sepsis-related pathways can be utilized for disease subtyping, diagnosis, prognosis, and drug screening.
Machine learning for the prediction of all-cause mortality in patients with sepsis-associated acute kidney injury during hospitalization
Authors: Zhou Hongshan , Liu Leping , Zhao Qinyu , Jin Xin , Peng Zhangzhe , Wang Wei , Huang Ling , Xie Yanyun , Xu Hui , Tao Lijian , Xiao Xiangcheng , Nie Wannian , Liu Fang , Li Li , Yuan Qiongjing
Published: April 2023

Background

Sepsis-associated acute kidney injury (S-AKI) is considered to be associated with high morbidity and mortality, a commonly accepted model to predict mortality is urged consequently. This study used a machine learning model to identify vital variables associated with mortality in S-AKI patients in the hospital and predict the risk of death in the hospital. We hope that this model can help identify high-risk patients early and reasonably allocate medical resources in the intensive care unit (ICU).

Methods

A total of 16,154 S-AKI patients from the Medical Information Mart for Intensive Care IV database were examined as the training set (80%) and the validation set (20%). Variables (129 in total) were collected, including basic patient information, diagnosis, clinical data, and medication records. We developed and validated machine learning models using 11 different algorithms and selected the one that performed the best. Afterward, recursive feature elimination was used to select key variables. Different indicators were used to compare the prediction performance of each model. The SHapley Additive exPlanations package was applied to interpret the best machine learning model in a web tool for clinicians to use. Finally, we collected clinical data of S-AKI patients from two hospitals for external validation.

Results

In this study, 15 critical variables were finally selected, namely, urine output, maximum blood urea nitrogen, rate of injection of norepinephrine, maximum anion gap, maximum creatinine, maximum red blood cell volume distribution width, minimum international normalized ratio, maximum heart rate, maximum temperature, maximum respiratory rate, minimum fraction of inspired O2, minimum creatinine, minimum Glasgow Coma Scale, and diagnosis of diabetes and stroke. The categorical boosting algorithm model presented significantly better predictive performance [receiver operating characteristic (ROC): 0.83] than other models [accuracy (ACC): 75%, Youden index: 50%, sensitivity: 75%, specificity: 75%, F1 score: 0.56, positive predictive value (PPV): 44%, and negative predictive value (NPV): 92%]. External validation data from two hospitals in China were also well validated (ROC: 0.75).

Conclusions

After selecting 15 crucial variables, a machine learning-based model for predicting the mortality of S-AKI patients was successfully established and the CatBoost model demonstrated best predictive performance.
Elevated circulating monocytes and monocyte activation in COVID-19 convalescent individuals
Authors: Park Juwon , Dean Logan S. , Jiyarom Boonyanudh , Gangcuangco Louie Mar , Shah Parthav , Awamura Thomas , Ching Lauren L. , Nerurkar Vivek R. , Chow Dominic C. , Igno Fritzie , Shikuma Cecilia M. , Devendra Gehan
Published: April 2023

Background

Monocytes and macrophages play a pivotal role in inflammation during acute SARS-CoV-2 infection. However, their contribution to the development of post-acute sequelae of SARS-CoV-2 infection (PASC) are not fully elucidated.

Methods

A cross-sectional study was conducted comparing plasma cytokine and monocyte levels among three groups: participants with pulmonary PASC (PPASC) with a reduced predicted diffusing capacity for carbon monoxide [DLCOc, <80%; (PG)]; fully recovered from SARS-CoV-2 with no residual symptoms (recovered group, RG); and negative for SARS-CoV-2 (negative group, NG). The expressions of cytokines were measured in plasma of study cohort by Luminex assay. The percentages and numbers of monocyte subsets (classical, intermediate, and non-classical monocytes) and monocyte activation (defined by CD169 expression) were analyzed using flow cytometry analysis of peripheral blood mononuclear cells.

Results

Plasma IL-1Ra levels were elevated but FGF levels were reduced in PG compared to NG. Circulating monocytes and three subsets were significantly higher in PG and RG compared to NG. PG and RG exhibited higher levels of CD169+ monocyte counts and higher CD169 expression was detected in intermediate and non-classical monocytes from RG and PG than that found in NG. Further correlation analysis with CD169+ monocyte subsets revealed that CD169+ intermediate monocytes negatively correlated with DLCOc%, and CD169+ non-classical monocytes positively correlated with IL-1α, IL-1β, MIP-1α, Eotaxin, and IFN-γ.

Conclusion

This study present evidence that COVID convalescents exhibit monocyte alteration beyond the acute COVID-19 infection period even in convalescents with no residual symptoms. Further, the results suggest that monocyte alteration and increased activated monocyte subsets may impact pulmonary function in COVID-19 convalescents. This observation will aid in understanding the immunopathologic feature of pulmonary PASC development, resolution, and subsequent therapeutic interventions.
Decreased breadth of the antibody response to the spike protein of SARS-CoV-2 after repeated vaccination
Authors: Horndler Lydia , Delgado Pilar , Romero-Pinedo Salvador , Quesada Marina , Balabanov Ivaylo , Laguna-Goya Rocío , Almendro-Vázquez Patricia , Llamas Miguel A. , Fresno Manuel , Paz-Artal Estela , van Santen Hisse M. , Álvarez-Fernández Stela , Olmo Asunción , Alarcón Balbino
Published: April 2023

Introduction

The rapid development of vaccines to prevent COVID-19 has raised the need to compare the capacity of different vaccines in terms of developing a protective humoral response. Previous studies have shown inconsistent results in this area, highlighting the importance of further research to evaluate the efficacy of different vaccines.

Methods

This study utilized a highly sensitive and reliable flow cytometry method to measure the titers of IgG1 isotype antibodies in the blood of healthy volunteers after receiving one or two doses of various vaccines administered in Spain. The method was also used to simultaneously measure the reactivity of antibodies to the S protein of the original Wuhan strain and variants B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.617.1 (Kappa).

Results

Significant differences were observed in the titer of anti-S antibodies produced after a first dose of the vaccines ChAdOx1 nCov-19/AstraZeneca, mRNA-1273/Moderna, BNT162b2/Pfizer-BioNTech, and Ad26.COV.S/Janssen. Furthermore, a relative reduction in the reactivity of the sera with the Alpha, Delta, and Kappa variants, compared to the Wuhan strain, was observed after the second boosting immunization.

Discussion

The findings of this study provide a comparison of different vaccines in terms of anti-S antibody generation and cast doubts on the convenience of repeated immunization with the same S protein sequence. The multiplexed capacity of the flow cytometry method utilized in this study allowed for a comprehensive evaluation of the efficacy of various vaccines in generating a protective humoral response. Future research could focus on the implications of these findings for the development of effective COVID-19 vaccination strategies.
Genomes of the human filarial parasites Mansonella perstans and Mansonella ozzardi
Authors: Sinha Amit , Li Zhiru , Poole Catherine B. , Morgan Richard D. , Ettwiller Laurence , Lima Nathália F. , Ferreira Marcelo U. , Fombad Fanny F. , Wanji Samuel , Carlow Clotilde K. S.
Published: April 2023

The filarial parasites Mansonella ozzardi and Mansonella perstans, causative agents of mansonellosis, infect hundreds of millions of people worldwide, yet remain among the most understudied of the human filarial pathogens. M. ozzardi is highly prevalent in Latin American countries and Caribbean Islands, while M. perstans is predominantly found in sub-Saharan Africa as well as in a few areas in South America. In addition to the differences in their geographical distribution, the two parasites are transmitted by different insect vectors, as well as exhibit differences in their responses to commonly used anthelminthic drugs. The lack of genome information has hindered investigations into the biology and evolution of Mansonella parasites and understanding the molecular basis of the clinical differences between species. In the current study, high quality genomes of two independent clinical isolates of M. perstans from Cameroon and two M. ozzardi isolates one from Brazil and one from Venezuela are reported. The genomes are approximately 76 Mb in size, encode about 10,000 genes each, and are largely complete based on BUSCO scores of about 90%, similar to other completed filarial genomes. These sequences represent the first genomes from Mansonella parasites and enabled a comparative genomic analysis of the similarities and differences between Mansonella and other filarial parasites. Horizontal DNA transfers (HDT) from mitochondria (nuMTs) as well as transfers from genomes of endosymbiotic Wolbachia bacteria (nuWTs) to the host nuclear genome were identified and analyzed. Sequence comparisons and phylogenetic analysis of known targets of anti-filarial drugs diethylcarbamazine (DEC), ivermectin and mebendazole revealed that all known target genes were present in both species, except for the DEC target encoded by gon-2 gene, which is fragmented in genome assemblies from both M. ozzardi isolates. These new reference genome sequences will provide a valuable resource for further studies on biology, symbiosis, evolution and drug discovery.
Transitioning from blue growth to the sustainable blue economy: A review of Ireland’s new marine governance in the aquaculture sector
Authors: Troya María Del Camino , Ansong Joseph Onwona , O’Hagan Anne Marie
Published: April 2023

This paper reviews the evolution of marine governance in Ireland in response to EU policy requirements in relation to the development of a sustainable blue economy in coherence with the United Nations Ocean Decade (2021-2030). In response to these EU requirements, Ireland has introduced the National Marine Planning Framework (NMPF) and Maritime Area Planning Act, 2021 (MAPA) in 2021 to deliver this sustainable blue economy. This new marine and coastal governance framework in Ireland reforms the consenting regime for key blue economy sectors such as Offshore Renewable Energy (ORE) and sets new policy requirements for the integration of aquaculture within the MSP framework. However, the exclusion of aquaculture from the new consenting regime may hinder the full integration of the sector into MSP and impede compliance with environmental goals established by EU Directives (e.g., WFD, MSFD, MSPD). This review identifies policy and legal gaps which may impede the integration of aquaculture into the new Irish marine governance and national MSP process. Furthermore, this paper analyses aquaculture licensing cases to assess the integration of environmental criteria into planning decisions to gather insight into the readiness of the sector’s transition towards a sustainable model. The analysis from this paper indicates that the legal framework underpinning MSP in Ireland may have a limited impact on the integration of aquaculture and hinder the delivery of sustainability across all marine sectors.
Shark bycatch of the acoupa weakfish, Cynoscion acoupa (Lacèpede, 1801), fisheries of the Amazon Shelf
Authors: Lutz Ítalo , Pinaya Walter Hugo Diaz , Nascimento Mayra , Lima Wellington , Silva Evaldo , Nunes Zélia , Bentes Bianca
Published: April 2023

In recent years, the populations of many shark species have been depleted drastically around the world. In the present study, we analyzed the shark bycatch in the monthly landing data of the acoupa weakfish (Cynoscion acoupa) gillnet fisheries of the state of Pará, on the northern coast of Brazil, between January 1995 and December 2007. Based on 4,659 landings, we estimated that a total of 1,972.50 tons of shark were taken as bycatch during the study period. The acoupa weakfish fisheries operate on the Amazon Shelf, an important fishing ground, and we analyzed the shark landings in relation to the Amazon River Discharge anomaly (ARD) and the climatic variability in the Atlantic Ocean. We applied cross-correlation, cross-wavelet, wavelet coherence, and redundancy analysis techniques to the analysis of the data time series. The shark bycatch landings peaked between 1998 and 2000, a period associated with an increase in fishing effort by the acoupa weakfish fisheries, in particular during the dry season of the Amazon basin. The cross-correlation analysis indicated that shark landings were associated with Sea Surface Temperatures (SSTs), the characteristics of the wind, and the Atlantic Multidecadal Oscillation (AMO), while the fishing effort of the acoupa weakfish fisheries was associated with the meridional wind component, the AMO, and the ARD. The cross-wavelet and coherence wavelet analyses indicated that environmental variability was linked systematically with shark landings and acoupa weakfish fishing effort. We observed a phase change in this signal between 1998 and 2000, due to a strong and persistent La Niña event. Despite the resistance from the fishing industry, development and deployment of devices designed to reduce bycatch should be incentivized in order to reduce the unintentional capture of endangered species such as sharks. The findings of the present study highlight the importance of a continuous and accurate fishery database, and the need for continuous fishery statistics to ensure adequate management practices. Adequate public fishery management policies must be implemented urgently to guarantee the survival of shark species, with the effective participation of all the actors involved in the process, including managers, researchers, and fishers.
Can stand the heat – ecology of the potentially invasive ascidian Styela plicata along the Mediterranean coast of Israel
Authors: Platin Raz , Shenkar Noa
Published: April 2023

Introduction

Both colonial and solitary ascidians (Chordata, Ascidiacea) have been gathering attention due to their impact on coastal environments. The solitary ascidian Styela plicata was first observed along the coast of Israel in 2014. It is considered a cosmopolitan species of unknown origin, and is well-known for its ability to create large aggregations on artificial substrates in the western Mediterranean Sea, North-Pacific Ocean and the Atlantic. The extreme environmental conditions that characterize the Mediterranean coast of Israel, with a salinity of 40 psu and sea-surface temperature reaching 33°C, may however present a barrier to its future spread.

Methods

We examined the seasonal reproduction patterns and population structure of three populations over two years, in addition to spatial surveys and monitoring oocyte release under laboratory conditions.

Results

Histological sections revealed significant differences in reproduction patterns between seasons and sites, with a higher proportion of the larger oocytes size group observed during the winter for all sites. Along the Israeli coast, with the exception of one site, S. plicata is currently restricted to marinas and ports.

Discussion

With an impressive ability to survive the extreme environmental conditions and sustain reproductive populations. Acquiring data on its spread and establishment is essential for modeling S. plicata’s distribution under the current and predicted global climate changes, and for developing tools for its mitigation and control.
Insight into the genomes of dominant yeast symbionts of European spruce bark beetle, Ips typographus
Authors: Cheng Tian , Veselská Tereza , Křížková Barbora , Švec Karel , Havlíček Václav , Stadler Marc , Kolařík Miroslav
Published: April 2023

Spruce bark beetleIps typographus can trigger outbreaks on spruce that results in significant losses in the forest industry. It has been suggested that symbiotic microorganisms inhabiting the gut of bark beetles facilitate the colonization of plant tissues as they play a role in the detoxification of plant secondary metabolites, degrade plant cell wall and ameliorate beetle’s nutrition. In this study, we sequenced and functionally annotated the genomes of five yeastsKuraishia molischiana,Cryptococcussp.,Nakazawaea ambrosiae,Ogataea ramenticola, andWickerhamomyces bisporusisolated from the gut ofIps typographus. Genome analysis identified 5314, 7050, 5722, 5502, and 5784 protein coding genes fromK. molischiana,Cryptococcussp.,N. ambrosiae,O. ramenticola, andW. bisporus, respectively. Protein-coding sequences were classified into biological processes, cellular and molecular function based on gene ontology terms enrichment. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation was used to predict gene functions. All analyzed yeast genomes contain full pathways for the synthesis of essential amino acids and vitamin B6, which have nutritional importance to beetle. Furthermore, their genomes contain diverse gene families related to the detoxification processes. The prevalent superfamilies are aldo-keto reductase, ATP-binding cassette and the major facilitator transporters. The phylogenetic relationships of detoxification-related enzymes aldo-keto reductase, and cytochrome P450 monooxygenase, and ATP-binding cassette are presented. Genome annotations also revealed presence of genes active in lignocellulose degradation.In vitroanalyses did not confirm enzymatic endolytic degradation of lignocellulose; however, all species can utilize and pectin and produce a large spectrum of exolytic enzymes attacking cellulose, chitin, and lipids.
Gene transfer and genome editing for familial hypercholesterolemia
Authors: Canepari Cesare , Cantore Alessio
Published: April 2023

Familial hypercholesterolemia (FH) is an autosomal dominant inherited disease characterized by high circulating low-density lipoprotein (LDL) cholesterol. High circulating LDL cholesterol in FH is due to dysfunctional LDL receptors, and is mainly expressed by hepatocytes. Affected patients rapidly develop atherosclerosis, potentially leading to myocardial infarction and death within the third decade of life if left untreated. Here, we introduce the disease pathogenesis and available treatment options. We highlight different possible targets of therapeutic intervention. We then review different gene therapy strategies currently under development, which may become novel therapeutic options in the future, and discuss their advantages and disadvantages. Finally, we briefly outline the potential applications of some of these strategies for the more common acquired hypercholesterolemia disease.
Pathological identification of HER2-low breast cancer: Tips, tricks, and troubleshooting for the optimal test
Authors: Sajjadi Elham , Guerini-Rocco Elena , De Camilli Elisa , Pala Oriana , Mazzarol Giovanni , Venetis Konstantinos , Ivanova Mariia , Fusco Nicola
Published: April 2023

The introduction of novel anti-HER2 antibody-drug conjugates (ADC) for the treatment of HER2-low breast cancers has transformed the traditional dichotomy of HER2 status to an expanded spectrum. However, the identification of HER2-low (i.e., immunohistochemistry (IHC) score 1 + or IHC score 2+, without gene amplification) tumors is challenged by methodological and analytical variables that might influence the sensitivity and reproducibility of HER2 testing. To open all possible therapeutic opportunities for HER2-low breast cancer patients the implementation of more accurate and reproducible testing strategies is mandatory. Here, we provide an overview of the existing barriers that may trouble HER2-low identification in breast cancer and discuss practical solutions that could enhance HER-low assessment.
Aphasic mild cognitive impairment in prodromal dementia with Lewy bodies
Authors: Watanabe Hiroyuki , Hikida Sakura , Ikeda Manabu , Mori Etsuro
Published: April 2023

Introduction

This study aimed to determine the characteristics of aphasic mild cognitive impairment (aphasic MCI), which is characterized by a progressive and relatively prominent language impairment compared with other cognitive impairments, in the prodromal phase of dementia with Lewy bodies (DLB).

Methods

Of the 26 consecutive patients with aphasic MCI who had been prospectively recruited at our hospital, 8 patients were diagnosed with prodromal DLB and underwent language, neurological, neuropsychological, and neuroimaging (N-isopropyl-p-[123I] iodoamphetamine single-photon emission computed tomography; IMP-SPECT) testing. Three of these patients also underwent cholinesterase inhibitor therapy with donepezil.

Results

In our aphasic MCI cohort, the clinical diagnosis of probable prodromal DLB accounted for more than 30% of cases; therefore, the presence of language impairment in prodromal DLB was not very uncommon. Five patients were diagnosed with progressive anomic aphasia and three with logopenic progressive aphasia. Anomic aphasia was characterized by apparent anomia but relatively preserved repetition and comprehension ability and logopenic progressive aphasia by anomia, phonemic paraphasia, and impaired repetition. IMP-SPECT revealed hypoperfusion of the temporal and parietal lobes in the left hemisphere in all but one patient. All patients who underwent cholinesterase inhibitor therapy with donepezil showed improvement in general cognitive function, including language function.

Discussion

The clinical and imaging features of aphasic MCI in prodromal DLB are similar to those observed in Alzheimer's disease. Progressive fluent aphasia, such as progressive anomic aphasia and logopenic progressive aphasia, is one of the clinical presentations in prodromal state of DLB. Our findings provide further insight into the clinical spectrum of prodromal DLB and may contribute to the development of medication for progressive aphasia caused by cholinergic insufficiency.
Global research trends on COVID-19 and stroke: A bibliometric analysis
Authors: Zeng Youjie , Cao Si , Yang Heng
Published: April 2023

Background

The pandemic of COVID-19 has had a profound influence on worldwide healthcare systems. Our study aimed to conduct a bibliometric analysis to explore the impact of COVID-19 on stroke and to highlight the major research trends in this field.

Methods

We searched the original articles and review articles regarding COVID-19 and stroke from the Web of Science collection (WOSCC) database between January 1, 2020 and December 30, 2022. Subsequently, we performed bibliometric analyses and visualization using VOSviewer, Citespace, and Scimago Graphica.

Results

A total of 608 original articles or review articles were included. JOURNAL OF STROKE and CEREBROVASCULAR DISEASES published the most studies on this subject (n = 76), while STROKE was the source of the most-cited references (n = 2,393). The United States is the most influential country in this field, with the highest number of publications (n = 223) and citations (n = 5,042). Shadi Yaghi from New York University is the most prolific author in the field, while Harvard Medical School is the most prolific institution. In addition, through keyword analysis and reference co-citation analysis, three major research topics were identified: (i) the impact of COVID-19 on stroke outcomes (including risk factors, clinical characteristics, mortality, stress, depression, comorbidities, etc.); (ii) the management and care of stroke patients during the COVID-19 pandemic (including thrombolysis, thrombectomy, telemedicine, anticoagulation, vaccination, etc.); and (iii) the potential relationship and pathological mechanism between COVID-19 and stroke (including renin-angiotensin system activation, SARS-CoV-2 virus-induced inflammation leading to endothelial impairment, coagulopathy, etc.).

Conclusion

Our bibliometric analysis provides a comprehensive overview of the current state of research on COVID-19 and stroke and highlights key areas of focus in the field. Optimizing the treatment of COVID-19-infected stroke patients and elucidating the underlying pathogenic mechanisms of COVID-19 and stroke co-morbidity are key areas of future research that will be beneficial in improving the prognosis of stroke patients during the ongoing COVID-19 epidemic.
Rhodopsin-associated retinal dystrophy: Disease mechanisms and therapeutic strategies
Authors: Zhen Fangyuan , Zou Tongdan , Wang Ting , Zhou Yongwei , Dong Shuqian , Zhang Houbin
Published: April 2023

Rhodopsin is a light-sensitive G protein-coupled receptor that initiates the phototransduction cascade in rod photoreceptors. Mutations in the rhodopsin-encoding gene RHO are the leading cause of autosomal dominant retinitis pigmentosa (ADRP). To date, more than 200 mutations have been identified in RHO. The high allelic heterogeneity of RHO mutations suggests complicated pathogenic mechanisms. Here, we discuss representative RHO mutations as examples to briefly summarize the mechanisms underlying rhodopsin-related retinal dystrophy, which include but are not limited to endoplasmic reticulum stress and calcium ion dysregulation resulting from protein misfolding, mistrafficking, and malfunction. Based on recent advances in our understanding of disease mechanisms, various treatment methods, including adaptation, whole-eye electrical stimulation, and small molecular compounds, have been developed. Additionally, innovative therapeutic treatment strategies, such as antisense oligonucleotide therapy, gene therapy, optogenetic therapy, and stem cell therapy, have achieved promising outcomes in preclinical disease models of rhodopsin mutations. Successful translation of these treatment strategies may effectively ameliorate, prevent or rescue vision loss related to rhodopsin mutations.
The cost of aiming for the best answers: Inconsistent perception
Authors: Smeets Jeroen B. J. , Brenner Eli
Published: April 2023

The laws of physics and mathematics describe the world we live in as internally consistent. As these rules provide a very effective description, and our interaction with the world is also very effective, it seems self-evident that our perception follows these laws. As a result, when trying to explain imperfections in perception, we tend to impose consistency and introduce concepts such as deformations of visual space. In this review, we provide numerous examples that show that in many situations we perceive related attributes to have inconsistent values. We discuss how our tendency to assume consistency leads to erroneous conclusions on how we process sensory information. We propose that perception is not about creating a consistent internal representation of the outside world, but about answering specific questions about the outside world. As the information used to answer a question is specific for that question, this naturally leads to inconsistencies in perception and to an apparent dissociation between some perceptual judgments and related actions.
Post-ischemic inflammatory response in the brain: Targeting immune cell in ischemic stroke therapy
Authors: Shen Xueyang , Li Mingming , Shao Kangmei , Li Yongnan , Ge Zhaoming
Published: April 2023

An ischemic stroke occurs when the blood supply is obstructed to the vascular basin, causing the death of nerve cells and forming the ischemic core. Subsequently, the brain enters the stage of reconstruction and repair. The whole process includes cellular brain damage, inflammatory reaction, blood–brain barrier destruction, and nerve repair. During this process, the proportion and function of neurons, immune cells, glial cells, endothelial cells, and other cells change. Identifying potential differences in gene expression between cell types or heterogeneity between cells of the same type helps to understand the cellular changes that occur in the brain and the context of disease. The recent emergence of single-cell sequencing technology has promoted the exploration of single-cell diversity and the elucidation of the molecular mechanism of ischemic stroke, thus providing new ideas and directions for the diagnosis and clinical treatment of ischemic stroke.
Effect of optimized germination technology on polyphenol content and hypoglycemic activity of mung bean
Authors: Li Bo , Shen Xinting , Shen Huifang , Zhou Ye , Yao Xinmiao
Published: April 2023

The study aimed to investigate the effect of germination conditions on the content of polyphenol extract in mung bean and to further investigate the effect of polyphenol extract in germinated mung bean on diabetic mice. Through single factor experiment and response surface experiment, the effects of soaking temperature, soaking time, germination temperature, germination time and soaking liquid CaCl2 concentration on the polyphenol content of mung bean were analyzed. The optimal germination conditions of mung bean were determined as soaking temperature 25°C, soaking time 11 h, germination temperature 28°C, germination time 3 days and CaCl2 concentration 2 mM. Under these conditions, the content of polyphenol extract in germinated mung bean was 4.878 ± 0.30 mg/g, which was 3.07 times higher than that in ungerminated mung bean. The structure and content of purified polyphenols in germinated mung bean were determined by HPLC-MS/MS. Quinic acid, Quercetin, Rutin, Vitexin, Isovitexin and other substances were identified, and the content of polyphenols was 65.19%. In addition, through the in vivo and in vitro hypoglycemic activity experimental study of germinated mung bean polyphenols extract, the results showed that germinated mung bean polyphenols had an in vitro inhibitory effect on α-glucosidase, IC50 was 44.45 mg/ml. In vitro inhibitory activity was stronger after digestion. Polyphenol extract can significantly reduce blood sugar and improve insulin resistance in Type 2 diabetic mice (T2DM). According to the results, germination treatment is an effective way to increase the content of polyphenols in mung bean, and the polyphenols extract has hypoglycemic activity.
A prediction nomogram for moderate-to-severe bronchopulmonary dysplasia in preterm infants < 32 weeks of gestation: A multicenter retrospective study
Authors: Zhang Jing , Mu Kai , Wei Lihua , Fan Chunyan , Zhang Rui , Wang Lingling
Published: April 2023

Background

Moderate-to-severe bronchopulmonary dysplasia (msBPD) is a serious complication in preterm infants. We aimed to develop a dynamic nomogram for early prediction of msBPD using perinatal factors in preterm infants born at <32 weeks' gestation.

Methods

This multicenter retrospective study conducted at three hospitals in China between January 2017 and December 2021 included data on preterm infants with gestational age (GA) < 32 weeks. All infants were randomly divided into training and validation cohorts (3:1 ratio). Variables were selected by Lasso regression. Multivariate logistic regression was used to build a dynamic nomogram to predict msBPD. The discrimination was verified by receiver operating characteristic curves. Hosmer-Lemeshow test and decision curve analysis (DCA) were used for evaluating calibration and clinical applicability.

Results

A total of 2,067 preterm infants. GA, Apgar 5-min score, small for gestational age (SGA), early onset sepsis, and duration of invasive ventilation were predictors for msBPD by Lasso regression. The area under the curve was 0.894 (95% CI 0.869–0.919) and 0.893 (95% CI 0.855–0.931) in training and validation cohorts. The Hosmer−Lemeshow test calculated P value of 0.059 showing a good fit of the nomogram. The DCA demonstrated significantly clinical benefit of the model in both cohorts. A dynamic nomogram predicting msBPD by perinatal days within postnatal day 7 is available at https://sdxxbxzz.shinyapps.io/BPDpredict/.

Conclusion

We assessed the perinatal predictors of msBPD in preterm infants with GA < 32 weeks and built a dynamic nomogram for early risk prediction, providing clinicians a visual tool for early identification of msBPD.
Phytochemical component and toxicological evaluation of purple sweet potato leaf extract in male Sprague–Dawley rats
Authors: Hisamuddin Ahmad Safiyyu’d-din Bin , Naomi Ruth , Bin Manan Khairul Aiman , Bahari Hasnah , Yazid Muhammad Dain , Othman Fezah , Embong Hashim , Hadizah Jumidil Siti , Hussain Mohd Khairi , Zakaria Zainul Amiruddin
Published: April 2023

This study assessed the toxicity of lutein-rich purple sweet potato leaf (PSPL) extract in male Sprague–Dawley rats.

Methods and study design: A total of 54 adult male Sprague–Dawley rats were used. For the acute toxicity study, three rats in the acute control group were fed 2,000 mg/kg of PSPL for 14 days. The subacute toxicity study included six rats each in four groups administered 50, 250, 500, or 1,000 mg/kg for 28 days and observed for further 14 days without treatment in the subacute control and subacute satellite groups. Changes in body weight; blood biochemistry; hematological parameters; relative organ weight; and histological sections of the heart, kidney, liver, pancreas, aorta, and retina were observed for signs of toxicity.

Results: The gradual increase in weekly body weight, normal level full blood count, normal liver and kidney profile, relative organ weight, and histological sections of all stained organ tissue in the treated group compared with the acute, subacute, and satellite control groups demonstrated the absence of signs of toxicity.

Conclusion: Lutein-rich PSPL extract shows no signs of toxicity up to 2,000 mg/kg/day.
Cationic lipid-assisted nanoparticles for simultaneous delivery of CD47 siRNA and R848 to promote antitumor immune responses
Authors: Li Simin , Chen Yichang , Ma Ruolin , Du Ye , Han Bing
Published: April 2023

Graphical Abstract

The PEG-PLGA nanoparticles effectively delivered R848 and CD47 siRNA into tumor cells, resulting in simultaneous activation of DCs and downregulation of CD47 expression on tumor cells, thereby enhancing antitumor immune responses by T cells.
Myelin sheath injury and repairment after subarachnoid hemorrhage
Authors: Chen Mao , Guo Peiwen , Ru Xufang , Chen Yujie , Zuo Shilun , Feng Hua
Published: April 2023

Subarachnoid hemorrhage (SAH) can lead to damage to the myelin sheath in white matter. Through classification and analysis of relevant research results, the discussion in this paper provides a deeper understanding of the spatiotemporal change characteristics, pathophysiological mechanisms and treatment strategies of myelin sheath injury after SAH. The research progress for this condition was also systematically reviewed and compared related to myelin sheath in other fields. Serious deficiencies were identified in the research on myelin sheath injury and treatment after SAH. It is necessary to focus on the overall situation and actively explore different treatment methods based on the spatiotemporal changes in the characteristics of the myelin sheath, as well as the initiation, intersection and common action point of the pathophysiological mechanism, to finally achieve accurate treatment. We hope that this article can help researchers in this field to further clarify the challenges and opportunities in the current research on myelin sheath injury and treatment after SAH.
Advances in computational frameworks in the fight against TB: The way forward
Authors: Naidu Akshayata , Nayak Smruti Sudha , Lulu S Sajitha , Sundararajan Vino
Published: April 2023

Around 1.6 million people lost their life to Tuberculosis in 2021 according to WHO estimates. Although an intensive treatment plan exists against the causal agent, Mycobacterium Tuberculosis, evolution of multi-drug resistant strains of the pathogen puts a large number of global populations at risk. Vaccine which can induce long-term protection is still in the making with many candidates currently in different phases of clinical trials. The COVID-19 pandemic has further aggravated the adversities by affecting early TB diagnosis and treatment. Yet, WHO remains adamant on its “End TB” strategy and aims to substantially reduce TB incidence and deaths by the year 2035. Such an ambitious goal would require a multi-sectoral approach which would greatly benefit from the latest computational advancements. To highlight the progress of these tools against TB, through this review, we summarize recent studies which have used advanced computational tools and algorithms for—early TB diagnosis, anti-mycobacterium drug discovery and in the designing of the next-generation of TB vaccines. At the end, we give an insight on other computational tools and Machine Learning approaches which have successfully been applied in biomedical research and discuss their prospects and applications against TB.
Active nematic multipoles: Flow responses and the dynamics of defects and colloids
Authors: Houston Alexander J. H. , Alexander Gareth P.
Published: April 2023

We introduce a general description of localised distortions in active nematics using the framework of active nematic multipoles. We give the Stokesian flows for arbitrary multipoles in terms of differentiation of a fundamental flow response and describe them explicitly up to quadrupole order. We also present the response in terms of the net active force and torque associated to the multipole. This allows the identification of the dipolar and quadrupolar distortions that generate self-propulsion and self-rotation respectively and serves as a guide for the design of arbitrary flow responses. Our results can be applied to both defect loops in three-dimensional active nematics and to systems with colloidal inclusions. They reveal the geometry-dependence of the self-dynamics of defect loops and provide insights into how colloids might be designed to achieve propulsive or rotational dynamics, and more generally for the extraction of work from active nematics. Finally, we extend our analysis also to two dimensions and to systems with chiral active stresses.
Passive control of wake flow behind a square cylinder using a flat plate
Authors: Abbasi Waqas Sarwar , Ismail Saba , Nadeem Sumaira , Rahman Hamid , Majeed Afraz Hussain , Khan Ilyas , Mohamed Abdullah
Published: April 2023

In this study, control over the wake flow of a single square cylinder exercised by a flat plate attached to the rear side of the cylinder is analyzed numerically via the lattice Boltzmann method. The Reynolds number (Re) is fixed at 150, and the length of the plate is varied from 0.1 to 8.5. Three distinct flow modes are observed in this study: unsteady, transient, and steady flow in the cases of plate lengths (L) in the ranges 0.1 ≤L≤ 6.5, 6.75 ≤L≤ 7.5, and 7.75 ≤L≤ 8.5, respectively. The streamlines exhibit different flow structures, termed hairpin-like, ellipse-like, and elongated bubble-like, at different values of L. Complete wake control is achieved at plate lengths beyond 7.75. This study reveals that the drag and lift coefficients exhibit unsteadiness at short plate lengths in early time steps, but as the plate length increases, unsteadiness slows down and eventually disappears, confirming the steady flow pattern. The mean drag coefficient (CDm), Strouhal number (St), and root-mean-square value of drag and lift coefficients (CDrms; CLrms) are reduced by maximums of 23.5%, 100%, 84.6%, and 99.5%, respectively, as a result of the presence of the plate.