bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceptions of impacts and management of invasive alien plants: a case study from Mirzapur, India
Authors: Kumar Sudhanshu , Meena Renu , Tiwari Amit Kumar , Singh Rinku , Patel Sanoj Kumar , Singh Gopal Shankar
Published: August 2023

Invasive alien plants (IAPs) have become a serious threat to biodiversity, agriculture and socio-economic development. Several aspects, including the ecological and economic impacts of IAPs have been explored in the recent past, however, perceptions of ecosystem services (ES) and ecosystem disservices (EDS) have not been well studied. IAPs affect the lives of local people both positively (providing ES) and negatively (providing EDS). IAPs in this region have not been studied through the aspects of ES and EDS that integrate the views and perceptions of local communities. Keeping in view this research gap, the present study was conducted in the Mirzapur district (Uttar Pradesh, India) where IAPs are widely distributed. In five sites covering a rural to urban gradient with increasing distance from forest, we randomly selected 100 respondents–20 from each of the five sites for the survey. A semi-structured questionnaire was used to collect respondents’ perceptions on ES and EDS supplied by IAPs in their local habitats. The questionnaire was designed to obtain data on awareness and knowledge, perceptions of ES and EDS, attitudes toward management, and socio-demographic information. Results indicated that 95% of respondents were familiar with at least one of the 12 IAPs identified as being important in the region. Ipomea carnea and Stylosanthes hamata were the most and least frequently cited plants, respectively. Medical use and reduction in soil fertility were most perceived as ES and EDS, respectively. The value of Spearman’s rank correlation coefficient (Spearman’s ρ = 0.487, p > 0.05) indicates a non-significant correlation between ranks of ES and EDS cited by respondents. Older and less educated people were more aware of the impacts of IAPs. Uprooting was the most commonly used management practice to control the invasion of plant species. People’s attitudes toward the management of IAPs seem to indicate that they prefer to eradicate species that have direct harmful effects on human health and biodiversity. This study provides inputs for incorporating people’s perceptions into the control and management of IAPs in the forest region.
Prenatal diagnosis and outcomes in 320 fetuses with nasal bone anomalies
Authors: Li Hui , Yao Yanyi , Zhang Chengcheng , Qin Yayun , Zeng Ling , Song Jieping , Lu Li , Wang Wei , Liu Lijun
Published: August 2023

Object: To investigate the chromosome abnormalities associated with absent or hypoplastic fetal nasal bone.

Methods: Patients with fetal nasal bone anomalies (NBA) referred to our center for prenatal diagnosis between 2017 and 2021 were retrospectively evaluated. All these patients underwent chromosomal microarray and/or karyotyping and received genetic counseling before and after testing.

Results: Among 320 fetuses with NBA, chromosomal abnormalities were diagnosed in 89 (27.8%) cases, including 53 cases of trisomy 21, which was the most common type of chromosomal aneuploidy, accounting for 59.6% of all detected abnormalities. In addition to aneuploidies, 29 cases of copy number variants (CNVs) were detected. In cases of isolated NBA with low-risk screening results and without other risk factors, the incidence of fetal chromosomal aneuploidies and pathogenic CNVs is 5.3% (7 in 132 cases).

Conclusion: This study suggests that parents of fetuses should be informed about the possibility of fetal aneuploidy and pathogenic CNVs and that discussion with the parents is also recommended, providing data support and reference for clinical counseling.
Mendelian randomization shows depression increases the risk of type 2 diabetes
Authors: Jin Heejin , Lee Sanghun , Won Sungho
Published: August 2023

Introduction: Type 2 diabetes (T2D) is associated with severe mental illnesses (SMIs), such as schizophrenia, bipolar disorder, and depression. However, causal relationships between SMIs and T2D remain unclear owing to potential bias in observational studies. We aimed to characterize the causal effect of SMI liability on T2D using two-sample Mendelian randomization (MR).

Methods: The causality between liability to SMI and T2D was investigated using the inverse-variance weighted (IVW), MREgger, MR-Egger with a simulation extrapolation, weighted median, and the MR pleiotropy residual sum and outlier method. Similarly, we performed additional MR which can detect the reverse causation effect by switching exposure and outcome for T2D liability for SMI. To further consider pleiotropic effects between SMIs, multivariable MR analysis was performed after accounting for the other traits.

Results: In the univariable IVW method, depression showed a causal effect on T2D (odds ratio [OR]: 1.128, 95% confidence interval [CI]: 1.024–1.245, p = 0.014). Multinomial MR more strongly supported these results (IVW OR: 1.197, 95% CI: 1.069, 1.340, p = 0.002; MR-Egger OR: 1.198, 95% CI: 1.062, 1.349, p = 0.003). Bidirectional MR showed absence of reversecausality between depression and T2D. However, causal relationship of bipolar and schizophrenia on T2D was not detected.

Discussion: Careful attention is needed for patients with depression regarding T2D prevention and treatment.
Probing the genomic landscape of human sexuality: a critical systematic review of the literature
Authors: Bragazzi Nicola Luigi , Converti Manlio , Crapanzano Andrea , Zerbetto Riccardo , Siri Anna , Khamisy-Farah Rola
Published: August 2023

Whether human sexuality is the result of nature or nurture (or their complex interplay) represents a hot, often ideologically driven, and highly polarized debate with political and social ramifications, and with varying, conflicting findings reported in the literature. A number of heritability and behavioral genetics studies, including pedigree-based investigations, have hypothesized inheritance patterns of human sexual behaviors. On the other hand, in most twin, adoption, and nuclear family studies, it was not possible to disentangle between underlying genetic and shared environmental sources. Furthermore, these studies were not able to estimate the precise extent of genetic loading and to shed light both on the number and nature of the putative inherited factors, which remained largely unknown. Molecular genetic studies offer an unprecedented opportunity to overcome these drawbacks, by dissecting the molecular basis of human sexuality and allowing a better understanding of its biological roots if any. However, there exists no systematic review of the molecular genetics of human sexuality. Therefore, we undertook this critical systematic review and appraisal of the literature, with the ambitious aims of filling in these gaps of knowledge, especially from the methodological standpoint, and providing guidance to future studies. Sixteen studies were finally retained and overviewed in the present systematic review study. Seven studies were linkage studies, four studies utilized the candidate gene approach, and five studies were GWAS investigations. Limitations of these studies and implications for further research are discussed.
Sperm quality parameters, fertilizing potential, metabolites, and DNA methylation in cold-stored and cryopreserved milt from Atlantic salmon (Salmo salar L.)
Authors: Narud Birgitte , Khezri Abdolrahman , Zeremichael Teklu T. , Eriksen Anne-Lene , Grevle Inger S. , Nordborg Anna , Klinkenberg Geir , Wilson Robert C. , Kommisrud Elisabeth
Published: August 2023

Cold storage and freezing/thawing of milt may affect sperm functionality and the subsequent fertilization ability of milt. This study aimed to investigate sperm quality parameters and fertilization potential of Atlantic salmon milt, stored cold and subsequently cryopreserved, using different storage conditions. The objective was also to assess if analysis of milt metabolites and sperm DNA methylation signatures could be applicable to further elucidate sperm quality and fertilization following preservation. Milt samples were collected from eight mature Atlantic salmon males and stored for 4 days at 2°C and 8°C. Samples were taken on day one of storage at 2°C and on day four of storage at 2°C and 8°C. Storage for 4 days at 8°C is expected to be detrimental to sperm quality, and was included to create contrasts. Correspondingly, aliquots of cold-stored milt were prepared for cryopreservation, resulting in a total of six experimental conditions. Samples from all six experimental conditions were used in fertilization trials and analyzed for sperm viability, motility, ATP content, DNA fragmentation index, and High DNA stainability. In addition, milt samples from four of the males were analyzed for targeted metabolites and DNA methylation signatures by reduced representation bisulfite sequencing. The fertilization trials were performed using sperm:egg ratios of 75 × 103and 500 × 103, respectively. Storage duration, temperature, and cryopreservation of cold-stored milt influenced several sperm quality parameters, metabolites, and DNA methylation signatures. The total motility, progressive motility, ATP, and velocity parameters were the sperm parameters with the strongest correlation to fertilization rates (p< 0.01). Several metabolites were correlated with fertility rates in both cold-stored and cryopreserved samples (p< 0.05). The fertilizing capacity of cold-stored milt was significantly reduced after 4 days of storage at 8°C, while corresponding cryopreserved milt showed reduced fertilization at both storage temperatures (2°C and 8°C) (p< 0.05). The results indicate that cryopreservation of milt stored for 1 day does not compromise either fertilization ability or DNA methylation signatures.
EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison
Authors: Alves Sandy Ingrid Aguiar , Ferreira Victor Benedito Costa , Dantas Carlos Willian Dias , Silva Artur Luiz da Costa da , Ramos Rommel Thiago Jucá
Published: August 2023

Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1–6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually—time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run. EasySSR requires only a FASTA and an optional GENBANK file of one or more genomes to identify and compare STRs. The tool can automatically analyze and compare SSRs in whole genomes, convert GenBank to PTT files, identify perfect and imperfect SSRs and coding and non-coding regions, compare their frequencies, abundancy, motifs, flanking sequences, and iterations, producing many outputs ready for download such as PTT files, interactive charts, and Excel tables, giving the user the data ready for further analysis in minutes. EasySSR was implemented as a web application, which can be executed from any browser and is available for free at https://computationalbiology.ufpa.br/easyssr/. Tutorials, usage notes, and download links to the source code can be found at https://github.com/engbiopct/EasySSR.
An efficient convolutional neural network-based diagnosis system for citrus fruit diseases
Authors: Huang Zhangcai , Jiang Xiaoxiao , Huang Shaodong , Qin Sheng , Yang Su
Published: August 2023

Introduction: Fruit diseases have a serious impact on fruit production, causing a significant drop in economic returns from agricultural products. Due to its excellent performance, deep learning is widely used for disease identification and severity diagnosis of crops. This paper focuses on leveraging the high-latitude feature extraction capability of deep convolutional neural networks to improve classification performance.

Methods: The proposed neural network is formed by combining the Inception module with the current state-of-the-art EfficientNetV2 for better multi-scale feature extraction and disease identification of citrus fruits. The VGG is used to replace the U-Net backbone to enhance the segmentation performance of the network.

Results: Compared to existing networks, the proposed method achieved recognition accuracy of over 95%. In addition, the accuracies of the segmentation models were compared. VGG-U-Net, a network generated by replacing the backbone of U-Net with VGG, is found to have the best segmentation performance with an accuracy of 87.66%. This method is most suitable for diagnosing the severity level of citrus fruit diseases. In the meantime, transfer learning is applied to improve the training cycle of the network model, both in the detection and severity diagnosis phases of the disease.

Discussion: The results of the comparison experiments reveal that the proposed method is effective in identifying and diagnosing the severity of citrus fruit diseases identification.
Insect-pathogen crosstalk and the cellular-molecular mechanisms of insect immunity: uncovering the underlying signaling pathways and immune regulatory function of non-coding RNAs
Authors: Mahanta Deepak Kumar , Bhoi Tanmaya Kumar , Komal J. , Samal Ipsita , Nikhil R. M. , Paschapur Amit Umesh , Singh Gaurav , Kumar P. V. Dinesh , Desai H. R. , Ahmad Mohammad Abbas , Singh P. P. , Majhi Prasanta Kumar , Mukherjee U. , Singh Pushpa , Saini Varun , Shahanaz  , Srinivasa N. , Yele Yogesh
Published: August 2023

Multicellular organisms are constantly subjected to pathogens that might be harmful. Although insects lack an adaptive immune system, they possess highly effective anti-infective mechanisms. Bacterial phagocytosis and parasite encapsulation are some forms of cellular responses. Insects often defend themselves against infections through a humoral response. This phenomenon includes the secretion of antimicrobial peptides into the hemolymph. Specific receptors for detecting infection are required for the recognition of foreign pathogens such as the proteins that recognize glucans and peptidoglycans, together referred to as PGRPs and βGRPs. Activation of these receptors leads to the stimulation of signaling pathways which further activates the genes encoding for antimicrobial peptides. Some instances of such pathways are the JAK-STAT, Imd, and Toll. The host immune response that frequently accompanies infections has, however, been circumvented by diseases, which may have assisted insects evolve their own complicated immune systems. The role of ncRNAs in insect immunology has been discussed in several notable studies and reviews. This paper examines the most recent research on the immune regulatory function of ncRNAs during insect-pathogen crosstalk, including insect- and pathogen-encoded miRNAs and lncRNAs, and provides an overview of the important insect signaling pathways and effector mechanisms activated by diverse pathogen invaders.
A novel signature constructed by differential genes of muscle-invasive and non-muscle-invasive bladder cancer for the prediction of prognosis in bladder cancer
Authors: Wang Weizhuo , Zhang Xi , Jiang Silin , Xu Peng , Chen Kang , Li Kai , Wang Fei , Le Xiang , Zhang Ke
Published: August 2023

Background

Bladder cancer (BCa) is a malignant tumor that usually forms cancer cells in the inner lining of the bladder. Hundreds of thousands of people worldwide have BCa diagnosed each year. The purpose of this study was to construct a prognostic model by differential expression of genes between muscular and non-muscular invasive BCa, and to investigate the prognosis of BCa patients.

Methods

The data of BCa patients was sourced from the GEO and TCGA database. Single-cell sequencing data was obtained from three patients in the GSE135337 database, and microarray data for verification was obtained from GSE32894. Univariate, Lasso and multivariate cox regression analyses were performed to construct the prognostic model. The prognostic features, immune features and drug sensitivity of the model were further evaluated. Single-cell data and microarray data were used to validate the differential expression of model genes between muscle-invasive and non-muscle-invasive BCa. The invasion and migration of BCa cells were evaluated using the transwell assay and wound-healing assay. The cell proliferation capacity was simultaneously evaluated using Colony formation experiments. The protein expression of the specific gene was detected by western blot analysis.

Results

We identified 183 differentially expressed muscle-invasive-related differential genes (MIRDGs), among which four were selected to establish a prognostic model. Based on our signature, patients in different groups displayed varying levels of immune infiltration and immunotherapy profiles. Single-cell sequencing data and microarray data confirmed that four invasion-related genes were expressed at higher levels in muscle-invasive BCa. Given the critical role of S100A9 in the progression of BCa, we performed further analysis. The results showed that protein expression of S100A9 was high in muscle-invasive BCa, and S100A9 knockdown could inhibit the proliferation, migration and invasion of BCa.

Conclusion

These findings demonstrated that the prognostic model for BCa patients was reasonably accurate and valid, and it may prove to be of considerable value for the treatment and prognosis of BCa patients in the future. S100A9 may become a better prognostic marker and potential therapeutic target to further guide clinical treatment decisions.
Cancer immunotherapies: advances and bottlenecks
Authors: Rui Rui , Zhou Liqun , He Shiming
Published: August 2023

Immunotherapy has ushered in a new era in cancer treatment, and cancer immunotherapy continues to be rejuvenated. The clinical goal of cancer immunotherapy is to prime host immune system to provide passive or active immunity against malignant tumors. Tumor infiltrating leukocytes (TILs) play an immunomodulatory role in tumor microenvironment (TME) which is closely related to immune escape of tumor cells, thus influence tumor progress. Several cancer immunotherapies, include immune checkpoint inhibitors (ICIs), cancer vaccine, adoptive cell transfer (ACT), have shown great efficacy and promise. In this review, we will summarize the recent research advances in tumor immunotherapy, including the molecular mechanisms and clinical effects as well as limitations of immunotherapy.
Impact of age on liver damage, inflammation, and molecular signaling pathways in response to femoral fracture and hemorrhage
Authors: Meng Fanshuai , Zhou Yuzhuo , Wagner Alessa , Bülow Jasmin Maria , Köhler Kernt , Neunaber Claudia , Bundkirchen Katrin , Relja Borna
Published: August 2023

Background

Trauma causes disability and mortality globally, leading to fractures and hemorrhagic shock. This can trigger an irregular inflammatory response that damages remote organs, including liver. Aging increases the susceptibility to dysregulated immune responses following trauma, raising the risk of organ damage, infections, and higher morbidity and mortality in elderly patients. This study investigates how aging affects liver inflammation and damage post-trauma.

Methods

24 male C57BL/6J mice were randomly divided into four groups. Twelve young (17-26 weeks) and 12 aged (64-72 weeks) mice were included. Mice further underwent either hemorrhagic shock (trauma/hemorrhage, TH), and femoral fracture (osteotomy) with external fixation (Fx) (THFx, n=6) or sham procedures (n=6). After 24 hours, mice were sacrificed. Liver injury and apoptosis were evaluated using hematoxylin-eosin staining and activated caspase-3 immunostaining. CXCL1 and infiltrating polymorphonuclear leukocytes (PMNL) in the liver were assessed by immunostaining, and concentrations of CXCL1, TNF, IL-1β, and IL-10 in the liver tissue were determined by ELISA. Gene expression of Tnf, Cxcl1, Il-1β, and Cxcl2 in the liver tissue was determined by qRT-PCR. Finally, western blot was used to determine protein expression levels of IκBα, Akt, and their phosphorylated forms.

Results

THFx caused liver damage and increased presence of active caspase-3-positive cells compared to the corresponding sham group. THFx aged group had more severe liver injury than the young group. CXCL1 and PMNL levels were significantly higher in both aged groups, and THFx caused a greater increase in CXCL and PMNL levels in aged compared to the young group. Pro-inflammatory TNF and IL-1β levels were elevated in aged groups, further intensified by THFx. Anti-inflammatory IL-10 levels were lower in aged groups. Tnf and Cxcl1 gene expression was enhanced in the aged sham group. Phosphorylation ratio of IκBα was significantly increased in the aged sham group versus young sham group. THFx-induced IκBα phosphorylation in the young group was significantly reduced in the aged THFx group. Akt phosphorylation was significantly reduced in the THFx aged group compared to the THFx young group.

Conclusion

The findings indicate that aging may lead to increased vulnerability to liver injury and inflammation following trauma due to dysregulated immune responses.
Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing
Authors: Kalomoiri Maria , Prakash Chandana Rao , Lagström Sonja , Hauschulz Kai , Ewing Ewoud , Shchetynsky Klementy , Kular Lara , Needhamsen Maria , Jagodic Maja
Published: August 2023

The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing an important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here, we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture related method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in HLA locus. Moreover, by the detection of differentially methylated positions in promoters of immune-related genes, we identified relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the interplay between genetic variance and epigenetic regulation in the HLA class II region, potentially, in a wide disease context.
4-Methoxy-2,2′-bipyrrole-5-carbaldehyde, a biosynthetic intermediate of bipyrrole-containing natural products from the Streptomyces culture, arrests the strobilation of moon jellyfish Aurelia coerulea
Authors: Misaki Yuya , Hirashima Tomomi , Fujii Karin , Hirata Asahi , Hoshino Yutaro , Sumiyoshi Miho , Masaki Sachiko , Suzuki Toshihiro , Inada Kuninobu , Koyama Hiroki , Kuniyoshi Hisato , Arakawa Kenji
Published: August 2023

Streptomyces spp. are well-known producers of secondary metabolites with diverse biological activities. We screened the substances that regulate polyp-to-jellyfish transition, called strobilation, of the moon jellyfish (Aurelia coerulea) from the Streptomyces culture library. Among the culture extracts of the strains tested, Streptomyces albus HUT6047 inhibited the strobilation of A. coerulea. The active component in strain HUT6047 was purified. Based on structure elucidation, this component was identified as 4-methoxy-2,2′-bipyrrole-5-carbaldehyde (MBC), a possible common biosynthetic intermediate of pyrrole-containing natural products including prodigiosins and tambjamines. Synthetic MBC arrested strobilation without inducing cytotoxicity and generated abnormal tentacle-like structures in a dose-dependent manner. Synthetic MBC also exhibited a minimum activity of 6.3 µM. To our knowledge, this study provides the first example of a biological activity of MBC.
Is my wound infected? A study on the use of hyperspectral imaging to assess wound infection
Authors: Ramirez-GarciaLuna Jose L. , Martinez-Jimenez Mario A. , Fraser Robert D. J. , Bartlett Robert , Lorincz Amy , Liu Zheng , Saiko Gennadi , Berry Gregory K.
Published: August 2023

Introduction

Clinical signs and symptoms (CSS) of infection are a standard part of wound care, yet they can have low specificity and sensitivity, which can further vary due to clinician knowledge, experience, and education. Wound photography is becoming more widely adopted to support wound care. Thermography has been studied in the medical literature to assess signs of perfusion and inflammation for decades. Bacterial fluorescence has recently emerged as a valuable tool to detect a high bacterial load within wounds. Combining these modalities offers a potential objective screening tool for wound infection.

Methods

A multi-center prospective study of 66 outpatient wound care patients used hyperspectral imaging to collect visible light, thermography, and bacterial fluorescence images. Wounds were assessed and screened using the International Wound Infection Institute (IWII) checklist for CSS of infection. Principal component analysis was performed on the images to identify wounds presenting as infected, inflamed, or non-infected.

Results

The model could accurately predict all three wound classes (infected, inflamed, and non-infected) with an accuracy of 74%. They performed best on infected wounds (100% sensitivity and 91% specificity) compared to non-inflamed (sensitivity 94%, specificity 70%) and inflamed wounds (85% sensitivity, 77% specificity).

Discussion

Combining multiple imaging modalities enables the application of models to improve wound assessment. Infection detection by CSS is vulnerable to subjective interpretation and variability based on clinicians' education and skills. Enabling clinicians to use point-of-care hyperspectral imaging may allow earlier infection detection and intervention, possibly preventing delays in wound healing and minimizing adverse events.
Association of high estimated glomerular filtration rate with risk of atrial fibrillation: a nationwide cohort study
Authors: Kang Min Kyoung , Ha Hee-Jung , Jung Raon , Oh YunSeo , Kim Dong-Hyeok , Song Tae-Jin
Published: August 2023

Aim

While the relationship between impaired kidney function and atrial fibrillation (AF) is well established, there is limited research exploring the association between elevated estimated glomerular filtration rate (eGFR) and AF development. This study aimed to examine the association between higher-than-normal eGFR and AF risk using a nationwide longitudinal study of the general population in Korea.

Materials and methods

This study utilized the National Health Insurance Service cohort database of Korea, analyzing data from 2,645,042 participants aged 20–79 years who underwent health examinations between 2010 and 2011. Participants with a history of end-stage renal disease, renal transplantation, and AF prior to the index date were excluded. Renal function was assessed using eGFR levels, calculated with the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. Baseline characteristics were gathered through questionnaires, while comorbidities and AF occurrence outcomes were identified and validated using diagnostic codes and medication histories. The study employed Kaplan–Meier survival curves and Cox proportional hazard models to evaluate the association between eGFR and AF occurrence.

Results

The mean age of subjects was 48.82 ± 10.08 years. Over a median follow-up of 9.58 years, 27,469 (1.04%) AF cases were identified. The risk for AF increased in the higher-than-normal decile, as demonstrated by Kaplan–Meier survival curves (p < 0.001). The eGFR <30 mL/min/1.73 m2 group was associated with an increased risk of AF [hazard ratio (HR): 1.22, 95% confidence interval (CI) (1.01, 1.46), p = 0.039], while the eGFR >120 mL/min/1.73 m2 group was associated with a decreased risk of AF [HR: 0.88, 95% CI (0.78, 0.98), p = 0.045]. Compared to the 5th decile, the 1st [HR: 1.08, 95% CI (1.03, 1.13), p = 0.010] eGFR decile was significantly associated with an increased risk of AF, while the 10th [HR: 0.77, 95% CI (0.70, 0.85), p < 0.001] eGFR decile was significantly associated with a reduced risk of AF.

Conclusion

The study revealed that individuals with eGFR>120 mL/min/1.73 m2 or those falling within eGFR 10th decile (>113.41 mL/min/1.73 m2) demonstrated an inverse association linked to a reduced risk of AF. Our study suggests that general population with higher-than-normal eGFR levels may have a lower risk of developing AF.
Prenatal phenotypes and pregnancy outcomes of fetuses with recurrent 1q21.1 microdeletions and microduplications
Authors: Yue Fagui , Yang Xiao , Jiang Yuting , Li Shibo , Liu Ruizhi , Zhang Hongguo
Published: August 2023

Objective

Chromosomal 1q21.1 deletions and duplications are genomic disorders that are usually diagnosed postnatally. However, the genotype–phenotype correlations of 1q21.1 copy number variants (CNVs) during the prenatal period are still not clear. This study aimed to provide a systematic summary of prenatal phenotypes for such genomic disorders.

Methods

In total, 26 prenatal amniotic fluid samples diagnosed with 1q21.1 microdeletions/microduplications were obtained from pregnant women who opted for invasive prenatal testing. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed for all cases simultaneously. The pregnancy outcomes and health conditions after birth in all cases were followed up. Meanwhile, prenatal cases with 1q21.1 microdeletions or microduplications in the literature were retrospectively collected.

Results

In total, 11 pregnancies (11/8,252, 0.13%) with 1q21.1 microdeletions and 15 (15/8,252, 0.18%) with 1q21.1 microduplications were identified. Among these 1q21.1 CNVs, 4 cases covered the thrombocytopenia-absent radius (TAR) region, 16 cases covered the 1q21.1 recurrent microdeletion/microduplication region, and 6 cases covered all regions mentioned above. The prenatal abnormal ultrasound findings were recorded in four participants with 1q21.1 deletions and seven participants with 1q21.1 duplications. Finally, three cases with 1q21.1 deletions and five with 1q21.1 duplications terminated their pregnancies.

Conclusion

In the prenatal setting, 1q21.1 microdeletions were associated with increased nuchal translucency (NT), anomalies of the urinary system, and cardiovascular abnormalities, while 1q21.1 microduplications were correlated with cardiovascular malformations, nasal bone dysplasia, and increased NT. In addition, cerebral ventriculomegaly might be correlated with 1q21.1 microduplications. Considering the variable expressivity and incomplete penetrance of 1q21.1 CNVs, long-term follow-up after birth should be carried out in these cases.
Bacillus subtilis ER-08, a multifunctional plant growth-promoting rhizobacterium, promotes the growth of fenugreek (Trigonella foenum-graecum L.) plants under salt and drought stress
Authors: Patel Margi , Islam Shaikhul , Husain Fohad Mabood , Yadav Virendra Kumar , Park Hyun-Kyung , Yadav Krishna Kumar , Bagatharia Snehal , Joshi Madhvi , Jeon Byong-Hun , Patel Ashish
Published: August 2023

Introduction

Sustainable agriculture and meeting the world's food needs face considerable obstacles from abiotic stresses such as soil salinity and drought. This critical issue was addressed by our current study, which sought to uncover multi-trait bioinoculants from hostile ecosystems that could help mitigate salinity and drought stresses at the same time.

Methods

The Bacillus subtilis ER-08 (BST) strain was isolated from the halotolerant plant Fagonia cretica which was collected from the Little Rann of Kachchh, India. Various biochemical and molecular approaches were applied for the detailed characterization of the BST isolate.

Results and discussion

The BST isolate demonstrated notable plant growth-promoting qualities. Fenugreek seed biopriming was performed using the BST isolate. The effect of BST seed treatment on fenugreek developmental indices as well as abiotic alleviation was examined under greenhouse conditions. The BST produced 83.7 g ml−1 gibberellins (GA3) and 176.1 g ml−1 indole-3 acetic acid. Moreover, hydrogen cyanide, siderophore, exopolysaccharides (EPS), ammonia, cellulase, protease, pectinase, and chitinase were also produced by the BST strain. Interestingly, 52% of Fusarium oxysporum mycelial growth was suppressed by the BST isolate under in vitro conditions. Furthermore, BST isolates functioned well under several abiotic stress conditions, for instance, salinity (4 and 6 ds m−1), pH (5, 7, and 9), drought (PEG6000 at 10%, 20%, and 30%), and temperature (25°C, 35°C, 37°C, and 55°C). This study indicates that the BST strain might serve as an effective bio-inoculant for minimizing the detrimental effects of abiotic stresses.
The core bacteriobiome of Côte d’Ivoire soils across three vegetation zones
Authors: Amon Chiguié Estelle Raïssa , Fossou Romain Kouakou , Ebou Anicet E. T. , Koua Dominiqueua K. , Kouadjo Claude Ghislaine , Brou Yao Casimir , Voko Bi Don Rodrigue Rosin , Cowan Don A. , Zézé Adolphe
Published: August 2023

The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d’Ivoire. 45 surface soil samples were collected from Côte d’Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d’Ivoire, provides insights into the distribution of bacterial taxa in Côte d’Ivoire soils, and the findings may serve as biological indicator for land management in Côte d’Ivoire.
Investigating the antidepressant effect of Ziyan green tea on chronic unpredictable mild stress mice through fecal metabolomics
Authors: Jia Wenbao , Tang Qian , Zou Yao , Yang Yang , Wu Wenliang , Xu Wei
Published: August 2023

Introduction

Some studies have shown the effectiveness of tea in reducing depression. Gut flora dysfunction is strongly associated with depression. The mechanism by which Ziyan green tea ameliorates depression is not clear.

Methods

In this study, we examined the impact of Ziyan green tea on mice exhibiting symptoms similar to depression. We specifically focused on the role of intestinal flora and its metabolites. We first established a chronic unpredictable mild stress (CUMS) mouse model to induce depressive symptoms and conducted behavioural tests, biochemical tests, and pathological tissue analysis. We also investigated gut microbiota changes by 16S rRNA sequencing and measured faecal metabolites in mice using UHPLC-MS/MS.

Results

The results showed that Ziyan green tea intervention improved depression-like behaviour, neurobiochemical factors, and reduced levels of pro-inflammatory factors in CUMS mice. Spearman’s correlation analysis showed that different microbial communities (Corynebacterium, Faecalibaculum, Enterorhabdus, Desulfovibrio) correlation with differential metabolites (Cholic acid, Deoxycholic acid, etc.) and depression-related biochemical indicators (5-HT, DA, BDNF, IL-6, and TNF-α).

Discussion

In conclusion, our findings suggest that both low and high-dose interventions of Ziyan green tea have positive preventive effects on CUMS mice without dose dependence, partly because they mainly affect intestinal Purine Metabolism, Bile Acid Biosynthesis and Cysteine Metabolism in CUMS mice, thus stimulating brain 5-HT, DA and BDNF, and decreasing the inflammatory factors IL-6, TNF-α, activate the composition of intestinal flora, improve the intestinal flora environment and thus promote the production of intestinal metabolites, which can be used for depression treatment. It is suggested that Ziyan green tea may achieve an antidepressant effect through the gut-microbiota-brain axis.
Aztreonam is a novel chemical inducer that promotes Agrobacteium transformation and lateral root development in soybean
Authors: Waqar Khan M. , Yang Wenqi , Yu Ke , Zhang Xuebin
Published: August 2023

Agrobacterium-mediated soybean transformation is the simplest method of gene transfer. However, the low transformation due to the intractable nature of soybean genotypes hinders this process. The use of biochemicals (acetosyringone, cinnamic acid, flavonoids, etc.) plays an important role in increasing soybean transformation. These biochemicals induce chemotaxis and virulence gene activation during the infection process. Here we identified a biochemical, aztreonam (a monobactam), for high agrobacterium-mediated transformation in soybean. The soybean explants from three genotypes were inoculated with A. tumefaciens (GV3101) harboring the pMDC32 vector containing hpt or the GmUbi-35S-GUS vector containing the GUS gene during two separate events. High transient GUS expression was obtained during cotyledon explant culture on MS media supplemented with 2.5 mg/L aztreonam. The aztreonam-treated explants showed high efficiency in transient and stable transformation as compared to the untreated control. The transformation of aztreonam-treated explants during seed imbibition resulted in an average of 21.1% as compared to 13.2% in control by using the pMDC32 vector and 28.5 and 20.7% while using the GUS gene cassette, respectively. Based on these findings, the metabolic analysis of the explant after aztreonam treatment was assessed. The high accumulation of flavonoids was identified during an untargeted metabolic analysis. The quantification results showed a significantly high accumulation of the four compounds, i.e., genistein, apigenin, naringenin, and genistin, in cotyledon explants after 18 hours of aztreonam treatment. Alongside this, aztreonam also had some surprising effects on root elongation and lateral root formation when compared to indole-3-butyric acid (IBA). Our findings were limited to soybeans. However, the discovery of aztreonam and its effect on triggering flavonoids could lead to the potential role of aztreonam in the agrobacterium-mediated transformation of different crops.
The effect of different sources of mesenchymal stem cells on microglia states
Authors: Xin Qiang , Zhu Wenhao , He Chuan , Liu Tianyi , Wang Haifeng
Published: August 2023

Microglial reaction plays a key role in the prognosis of traumatic CNS injuries (TBI and SCI). A growing number of studies have shown that mesenchymal stem cells (MSCs) play an important role in regulating microglial states. This review summarizes the effects and mechanisms of different sources of MSCs on microglial states in the last 5 years. In general, bone marrow-derived mesenchymal stem cells are the most accessible and widely used, and can produce immunosuppressive effects on a variety of brain injuries including TBI through tissue engineering in situ implantation; MSCs mainly regulate inflammatory pathways and promote the states of microglia in the anti-inflammatory direction, which also secrete certain cytokines or extracellular vesicles to affect apoptotic pathways, such as the extracellular vesicles miR-21-5p, acting as a neuronal protector.
Transcranial direct current stimulation (tDCS) over the orbitofrontal cortex reduces delay discounting
Authors: Moro Andrea Stefano , Saccenti Daniele , Vergallito Alessandra , Scaini Simona , Malgaroli Antonio , Ferro Mattia , Lamanna Jacopo
Published: August 2023

Delay discounting (DD) is a quantifiable psychological phenomenon that regulates decision-making. Nevertheless, the neural substrates of DD and its relationship with other cognitive domains are not well understood. The orbitofrontal cortex (OFC) is a potential candidate for supporting the expression of DD, but due to its wide involvement in several psychological functions and neural networks, its central role remains elusive. In this study, healthy subjects underwent transcranial direct current stimulation (tDCS) while performing an intertemporal choice task for the quantification of DD and a working memory task. To selectively engage the OFC, two electrode configurations have been tested, namely, anodal Fp1–cathodal Fp2 and cathodal Fp1–anodal Fp2. Our results show that stimulation of the OFC reduces DD, independently from electrode configuration. In addition, no relationship was found between DD measures and either working memory performance or baseline impulsivity assessed through established tests. Our work will direct future investigations aimed at unveiling the specific neural mechanisms underlying the involvement of the OFC in DD, and at testing the efficacy of OFC tDCS in reducing DD in psychological conditions where this phenomenon has been strongly implicated, such as addiction and eating disorders.
A novel approach to attention mechanism using kernel functions: Kerformer
Authors: Gan Yao , Fu Yanyun , Wang Deyong , Li Yongming
Published: August 2023

Artificial Intelligence (AI) is driving advancements across various fields by simulating and enhancing human intelligence. In Natural Language Processing (NLP), transformer models like the Kerformer, a linear transformer based on a kernel approach, have garnered success. However, traditional attention mechanisms in these models have quadratic calculation costs linked to input sequence lengths, hampering efficiency in tasks with extended orders. To tackle this, Kerformer introduces a nonlinear reweighting mechanism, transforming maximum attention into feature-based dot product attention. By exploiting the non-negativity and non-linear weighting traits of softmax computation, separate non-negativity operations for Query(Q) and Key(K) computations are performed. The inclusion of the SE Block further enhances model performance. Kerformer significantly reduces attention matrix time complexity from O(N2) to O(N), with N representing sequence length. This transformation results in remarkable efficiency and scalability gains, especially for prolonged tasks. Experimental results demonstrate Kerformer's superiority in terms of time and memory consumption, yielding higher average accuracy (83.39%) in NLP and vision tasks. In tasks with long sequences, Kerformer achieves an average accuracy of 58.94% and exhibits superior efficiency and convergence speed in visual tasks. This model thus offers a promising solution to the limitations posed by conventional attention mechanisms in handling lengthy tasks.
Smoking behavior detection algorithm based on YOLOv8-MNC
Authors: Wang Zhong , Lei Lanfang , Shi Peibei
Published: August 2023

Introduction

The detection of smoking behavior is an emerging field faced with challenges in identifying small, frequently occluded objects like cigarette butts using existing deep learning technologies. Such challenges have led to unsatisfactory detection accuracy and poor model robustness.

Methods

To overcome these issues, this paper introduces a novel smoking detection algorithm, YOLOv8-MNC, which builds on the YOLOv8 network and includes a specialized layer for small target detection. The YOLOv8-MNC algorithm employs three key strategies: (1) It utilizes NWD Loss to mitigate the effects of minor deviations in object positions on IoU, thereby enhancing training accuracy; (2) It incorporates the Multi-head Self-Attention Mechanism (MHSA) to bolster the network’s global feature learning capacity; and (3) It implements the lightweight general up-sampling operator CARAFE, in place of conventional nearest-neighbor interpolation up-sampling modules, minimizing feature information loss during the up-sampling process.

Results

Experimental results from a customized smoking behavior dataset demonstrate significant improvement in detection accuracy. The YOLOv8-MNC model achieved a detection accuracy of 85.887%, signifying a remarkable increase of 5.7% in the mean Average Precision (mAP@0.5) when compared to the previous algorithm.

Discussion

The YOLOv8-MNC algorithm represents a valuable step forward in resolving existing problems in smoking behavior detection. Its enhanced performance in both detection accuracy and robustness indicates potential applicability in related fields, thus illustrating a meaningful advancement in the sphere of smoking behavior detection. Future efforts will focus on refining this technique and exploring its application in broader contexts.
Selective dopaminergic vulnerability in Parkinson’s disease: new insights into the role of DAT
Authors: Harraz Maged M.
Published: August 2023

One of the hallmarks of Parkinson’s disease (PD) is the progressive loss of dopaminergic neurons and associated dopamine depletion. Several mechanisms, previously considered in isolation, have been proposed to contribute to the pathophysiology of dopaminergic degeneration: dopamine oxidation-mediated neurotoxicity, high dopamine transporter (DAT) expression density per neuron, and autophagy-lysosome pathway (ALP) dysfunction. However, the interrelationships among these mechanisms remained unclear. Our recent research bridges this gap, recognizing autophagy as a novel dopamine homeostasis regulator, unifying these concepts. I propose that autophagy modulates dopamine reuptake by selectively degrading DAT. In PD, ALP dysfunction could increase DAT density per neuron, and enhance dopamine reuptake, oxidation, and neurotoxicity, potentially contributing to the progressive loss of dopaminergic neurons. This integrated understanding may provide a more comprehensive view of aspects of PD pathophysiology and opens new avenues for therapeutic interventions.