bluuebunny/crossref_metadata_2025 huggingface dataset:
Refining the relationship between gut microbiota and common hematologic malignancies: insights from a bidirectional Mendelian randomization study
Authors: Chen Pengyin , Guo Jiaxin , Wang Wei , Feng Anhua , Qin Lili , Hu Yuyuan , Lyu Nannan , Wang Haiying
Published: June 2024

Background

The relationship between gut microbiota and hematologic malignancies has attracted considerable attention. As research progresses, it has become increasingly clear that the composition of gut microbiota may influence the onset and progression of hematologic malignancies. However, our understanding of this association remains limited.

Methods

In our study, we classified gut microbiota into five groups based on information at the phylum, class, order, family, and genus levels. Subsequently, we obtained data related to common hematologic malignancies from the IEU Open GWAS project. We then employed a bidirectional Mendelian Randomization (MR) approach to determine whether there is a causal relationship between gut microbiota and hematologic malignancies. Additionally, we conducted bidirectional MR analyses to ascertain the directionality of this causal relationship.

Results

Through forward and reverse MR analyses, we found the risk of lymphoid leukemia was significantly associated with the abundance of phylum Cyanobacteria, order Methanobacteriales, class Methanobacteria, family Peptococcaceae, family Methanobacteriaceae, and genera Lachnospiraceae UCG010, Methanobrevibacter, Eubacterium brachy group, and Butyrivibrio. The risk of myeloid leukemia was significantly associated with the abundance of phylum Actinobacteria, phylum Firmicutes, order Bifidobacteriales, order Clostridiales, class Actinobacteria, class Gammaproteobacteria, class Clostridia, family Bifidobacteriaceae, and genera Fusicatenibacter, Eubacterium hallii group, Blautia, Collinsella, Ruminococcus gauvreauii group, and Bifidobacterium. The risk of Hodgkin lymphoma was significantly associated with the abundance of family Clostridiales vadinBB60 group, genus Peptococcus, and genus Ruminococcaceae UCG010. The risk of malignant plasma cell tumor was significantly associated with the abundance of genera Romboutsia and Eubacterium rectale group. The risk of diffuse large B-cell lymphoma was significantly associated with the abundance of genera Erysipelatoclostridium and Eubacterium coprostanoligenes group. The risk of mature T/NK cell lymphomas was significantly associated with the abundance of phylum Verrucomicrobia, genus Ruminococcaceae UCG013, genus Lachnoclostridium, and genus Eubacterium rectale group. Lastly, the risk of myeloproliferative neoplasms was significantly associated with the abundance of genus Coprococcus 3 and Eubacterium hallii group.

Conclusion

Our study provided new evidence for the causal relationship between gut microbiota and hematologic malignancies, offering novel insights and approaches for the prevention and treatment of these tumors.
Academic activism: learning and self-transformation through collective action taking
Authors: Zourou Katerina , Potolia Anthippi , Oikonomou Stefania
Published: June 2024

Activism, as a manifestation of citizen engagement for social purposes, can be practiced by individuals and communities alike, such as communities of professionals and, in this case, professionals in academia. Academic activism is a novel form of socio-political engagement in scholarly communities. Recently, communities engaged in academic activism have multiplied, mostly due to the climate emergency and increased awareness on human-induced climate change. This paper focuses on the learning elements and self-transformative potential of becoming an academic activist. This is done by analyzing three key areas: (a) the perceptions of self, (b) the learning component, and (c) the educational component, namely teaching the very activities that activists carry out at their universities. To serve these objectives, we conducted eight semi-directive interviews during the summer of 2022 in which participants drew upon their personal experience and life trajectories in their journey to becoming academic activists. Using a Discourse Analytical framework, we scrutinized the semantic fields summoned and the discursive spaces mobilized by the interviewees. The findings of this study highlight the participants' determination for activism, depicting it as a conscious act, a duty. Moreover, three types of learning have been depicted, demonstrating the wealth of learning trajectories experienced. The potential impact of academic activism on teaching practices (societal role of education) has also been depicted.
Reading self-concept, trait emotional intelligence and anxiety of primary school children with dyslexia
Authors: Polychroni Fotini , Antoniou Alexandros-Stamatios , Kofa Olga , Charitaki Garyfalia
Published: June 2024

Introduction

The association between the cognitive and the affective domain in reading is well documented in research, especially when difficulties are manifested. The aim of this study was (a) to investigate levels of reading self-concept, trait emotional intelligence, and anxiety of students with dyslexia and compare them to students with no previous assessment and (b) explore the hypothesis that reading self-concept and trait emotional intelligence are negative predictors of state and trait anxiety taking into account students’ individual characteristics such as gender, school year, and school performance.

Methods

A total of 794, fifth- and sixth-grade Greek primary school children aged 10 to 12 years old participated in the study. Of them, 50 children had a statement of dyslexia. The State and Trait Anxiety Inventory for Children, the Reading Self-Concept Scale, and the Trait Emotional Intelligence Questionnaire—Short Form were administered to the participants.

Results

The results showed that children with dyslexia were more vulnerable in terms of their perceptions of reading self-concept and emotional intelligence as compared to typical peers. Moreover, students’ characteristics, i.e., grades in math and language and dyslexia, had a direct positive path to trait emotional intelligence and reading self-concept while trait emotional intelligence and reading self-concept predicted negative anxiety.

Discussion

The implications of the results in terms of the possible protective role of reading self-concept and emotional intelligence on anxiety for children with dyslexia are discussed, and suggestions for future research are presented.
Puberty suppression in adolescents with gender dysphoria: an emerging issue with multiple implications
Authors: Betsi Grigoria , Goulia Panagiota , Sandhu Sophia , Xekouki Paraskevi
Published: June 2024

Controversy exists over puberty suppression (PS) in adolescents with gender dysphoria (GD). PS is preferentially achieved with GnRH analogues. By preventing the development of secondary sex characteristics, PS may improve psychological functioning, well-being, quality of life, emotional and behavioral (especially internalizing) problems and depressive symptoms, thus decreasing suicidality. PS can also extend the diagnostic period and give transgender adolescents time to explore their gender identity. GnRHa may also decrease the need for feminization/masculinization surgery. However, 2-year treatment with GnRHa may result in bone mass accrual retardation (decrease in BMD/BMAD z-scores), growth velocity deceleration (decrease in height SDS), increase in fat mass, temporary pause in oocyte/sperm maturation. The most common side effects of GnRHa are hot flashes, mood fluctuations, fatigue and headache. They are usually mild and rarely lead to GnRHa discontinuation. Based on current scientific evidence, PS could be recommended to adolescents who meet the diagnostic criteria of gender incongruence (by DSM-5 and/or ICD-11) and have long-lasting intense GD, which aggravates with puberty onset. Before initiating PS, possible mental issues should be addressed and informed consent (by the adolescent/caregiver) should be given, after counseling on probable reproductive effects of GnRHa. GnRHa can only be started after the adolescent has entered Tanner stage 2. Nevertheless, published studies are inadequate in number, small in size, uncontrolled and relatively short-term, so that it is difficult to draw safe conclusions on efficacy and safety of GnRHa. Large long-term randomized controlled trials are needed to expand knowledge on this controversial issue and elucidate the benefit and risks of PS.
Changes in the serum metabolomics of polycystic ovary syndrome before and after compound oral contraceptive treatment
Authors: Zhao Ting , Xiao Xiao , Li Lingchuan , Zhu Jing , He Wenli , Zhang Qiong , Wu Jiaqi , Wu Xiaomei , Yuan Tao
Published: June 2024

Background

Polycystic ovary syndrome (PCOS) is both a common endocrine syndrome and a metabolic disorder that results in harm to the reproductive system and whole-body metabolism. This study aimed to investigate differences in the serum metabolic profiles of patients with PCOS compared with healthy controls, in addition to investigating the effects of compound oral contraceptive (COC) treatment in patients with PCOS.

Materials and methods

50 patients with PCOS and 50 sex-matched healthy controls were recruited. Patients with PCOS received three cycles of self-administered COC treatment. Clinical characteristics were recorded, and the laboratory biochemical data were detected. We utilized ultra-performance liquid chromatography–high-resolution mass spectrometry to study the serum metabolic changes between patients with PCOS, patients with PCOS following COC treatment, and healthy controls.

Result

Patients with PCOS who received COC treatment showed significant improvements in serum sex hormone levels, a reduction in luteinising hormone levels, and a significant reduction in the levels of biologically active free testosterone in the blood. Differential metabolite correlation analysis revealed differences between PCOS and healthy control groups in N-tetradecanamide, hexadecanamide, 10E,12Z-octadecadienoic acid, and 13-HOTrE(r); after 3 months of COC treatment, there were significant differences in benzoic acid, organic acid, and phenolamides. Using gas chromatography–mass spectrometry to analyse blood serum in each group, the characteristic changes in PCOS were metabolic disorders of amino acids, carbohydrates, and purines, with significant changes in the levels of total cholesterol, uric acid, phenylalanine, aspartic acid, and glutamate.

Conclusion

Following COC treatment, improvements in sex hormone levels, endocrine factor levels, and metabolic levels were better than in the group of PCOS patients receiving no COC treatment, indicating that COC treatment for PCOS could effectively regulate the levels of sex hormones, endocrine factors, and serum metabolic profiles.
Optimization of pore size and filter material for better enrichment of environmental DNA
Authors: Liu Qianqian , Tan Juan , Wang Min , Xin Ni , Qi Rui , Wang Hui
Published: June 2024

In the study of environmental DNA (eDNA), the rate of water filtration and the amount of DNA obtained are of general interest to researchers. We compared the PCTE filters with different pore sizes in enriching total DNA and fish eDNA from water samples. We also designed and tested a new filter device with a PET pad (5 µm) superimposed on a PCTE membrane (3 µm) and compared it to a pure PCTE filter. A comprehensive evaluation of filtration time, eDNA concentration, fish DNA quantification, and fish species detected showed that the shortest average filtration time was obtained with the 8 μm pore size (2 min 9 s) and the longest average filtration time was obtained with the 0.2 μm pore size (32 min 6 s). The highest average DNA concentration was 3.785 ng/μL for the 0.2 μm filter and the lowest was 0.577 ng/μL for the 8 μm filter; meanwhile, the concentrations of fish DNA measured by quantitative PCR were 5.02E+02(8 μm), 4.79E+02(3 μm), 1.63E+03(1.2 μm), 5.95E+03(0.2 μm) copies of fish DNA per µl and there was no significant difference in the results between them (p > 0.05). The sequencing results showed that 17 fish species were detected in the 0.2 μm filter, 10 species in the 1.2 μm filter, 12 species in the 3 μm filter and 11 species in the 8 μm filter. Comparing to 3 μm and 0.2 um, the average filtration time in stacked-filter was reduced by 4 and 24 min, respectively, while the average concentration was 2.46 and 1.55 times higher than the former. The qPCR results showed that the number of eDNA copies of the samples enriched with the 3 µm and stacked-filter was 4.79E+02 and 1.53E+04, respectively. 3 μm and stacked-filter showed significant differences (p < 0.05), while 0.2 µm and stacked-filter did not show significant differences (p > 0.05). Sixteen fish species were detected by the stacked-filter. The number of eDNA obtained and the number of fish species detected were higher than those of the pure PCTE filter, while clogging during filtration was effectively avoided. We recommend using the stacked-filter to enrich eDNA from water samples.
Ehmt2 inactivation in pancreatic epithelial cells shapes the transcriptional landscape and inflammation response of the whole pancreas
Authors: Pollin Gareth , Mathison Angela J. , de Assuncao Thiago M. , Thomas Anju , Zeighami Atefeh , Salmonson Ann , Liu Hongfei , Urrutia Guillermo , Vankayala Pallavi , Pandol Stephen J. , Hong Johnny C. , Zimmermann Michael T. , Iovanna Juan , Jin Victor X. , Urrutia Raul , Lomberk Gwen
Published: June 2024

Introduction: The Euchromatic Histone Methyl Transferase Protein 2 (EHMT2), also known as G9a, deposits transcriptionally repressive chromatin marks that play pivotal roles in the maturation and homeostasis of multiple organs. Recently, we have shown that Ehmt2 inactivation in the mouse pancreas alters growth and immune gene expression networks, antagonizing Kras-mediated pancreatic cancer initiation and promotion. Here, we elucidate the essential role of Ehmt2 in maintaining a transcriptional landscape that protects organs from inflammation.

Methods: Comparative RNA-seq studies between normal postnatal and young adult pancreatic tissue from Ehmt2 conditional knockout animals (Ehmt2fl/fl) targeted to the exocrine pancreatic epithelial cells (Pdx1-Cre and P48Cre/+), reveal alterations in gene expression networks in the whole organ related to injury-inflammation-repair, suggesting an increased predisposition to damage. Thus, we induced an inflammation repair response in the Ehmt2fl/fl pancreas and used a data science-based approach to integrate RNA-seq-derived pathways and networks, deconvolution digital cytology, and spatial transcriptomics. We also analyzed the tissue response to damage at the morphological, biochemical, and molecular pathology levels.

Results and discussion: The Ehmt2fl/fl pancreas displays an enhanced injury-inflammation-repair response, offering insights into fundamental molecular and cellular mechanisms involved in this process. More importantly, these data show that conditional Ehmt2 inactivation in exocrine cells reprograms the local environment to recruit mesenchymal and immunological cells needed to mount an increased inflammatory response. Mechanistically, this response is an enhanced injury-inflammation-repair reaction with a small contribution of specific Ehmt2-regulated transcripts. Thus, this new knowledge extends the mechanisms underlying the role of the Ehmt2-mediated pathway in suppressing pancreatic cancer initiation and modulating inflammatory pancreatic diseases.
Dual immunotherapy alternating with anti-PD-1 antibody plus liposomal doxorubicin show good efficacy in prostate epithelioid hemangioendothelioma: a case report
Authors: Zhang Jie , Ye Qin , Yang Xudan , Li Tenglong , Huang Shan , Zhou Ping , Feng Yumei , Liu Hao , Xie Ke
Published: June 2024

Epithelioid hemangioendothelioma is a rare vascular malignancy, and currently, there is no standard treatment regimen for this disease and existing treatment options have limited efficacy. In this case report, we present a patient with lung and lymph node metastases from prostate epithelioid hemangioendothelioma who achieved a significant partial response. This was accomplished through alternating nivolumab therapy with ipilimumab and liposomal doxorubicin, resulting in a progression-free-survival more than 6 months to date. The treatment was well-tolerated throughout. Our report suggests that dual immunotherapy alternating with anti-PD-1antibody plus doxorubicin may be a potential treatment modality for epithelioid hemangioendothelioma. However, larger sample studies are necessary to ascertain the effectiveness of this treatment strategy and it is essential to continue monitoring this patient to sustain progression-free survival and overall survival.
Identification of functional enhancer variants associated with type I diabetes in CD4+ T cells
Authors: Mishra Arpit , Jajodia Ajay , Weston Eryn , Jayavelu Naresh Doni , Garcia Mariana , Hossack Daniel , Hawkins R. David
Published: June 2024

Type I diabetes is an autoimmune disease mediated by T-cell destruction of β cells in pancreatic islets. Currently, there is no known cure, and treatment consists of daily insulin injections. Genome-wide association studies and twin studies have indicated a strong genetic heritability for type I diabetes and implicated several genes. As most strongly associated variants are noncoding, there is still a lack of identification of functional and, therefore, likely causal variants. Given that many of these genetic variants reside in enhancer elements, we have tested 121 CD4+ T-cell enhancer variants associated with T1D. We found four to be functional through massively parallel reporter assays. Three of the enhancer variants weaken activity, while the fourth strengthens activity. We link these to their cognate genes using 3D genome architecture or eQTL data and validate them using CRISPR editing. Validated target genes include CLEC16A and SOCS1. While these genes have been previously implicated in type 1 diabetes and other autoimmune diseases, we show that enhancers controlling their expression harbor functional variants. These variants, therefore, may act as causal type 1 diabetic variants.
Molecular mimicry of SARS-COV-2 antigens as a possible natural anti-cancer preventive immunization
Authors: Ragone Concetta , Mauriello Angela , Cavalluzzo Beatrice , Cavalcanti Ernesta , Russo Luigi , Manolio Carmen , Mangano Simona , Cembrola Biancamaria , Tagliamonte Maria , Buonaguro Luigi
Published: June 2024

Background

In the present study we investigated whether peptides derived from the entire SARS-CoV-2 proteome share homology to TAAs (tumor-associated antigens) and cross-reactive CD8+ T cell can be elicited by the BNT162b2 preventive vaccine or the SARS-CoV-2 natural infection.

Methods and results

Viral epitopes with high affinity (<100nM) to the HLA-A*02:01 allele were predicted. Shared and variant-specific epitopes were identified. Significant homologies in amino acidic sequence have been found between SARS-CoV-2 peptides and multiple TAAs, mainly associated with breast, liver, melanoma and colon cancers. The molecular mimicry of the viral epitopes and the TAAs was found in all viral proteins, mostly the Orf 1ab and the Spike, which is included in the BNT162b2 vaccine. Predicted structural similarities confirmed the sequence homology and comparable patterns of contact with both HLA and TCR α and β chains were observed. CD8+ T cell clones cross-reactive with the paired peptides have been found by MHC class l-dextramer staining.

Conclusions

Our results show for the first time that several SARS-COV-2 antigens are highly homologous to TAAs and cross-reactive T cells are identified in infected and BNT162b2 preventive vaccinated individuals. The implication would be that the SARS-Cov-2 pandemic could represent a natural preventive immunization for breast, liver, melanoma and colon cancers. In the coming years, real-world evidences will provide the final proof for such immunological experimental evidence. Moreover, such SARS-CoV-2 epitopes can be used to develop “multi-cancer” off-the-shelf preventive/therapeutic vaccine formulations, with higher antigenicity and immunogenicity than over-expressed tumor self-antigens, for the potential valuable benefit of thousands of cancer patients around the World.
Unraveling gene regulation mechanisms in fish: insights into multistress responses and mitigation through iron nanoparticles
Authors: Kumar Neeraj , Thorat Supriya Tukaram , Gunaware Meghana Ajit , Kumar Paritosh , Reddy Kotha Sammi
Published: June 2024

The recent trend of global warming poses a significant threat to ecosystems worldwide. This global climate change has also impacted the pollution levels in aquatic ecosystems, subsequently affecting human health. To address these issues, an experiment was conducted to investigate the mitigating effects of iron nanoparticles (Fe-NPs) on arsenic and ammonia toxicity as well as high temperature stress (As+NH3+T). Fe-NPs were biologically synthesized using fish waste and incorporated into feed formulations at 10, 15, and 20 mg kg-1 diet. A total of 12 treatments were designed in triplicate following a completely randomized design involving 540 fish. Fe-NPs at 15 mg kg-1 diet notably reduced the cortisol levels in fish exposed to multiple stressors. The gene expressions of HSP 70, DNA damage-inducible protein (DDIP), and DNA damage were upregulated by stressors (As+NH3+T) and downregulated by Fe-NPs. Apoptotic genes (Cas 3a and 3b) and detoxifying genes (CYP 450), metallothionein (MT), and inducible nitric oxide synthase (iNOS) were downregulated by Fe-NPs at 15 mg kg-1 diet in fish subjected to As+NH3+T stress. Immune-related genes such as tumor necrosis factor (TNFα), immunoglobulin (Ig), and interleukin (IL) were upregulated by Fe-NPs, indicating enhanced immunity in fish under As+NH3+T stress. Conversely, Toll-like receptor (TLR) expression was notably downregulated by Fe-NPs at 15 mg kg-1 diet in fish under As+NH3+T stress. Immunological attributes such as nitro blue tetrazolium chloride, total protein, albumin, globulin, A:G ratio, and myeloperoxidase (MPO) were improved by dietary Fe-NPs at 15 mg kg-1 diet in fish, regardless of stressors. The antioxidant genes (CAT, SOD, and GPx) were also strengthened by Fe-NPs in fish. Genes associated with growth performance, such as growth hormone regulator (GHR1 and GHRβ), growth hormone (GH), and insulin-like growth factor (IGF 1X and IGF 2X), were upregulated, enhancing fish growth under stress, while SMT and MYST were downregulated by Fe-NPs in the diet. Various growth performance indicators were improved by dietary Fe-NPs at 15 mg kg-1 diet. Notably, Fe-NPs also enhanced arsenic detoxification and reduced the cumulative mortality after a bacterial infection. In conclusion, this study highlights that dietary Fe-NPs can effectively mitigate arsenic and ammonia toxicity as well as high temperature stress by modulating gene expression in fish.
C-reactive protein: structure, function, regulation, and role in clinical diseases
Authors: Zhou Hai-Hong , Tang Yu-Long , Xu Tian-Hao , Cheng Bin
Published: June 2024

C-reactive protein (CRP) is a plasma protein that is evolutionarily conserved, found in both vertebrates and many invertebrates. It is a member of the pentraxin superfamily, characterized by its pentameric structure and calcium-dependent binding to ligands like phosphocholine (PC). In humans and various other species, the plasma concentration of this protein is markedly elevated during inflammatory conditions, establishing it as a prototypical acute phase protein that plays a role in innate immune responses. This feature can also be used clinically to evaluate the severity of inflammation in the organism. Human CRP (huCRP) can exhibit contrasting biological functions due to conformational transitions, while CRP in various species retains conserved protective functions in vivo. The focus of this review will be on the structural traits of CRP, the regulation of its expression, activate complement, and its function in related diseases in vivo.
Investigation of AA6063-based metal–matrix composites reinforced with TiO2 dispersoids through digitally assisted techniques for mechanical, tribological, and microstructural characterizations
Authors: Pattar Jagannath , Ramesh Dasappa , Malghan Rashmi Laxmikant , Kumar Ajay , Kumar Pawan , H. M. Vishwanatha
Published: June 2024

Aluminum metal–matrix composites (AMMCs) were prepared by dispersing TiO2 dispersoids of different volume fractions into an AA6063 matrix via stir casting and subjected to process–structure correlation studies. Four different samples based on weight ratio were considered herein: 99Al-1TiO2, 97Al-3TiO2, 95Al-5TiO2, and the as-received AA6063. Their mechanical properties namely, microhardness, tensile strength, and tribological behavior, were determined. In addition, the microstructure of the samples was also analysed. It was observed that the addition of 5% TiO2 particles enabled the AA6063 matrix to accommodate a higher strain energy while providing the required driving force to generate dislocations and substructures. Therefore, considering the plastic deformation, the ultimate tensile strength σut increased gradually with the addition of TiO2 (in weight%). The flow curves of the 95Al-5TiO2 sample showed the highest value of σut, whereas the as-received AA6063 matrix exhibited the lowest value. For linear elastic deformation, AA6063 showed the lowest yield strength (σys) as compared to the AMMC samples for all TiO2 weight% values; however, the variation in σys among the AMMC samples was minimal. The microhardness of the samples increased gradually with the addition of TiO2, and the percentage reduction in area at the fracture was largest for 95Al-5TiO2. The Taguchi’s L9 array and variance analysis of the process parameters indicated that the material wear was largely affected by the normal load, followed by weight% of TiO2 and sliding speed. Wear surface characteristics, such as microvoids, delamination, microcracks, and wear debris, were qualitatively observed in all the AMMC samples. The overall strength improvement was attributable to the effects of addition of the dispersoids. During melt solidification, the TiO2 particles surpassed/pinned and hindered the grain growth, resulting in grain-size refinement.
Bacterial and fungal communities regulated directly and indirectly by tobacco-rape rotation promote tobacco production
Authors: Liu Lu , Miao Qi , Guo Yingxin , Wang Chen , Sun Junwei , Fan Zhiyong , Wang Dexun , Hu Yanxia , Li Junying , Cui Zhenling
Published: June 2024

Tobacco continuous cropping is prevalent in intensive tobacco agriculture but often leads to microbial community imbalance, soil nutrient deficiency, and decreased crop productivity. While the tobacco-rape rotation has demonstrated significant benefits in increasing tobacco yield. Microorganisms play a crucial role in soil nutrient cycling and crop productivity. However, the internal mechanism of tobacco-rape rotation affecting tobacco yield through microbe-soil interaction is still unclear. In this study, two treatments, tobacco continuous cropping (TC) and tobacco-rape rotation (TR) were used to investigate how planting systems affect soil microbial diversity and community structure, and whether these changes subsequently affect crop yields. The results showed that compared with TC, TR significantly increased the Shannon index, Chao1 index, ACE index of bacteria and fungi, indicating increased microbial α-diversity. On the one hand, TR may directly affect the bacterial and fungal community structure due to the specificity of root morphology and root exudates in rape. Compared with TC, TR significantly increased the proportion of beneficial bacterial and fungal taxa while significantly reduced soil-borne pathogens. Additionally, TR enhanced the scale and complexity of microbial co-occurrence networks, promoting potential synergies between bacterial OTUs. On the other hand, TR indirectly changed microbial community composition by improving soil chemical properties and changing microbial life history strategies. Compared with TC, TR significantly increased the relative abundance of copiotrophs while reduced oligotrophs. Notably, TR significantly increased tobacco yield by 39.6% compared with TC. The relationships among yield, microbial community and soil chemical properties indicated that planting systems had the greatest total effect on tobacco yield, and the microbial community, particularly bacteria, had the greatest direct effect on tobacco yield. Our findings highlighted the potential of tobacco-rape rotation to increase yield by both directly and indirectly optimizing microbial community structure.
Molecular epidemiology, genetic diversity, antibiotic resistance and pathogenicity of Stenotrophomonas maltophilia complex from bacteremia patients in a tertiary hospital in China for nine years
Authors: Wang Lifeng , Wang Yu , Ye Kun , Qiu Xuemei , Zhao Qiang , Ye LiYan , Yang Jiyong
Published: June 2024

Background

The Stenotrophomonas maltophilia complex (Smc) has emerged as a significant nosocomial pathogen contributing to increased mortality rates, particularly in case of bloodstream infections.

Methods

This study employed whole-genome sequencing (WGS) to assess the genetic diversity, antimicrobial resistance profiles, molecular epidemiology and frequencies of virulence genes among 55 S. maltophilia isolates obtained from bacteremic cases over a 9-year period.

Results

Based on the threshold of 95% average nucleotide identity (ANI) and 70% digital DNA–DNA hybridization (dDDH) for genospecies delineation, we classified 37 isolates into 6 known species, all belonging to the Smc. The remaining 18 isolates sequenced in this study were assigned to 6 new genomospecies. Among the 55 isolates, we identified 44 different sequence types (STs), comprising 22 known and 22 novel allele combinations. The resistance rate of Smc against trimethoprim-sulfamethoxazole (TMP/SMX) was found to be 3.6%, with the sul1 and class one integron integrase genes (intI) detected in these isolates. All Smc isolates were susceptible to minocycline. Furthermore, all Smc strains harbored the motA, pilU, smf-1 and Stmpr2 genes. Genomospecies 1 (100%, n = 9), Stenotrophomonas maltophilia (84.21%, n = 19) and Stenotrophomonas sepilia (71.43%, n = 7) demonstrated a higher percentage of the afaD gene, which was also associated with a higher separation rate. In addition to motA, pilU, smf-1, and Stmpr2 genes, all S. maltophilia strains (100%) contained entA, gspD, KatA, and stmPr1 genes, while all genomospecies 1 strains (100%) contained afaD, entA, gspD, and KatA genes.

Conclusion

Our study highlights the genetic diversity among Smc isolates from patients with bacteremia, revealing 22 novel ST types, 58 new alleles and 6 new genomospecies. S. maltophilia and S. pavanii were found to carry more virulence factors, emphasizing the importance of accurate strain identification. Minocycline emerged as a promising alternative antibiotic for patients who were resistant to TMP/SMX.
Effect of preconception multiple micronutrients vs. iron–folic acid supplementation on maternal and birth outcomes among women from developing countries: a systematic review and meta-analysis
Authors: Das Rashmi Ranjan , Sankar Jhuma , Jaiswal Nishant , Dwibedi Bhagirathi , Satapathy Amit Kumar , Pradhan Pranita , Sahu Prajyoti
Published: June 2024

Background

Maternal malnutrition affects the somatic growth of the fetus and subsequent adverse events during infancy and childhood period. Though trials have been conducted on multiple micronutrient (MMN) supplements initiated during the preconception period, there is no collated evidence on this.

Materials and methods

We performed a systematic review of published trials with the application of Grading of Recommendations Assessment, Development, and Evaluation (GRADE). The searches were conducted until 30 September 2023. Meta-analysis was performed using Review Manager 5 software. The primary objective was to compare the effect of preconception MMN vs. iron–folic acid (IFA) supplementation on newborn anthropometric parameters at birth.

Results

Of the 11,832 total citations retrieved, 12 studies with data from 11,391 participants [Intervention = 5,767; Control = 5,624] were included. For the primary outcome, there was no significant difference in the birth weight [MD, 35.61 (95% CI, −7.83 to 79.06), p = 0.11], birth length [MD, 0.19 (95% CI, −0.03 to 0.42), p = 0.09], and head circumference [MD, −0.25 (95% CI, −0.64 to −0.14), p = 0.22] between the MMN and control groups. For all the secondary outcomes [except for small for gestational age (SGA) and low birth weight (LBW)], the difference between the MMN and control groups was not significant. The GRADE evidence generated for all the outcomes varied from “very low to moderate certainty.”

Conclusion

A “very low certainty” of evidence suggests that MMN supplementation may not be better than routine IFA supplementation in improving newborn anthropometric parameters (weight, length, and head circumference). The adverse events resulting from the supplementation were not significant. We need better quality uniformly designed RCTs before any firm recommendation can be made.

Systematic review registration: identifier (CRD42019144878: https://www.crd.york.ac.uk/prospero/#searchadvanced).
Causal associations between the gut microbiota and multiple myeloma: a two-sample Mendelian randomization study
Authors: Zhang Chun-Yan , Zhang Dong , Sun Wen-Rui , Tang Hai-Long , Tian Biao , Hu Li-Hong , Hu Wu-Yue , Gao Ya-Ya , Li Miao-Yu , Xiao Wan-Ting , Gao Shan , Gao Guang-Xun
Published: June 2024

Background

Previous observational studies have indicated a potential association between the gut microbiota and multiple myeloma (MM). However, the relationship between the gut microbiota and MM remains unclear. This study aimed to ascertain the existence of a causal link between the gut microbiota and MM.

Methods

To investigate the potential causal relationship between gut microbiota and MM, a two-sample Mendelian randomization (MR) analysis was conducted. Exposure data was obtained from the MiBioGen consortium, which provided genetic variants associated with 211 bacterial traits. MM outcome data was obtained from the FinnGen consortium. The selection of Single nucleotide polymorphisms estimates was performed through meta-analysis using inverse-variance weighting, and sensitivity analyses were conducted using weighted median, MR Egger, Simple mode, and MR-PRESSO.

Results

The results of the study demonstrated a significant positive correlation between the genus Eubacterium ruminantium group and the risk of MM (OR 1.71, 95% CI 1.21 to 2.39). Conversely, the genus: Dorea (OR 0.46, 95% CI 0.24 to 0.86), Coprococcus1 (OR 0.47, 95% CI 0.22 to 1.00), RuminococcaceaeUCG014 (OR 0.57, 95% CI 0.33 to 0.99), Eubacterium rectale group (OR 0.37, 95% CI 0.18 to 0.77), and order: Victivallales (OR 0.62, 95% CI 0.41–0.94), class: Lentisphaeria (OR 0.62, 95% CI 0.41 to 0.94), exhibited a negative association with MM. The inverse variance weighting analysis provided additional support for these findings.

Conclusion

This study represents an inaugural exploration of MR to investigate the connections between gut microbiota and MM, thereby suggesting potential significance for the prevention and treatment of MM.
Improvement and application of recommended food score for hypertension in Korean adults: the Korean Genome and Epidemiology Study
Authors: Hwang Jiyoung , Kim Jeongsu , Kim Hyesook
Published: June 2024

Background

Addressing dietary factors to lower blood pressure can be a crucial strategy at the population level to mitigate the risk of hypertension. In a prior investigation, a tailored food score was used as a dietary index relevant to hypertension among Korean adults. This current study aims to assess the association between the overall quality of the diet, taking into account more precise food components, and evaluate the risk of developing hypertension.

Methods

This prospective cohort study included 5,342 adults aged 40–70 without hypertension who participated in the Korean Genome and Epidemiology Study (KoGES) from 2001 to 2016. The improved Recommended Food Score for Hypertension (iRFSH) is a modified version of the Recommended Food Score to assess the consumption of foods recommended in the Dietary Approaches to Stop Hypertension (DASH) diet for Korean foods. A higher score reflects greater consumption of recommended foods, indicative of higher dietary quality. The maximum total score is 65. High blood pressure, which includes both hypertension and prehypertension, was analyzed using Cox proportional hazard regression models to examine its prospective relationship with iRFSH.

Results

Among 2,478 males and 2,864 females with 10.8 mean years of follow-up, a higher score of iRFSH was associated with a lower risk of hypertension in the highest quintile compared to the lowest quintile [total: hazard ratio (HR): 0.79; 95% confidence interval (CI): 0.72, 0.87; female: HR: 0.71; 95% CI: 0.62, 0.83].

Conclusion

Higher iRFSH is associated with a lower incidence of hypertension. Our results suggest that the iRFSH may be a potential tool for assessing dietary quality and dietary patterns and predicting the risk of hypertension in Korean adults.
Association between dietary protein intake and risk of chronic kidney disease: a systematic review and meta-analysis
Authors: Cheng Yu , Zheng Guanghao , Song Zhen , Zhang Gan , Rao Xuepeng , Zeng Tao
Published: June 2024

Objective

There is suggestive data indicating a correlation among dietary protein intake and the progression of chronic kidney disease (CKD). Nonetheless, the exact associations between dietary protein intake and the incidence of CKD have remained uncertain. We performed the first meta-analysis to explore the correlation among total protein, plant protein, animal protein intake and CKD risk.

Methods

The study conformed the PRISMA statement guidelines. We comprehensively searched PubMed, Web of Science, and Embase until to December 2023. The retrieved studies underwent rigorous evaluation for eligibility, and relevant data were meticulously extracted. The Newcastle-Ottawa Scale (NOS) tool was applied to evaluate the risk of bias. Subsequently, relevant data were extracted and pooled to evaluate the relations among dietary protein intake and CKD incidence.

Results

Totally, 6,191 articles were identified, six studies were eligible. A total of 148,051 participants with 8,746 CKD cases were included. All studies had a low overall risk of bias. Higher total, plant and animal protein intake were all correlated with decreased CKD incidence, pooled risk ratios (RRs) and 95% confidence intervals (CIs) were as follows: (RR = 0.82, 95% CI = 0.71–0.94, p = 0.005; I2 = 38%, p = 0.17); (RR = 0.77, 95% CI = 0.61–0.97, p = 0.03; I2 = 77%, p = 0.001); (RR = 0.86, 95% CI = 0.76–0.97, p = 0.02; I2 = 0%, p = 0.59), respectively. For fish and seafood within animal protein: RR = 0.84, 95% CI = 0.74–0.94. Subgroup analysis showed that geographical region, sample size, follow-up time, not assessing protein by food frequency questionnaire, using %energy as the measurement index, not adjusting for several covariates may be the sources of heterogeneity for plant protein. A significant non-linear relation among plant protein and incident CKD was observed by dose–response analysis.

Conclusion

The data showed a lower CKD risk significantly associated higher-level dietary total, plant or animal protein (especially for fish and seafood) intake. Further prospective studies demonstrating the correlations of precise sources, intake and duration of dietary protein and incident CKD are warranted.
Prognostic and clinicopathological significance of systemic immune-inflammation index in upper tract urothelial carcinoma: a meta-analysis of 3911 patients
Authors: Yu Ziyi , Xiong Zhencheng , Ma Jinchao , Du Peng , Wang Shuo , Liu Jia , Cao Yudong , Yang Yong
Published: June 2024

Background

Systemic immune-inflammation index (SII), a novel prognostic indicator, is being more commonly utilized in different types of cancer. This research project involved combining information from previously published studies to examine how pre-treatment SII can predict outcomes in individuals with upper tract urothelial carcinoma (UTUC). Further examination of the correlation between SII and clinical and pathological features in UTUC.

Methods

We thoroughly chose pertinent articles from various databases including PubMed, Embase, Cochrane Library, Web of Science, Chinese National Knowledge Infrastructure (CNKI), WanFang database, and Chinese Scientific Journal Database (VIP) until March 10, 2022.The data collected was analyzed using Stata 17.0 software (Stat Corp, College Station, TX). Subsequently, the impact of SII on the survival outcomes of UTUC patients was evaluated by combining HRs with 95% confidence intervals.

Results

Six included studies were finally confirmed, including 3911 UTUC patients in seven cohorts. The results showed that high SII before treatment predicted poor overall survival (HR =1.87, 95%CI 1.20-2.92, p=0.005), cancer specific survival (HR=2.70, 95%CI 1.47-4.96, P=0.001), and recurrence‐free survival (HR =1.52, 95%CI 1.12-2.07, P=0.007). And the elevated SII may be related to LVI (present vs. absent) (OR=0.83, 95% CI=0.71-0.97, p=0.018), pT stage (pT ≥3 vs. < 3) (OR=1.82, 95% CI=1.21-2.72, p=0.004), and pN stage (N+ vs. N0) (OR=3.27, 95% CI=1.60-6.71, p=0.001).

Conclusion

A comprehensive analysis of all included articles in this study showed that higher pretreatment SII was related to poorer survival outcomes and adverse pathological features independently.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier CRD42022316333.
Construction of a predictive model for postoperative hospitalization time in colorectal cancer patients based on interpretable machine learning algorithm: a prospective preliminary study
Authors: Wen Zhongjian , Wang Yiren , Chen Shouying , Li Yunfei , Deng Hairui , Pang Haowen , Guo Shengmin , Zhou Ping , Zhu Shiqin
Published: June 2024

Objective

This study aims to construct a predictive model based on machine learning algorithms to assess the risk of prolonged hospital stays post-surgery for colorectal cancer patients and to analyze preoperative and postoperative factors associated with extended hospitalization.

Methods

We prospectively collected clinical data from 83 colorectal cancer patients. The study included 40 variables (comprising 39 predictor variables and 1 target variable). Important variables were identified through variable selection via the Lasso regression algorithm, and predictive models were constructed using ten machine learning models, including Logistic Regression, Decision Tree, Random Forest, Support Vector Machine, Light Gradient Boosting Machine, KNN, and Extreme Gradient Boosting, Categorical Boosting, Artificial Neural Network and Deep Forest. The model performance was evaluated using Bootstrap ROC curves and calibration curves, with the optimal model selected and further interpreted using the SHAP explainability algorithm.

Results

Ten significantly correlated important variables were identified through Lasso regression, validated by 1000 Bootstrap resamplings, and represented through Bootstrap ROC curves. The Logistic Regression model achieved the highest AUC (AUC=0.99, 95% CI=0.97–0.99). The explainable machine learning algorithm revealed that the distance walked on the third day post-surgery was the most important variable for the LR model.

Conclusion

This study successfully constructed a model predicting postoperative hospital stay duration using patients’ clinical data. This model promises to provide healthcare professionals with a more precise prediction tool in clinical practice, offering a basis for personalized nursing interventions, thereby improving patient prognosis and quality of life and enhancing the efficiency of medical resource utilization.
Risk of immune system and skin and subcutaneous tissue related adverse events associated with oxaliplatin combined with immune checkpoint inhibitors: a pharmacovigilance study
Authors: Zhang Chunhong , Li Furong , Dai Ying , Zeng Yifan , Yu Xuben , Shi Dawei
Published: June 2024

Background

Few studies have analysed oxaliplatin-induced adverse events (ADEs) in the immune system and skin and subcutaneous tissues through pharmacovigilance. We used this approach to analyse the risk of such ADEs when oxaliplatin combined with immune checkpoint inhibitors (ICIs).

Methods

We evaluated the association between oxaliplatin and ADEs in the immune system and skin and subcutaneous tissues using the reporting odd ratio (ROR) for mining the ADE report signals in the FDA Adverse Event Reporting System database. Risk factors were analyzed using a binary logistic regression analysis using the sex and age of the patients.

Results

There were 40,474 reports of oxaliplatin as primary suspect drug or second suspect drug. The signal intensities of ADEs such as type II hypersensitivity, type I hypersensitivity, type III immune complex–mediated reaction, anaphylactoid shock and cytokine release syndrome were high in PTs classified by SOC as immune system disorders; in the PTs classified as skin and subcutaneous tissue disorders by SOC, the signal intensities of ADEs such as skin toxicity, skin reaction, rash maculo-papular and skin fissures were higher. In the risk assessment between the two groups, rash showed an increased risk in the oxaliplatin-ICI group, with an OR of 1.96. Nivolumab in combination with oxaliplatin had an OR of 2.196 and an adjusted OR of 2.231. Combined with pembrolizumab, OR was 2.762 and the adjusted OR was 2.678.

Conclusion

Type II hypersensitivity shows a stronger pharmacovigilance signal. Oxaliplatin in combination with nivolumab or pembrolizumab has been shown to increase the risk of rash.
Understanding copy number variations through their genes: a molecular view on 16p11.2 deletion and duplication syndromes
Authors: Leone Roberta , Zuglian Cecilia , Brambilla Riccardo , Morella Ilaria
Published: June 2024

Neurodevelopmental disorders (NDDs) include a broad spectrum of pathological conditions that affect >4% of children worldwide, share common features and present a variegated genetic origin. They include clinically defined diseases, such as autism spectrum disorders (ASD), attention-deficit/hyperactivity disorder (ADHD), motor disorders such as Tics and Tourette’s syndromes, but also much more heterogeneous conditions like intellectual disability (ID) and epilepsy. Schizophrenia (SCZ) has also recently been proposed to belong to NDDs. Relatively common causes of NDDs are copy number variations (CNVs), characterised by the gain or the loss of a portion of a chromosome. In this review, we focus on deletions and duplications at the 16p11.2 chromosomal region, associated with NDDs, ID, ASD but also epilepsy and SCZ. Some of the core phenotypes presented by human carriers could be recapitulated in animal and cellular models, which also highlighted prominent neurophysiological and signalling alterations underpinning 16p11.2 CNVs-associated phenotypes. In this review, we also provide an overview of the genes within the 16p11.2 locus, including those with partially known or unknown function as well as non-coding RNAs. A particularly interesting interplay was observed between MVP and MAPK3 in modulating some of the pathological phenotypes associated with the 16p11.2 deletion. Elucidating their role in intracellular signalling and their functional links will be a key step to devise novel therapeutic strategies for 16p11.2 CNVs-related syndromes.