bluuebunny/crossref_metadata_2025 huggingface dataset:
BIOLOGICAL AND ECONOMICALLY USEFUL FEATURES OF RED TOP VARIETIES CHARA AND ALBA
Authors: Zolotarev Vladimir
Published: October 2023

From the genus bentgrass (Agrostis L.) red top (A. gigantea Roth.) is the most adaptive species. Red top varieties Chara and Alba have been created and registered in the State Register of Breeding Achievements Approved for Use in the territory of the Russian Federation in the Federal Scientific Center "VIK named after V.R. Williams". The varieties are characterized by high adaptive potential and unpretentiousness. They are characterized by competitiveness when cultivated in poly-species grass mixtures. In the conditions of the Central region of Russia, the Chara variety forms high yields of green mass in the mode of triple mowing, up to 47.2 t/ha, dry weight 12.1 t/ha, which is 25.4 and 38.3% higher than the standard. The yield of seeds of the Chara variety from grass stands of the first year of use is 400 kg/ha, which is 36.8% higher than the standard. The Alba variety is characterized by increased drought resistance. Designed for lawn and pasture use. In the conditions of the Central Chernozem region, the yield of green mass is 27.3–34.5 t/ha, seeds — depending on the year of use of the herbage, 412–194 kg/ha. When lawn varieties are used, the density of shoots in the herbage of the second year of life can reach 76.0 thousand pcs/m2. In conditions of sufficient moisture, with the observance of lawn care technology, a high density of shoots can be maintained for 6 years. The varieties are resistant to disease.
Avaliação de custos e rentabilidade do milho convencional no município de Nova Mutum – MT
Authors: Gonzaga Douglas de Araujo , Varnier João Paulo , Possamai Ana Cássia Silva , Franz Gabriela Maria
Published: October 2023

O estudo objetivou analisar e demonstrar os custos de produção e rentabilidade de milho convencional no período safrinha de 2017 no sistema de plantio direto em uma lavoura de Nova Mutum-MT. Os dados foram obtidos através de uma entrevista semiestruturada juntamente com o produtor, onde além de coletar os dados do processo de produção, foi realizado um acompanhamento do ciclo de produção. Os resultados alcançados mostraram que o cultivo do milho não possui um valor de lucratividade muito elevado, porém possui grande importância na economia do estado, tendo em vista que é um dos grãos mais exportado do país.
Desempenho agronômico da figueira Roxo de Valinhos submetida a diferentes épocas de poda, em Nova Xavantina
Authors: Euzébio Manuel , Lima Eliane Moreira
Published: October 2023

A figueira (Ficus carica L.) é conduzida pelo sistema de poda, o que mantém seu porte arbustivo, produzindo precocemente em ramos do ano. O objetivo deste trabalho foi avaliar o efeito de épocas de poda quanto ao potencial produtivo e a qualidade dos frutos da figueira Roxo de Valinhos, em Nova Xavantina, MT. O experimento foi realizado em delineamento inteiramente casualizado, com três tratamentos (épocas de poda) e dez repetições. As variáveis avaliadas foram: crescimento (comprimento de ramo em cm, diâmetro de ramo em mm e número de folhas), produção (número de frutos maduros por planta e produção por planta em kg pl-1) e qualidade (peso médio dos frutos em gramas, diâmetro longitudinal, equatorial e do ostíolo dos frutos em mm, pH, sólidos solúveis e acidez titulável). De acordo com os resultados, a poda de julho foi a mais efetiva para o crescimento e produção da figueira Roxo de Valinhos. Porém não houve diferença estatística entre as épocas de poda para a maioria dos atributos de qualidade avaliados, exceto para os sólidos solúveis totais, onde a poda de julho proporcionou maiores médias para essa característica. O mês de janeiro apresentou maior produção acumulada de figo em todas as épocas de poda.
RANCANG BANGUN SISTEM INFORMASI MANAJEMEN SPARE PART MENGGUNAKAN QR CODE DI PT SAT NUSAPERSADA TBK
Authors: Tukino Tukino
Published: October 2023

This study aims to describe the information system management of spare parts in PT Sat Nusapersada Tbk that has been applied and what problems have arisen and design a new system as a proposal of the problem of spare part management in PT Sat Nusapersada Tbk. To give an idea through the system design of the benefits of the system that makes it easy for users, the method used in this study is the waterfall. The results of this study indicate that the current system has the potential for errors in checking spare part stock data, reading the size of parts and also the slow management of stock data. With the new system design, it is expected to be able to control stock quickly, facilitate users in making reports, maximize business operations by using technology, and efficiently manage spare parts using qr code.
Calibration methods to fit parameters within complex biological models
Authors: Nanda Pariksheet , Kirschner Denise E.
Published: October 2023

Mathematical and computational models of biological systems are increasingly complex, typically comprised of hybrid multi-scale methods such as ordinary differential equations, partial differential equations, agent-based and rule-based models, etc. These mechanistic models concurrently simulate detail at resolutions of whole host, multi-organ, organ, tissue, cellular, molecular, and genomic dynamics. Lacking analytical and numerical methods, solving complex biological models requires iterative parameter sampling-based approaches to establish appropriate ranges of model parameters that capture corresponding experimental datasets. However, these models typically comprise large numbers of parameters and therefore large degrees of freedom. Thus, fitting these models to multiple experimental datasets over time and space presents significant challenges. In this work we undertake the task of reviewing, testing, and advancing calibration practices across models and dataset types to compare methodologies for model calibration. Evaluating the process of calibrating models includes weighing strengths and applicability of each approach as well as standardizing calibration methods. Our work compares the performance of our model agnostic Calibration Protocol (CaliPro) with approximate Bayesian computing (ABC) to highlight strengths, weaknesses, synergies, and differences among these methods. We also present next-generation updates to CaliPro. We explore several model implementations and suggest a decision tree for selecting calibration approaches to match dataset types and modeling constraints.
Quantitative and modularized CRISPR/dCas9-dCpf1 dual function system in Saccharomyces cerevisiae
Authors: Feng Qing , Ning Xiaoyu , Qin Lei , Li Jun , Li Chun
Published: October 2023

Introduction: Both CRISPR/dCas9 and CRISPR/dCpf1 genome editing systems have shown exciting promises in modulating yeast cell metabolic pathways. However, each system has its deficiencies to overcome. In this study, to achieve a compensatory effect, we successfully constructed a dual functional CRISPR activation/inhibition (CRISPRa/i) system based on Sp-dCas9 and Fn-dCpf1 proteins, along with their corresponding complementary RNAs.

Methods: We validated the high orthogonality and precise quantity targeting of selected yeast promoters. Various activating effector proteins (VP64, p65, Rta, and VP64-p65-Rta) and inhibiting effector proteins (KRAB, MeCP2, and KRAB-MeCP2), along with RNA scaffolds of MS2, PP7 and crRNA arrays were implemented in different combinations to investigate quantitative promoter strength. In the CRISPR/dCas9 system, the regulation rate ranged from 81.9% suppression to 627% activation in the mCherry gene reporter system. Studies on crRNA point mutations and crRNA arrays were conducted in the CRISPR/dCpf1 system, with the highest transcriptional inhibitory rate reaching up to 530% higher than the control. Furthermore, the orthogonal CRISPR/dCas9-dCpf1 inhibition system displayed distinct dual functions, simultaneously regulating the mCherry gene by dCas9/gRNA (54.6% efficiency) and eGFP gene by dCpf1/crRNA (62.4% efficiency) without signal crosstalk.

Results and discussion: Finally, we established an engineered yeast cell factory for β-carotene production using the CRISPR/dCas9-dCpf1 bifunctional system to achieve targeted modulation of both heterologous and endogenous metabolic pathways in Saccharomyces cerevisiae. The system includes an activation module of CRISPRa/dCas9 corresponding to a gRNA-protein complex library of 136 plasmids, and an inhibition module of CRISPRi/dCpf1 corresponding to a small crRNA array library. Results show that this CRISPR/dCas9-dCpf1 bifunctional orthogonal system is more quantitatively effective and expandable for simultaneous CRISPRa/i network control compared to single-guide edition, demonstrating higher potential of future application in yeast biotechnology.
Expanding flavone and flavonol production capabilities in Escherichia coli
Authors: Yiakoumetti Andrew , Hanko Erik K. R. , Zou Yutong , Chua Jeremy , Chromy Jakub , Stoney Ruth A. , Valdehuesa Kris Niño G. , Connolly Jack A. , Yan Cunyu , Hollywood Katherine A. , Takano Eriko , Breitling Rainer
Published: October 2023

Flavones and flavonols are important classes of flavonoids with nutraceutical and pharmacological value, and their production by fermentation with recombinant microorganisms promises to be a scalable and economically favorable alternative to extraction from plant sources. Flavones and flavonols have been produced recombinantly in a number of microorganisms, withSaccharomyces cerevisiaetypically being a preferred production host for these compounds due to higher yields and titers of precursor compounds, as well as generally improved ability to functionally express cytochrome P450 enzymes without requiring modification to improve their solubility. Recently, a rapid prototyping platform has been developed for high-value compounds inE. coli, and a number of gatekeeper (2S)-flavanones, from which flavones and flavonols can be derived, have been produced to high titers inE. coliusing this platform. In this study, we extended these metabolic pathways using the previously reported platform to produce apigenin, chrysin, luteolin and kaempferol from the gatekeeper flavonoids naringenin, pinocembrin and eriodictyol by the expression of either type-I flavone synthases (FNS-I) or type-II flavone synthases (FNS-II) for flavone biosynthesis, and by the expression of flavanone 3-dioxygenases (F3H) and flavonol synthases (FLS) for the production of the flavonol kaempferol. In our best-performing strains, titers of apigenin and kaempferol reached 128 mg L−1and 151 mg L−1in 96-DeepWell plates in cultures supplemented with an additional 3 mM tyrosine, though titers for chrysin (6.8 mg L−1) from phenylalanine, and luteolin (5.0 mg L−1) from caffeic acid were considerably lower. In strains with upregulated tyrosine production, apigenin and kaempferol titers reached 80.2 mg L−1and 42.4 mg L−1respectively, without the further supplementation of tyrosine beyond the amount present in the rich medium. Notably, the highest apigenin, chrysin and luteolin titers were achieved with FNS-II enzymes, suggesting that cytochrome P450s can show competitive performance compared with non-cytochrome P450 enzymes in prokaryotes for the production of flavones.
Progressive insights into fibrosarcoma diagnosis and treatment: leveraging fusion genes for advancements
Authors: Tang Xiaodi , Hu Xin , Wen Yang , Min Li
Published: October 2023

Fibrosarcoma, originating from fibroblast cells, represents a malignant neoplasm that can manifest across all genders and age groups. Fusion genes are notably prevalent within the landscape of human cancers, particularly within the subtypes of fibrosarcoma, where they exert substantial driving forces in tumorigenesis. Many fusion genes underlie the pathogenic mechanisms triggering the onset of this disease. Moreover, a close association emerges between the spectrum of fusion gene types and the phenotypic expression of fibrosarcoma, endowing fusion genes not only as promising diagnostic indicators for fibrosarcoma but also as pivotal foundations for its subcategorization. Concurrently, an increasing number of chimeric proteins encoded by fusion genes have been substantiated as specific targets for treating fibrosarcoma, consequently significantly enhancing patient prognoses. This review comprehensively delineates the mechanisms behind fusion gene formation in fibrosarcoma, the lineage of fusion genes, methodologies employed in detecting fusion genes within fibrosarcoma, and the prospects of targeted therapeutic interventions driven by fusion genes within the fibrosarcoma domain.
Sound effect of transmitting specific emotions in music performance based on the acoustic properties of conjugated materials
Authors: Li Yangjingyi , Lee Fenghsu
Published: October 2023

In music performances, instruments made of traditional materials often cannot accurately express specific emotions through means such as tone, pitch, and timbre, and it is difficult to adjust the sound effects according to specific emotions. This article studies the impact of conjugated materials on the timbre, frequency response, etc. of musical instruments, hoping to achieve sound effects that better convey specific emotions. This article analyzes the acoustic properties of conjugated materials and applies them to musical performances. It is found that conjugated materials can provide a wider selection of tones, pitches and timbres, performers can choose appropriate tone, pitch, and timbre from conjugated materials to express emotions according to specific emotional needs, or adjust and transform the tone, pitch, and timbre for specific emotions, thereby arousing emotional resonance from the audience, so that specific emotions can be conveyed to the audience more accurately and powerfully. At the same time, this research also found that compared with an environment with poor sound insulation, the average sound absorption coefficient of metal materials in a room with good sound insulation increased by 6.5%, and the average sound absorption coefficient of conjugate materials increased by 25.4%, which shows that the increase in the average sound absorption coefficient of conjugate materials is much greater than that of metallic materials. The research shows that studying the sound effects of musical performances based on the acoustic properties of conjugated materials will help explore and develop more immersive and emotionally rich musical experiences.
Cardiac cellular diversity and functionality in cardiac repair by single-cell transcriptomics
Authors: Chen Wei , Li Chuling , Chen Yijin , Bin Jianping , Chen Yanmei
Published: October 2023

Cardiac repair after myocardial infarction (MI) is orchestrated by multiple intrinsic mechanisms in the heart. Identifying cardiac cell heterogeneity and its effect on processes that mediate the ischemic myocardium repair may be key to developing novel therapeutics for preventing heart failure. With the rapid advancement of single-cell transcriptomics, recent studies have uncovered novel cardiac cell populations, dynamics of cell type composition, and molecular signatures of MI-associated cells at the single-cell level. In this review, we summarized the main findings during cardiac repair by applying single-cell transcriptomics, including endogenous myocardial regeneration, myocardial fibrosis, angiogenesis, and the immune microenvironment. Finally, we also discussed the integrative analysis of spatial multi-omics transcriptomics and single-cell transcriptomics. This review provided a basis for future studies to further advance the mechanism and development of therapeutic approaches for cardiac repair.
An implementation analysis of a Cognitively Guided Instruction (CGI) teacher professional development program
Authors: Tazaz Amanda M. , Schoen Robert C.
Published: October 2023

Information about program implementation provides critical information for the interpretation of results from randomized trials. The present study provides an evaluation of the implementation of a Cognitively Guided Instruction mathematics teacher professional development as part of a large scale randomized controlled trial with teachers in first- and second- grade in eleven elementary schools in two adjacent school districts. We developed a measure of fidelity of implementation and used it during the in-person training sessions to determine the extent to which the training program was implemented as intended. The results from this study suggest that the program was implemented with high fidelity providing context for interpretation of overall program outcomes on teachers and students.
GNAS locus: bone related diseases and mouse models
Authors: Yang Wan , Zuo Yiyi , Zhang Nuo , Wang Kangning , Zhang Runze , Chen Ziyi , He Qing
Published: October 2023

GNASis a complex locus characterized by multiple transcripts and an imprinting effect. It orchestrates a variety of physiological processes via numerous signaling pathways. Human diseases associated with the GNAS gene encompass fibrous dysplasia (FD), Albright’s Hereditary Osteodystrophy (AHO), parathyroid hormone(PTH) resistance, and Progressive Osseous Heteroplasia (POH), among others. To facilitate the study of the GNAS locus and its associated diseases, researchers have developed a range of mouse models. In this review, we will systematically explore the GNAS locus, its related signaling pathways, the bone diseases associated with it, and the mouse models pertinent to these bone diseases.
GAS-STING: a classical DNA recognition pathways to tumor therapy
Authors: Wang Xinrui , Lin Meijia , Zhu Liping , Ye Zhoujie
Published: October 2023

Cyclic GMP-AMP synthetase (cGAS), recognized as the primary DNA sensor within cells, possesses the capability to identify foreign DNA molecules along with free DNA fragments. This identification process facilitates the production of type I IFNs through the activator of the interferon gene (STING) which induces the phosphorylation of downstream transcription factors. This action characterizes the most archetypal biological functionality of the cGAS-STING pathway. When treated with anti-tumor agents, cells experience DNA damage that triggers activation of the cGAS-STING pathway, culminating in the expression of type I IFNs and associated downstream interferon-stimulated genes. cGAS-STING is one of the important innate immune pathways,the role of type I IFNs in the articulation between innate immunity and T-cell antitumour immunity.type I IFNs promote the recruitment and activation of inflammatory cells (including NK cells) at the tumor site.Type I IFNs also can promote the activation and maturation of dendritic cel(DC), improve the antigen presentation of CD4+T lymphocytes, and enhance the cross-presentation of CD8+T lymphocytes to upregulating anti-tumor responses. This review discussed the cGAS-STING signaling and its mechanism and biological function in traditional tumor therapy and immunotherapy.
T cell biology in neuromuscular disorders: a focus on Duchenne Muscular Dystrophy and Amyotrophic Lateral Sclerosis
Authors: Lemos Julia Pereira , Tenório Liliane Patrícia Gonçalves , Mouly Vincent , Butler-Browne Gillian , Mendes-da-Cruz Daniella Arêas , Savino Wilson , Smeriglio Piera
Published: October 2023

Growing evidence demonstrates a continuous interaction between the immune system, the nerve and the muscle in neuromuscular disorders of different pathogenetic origins, such as Duchenne Muscular Dystrophy (DMD) and Amyotrophic Lateral Sclerosis (ALS), the focus of this review. Herein we highlight the complexity of the cellular and molecular interactions involving the immune system in neuromuscular disorders, as exemplified by DMD and ALS. We describe the distinct types of cell-mediated interactions, such as cytokine/chemokine production as well as cell-matrix and cell-cell interactions between T lymphocytes and other immune cells, which target cells of the muscular or nervous tissues. Most of these interactions occur independently of exogenous pathogens, through ligand-receptor binding and subsequent signal transduction cascades, at distinct levels of specificity. Although this issue reveals the complexity of the system, it can also be envisioned as a window of opportunity to design therapeutic strategies (including synthetic moieties, cell and gene therapy, as well as immunotherapy) by acting upon one or more targets. In this respect, we discuss ongoing clinical trials using VLA-4 inhibition in DMD, and in ALS, with a focus on regulatory T cells, both revealing promising results.
STAT1 deficiency underlies a proinflammatory imprint of naive CD4+ T cells in spondyloarthritis
Authors: Cherqaoui Bilade , Crémazy Frédéric , Lauraine Marc , Shammas Ghazal , Said-Nahal Roula , Mambu Mambueni Hendrick , Costantino Félicie , Fourmont Marine , Hulot Audrey , Garchon Henri-Jean , Glatigny Simon , Araujo Luiza M. , Breban Maxime
Published: October 2023

Introduction

In spondyloarthritis (SpA), an increased type 3 immune response, including T helper cells (Th) 17 excess, is observed in both human and SpA animal models, such as the HLA-B27/human β2-microglobulin transgenic rat (B27-rat).

Methods

To investigate this unexplained Th17-biased differentiation, we focused on understanding the immunobiology of B27-rat naive CD4+ T cells (Tn).

Results

We observed that neutrally stimulated B27-rat Tn developed heightened Th17 profile even before disease onset, suggesting an intrinsic proinflammatory predisposition. In parallel with this observation, transcriptomic and epigenomic analyses showed that B27-rat Tn exhibited a decreased expression of Interferon/Th1- and increased expression of Th17-related genes. This molecular signature was predicted to be related to an imbalance of STAT1/STAT3 transcription factors activity. Stat1 mRNA and STAT1 protein expression were decreased before disease onset in Tn, even in their thymic precursors, whereas Stat3/STAT3 expression increased upon disease establishment. Confirming the relevance of these results, STAT1 mRNA expression was also decreased in Tn from SpA patients, as compared with healthy controls and rheumatoid arthritis patients. Finally, stimulation of B27-rat Tn with a selective STAT1 activator abolished this preferential IL-17A expression, suggesting that STAT1-altered activity in B27-rats allows Th17 differentiation.

Discussion

Altogether, B27-rat Tn harbor a STAT1 deficiency preceding disease onset, which may occur during their thymic differentiation, secondarily associated with a persistent Th17 bias, which is imprinted at the epigenomic level. This early molecular phenomenon might lead to the persistent proinflammatory skew of CD4+ T cells in SpA patients, thus offering new clues to better understand and treat SpA.
It’s high-time to re-evaluate the value of induced-chemotherapy for reinforcing immunotherapy in colorectal cancer
Authors: Yao Shiya , Han Yuejun , Yang Mengxiang , Jin Ketao , Lan Huanrong
Published: October 2023

Immunotherapy has made significant advances in the treatment of colorectal cancer (CRC), revolutionizing the therapeutic landscape and highlighting the indispensable role of the tumor immune microenvironment. However, some CRCs have shown poor response to immunotherapy, prompting investigation into the underlying reasons. It has been discovered that certain chemotherapeutic agents possess immune-stimulatory properties, including the induction of immunogenic cell death (ICD), the generation and processing of non-mutated neoantigens (NM-neoAgs), and the B cell follicle-driven T cell response. Based on these findings, the concept of inducing chemotherapy has been introduced, and the combination of inducing chemotherapy and immunotherapy has become a standard treatment option for certain cancers. Clinical trials have confirmed the feasibility and safety of this approach in CRC, offering a promising method for improving the efficacy of immunotherapy. Nevertheless, there are still many challenges and difficulties ahead, and further research is required to optimize its use.
Causal relationship between spondylarthritis and stroke in a European population: a two sample Mendelian randomization study
Authors: Zhang Luofei , Yu Kefu , Huo Jiping , Mei Shenghui , Zhao Zhigang , Zhu Bin
Published: October 2023

Background

Observational studies have found an increased risk of stroke in patients with spondyloarthritis, but the results are susceptible to reverse causality and confounders. Therefore, the study aimed to further explore the association between spondyloarthritis and different subtypes of stroke by using a two sample Mendelian randomization (MR) analysis.

Methods

Genetic instrumental variables for spondyloarthritis were identified using summary level data from a genome-wide association study involving 201,581 people. Summary statistics from the Multiancestry Genome-wide Association Study of Stroke Consortium were used to obtain genetic data on stroke. There was no sample overlap between the exposure and outcome datasets. Inverse-variance weighted was considered the primary MR method for causal analysis. Heterogeneity, pleiotropy and sensitivity analyses were performed to ensure robustness, and single nucleotide polymorphism (SNP) with potential confounders was further screened in the PhenoScanner database to better evaluate the stability of our study.

Results

One SNP (rs1065045) was excluded due to schizophrenia. After excluding SNP (rs1065045), results of the second MR analysis were slightly different from the first, which were considered as the final result: a significant positive causality between spondyloarthritis and cardioembolic stroke (OR=1.296, 95% CI:1.094-1.534, p=0.003); a possible positive causality between spondyloarthritis and any stroke (OR=1.082, 95% CI:1.016-1.152, p=0.013)/any ischemic stroke (OR=1.086, 95% CI:1.013-1.163, p=0.020); no significant/possible causality between spondyloarthritis and small vessel stroke (OR=1.168, 95% CI:0.993-1.375, p=0.061). Insufficient power may be one possible reason why a causality was not observed between spondyloarthritis in our study.

Conclusions

This study suggests that the possible causative effects of spondyloarthritis predicted by genetics on stroke may be limited to any stroke, any ischemic stroke, and cardioembolic stroke, especially the last.
Hepatitis B surface antigen reduction is associated with hepatitis B core-specific CD8+ T cell quality
Authors: Takahama Shokichi , Yoshio Sachiyo , Masuta Yuji , Murakami Hirotomo , Sakamori Ryotaro , Kaneko Shun , Honda Takashi , Murakawa Miyako , Sugiyama Masaya , Kurosaki Masayuki , Asahina Yasuhiro , Takehara Tetsuo , Appay Victor , Kanto Tatsuya , Yamamoto Takuya
Published: October 2023

Despite treatment, hepatitis B surface antigen (HBsAg) persists in patients with chronic hepatitis B (CHB), suggesting the likely presence of the virus in the body. CD8+ T cell responses are essential for managing viral replication, but their effect on HBsAg levels remains unclear. We studied the traits of activated CD8+ T cells and HBV-specific CD8+ T cells in the blood of CHB patients undergoing nucleos(t)ide analog (NUC) therapy. For the transcriptome profiling of activated CD8+ T cells in peripheral blood mononuclear cells (PBMCs), CD69+ CD8+ T cells were sorted from six donors, and single-cell RNA sequencing (scRNA-seq) analysis was performed. To detect HBV-specific CD8+ T cells, we stimulated PBMCs from 26 donors with overlapping peptides covering the HBs, HBcore, and HBpol regions of genotype A/B/C viruses, cultured for 10 days, and analyzed via multicolor flow cytometry. scRNA-seq data revealed that CD8+ T cell clusters harboring the transcripts involved in the cytolytic functions were frequently observed in donors with high HBsAg levels. Polyfunctional analysis of HBV-specific CD8+ T cells utilized by IFN-γ/TNFα/CD107A/CD137 revealed that HBcore-specific cells exhibited greater polyfunctionality, suggesting that the quality of HBV-specific CD8+ T cells varies among antigens. Moreover, a subset of HBcore-specific CD8+ T cells with lower cytolytic potential was inversely correlated with HBsAg level. Our results revealed a stimulant-dependent qualitative difference in HBV-specific CD8+ T cells in patients with CHB undergoing NUC therapy. Hence, the induction of HBcore-specific CD8+ T cells with lower cytolytic potential could be a new target for reducing HBsAg levels.
Response to visual and mechano-acoustic predator cues is robust to ocean warming and acidification and is highly variable in European sea bass
Authors: Cohen-Rengifo Mishal , Mazurais David , Bégout Marie-Laure
Published: October 2023

Predator-prey interactions and, especially, the success of anti-predator responses are modulated by the sensory channels of vision, olfaction, audition and mechanosensation. If climate change alters fish sensory ability to avoid predation, community dynamics can be affected. We investigated whether mid-duration exposure to warming and/or acidification alters behavioural response to visual or mechano-acoustic predator cues in juvenile Dicentrarchus labrax. We measured kinematic variables before and after a visual or a mechano-acoustic challenge which mimicked an overflying bird shadow or a bird swoop attack, respectively. Due to large interindividual variability in responses before cue presentation, fish were categorized as slow and fast to account for baseline individual variability. Treatment did not impact kinematic variables as both slow and fast fish of every treatment elicited precautionary and escape responses. Interestingly, even slow fish swam as fast as fast fish after the cue, suggesting that regardless of initial category, fish managed to escape facing a danger. Anti-predator response varied according to the level of threat to survival with greater responses elicited after the swoop attack. Although wild juvenile sea bass aggregate in schools, school dynamics rely on single leaders which highlights the importance of the variability in individual behaviours. We demonstrated that anti-predator response in juvenile D. labrax is robust to mid-duration exposure to independent and combined effects of warming and acidification. If robustness is confirmed over long-duration, it could provide D. labrax with an evolutionary advantage in the future ocean, where cue transmission through changing environments can further modulate cue perception and predator-prey interactions.
Impact of freshwater diversions on vegetation in coastal wetlands based on remote sensing derived vegetation index
Authors: Wu Wei , Grimes Evan , Suir Glenn
Published: October 2023

There exist contrasting results on the impact of large-scale freshwater and sediment diversions on land gain/loss. To improve understanding on the efficacy of diversion projects in restoring coastal wetlands, we aim to evaluate the long-term impacts of diversion-altered salinity and water level on vegetation productivity in coastal wetlands. Two freshwater diversion projects Caernarvon and Davis Pond in Louisiana, U.S. and associated reference sites were selected for inclusion in this study. We implemented multi-level Bayesian models to evaluate 1) how vegetation productivity approximated by Landsat-derived Normalized Difference Vegetation Index (NDVI) in peak biomass season changed over time (pre- and post-construction and operation of the freshwater diversions), and 2) how peak-season NDVI responded to mean and variability of water level and salinity among a suite of factors that could affect vegetation productivity. Analysis showed difference in temporal trends of NDVI between the reference and diversion site for the Caernarvon project with a significant increase at the diversion site although NDVI negatively responded to diversion at the beginning. Diversion did not seem to negatively affect NDVI for the Davis Pond project and NDVI only marginally increased at the diversion site. For both projects, NDVI negatively responded to water level, while salinity negatively affected NDVI or showed quadratic relation with NDVI. At the Caernarvon diversion project, the negative impact of water level on NDVI was greater at the diversion site than at the reference site. At the Davis Pond project, it was the salinity that showed different impact between the diversion and reference site. The temporal increase of NDVI at the Caernarvon diversion site can be explained by the lower salinity driven by diversion. The quadratic relation between salinity and NDVI at the Davis Pond diversion project led to only marginal increase at the diversion site. This study provided uncertainty estimates in temporal trend of NDVI and the impact of two key abiotic drivers on NDVI. The improved understanding on vegetation productivity will help predict landscape change in response to freshwater diversions.
An empirical formula of bottom friction coefficient with a dependence on the current speed for the tidal models
Authors: Dong Yakang , Jiang Jinglu , Liu Xiujuan , Wang Daosheng , Zhang Jicai
Published: October 2023

Tides are of great importance for ocean mixing and nearshore ocean engineering. Bottom friction is a major factor in tidal dissipation and is usually parameterized by the bottom friction coefficient (BFC). BFC is a critical parameter in numerical tidal models and is known to vary with time and space, as calculated with measured data. However, it is difficult to accurately adjust the spatially-temporally varying BFC in numerical tidal models. Based on the relationship between the spatially-temporally varying BFC estimated by adjoint data assimilation and the simultaneously simulated current speed, an empirical formula of BFC with a dependence on the current speed is proposed. This new empirical formula of BFC is compared with several traditional empirical formulas, including the constant BFC, the Chezy-Manning BFC, and two depth-dependent BFCs. When the four principal tidal constituents (M2, S2, K1, and O1) in the Bohai, Yellow and East China Seas (BYECS) are simulated, the mean vector error between the simulated results obtained using the current speed-dependent BFC and the TOPEX/Poseidon satellite altimetry data (the tidal gauge data) is 8.81 cm (10.62 cm), which is decreased by up to 8.1% (18.2%) compared with those using the several commonly used empirical formulas of BFC. Furthermore, in the sensitivity experiments where only the M2 tide in the BYECS, the M2, S2, K1, and O1 tides in the Bohai and Yellow Sea (BYS), and the M2, S2, K1, and O1 tides in the South China Sea (SCS) are simulated, the errors between the simulated results obtained by using current speed-dependent BFC and the tidal gauge data are less than those using the other empirical formulas of BFC, further demonstrating the superiority of the current speed-dependent BFC proposed in this study. From numerical model experiments, the current speed-dependent BFC can adequately reflect the spatial and temporal variations of BFC and improve the simulation accuracy of tides, thus having a broad application scope.
Prevalence of diagnostically-discrepant Clostridioides difficile clinical specimens: insights from longitudinal surveillance
Authors: Anwar Farhan , Clark Marielle , Lindsey Jason , Claus-Walker Rachel , Mansoor Asad , Nguyen Evy , Billy Justin , Lainhart William , Shehab Kareem , Viswanathan V. K. , Vedantam Gayatri
Published: October 2023

Background

Clostridioides difficile Infection (CDI) is a healthcare-associated diarrheal disease prevalent worldwide. A common diagnostic algorithm relies on a two-step protocol that employs stool enzyme immunoassays (EIAs) to detect the pathogen, and its toxins, respectively. Active CDI is deemed less likely when the Toxin EIA result is negative, even if the pathogen-specific EIA is positive for C. difficile. We recently reported, however, that low-toxin-producing C. difficile strains recovered from Toxin-negative (‘discrepant’) clinical stool specimens can be fully pathogenic, and cause lethality in a rodent CDI model. To document frequency of discrepant CDI specimens, and evaluate C. difficile strain diversity, we performed longitudinal surveillance at a Southern Arizona tertiary-care hospital.

Methods

Diarrheic stool specimens from patients with clinical suspicion of CDI were obtained over an eight-year period (2015–2022) from all inpatient and outpatient Units of a > 600-bed Medical Center in Southern Arizona. Clinical laboratory EIA testing identified C. difficile-containing specimens, and classified them as Toxin-positive or Toxin-negative. C. difficile isolates recovered from the stool specimens were DNA fingerprinted using an international phylogenetic lineage assignment system (“ribotyping”). For select isolates, toxin abundance in stationary phase supernatants of pure cultures was quantified via EIA.

Results

Of 8,910 diarrheic specimens that underwent diagnostic testing, 1733 (19.4%) harbored C. difficile. Our major findings were that: (1) C. difficile prevalence and phylogenetic diversity was stable over the 8-year period; (2) toxigenic C. difficile was recovered from 69% of clinically Tox-neg (‘discrepant’) specimens; (3) the six most prevalent USA ribotypes were recovered in significant proportions (>60%) from Tox-neg specimens; and (4) toxin–producing C. difficile recovered from discrepant specimens produced less toxin than strains of the same ribotype isolated from non-discrepant specimens.

Conclusion

Our study highlights the dominance of Toxin EIA-negative CDI specimens in a clinical setting and the high frequency of known virulent ribotypes in these specimens. Therefore, a careful reevaluation of the clinical relevance of diagnostically-discrepant specimens particularly in the context of missed CDI diagnoses and C. difficile persistence, is warranted.
Identification and characterization of a novel 6′-N-aminoglycoside acetyltransferase AAC(6′)-Va from a clinical isolate of Aeromonas hydrophila
Authors: Zhang Guozhi , Zhang Lei , Sha Yuning , Chen Qiaoying , Lin Naru , Zhao Jingxuan , Zhang Yuan , Ji Yongan , Jiang Weiyan , Zhang Xueya , Li Qiaoling , Lu Junwan , Lin Xi , Li Kewei , Zhang Hailin , Bao Qiyu , Lu Jun , Hu Yunliang , Zhu Tingting
Published: October 2023

Background

Aeromonas species have been identified as agents responsible for various diseases in both humans and animals. Multidrug-resistant Aeromonas strains pose a significant public health threat due to their emergence and spread in clinical settings and the environment. The aim of this study was to determine a novel resistance mechanism against aminoglycoside antimicrobials in a clinical isolate.

Methods

The function of aac(6′)-Va was verified by gene cloning and antibiotic susceptibility tests. To explore the in vivo activity of the enzyme, recombinant proteins were expressed, and enzyme kinetics were tested. To determine the molecular background and mechanism of aac(6′)-Va, whole-genome sequencing and bioinformatic analysis were performed.

Results

The novel aminoglycoside N-acetyltransferase gene aac(6′)-Va confers resistance to several aminoglycosides. Among the antimicrobials tested, ribostamycin showed the highest increase (128-fold) in the minimum inhibitory concentration (MIC) compared with the control strains. According to the MIC results of the cloned aac(6′)-Va, AAC(6′)-Va also showed the highest catalytic efficiency for ribostamycin [kcat/Km ratio = (3.35 ± 0.17) × 104 M−1 s−1]. Sharing the highest amino acid identity of 54.68% with AAC(6′)-VaIc, the novel aminoglycoside N-acetyltransferase constituted a new branch of the AAC(6′) family due to its different resistance profiles. The gene context of aac(6′)-Va and its close relatives was conserved in the genomes of species of the genus Aeromonas.

Conclusion

The novel resistance gene aac(6′)-Va confers resistance to several aminoglycosides, especially ribostamycin. Our finding of a novel resistance gene in clinical A. hydrophila will help us develop more effective treatments for this pathogen’s infections.
Mechanism of fungal remediation of wetland water: Stropharia rugosoannulata as promising fungal species for the development of biofilters to remove clinically important pathogenic and antibiotic resistant bacteria in contaminated water
Authors: Sen Keya , Llewellyn Marina , Taheri Babak , Turner Robert J. , Berglund Tanner , Maloney Kellen
Published: October 2023

Mycoremediation uses mushroom forming fungi for remediation of sites contaminated with biotic and abiotic contaminants. The root-like hyphae of many fungi, the mycelia, have been used to remediate soil and water. In this study mushroom mycelia biofilters were evaluated for remediation efficacy of wetland water polluted with crow feces containing antibiotic resistant (AMR) bacteria. Three strains of fungi, Pleurotus ostreatus, Stropharia rugosoannulata, and Pleurotus pulmonarius, were allowed to develop dense mycelia for 3-5 weeks on wood chips within cylindrical jars. Biofilter jars were incubated with wetland water (WW) obtained from a crow roost area that was additionally spiked with AMR bacteria isolated from previous crow fecal collections. E. coli, Staphylococcus aureus, Enterococcus faecium, Campylobacter jejuni, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella enteritidis were added at concentrations of 1,500–3,500 CFU/100 ml. Remediation was calculated from bacterial counts or gene copy numbers (GCN), before and after passage of water through jars. Stropharia and P. pulmonarius biofilters remediated all bacteria, but Klebsiella, in the range of 43-78%, after 1 h. Incubation of water for 24 h showed Stropharia remediation to be superior relative to other tested fungi. Percent remediation varied as follows: S. aureus-100%, E. faecium-97%, C. jejuni-59%, P. aeruginosa-54%, E. coli-65% and S. enteritidis-27%. The mechanism of remediation was tested by removing the mycelium from the biofilter column after passage of water, followed by extraction of DNA. Association of bacterial DNA with the mycelia was demonstrated by qPCR for all bacteria, except S. aureus and Salmonella. Depending on the bacteria, the GCN ranged from 3,500 to 54,000/250 mg of mycelia. Thus, some of the ways in which mycelia biofilters decrease bacteria from water are through bio-filtration and bio-absorption. Active fungal growth and close contact with bacteria appear necessary for removal. Overall these results suggest that mushroom mycelia biofilters have the potential to effectively remediate water contaminated with pathogenic and AMR bacteria.
Colorectal cancer and gut viruses: a visualized analysis based on CiteSpace knowledge graph
Authors: Jian Chu , Jing Zhuang , Yinhang Wu , Jinlong Duan , Yuefen Pan , Quan Qi , Shuwen Han
Published: October 2023

Background

Gut microbiome is a complex community of microbes present in the human gut and plays an important role in the occurrence and progression of colorectal cancer (CRC). However, the relationship between virus and CRC has not been fully understood.

Objective

To explore the hot spots and research trends in the field of CRC and virus.

Methods

By using the bibliometric analysis tool CiteSpace and based on the articles of the Web of Science Core Collection (WoSCC) database, the country, institution, highly cited literature, keywords and so on were visually analyzed.

Results

A total of 356 research articles on CRC from 2001 to 2023 were thoroughly analyzed. The USA and China have made the largest contribution in the field of virus and CRC. The Helmholtz Association published the most papers. There were relatively few cooperations among institutions from different countries. The results of keyword cluster analysis proved that the literature on the relationship between human cytomegalovirus (CMV) and CRC was the most widely studied aspect in this field. “Gut microbiota,” “inflammatory bowel disease,” “hepatitis b virus,” and “human papillomavirus infection” are the current research hotspots; “oncolytic virus,” “apoptosis,” and “gut microbiome” are the recent research frontiers and should be paid closer attention.

Conclusion

By using CiteSpace bibliometric software, the visual analysis reflected the research trends and hot topics of virus and CRC. In addition, the prevalence and mechanism of specific virus on CRC were also reviewed, which provides valuable references for future CRC research.
Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios
Authors: Poirier Simon , Coeuret Gwendoline , Champomier-Vergès Marie-Christine , Desmonts Marie-Hélène , Werner Dalal , Feurer Carole , Frémaux Bastien , Guillou Sandrine , Luong Ngoc-Du Martin , Rué Olivier , Loux Valentin , Zagorec Monique , Chaillou Stéphane ,   on behalf of the ANR Redlosses Consortium Group
Published: October 2023

Background

The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.

Methods

Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.

Results

Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.

Conclusion

We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.