bluuebunny/crossref_metadata_2025 huggingface dataset:
Oral phytate supplementation on the progression of mild cognitive impairment, brain iron deposition and diabetic retinopathy in patients with type 2 diabetes: a concept paper for a randomized double blind placebo controlled trial (the PHYND trial)
Authors: Pujol Antelm , Sanchis Pilar , Tamayo María I. , Nicolau Joana , Grases Félix , Espino Ana , Estremera Ana , Rigo Elena , Amengual Guillermo J. , Rodríguez Manuel , Ribes José L. , Gomila Isabel , Simó-Servat Olga , Masmiquel Lluís
Published: May 2024

Type 2 diabetes mellitus has a worldwide prevalence of 10.5% in the adult population (20–79 years), and by 2045, the prevalence is expected to keep rising to one in eight adults living with diabetes. Mild cognitive impairment has a global prevalence of 19.7% in adults aged 50 years. Both conditions have shown a concerning increase in prevalence rates over the past 10 years, highlighting a growing public health challenge. Future forecasts indicate that the prevalence of dementia (no estimations done for individuals with mild cognitive impairment) is expected to nearly triple by 2050. Type 2 diabetes mellitus is a risk factor for the development of cognitive impairment, and such impairment increase the likelihood of poor glycemic/metabolic control. High phytate intake has been shown to be a protective factor against the development of cognitive impairment in observational studies. Diary phytate intake might reduce the micro- and macrovascular complications of patients with type 2 diabetes mellitus through different mechanisms. We describe the protocol of the first trial (the PHYND trial) that evaluate the effect of daily phytate supplementation over 56 weeks with a two-arm double-blind placebo-controlled study on the progression of mild cognitive impairment, cerebral iron deposition, and retinal involvement in patients with type 2 diabetes mellitus. Our hypothesis proposes that phytate, by inhibiting advanced glycation end product formation and chelating transition metals, will improve cognitive function and attenuate the progression from Mild Cognitive Impairment to dementia in individuals with type 2 diabetes mellitus and mild cognitive impairment. Additionally, we predict that phytate will reduce iron accumulation in the central nervous system, mitigate neurodegenerative changes in both the central nervous system and retina, and induce alterations in biochemical markers associated with neurodegeneration.
A new prognostic model for recurrent pregnancy loss: assessment of thyroid and thromboelastograph parameters
Authors: Mu Fangxiang , Huo Huyan , Wang Chen , Hu Ning , Wang Fang
Published: May 2024

Objective

This study aimed to identify predictors associated with thyroid function and thromboelastograph (TEG) examination parameters and establish a nomogram for predicting the risk of subsequent pregnancy loss in recurrent pregnancy loss (RPL).

Methods

In this retrospective study, we analyzed the medical records of 575 RPL patients treated at Lanzhou University Second Hospital, China, between September 2020 and December 2022, as a training cohort. We also included 272 RPL patients from Ruian People’s Hospital between January 2020 and July 2022 as external validation cohort. Predictors included pre-pregnancy thyroid function and TEG examination parameters. The study outcome was pregnancy loss before 24 weeks of gestation. Variable selection was performed using least absolute shrinkage and selection operator regression and stepwise regression analyses, and the prediction model was developed using multivariable logistic regression. The study evaluated the model’s performance using the area under the curve (AUC), calibration curve, and decision curve analysis. Additionally, dynamic and static nomograms were constructed to provide a visual representation of the models.

Results

The predictors used to develop the model were body mass index, previous pregnancy losses, triiodothyronine, free thyroxine, thyroid stimulating hormone, lysis at 30 minutes, and estimated percent lysis which were determined by the multivariable logistic regression with the minimum Akaike information criterion of 605.1. The model demonstrated good discrimination with an AUC of 0.767 (95%CI 0.725-0.808), and the Hosmer-Lemeshow test indicated good fitness of the predicting variables with a P value of 0.491. Identically, external validation confirmed that the model exhibited good performance with an AUC of 0.738. Moreover, the clinical decision curve showed a positive net benefit in the prediction model. Meanwhile, the web version we created was easy to use. The risk stratification indicated that high-risk patients with a risk score >147.9 had a higher chance of pregnancy loss (OR=6.05, 95%CI 4.09-8.97).

Conclusions

This nomogram well-predicted the risk of future pregnancy loss in RPL and can be used by clinicians to identify high-risk patients and provide a reference for pregnancy management of RPL.
Evolution of pore structure during fines migration in sand pack: NMR experimental and numerical investigations
Authors: Haoxuan Tang , Chunsheng Jia , Ziyi Wang , Hao Lu , Zhao Wang , Hongming Tang , Baiyu Zhu
Published: May 2024

Unconsolidated sand reservoirs containing heavy oil play a significant role in hydrocarbon resources, characterized by high porosity and permeability alongside abundant movable fines. During production, these fines can detach and migrate with the reservoir fluids, causing pore plugging and reduced productivity. Visualizing and quantitatively evaluating the evolution of pore structure caused by fines migration under various influencing factors at the microscale is fundamental for devising effective prevention and mitigation measures. This study employs on-line NMR experiments and CFD-DEM simulations to investigate fines migration processes and their effects on physical properties and pore structure at the pore scale. Results indicate that fines migration initiates the formation of a preferential network of migration pathways. The evolution of pore structure demonstrates zonal characteristics along the flow direction, with fines plugging and residual accumulation primarily occurring in the middle/rear section of the core. As the core’s skeleton porosity decreases, fines plugging intensifies; however, at high injection velocity, new dominant flow channels may emerge, leading to a transition from a single-peak to a double-peak T2 spectrum. Below the critical velocity (0.5–1 mL/min), an increase in flow velocity exacerbates severe fines plugging. Conversely, above the critical velocity, an increase in flow velocity results in a more pronounced enhancement of permeability.
Research on variable pairing scheme for V/f controlled MMC station
Authors: Ma Junchao , Wu Zhe , Sun Ke , Wang Chenxu , Lu Chengyu , Gu Yilei , Liu Jianing , Zhu Chengzhi , Guo Hanlin , Zhang Zheren , Xu Zheng
Published: May 2024

Grid-forming control is a promising solution for renewable power integration. This work presents a variable pairing scheme for the voltage controller of V/f controlled modular multilevel converter in an islanded network with a synchronous machine, which is a special type of grid-forming control. Based on the concept of the relative gain array (RGA), it is found that the RGA can be derived using steady-state sensitivity analysis. Then, the steady-state characteristics of the typical electrical components in the islanded network are considered, and the analytical expression for calculating the RGA is derived. Based on a typical system, a variable pairing scheme is then suggested using the calculated RGA elements. The time-domain simulations are conducted using PSCAD/EMTDC, and the results verify the feasibility and advantages of the suggested variable pairing scheme.
Setting-aside cropland did not reduce greenhouse gas emissions from a drained peat soil in Sweden
Authors: Keck Hannes , Meurer Katharina H. E. , Jordan Sabine , Kätterer Thomas , Hadden David , Grelle Achim
Published: May 2024

In the process of their formation, northern peatlands were accumulating vast amounts of carbon (C). When drained for agricultural use, a large proportion of that C is oxidized and emitted as carbon dioxide (CO2), turning those peatlands to strong CO2 emitters. As a mitigation option, setting-aside farmland on drained peat is being incentivized by policies, but recent evidence casts doubt on these policies’ efficiency for greenhouse gas (GHG) emission mitigation. To investigate the effects of setting-aside farmland on GHG fluxes from a Swedish peatland, we measured CO2, nitrous oxide (N2O), and methane (CH4) fluxes on two adjacent sites under contrasting management. The cultivated (CL) site was used for cereal production (wheat or barley) and the set-aside (SA) site was under permanent grassland. Carbon dioxide fluxes were measured from 2013 to 2019 using the eddy covariance (EC) method. Additionally, CO2, N2O, and CH4 fluxes were measured during the growing seasons of 2018–2020, using transparent and opaque chambers on vegetated plots and on bare peat. The cumulative CO2 fluxes measured by EC over the measurement period were 0.97 (±0.05) and 2.09 (±0.17) kg m−2 with annual average losses of 0.16 and 0.41 kg CO2 m−2 yr−1 for the CL and SA site, respectively. Thus, the SA site acted as a stronger CO2 source than the CL site. Both sites’ contribution to global warming, calculated on basis of the chamber measurements, was dominated by CO2. The contribution of the SA site was higher than that of the CL site. Nitrous oxide emissions were low at both sites with higher emissions from the CL site for transparent measurements and measurements on bare peat. Whereas, CH4 uptake was highest on the SA grassland. Thus, on the basis of our study, we found no evidence that setting-aside farmland on shallow drained peat soils will reduce GHG emissions or even turn the peatland into a C sink.
Everyday discrimination and satisfaction with nature experiences
Authors: Schinasi Leah H. , Lawrence Jourdyn A.
Published: May 2024

Introduction

There is growing interest in creating public green spaces to promote health. Yet, discussions about these efforts often overlook how experiences of chronic discrimination—which may manifest as racism, sexism, or homophobia, and more—could undermine satisfaction with nature experiences.

Methods

Using data from the 2018 wave of the National Opinion Research Center (NORC) General Social Survey (GSS), we quantified associations of frequency of everyday discrimination, operationalized using the Everyday Discrimination Scale (EDS, the primary independent variable), with respondents' perceptions of nature experiences and with their reported time spent in nature. Specifically, we quantified associations with the following three variables: (1) dissatisfaction with day-to-day experiences of nature, (2) not spending as much time as they would like in natural environments, and (3) usually spending at least one day per week in nature. We used survey-weighted robust Poisson models to estimate overall associations, and also stratified analyses by racial/ethnic and gender identity categories.

Results

Of 768 GSS respondents, 14% reported dissatisfaction with nature experiences, 36% reported not spending as much time as they would like in nature, and 33% reported that they did not spend at least one day per week in nature. The median non-standardized EDS, coded such that a higher value indicates greater frequency of discrimination, was 11 (interquartile range: 8, 15). Prevalence of reporting dissatisfaction with day-to-day experiences in nature was 7% higher in association with every one unit increase in EDS score above the median (PR: 1.07, 95% CI: 1.02–1.11). The prevalence of reporting not spending as much time as one would like in nature was 2% higher for every unit increase in higher than median everyday discrimination frequency (PR: 1.02, 95% CI: 1.00–1.05). Higher than median frequency in everyday discrimination was not associated with spending less than one day per week in nature. Race/ethnicity and gender identity did not modify associations.

Conclusion

Greater frequency of everyday discrimination is associated with less satisfaction with experiences in nature. This relationship could undermine efforts to promote health equity through green interventions.
Developing a DNA metabarcoding method to identify diet taxa in Neotropical foxes
Authors: Mannise Natalia , Cosse Mariana , Greif Gonzalo , Bou Nadia , Robello Carlos , González Susana , Iriarte Andres
Published: May 2024

Pampas and crab-eating foxes are medium-sized canids living in sympatry in the middle east of South America. Studies on the diet composition of these species provide a deep understanding of their ecological roles in the ecosystem structure and regulation. Using the metabarcoding technique, we analyzed the diet of both fox species in order to identify the vertebrate taxa included as food items. A fragment of the 12S ribosomal gene of the mtDNA was amplified using DNA extracted from 27 scat samples collected in south-central Uruguay during cold (June 2015) and warm (January – April 2016) seasons. A fox DNA blocking primer was designed to minimize the host amplicon products, and pooled samples were sequenced through paired-end reads (100 bp library) on a MiSeq Illumina Platform. The generated sequences were compared to a reference database built with sequences available in GenBank. In concordance with previous studies using traditional methods, we found that the most common food taxon were rodents. Qualitative differences in diet composition between both fox species were identified. Armadillo species were only found in pampas fox diet, while a greater variety of amphibians and birds were detected in crab-eating fox feces. Additionally, an innovative approach to differentiate between real and artifact sequences was employed. This method was based on comparing mutations at conserved and non-conserved positions within the secondary structure of the 12S rRNA, combined with network sequence reconstruction. Our results demonstrate the efficacy of the methodology in detecting the food species present in both fox diets, enabling the evaluation of intraspecific diversity among these species and facilitating the discarding of sequencing errors. This makes the methodology applicable to a wide range of studies.
Identification and expression of the Di19 gene family in response to abiotic stress in common bean (Phaseolus vulgaris L.)
Authors: Guo Wei , Li Xinhui , Yang Tao , Huang Chunguo , Zhao Bo , Wang Peng
Published: May 2024

Drought-induced 19 (Di19) protein plays critical biological functions in response to adversity as well as in plant growth and development. Exploring the role and mechanism of Di19 in abiotic stress responses is of great significance for improving plant tolerance. In this study, six Di19 genes were identified in the common bean (Phaseolus vulgaris L.), which were mainly derived from segmental duplications. These genes share conserved exon/intron structures and were classified into three subfamilies based on their phylogenetic relationships. The composition and arrangement of conserved motifs were consistent with their phylogenetic relationships. Many hormone- and stress-responsive elements were distributed in the promoters region of PvDi19 genes. Variations in histidine residues in the Cys2/His2 (C2H2) zinc-finger domains resulted in an atypical tertiary structure of PvDi19-5. Gene expression analysis showed rapid induction of PvDi19-1 in roots by 10% PEG treatment, and PvDi19-2 in leaves by 20% PEG treatment, respectively. Most PvDi19s exhibited insensitivity to saline-alkali stress, except for PvDi19-6, which was notably induced during later stages of treatment. The most common bean Di19 genes were inhibited or not regulated by cadmium stress, but the expression of PvDi19-6 in roots was significantly upregulated when subjected to lower concentrations of cadmium (5 mmol). Moreover, Di19s exhibited greater sensitivity to severe cold stress (6°C). These findings enhance our understanding of the role of PvDi19s in common bean abiotic stress responses and provide a basis for future genetic enhancements in common bean stress tolerance.
A multiscale spatial modeling framework for the germinal center response
Authors: Mu Derek P. , Scharer Christopher D. , Kaminski Norbert E. , Zhang Qiang
Published: May 2024

The germinal center response or reaction (GCR) is a hallmark event of adaptive humoral immunity. Unfolding in the B cell follicles of the secondary lymphoid organs, a GC culminates in the production of high-affinity antibody-secreting plasma cells along with memory B cells. By interacting with follicular dendritic cells (FDC) and T follicular helper (Tfh) cells, GC B cells exhibit complex spatiotemporal dynamics. Driving the B cell dynamics are the intracellular signal transduction and gene regulatory network that responds to cell surface signaling molecules, cytokines, and chemokines. As our knowledge of the GC continues to expand in depth and in scope, mathematical modeling has become an important tool to help disentangle the intricacy of the GCR and inform novel mechanistic and clinical insights. While the GC has been modeled at different granularities, a multiscale spatial simulation framework – integrating molecular, cellular, and tissue-level responses – is still rare. Here, we report our recent progress toward this end with a hybrid stochastic GC framework developed on the Cellular Potts Model-based CompuCell3D platform. Tellurium is used to simulate the B cell intracellular molecular network comprising NF-κB, FOXO1, MYC, AP4, CXCR4, and BLIMP1 that responds to B cell receptor (BCR) and CD40-mediated signaling. The molecular outputs of the network drive the spatiotemporal behaviors of B cells, including cyclic migration between the dark zone (DZ) and light zone (LZ) via chemotaxis; clonal proliferative bursts, somatic hypermutation, and DNA damage-induced apoptosis in the DZ; and positive selection, apoptosis via a death timer, and emergence of plasma cells in the LZ. Our simulations are able to recapitulate key molecular, cellular, and morphological GC events, including B cell population growth, affinity maturation, and clonal dominance. This novel modeling framework provides an open-source, customizable, and multiscale virtual GC simulation platform that enables qualitative and quantitative in silico investigations of a range of mechanistic and applied research questions on the adaptive humoral immune response in the future.
A meta-analysis of idiopathic granulomatous mastitis treatments for remission and recurrence prevention
Authors: Ong Seeu Si , Ho Peh Joo , Liow Jonathan Jun Kit , Tan Qing Ting , Goh Serene Si Ning , Li Jingmei , Hartman Mikael
Published: May 2024

Purpose

The major aim of our meta-analysis was to review the effectiveness of various treatment modalities for achieving successful remission and preventing recurrence for women with idiopathic granulomatous mastitis (IGM). This knowledge is instrumental in developing evidence-based guidelines for clinicians to improve management strategies and outcomes for patients with IGM.

Methods

A systematic literature search was performed on MEDLINE (Ovid), Embase (Elsevier), PubMed, Cochrane Library, Web of Science, and Google Scholar; studies published to 19 January 2022 were included. A meta-analysis of 57 observational studies was performed. The results of two randomized controlled trials were also examined.

Results

There were 3,035 IGM patients across the observational and randomised studies. Overall recurrence and remission rates across all treatment strategies in 59 studies are 87.9% (2,667/3035) and 13.5% (359/2667), respectively. The studies reported 19 different treatment strategies, comprising observation, medical monotherapies, surgery, and combinations involving medical therapies, with and without surgery. Among monotherapy treatment, surgical management had the highest pooled remission rate (0.99 [95% confidence interval (CI) = 0.97–1.00]); among combination therapy, this was steroids and surgery (0.99 [0.94–1.00]). Antibiotic monotherapy had the lowest remission rate (0.72 [0.37–0.96]). The highest recurrence rates belonged to treatments that combined antibiotics and surgery (0.54 [0.02–1.00]), and antibiotics, steroids, and surgery (0.57 [0.00–1.00]). Most successful for preventing recurrence were observation (0.03 [0.00–0.10]), methotrexate (0.08 [0.00–0.24]), and steroids and surgery (0.05 [0.01–0.12]). There is a significant association between longer follow-up duration and recurrence rate reported, p = 0.002.

Conclusion

Combination therapies, especially those incorporating antibiotics, steroids, and surgery, have demonstrated higher remission rates, challenging the use of antibiotic monotherapy. There is an increased emphasis on the need for personalised, multi-pronged approach for preventing IGM recurrence, with longer follow-up care. More prospective future work in IGM research, with standardised diagnostic criteria, treatment protocols, and reporting guidelines will be important for developing treatment protocols and guidelines clinicians can adhere to in the clinical management of IGM patients.

Systematic review registration: PROSPERO (CRD42022301386).
Case report: Autoimmune encephalomyelitis following cytomegalovirus infection after allogeneic hematopoietic stem cell transplantation
Authors: Yang Min , Cai Yu , Wan Liping , Ji Linhua , Song Xian M.
Published: May 2024

Introduction

Cytomegalovirus (CMV) can cause various end-organ diseases in immunocompromised hosts, including allogeneic hematopoietic cell transplant (allo-HSCT) recipients. Interestingly, CMV viremia has been associated with various complications and poor prognosis in allo-HSCT recipients. Complications involving the central nervous system (CNS) occur in 9–14% of patients following allo-HSCT. However, autoimmune encephalitis (AE) secondary to CMV infection after allo-HSCT has rarely been reported. Here we report a case of possible AE following CMV viremia after allo-HSCT, which was successfully treated with high-dose pulsed methylprednisolone and intravenous immunoglobulins (IVIg).

Case description

A 53-year-old female underwent allo-HSCT for T-lymphoblastic lymphoma/leukemia. The patient developed CMV viremia on day 36 after transplantation, and serum CMV-DNA remained positive after initiating ganciclovir antiviral therapy, turning negative one month later. Four months later, she started experiencing memory impairment, weakness in the left limbs, cognitive dysfunction, and hallucinations. A magnetic resonance imaging brain scan showed scattered ischemic lesions under the bilateral frontal cortex. Viral detection in cerebral spinal fluid (CSF) by next-generation gene sequencing technology showed no obvious abnormality. Antibodies specific to AE and paraneoplastic diseases in serum and CSF were absent. The oligoclonal bands in the CSF were detected using isoelectric focusing and immunofixation, and the results were negative. However, after extensive investigation regarding infections, autoimmune disorders, and recurrence of the malignancy, possible AE could not be excluded. The patient was treated with high-dose steroids combined with IVIg therapy; the patient’s symptoms were significantly improved.

Conclusion

The mechanisms of AE after allo-HSCT and the relationship with CMV infection should be further studied. Therefore, reporting this and similar cases will improve our awareness and understanding of the underlying disease mechanisms.
A new prediction model for acute kidney injury following liver transplantation using grafts from donors after cardiac death
Authors: Liu Hai-Xia , Wang Xin , Xu Man-Man , Wang Yi , Lai Man , Li Guang-Ming , Meng Qing-Hua
Published: May 2024

Acute kidney injury (AKI) is a major complication following liver transplantation (LT), which utilizes grafts from donors after cardiac death (DCD). We developed a machine-learning-based model to predict AKI, using data from 894 LT recipients (January 2015–March 2021), split into training and testing sets. Five machine learning algorithms were employed to construct the prediction models using 17 clinical variables. The performance of the models was assessed by the area under the receiver operating characteristic curve (AUC), accuracy, F1-score, sensitivity and specificity. The best-performing model was further validated in an independent cohort of 195 LT recipients who received DCD grafts between April 2021 and December 2021. The Shapley additive explanations method was utilized to elucidate the predictions and identify the most crucial features. The gradient boosting machine (GBM) model demonstrated the highest AUC (0.76, 95% CI: 0.70–0.82), F1-score (0.73, 95% CI: 0.66–0.79) and sensitivity (0.74, 95% CI: 0.66–0.80) in the testing set and a comparable AUC (0.75, 95% CI: 0.67–0.81) in the validation set. The GBM model identified high preoperative indirect bilirubin, low intraoperative urine output, prolonged anesthesia duration, low preoperative platelet count and graft steatosis graded NASH Clinical Research Network 1 and above as the top five important features for predicting AKI following LT using DCD grafts. The GBM model is a reliable and interpretable tool for predicting AKI in recipients of LT using DCD grafts. This model can assist clinicians in identifying patients at high risk and providing timely interventions to prevent or mitigate AKI.
Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila
Authors: Rodríguez-Cruz Ulises E. , Castelán-Sánchez Hugo G. , Madrigal-Trejo David , Eguiarte Luis E. , Souza Valeria
Published: May 2024

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the “Archaean Domes” (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5–9.8) and high salinity (5.28% to saturation).
Genomic and functional diversity of the human-derived isolates of Faecalibacterium
Authors: Li Wenxi , Lin Xiaoqian , Liang Hewei , Wu Zhinan , Wang Mengmeng , Sun Jingxi , Li Xiaofang , He Wenxin , Gao Xiaowei , Hu Tongyuan , Xiao Liang , Zou Yuanqiang
Published: May 2024

Introduction

Faecalibacterium is one of the most abundant bacteria in the gut microbiota of healthy adults, highly regarded as a next-generation probiotic. However, the functions of Faecalibacterium genomes from cultured strains and the distribution of different species in populations may differ among different sources.

Methods

We here performed an extensive analysis of pan-genomes, functions, and safety evaluation of 136 Faecalibacterium genomes collected from 10 countries.

Results

The genomes are clustered into 11 clusters, with only five of them were characterized and validly nomenclated. Over 80% of the accessory genes and unique genes of Faecalibacterium are found with unknown function, which reflects the importance of expanding the collection of Faecalibacterium strains. All the genomes have the potential to produce acetic acid and butyric acid. Nine clusters of Faecalibacterium are found significantly enriched in the healthy individuals compared with patients with type II diabetes..

Discussion

This study provides a comprehensive view of genomic characteristic and functions and of culturable Faecalibacterium bacterium from human gut, and enables clinical advances in the future.
Study on biodegradation mechanism of Fusarium solani NK-NH1 on the hull wood of the Nanhai No. 1 shipwreck
Authors: Wang Yu , Han Yeqing , Li Naisheng , Wang Cen , Ma Kaixuan , Huang Xinduo , Du Jing , Guo Hong , Pan Jiao
Published: May 2024

The Nanhai No. 1 shipwreck is an ancient wooden ship in the Southern Song Dynasty. Currently, serious challenges of microbial diseases exist on the hull wood. This study aimed to obtain microbial samples from the ship hull in December 2021 and analyze the microbial diseases through scanning electron microscopy and high-throughput sequencing to preserve the Nanhai No. 1 shipwreck. The biodegradation mechanism of diseased microorganisms was explored through whole genome sequencing and the detection of enzyme activity and gene expression levels of diseased microorganisms under different conditions. The results showed that there was obvious fungal colonization on the surface of the hull wood and Fusarium solani NK-NH1 was the dominant disease fungus on the surface. NK-NH1 has strong cellulose and lignin degradation ability. Its whole genome size is 52,389,955 bp, and it contains 17,402 genes. It has a variety of key enzyme genes involved in cellulose and lignin degradation. The NK-NH1 dominant degrading enzyme lignin peroxidase has the highest enzyme activity at pH = 4, NaCl concentration of 30%, and FeSO4 concentration of 50 mg/L, while laccase has the highest enzyme activity at pH = 4, NaCl concentration of 10%, and FeSO4 concentration of 100 mg/L. The above research results prove that NK-NH1 is a key fungus to the biodegradation of ship hull wood when it is exposed to air, low pH, high salt, and rich in sulfur iron compounds. This study provides a theoretical basis for the preservation of the Nanhai No. 1 shipwreck.
Isolation, characterization, and pathogenicity of Fusarium species causing crown rot of wheat
Authors: Ma Guoping , Wang Heng , Qi Kai , Ma Liguo , Zhang Bo , Zhang Yueli , Jiang Hang , Wu Xuehong , Qi Junshan
Published: May 2024

Fusarium crown rot (FCR) is one of the most important soilborne diseases affecting wheat production. To investigate the diversity of the pathogens causing this disease, 199 diseased wheat samples were collected from 13 cities in Shandong province. In total, 468 isolates were obtained, and from these isolates, 11 Fusarium species were identified based on phylogenetic analyses with the translation elongation factor-1α (TEF-1α), RNA polymerase II largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) gene sequences. Of these Fusarium isolates, 283 were identified as Fusarium pseudograminearum and the remaining isolates were identified as Fusarium graminearum (n = 113), Fusarium sinensis (n = 28), Fusarium acuminatum (n = 18), Fusarium incarnatum (n = 13), Fusarium ipomoeae (n = 5), Fusarium flocciferum (n = 3), Fusarium proliferatum (n = 2), Fusarium asiaticum (n = 1), Fusarium culmorum (n = 1), and Fusarium oxysporum (n = 1), suggesting that F. pseudograminearum is the dominant pathogen of FCR of wheat in Shandong province. Pathogenicity tests demonstrated that all 11 Fusarium species could cause typical symptoms of FCR on wheat seedlings. The results of the study indicate that a greater diversity of Fusarium species can cause FCR of wheat in Shandong province than that has been previously reported. This is the first report in the world of Fusarium incarnatum, Fusarium ipomoeae, and Fusarium flocciferum as pathogens causing FCR in wheat.
Breeding a new Ganoderma lucidum strain with increased contents of individual ganoderic acids by mono–mono crossing of genetically modified monokaryons
Authors: Zhou Ding-Xi , Kong Xiang-Ming , Huang Xiong-Min , Li Na , Feng Na , Xu Jun-Wei
Published: May 2024

Ganoderic acids (GAs) are major functional components of Ganoderma lucidum. The study aimed to breed a new G. lucidum strain with increased contents of individual GAs. Two mating-compatible monokaryotic strains, G. 260125 and G. 260124, were successfully isolated from the dikaryotic G. lucidum CGMCC 5.0026 via protoplast formation and regeneration. The Vitreoscilla hemoglobin gene (vgb) and squalene synthase gene (sqs) were overexpressed in the monokaryotic G. 260124 and G. 260125 strain, respectively. Mating between the G. 260124 strain overexpressing vgb and the G. 260125 strain overexpressing sqs resulted in the formation of the new hybrid dikaryotic G. lucidum strain sqs-vgb. The maximum contents of ganoderic acid (GA)-T, GA-Me, and GA-P in the fruiting body of the mated sqs-vgb strain were 23.1, 15.3, and 39.8 μg/g dry weight (DW), respectively, 2.23-, 1.75-, and 2.69-fold greater than those in G. lucidum 5.0026. The squalene and lanosterol contents increased 2.35- and 1.75-fold, respectively, in the fruiting body of the mated sqs-vgb strain compared with those in the G. lucidum 5.0026. In addition, the maximum expression levels of the sqs and lanosterol synthase gene (ls) were increased 3.23- and 2.13-fold, respectively, in the mated sqs-vgb strain. In summary, we developed a new G. lucidum strain with higher contents of individual GAs in the fruiting body by integrating genetic engineering and mono–mono crossing.
Identification and validation of a novel Parkinson-Glioma feature gene signature in glioma and Parkinson’s disease
Authors: Zhang Hengrui , Wang Jiwei , Su Nan , Yang Ning , Wang Xinyu , Li Chao
Published: May 2024

Introduction

The prognosis for glioma is generally poor, and the 5-year survival rate for patients with this disease has not shown significant improvement over the past few decades. Parkinson’s disease (PD) is a prevalent movement disorder, ranking as the second most common neurodegenerative disease after Alzheimer’s disease. Although Parkinson’s disease and glioma are distinct diseases, they may share certain underlying biological pathways that contribute to their development.

Objective

This study aims to investigate the involvement of genes associated with Parkinson’s disease in the development and prognosis of glioma.

Methods

We obtained datasets from the TCGA, CGGA, and GEO databases, which included RNA sequencing data and clinical information of glioma and Parkinson’s patients. Eight machine learning algorithms were used to identify Parkinson-Glioma feature genes (PGFGs). PGFGs associated with glioma prognosis were identified through univariate Cox analysis. A risk signature was constructed based on PGFGs using Cox regression analysis and the Least Absolute Shrinkage and Selection Operator (LASSO) method. We subsequently validated its predictive ability using various methods, including ROC curves, calibration curves, KM survival analysis, C-index, DCA, independent prognostic analysis, and stratified analysis. To validate the reproducibility of the results, similar work was performed on three external test datasets. Additionally, a meta-analysis was employed to observe the heterogeneity and consistency of the signature across different datasets. We also compared the differences in genomic variations, functional enrichment, immune infiltration, and drug sensitivity analysis based on risk scores. This exploration aimed to uncover potential mechanisms of glioma occurrence and prognosis.

Results

We identified 30 PGFGs, of which 25 were found to be significantly associated with glioma survival. The prognostic signature, consisting of 19 genes, demonstrated excellent predictive performance for 1-, 2-, and 3-year overall survival (OS) of glioma. The signature emerged as an independent prognostic factor for glioma overall survival (OS), surpassing the predictive performance of traditional clinical variables. Notably, we observed differences in the tumor microenvironment (TME), levels of immune cell infiltration, immune gene expression, and drug resistance analysis among distinct risk groups. These findings may have significant implications for the clinical treatment of glioma patients.

Conclusion

The expression of genes related to Parkinson’s disease is closely associated with the immune status and prognosis of glioma patients, potentially regulating glioma pathogenesis through multiple mechanisms. The interaction between genes associated with Parkinson’s disease and the immune system during glioma development provides novel insights into the molecular mechanisms and targeted therapies for glioma.
Awareness of episodic memory and meta-cognitive profiles: associations with cerebrospinal fluid biomarkers at the preclinical stage of the Alzheimer’s continuum
Authors: López-Martos David , Suárez-Calvet Marc , Milà-Alomà Marta , Gispert Juan Domingo , Minguillon Carolina , Quijano-Rubio Clara , Kollmorgen Gwendlyn , Zetterberg Henrik , Blennow Kaj , Grau-Rivera Oriol , Sánchez-Benavides Gonzalo
Published: May 2024

Introduction

The lack of cognitive awareness, anosognosia, is a clinical deficit in Alzheimer’s disease (AD) dementia. However, an increased awareness of cognitive function, hypernosognosia, may serve as a marker in the preclinical stage. Subjective cognitive decline (SCD) might correspond to the initial symptom in the dynamic trajectory of awareness, but SCD might be absent along with low awareness of actual cognitive performance in the preclinical stage. We hypothesized that distinct meta-cognitive profiles, both hypernosognosia and anosognosia, might be identified in preclinical-AD. This research evaluated the association between cerebrospinal fluid (CSF) AD biomarkers and the awareness of episodic memory, further exploring dyadic (participant-partner) SCD reports, in the preclinical Alzheimer’s continuum.

Methods

We analyzed 314 cognitively unimpaired (CU) middle-aged individuals (mean age: 60, SD: 4) from the ALFA+ cohort study. Episodic memory was evaluated with the delayed recall from the Memory Binding Test (MBT). Awareness of episodic memory, meta-memory, was defined as the normalized discrepancy between objective and subjective performance. SCD was defined using self-report, and dyadic SCD profiles incorporated the study partner’s report using parallel SCD-Questionnaires. The relationship between CSF Aβ42/40 and CSF p-tau181 with meta-memory was evaluated with multivariable regression models. The role of SCD and the dyadic contingency was explored with the corresponding stratified analysis.

Results

CSF Aβ42/40 was non-linearly associated with meta-memory, showing an increased awareness up to Aβ-positivity and a decreased awareness beyond this threshold. In the non-SCD subset, the non-linear association between CSF Aβ42/40 and meta-memory persisted. In the SCD subset, higher Aβ-pathology was linearly associated with increased awareness. Individuals presenting only study partner’s SCD, defined as unaware decliners, exhibited higher levels of CSF p-tau181 correlated with lower meta-memory performance.

Discussion

These results suggested that distinct meta-cognitive profiles can be identified in preclinical-AD. While most individuals might experience an increased awareness associated with the entrance in the AD continuum, hypernosognosia, some might be already losing insight and stepping into the anosognosic trajectory. This research reinforced that an early anosognosic profile, although at increased risk of AD-related decline, might be currently overlooked considering actual diagnostic criteria, and therefore its medical attention delayed.
Evaluating normalized registration and preprocessing methodologies for the analysis of brain MRI in pediatric patients with shunt-treated hydrocephalus
Authors: Ragguett Renee-Marie , Eagleson Roy , de Ribaupierre Sandrine
Published: May 2024

Introduction

Registration to a standardized template (i.e. “normalization”) is a critical step when performing neuroimaging studies. We present a comparative study involving the evaluation of general-purpose registration algorithms for pediatric patients with shunt treated hydrocephalus. Our sample dataset presents a number of intersecting challenges for registration, representing the potentially large deformations to both brain structures and overall brain shape, artifacts from shunts, and morphological differences corresponding to age. The current study assesses the normalization accuracy of shunt-treated hydrocephalus patients using freely available neuroimaging registration tools.

Methods

Anatomical neuroimages from eight pediatric patients with shunt-treated hydrocephalus were normalized. Four non-linear registration algorithms were assessed in addition to the preprocessing steps of skull-stripping and bias-correction. Registration accuracy was assessed using the Dice Coefficient (DC) and Hausdorff Distance (HD) in subcortical and cortical regions.

Results

A total of 592 registrations were performed. On average, normalizations performed using the brain extracted and bias-corrected images had a higher DC and lower HD compared to full head/ non-biased corrected images. The most accurate registration was achieved using SyN by ANTs with skull-stripped and bias corrected images. Without preprocessing, the DARTEL Toolbox was able to produce normalized images with comparable accuracy. The use of a pediatric template as an intermediate registration did not improve normalization.

Discussion

Using structural neuroimages from patients with shunt-treated pediatric hydrocephalus, it was demonstrated that there are tools which perform well after specified pre-processing steps were taken. Overall, these results provide insight to the performance of registration programs that can be used for normalization of brains with complex pathologies.
Microglia and infiltrating macrophages in ictogenesis and epileptogenesis
Authors: Bröer Sonja , Pauletti Alberto
Published: May 2024

Phagocytes maintain homeostasis in a healthy brain. Upon injury, they are essential for repairing damaged tissue, recruiting other immune cells, and releasing cytokines as the first line of defense. However, there seems to be a delicate balance between the beneficial and detrimental effects of their activation in a seizing brain. Blocking the infiltration of peripheral phagocytes (macrophages) or their depletion can partially alleviate epileptic seizures and prevent the death of neurons in experimental models of epilepsy. However, the depletion of resident phagocytes in the brain (microglia) can aggravate disease outcomes. This review describes the role of resident microglia and peripheral infiltrating monocytes in animal models of acutely triggered seizures and epilepsy. Understanding the roles of phagocytes in ictogenesis and the time course of their activation and involvement in epileptogenesis and disease progression can offer us new biomarkers to identify patients at risk of developing epilepsy after a brain insult, as well as provide novel therapeutic targets for treating epilepsy.
A novel and efficient surgical procedure for pyriform sinus fistulas in children
Authors: Chen Jiarui , Wang Ying , Shen Chenling , Wang Jing , Li Xiaoyan
Published: May 2024

Objective

This study aims to evaluate the efficacy of a novel surgical procedure for pyriform sinus fistulas in children via the external cervical approach through the hypopharynx.

Methods

A retrospective analysis was conducted on 71 pediatric patients with pyriform sinus fistula (PSF) who underwent treatment at the Department of Otolaryngology Head and Neck Surgery, Shanghai Children's Hospital, from 2012 July to 2022 July. Surgical treatment of PSF was performed via the external cervical approach through the hypopharynx, with dye instilled through the internal opening to serve as a guide for tract identification.

Results

All the internal orifices were found in the pyriform sinus by direct laryngoscopy in all 71 patients under general anesthesia. Two patients had a postoperative temporary hoarseness that resolved after 3 months. The other patients had no complications such as parapharyngeal abscess and incision infection. All patients were followed up for 23 months–70 months, and no recurrence was found.

Conclusion

The novel surgical procedure of PSF performed via the hypopharynx has advantages such as a short operation path, quick recovery, fewer complications, and a low recurrence rate. This method is a better choice for managing recurrence cases after repeated cauterization endoscopic surgeries, as well as for patients with visible cervical surgical scars or masses.
Teachers as caregivers of grieving children in school in the post-COVID-19 era: using the self-determination theory to conceptualize teachers' needs when supporting grieving children's mental health
Authors: Frei-Landau Rivi
Published: May 2024

Background

It has been estimated in recent studies that more than 1.5 million children worldwide lost a caregiver due to the COVID-19 pandemic. Childhood bereavement is associated with heightened risks of impaired academic and social performance, mental health issues, substance use disorders, and higher mortality rates. Yet children may receive insufficient support post-loss. Although the role of school psychologists in supporting grieving students has been examined, little is known about the role of teachers in this context. Specifically, knowledge about teachers' needs when supporting bereaved children is lacking.

Objective

The study's aim was to explore teachers' needs, drawing upon a well-established framework—self-determination theory (SDT)—which focuses on three human needs considered essential for optimal functioning: autonomy, competence, and relatedness.

Methods

Employing a qualitative approach, 36 teachers were interviewed about their needs when supporting grieving students. Interviews were transcribed and then analyzed using thematic content analysis.

Results

Analysis revealed three SDT-related needs: knowledge (theory- and practice-related), acknowledgment, and support (emotional and practical).

Conclusions

The findings enhance our theoretical understanding of childhood bereavement and may promote policy changes that ensure teachers' needs satisfaction. Its significance lies in the basic premise that supporting teachers' needs in the context of pediatric grief may eventually lead to their optimal ability to enact best practices for supporting grieving students' well-being.