bluuebunny/crossref_metadata_2025 huggingface dataset:
Methodological aspects of correlative, multimodal, multiparametric breast cancer imaging: from data acquisition to image processing for AI-based radioproteomics in a preclinical setting
Authors: Bartsch Silvester J. , Brožová Klára , Fürböck Christoph , Friske Joachim , Laimer-Gruber Daniela , Helbich Thomas H. , Hacker Marcus , Kuntner Claudia , Kratochwill Klaus , Kenner Lukas , Langs Georg , Pinker Katja , Wanek Thomas
Published: October 2024

Preclinical high-field magnetic resonance imaging (MRI) systems offer a diverse array of MRI techniques, providing rich multiparametric MRI (mpMRI) platforms for studying numerous biological parameters. mpMRI platforms prove particularly indispensable when investigating tumors that exhibit profound intratumoral heterogeneity, such as breast cancer. A thoughtful comprehension of the origins of intratumoral heterogeneity is imperative for the judicious assessment of new targeted therapies and treatment interventions. Furthermore, when data from mpMRI are complemented with data from other in vivo imaging modalities, such as positron emission tomography (PET), and correlated with data from ex vivo modalities, such as matrix-assisted laser desorption imaging mass spectrometry (MALDI IMS), the in vivo parameters can be further elucidated at a molecular level and microscopic scale. Nevertheless, extracting meaningful scientific insights from such complex datasets necessitates the utilization of machine learning (ML) approaches to discern region-specific radiomic features. The development of correlative, multimodal imaging (CMI) workflows, such as one incorporating MRI, PET and MALDI IMS, is inherently challenging, given the many technological and methodological challenges related to multimodal data acquisition as well as the physiological limitations of the laboratory mice of the investigation. Standardization efforts in image acquisition and processing are required to increase the reproducibility and translatability of CMI data. To address the challenges of developing standardized CMI workflows and stimulate dialog regarding this area of need, we present a practical workflow to investigate tumor heterogeneity in breast cancer xenografts across various spatial scales. Our workflow entails simultaneous functional MRI and PET acquisitions in living mice, followed by correlation with post-imaging MALDI IMS and histologic data. Additionally, we propose data preprocessing steps for potential ML applications. We illustrate the feasibility of this workflow through two examples, showcasing its effectiveness in comparing in vivo and ex vivo images to evaluate tumor metabolism and hypoxia in mice with breast cancer xenografts.
Predicting the microalgae lipid profile obtained by supercritical fluid extraction using a machine learning model
Authors: Rangel Pinto Juan David , Guerrero Jose L. , Rivera Lorena , Parada-Pinilla María Paula , Cala Mónica P. , López Gina , González Barrios Andrés Fernando
Published: October 2024

In this study a Machine Learning model was employed to predict the lipid profile from supercritical fluid extraction (SFE) of microalgae Galdieria sp. USBA-GBX-832 under different temperature (40, 50, 60°C), pressure (150, 250 bar), and ethanol flow (0.6, 0.9 mL min-1) conditions. Six machine learning regression models were trained using 33 independent variables: 29 from RD-Kit molecular descriptors, three from the extraction conditions, and the infinite dilution activity coefficient (IDAC). The lipidomic characterization analysis identified 139 features, annotating 89 lipids used as the entries of the model, primarily glycerophospholipids and glycerolipids. It was proposed a methodology for selecting the representative lipids from the lipidomic analysis using an unsupervised learning method, these results were compared with Tanimoto scores and IDAC calculations using COSMO-SAC-HB2 model. The models based on decision trees, particularly XGBoost, outperformed others (RMSE: 0.035, 0.095, 0.065 and coefficient of determination (R2): 0.971, 0.933, 0.946 for train, test and experimental validation, respectively), accurately predicting lipid profiles for unseen conditions. Machine Learning methods provide a cost-effective way to optimize SFE conditions and are applicable to other biological samples.
Systematic identification of therapeutic targets for coronary artery calcification: an integrated transcriptomic and proteomic Mendelian randomization
Authors: Chen Lihong , Ye Xiaoqi , Li Yan , Ran Xingwu
Published: October 2024

Background

Coronary artery calcification (CAC) is associated with an increased risk of mortality and cardiovascular events. However, none therapeutic drugs have been proven effective for CAC treatment. The objective of this study was to identify potential therapeutic targets for CAC through the utilization of Mendelian randomization (MR) and colocalization analysis.

Methods

The expression quantitative trait loci (eQTLs) of 16,943 genes from the eQTLGen consortium and protein quantitative trait loci (pQTLs) of 4,412 proteins from a plasma proteome were utilized as genetic instruments. Genetic associations with CAC were derived from a GWAS meta-analysis of 26,909 individuals. The MR and colocalization analysis were utilized to identify potential target genes.

Results

A total of 671 genes were found to be significantly associated with the risk of CAC based on transcriptomic MR analysis at a false discovery rate <0.05, while proteomic MR analysis identified 15 genes with significant associations with CAC at the same threshold. With robust evidence from colocalization analysis, we observed positive associations between CWF19L2, JARID2, and MANBA and the risk of CAC, while KLB exhibited an inverse association. In summary, our study identified 23 potential therapeutic targets for CAC. Further downstream analysis revealed IGFBP3, ABCC6, ULK3, DOT1L, KLB and AMH as promising candidates for repurposing in the treatment of CAC.

Conclusion

The integrated MR analysis of transcriptomic and proteomic data identified multiple potential drug targets for the treatment of CAC. ULK3, DOT1L, and AMH were recognized as novel targets for drug repurposing for CAC and deserve further investigation.
A qualitative study illustrating factors that enable and constrain academic advising practices in a Global South context
Authors: Versfeld Jessica , Mapaling Curwyn
Published: October 2024

Introduction

Academic advising plays a crucial role in South African higher education, especially considering the country’s diverse student population, historical injustices, and socio-economic inequalities. However, there is a lack of research supporting academic advising practices in this context.

Methods

This study employs a qualitative methodology, using semi-structured in-depth interviews with four academic advisors from the Engineering, Built Environment, and Information Technology (EBIT) department at a South African university. A socio-ecological lens is applied to explore the factors enabling and constraining best practices in academic advising.

Results

Key findings reveal that academic advisors face challenges such as limited resources and institutional support. However, opportunities exist for fostering student resilience and academic success. The study identifies enablers and constraints across microsystemic (e.g., advisor passion and resilience), mesosystemic (e.g., interdepartmental collaboration), and macrosystemic (e.g., institutional policies, socio-economic factors) levels.

Discussion

As part of the Global South, South Africa shares many socio-economic and educational challenges with other countries in the region. The study’s findings offer insights that may be relevant to similar contexts. By illuminating the mechanisms that empower the academic advising community, this research seeks to inform the development of more effective student support interventions. The socio-ecological framework provides a comprehensive understanding of the interconnected influences contributing to the efficacy and challenges faced by academic advisors in engineering departments.
Association between hypothyroidism and metabolic syndrome in Qinghai, China
Authors: Fan Xiaoxia , Yao Yongli , Chai Shengjun , Wang Beibei , Xie Yanling , Jiang Yanping , Lin Lijun , Li Yanan , Fan Peiyun , Luo Wei , Wang Shuqiong , Song Kang , Zhao Lingling , Cai Chunmei
Published: October 2024

Objective

To investigate the epidemiological characteristics of hypothyroidism in Qinghai Province, analyze its related influencing factors, establish the normal reference range of thyroid function, and explore the relationship between thyroid hormone (THs), thyroid stimulating hormone (TSH) and metabolic syndrome (MS) in Qinghai population within the normal range, so as to provide some scientific basis for the prevention and treatment of hypothyroidism in Qinghai Province.

Methods

A total of 2790 residents aged 18 and over from Qinghai were selected through stratified cluster random sampling. Data were collected via questionnaires, physical examinations, and laboratory tests.

Results

1. A total of 2628 eligible residents in Qinghai were included in this study, and the total prevalence of hypothyroidism was 30.25%, among which the prevalence of subclinical hypothyroidism was 29.22%, and the prevalence of clinical hypothyroidism was 1.03%. 2. The prevalence of hypothyroidism in women was significantly higher than that in men (36.69% vs 24.30%); smoking and drinking were risk factors for hypothyroidism. 3. In the excluded subjects, 1544 were abnormal thyroid ultrasound, abnormal thyroid function and/or positive thyroid autoantibodies, and the remaining 1084 were reference populations. According to the reference population data, the 95% reference ranges of TSH, FT4, FT3 were 0.43-5.51 mIU/L, 11.0-20.4 pmol/L, 3.63-5.73 pmol/L, respectively. 4. In the normal thyroid function population in Qinghai, MS and its related components were positively correlated with FT3 and FT4 levels, but not significantly correlated with TSH levels.

Conclusion

1. The prevalence of hypothyroidism in adults in Qinghai is relatively high, accounting for about one-thirtieth of the total population. Smoking and drinking have a certain impact on the incidence of hypothyroidism. 2. It provides a reference range for the diagnosis of thyroid diseases in Qinghai province, which is different from that of reagent suppliers, and has certain promotion significance in the western region. 3. MS and its related components are positively correlated with FT3 and FT4 levels, but not with TSH levels in people with normal thyroid function in Qinghai. Early thyroid function screening is of great significance for the prevention of MS.
Case report: exome sequencing identified mutations in the LRP5 and LGR4 genes in a case of osteoporosis with recurrent fractures and extraskeletal manifestations
Authors: Mehta Poonam , Sharma Aakriti , Goswami Anupam , Gupta Sushil Kumar , Singhal Vaibhav , Srivastava Kinshuk Raj , Chattopadhyay Naibedya , Singh Rajender
Published: October 2024

Background

Genetic mutations have been reported in a number of bone disorders with or without extra-skeletal manifestations. The purpose of the present study was to investigate the genetic cause in a middle-aged woman with osteoporosis, recurrent fractures and extraskeletal manifestations.

Methods

A 56-year-old Indian woman presented to the clinic with complaints of difficulty in walking, recurrent fractures, limb bending, progressive skeletal deformities, and poor overall health. At the age of 37, she had experienced severe anemia with diarrhea, significant weight loss, knuckle pigmentation, and a significant loss of scalp hair. She had received multiple blood transfusions and parenteral iron supplementation with normalization of hemoglobin. Subsequently, she had premature menopause at the age of 37. She died at the age of 61 due to liver failure. Exome sequencing followed by Sanger sequencing were undertaken to identify the potential pathogenic mutations.

Results

Genetic investigation identified likely pathogenic mutations in the LRP5 and LGR4 genes. Out of the two mutations, the heterozygous mutation (c.1199C>T) in the LRP5 gene resulted in a non-synonymous substitution of alanine with valine at the 400th position, and the second mutation (c.1403A>C) in the LGR4 gene led to a non-synonymous substitution of tyrosine with serine at the 468th residue of the protein. The minor allele frequencies of the c.1199C>T (LRP5) substitution in the 1000 genomes and IndiGenomes databases are 0.0003 and 0.001, while the c.1403A>C (LGR4) substitution has not been reported in these databases. Various in silico prediction tools suggested LGR4 mutation to be pathogenic and LRP5 mutation to be likely pathogenic.

Conclusion

Heterozygous mutations in the LRP5 and LGR4 genes had additive deteriorative effects on BMD, resulting in recurrent fractures and bone deformities, and extended the effect to extraskeletal sites, contributing to the poor overall health in this patient.
Evolution of the ecological security pattern of the Yellow River Basin based on ecosystem services: a case study of the Shanxi section, China
Authors: Wang Jinfang , Lv Zhihong , Zhen Zhilei , Wu Qian
Published: October 2024

Identifying and evaluating the ecological security pattern (ESP) of region can provide a solid foundation for optimizing regional ecosystem elements and improving regional ecological security. The PLUS model, InVEST model, and circuit theory were used to analyze the ecosystem services and ESP of the Shanxi section of the Yellow River Basin (SYRB) between 2005 and 2035. The findings revealed that 1) The total area of land use shift across categories between 2005 and 2020 was 6,080.99 km2, or 5.22% of the SYRB’s total area. Under the natural development scenario, the total land transfer area from 2020 to 2035 was predicted to be 4,605.10 km2. Among these, the tendency for construction and forest land was expanding, while the tendency for cultivated land, grassland, water area, and unused land was shrinking; 2) From 2005 to 2035, the SYRB’s water yield and soil conservation all decreased, while the habitat quality and carbon storage showed a declining tendency; 3) The ecological source increased from 35,767.00 km2 in 2005 to 39,931.00 km2 in 2035; the total length of the ecological corridors expanded from 2,792.24 km to 3,553.18 km between 2005 and 2035; the ecological pinch points increased from 27 in 2005 to 40 in 2035; the ecological barrier points increased from 21 in 2005 to 28 in 2035, which show that the ESP remained unstable; 4) According to the ecosystem service characteristics of the SYRB in 2020, an ESP of “one axis, two zones, four corridors, and multiple points” was constructed. This study could provide useful guidance for improving the spatial pattern of land use and maintaining ecosystem services.
Assessment of pollution and other impairments of US reservoirs based on expert opinion
Authors: Miranda L. E. , Shoemaker D. J. , Krogman R. M.
Published: October 2024

A comprehensive understanding of the prevailing pollution and other impairments to reservoirs is necessary at the national level to analyze patterns and causes as well as allocate national resources effectively. Most of these impairments are associated with sedimentation, nutrient contamination, and other pollution factors. The costs involved in conducting on-site surveys at multiple locations are potential obstacles for obtaining empirical data on large-scale spatial impairments. In such cases, inputs from specialists may be required to offset the absence of empirical data for determining the impairment statuses of thousands of geographically dispersed reservoirs. Thus, our aim was to examine whether expert opinion could offer a comprehensive review of the impairment statuses of numerous reservoirs in the United States. We designed and executed an internet-based survey of reservoir specialists to gather their ratings on visually evident elements of reservoir impairment. To evaluate the ratings, we searched for correlations with factors known to have impacts on reservoir impairment. Canonical correlation analyses indicated that nine metrics used by experts to rate impairment levels on an ordinal scale were correlated with metrics descriptive of the physical qualities of reservoirs, land use in catchments, and prevailing local climate. We thus conclude that expert opinions may facilitate assessments of impairment levels over large geographical areas. Lastly, we define the circumstances under which it is permissible to rely on expert opinions and propose criteria that could improve the quality of the data collected.
Determinants of micronutrient supplementation during pregnancy among women in three sub-Saharan African countries: a multilevel logistic regression model
Authors: Mekonen Enyew Getaneh , Zegeye Alebachew Ferede , Workneh Belayneh Shetie , Ali Mohammed Seid , Gonete Almaz Tefera , Alemu Tewodros Getaneh , Tamir Tadesse Tarik , Tekeba Berhan , Wassie Mulugeta , Kassie Alemneh Tadesse
Published: October 2024

Background

Poor maternal nutrition during pregnancy is a common cause of poor maternal and infant outcomes. Micronutrient deficiencies are common among pregnant women in low- and middle-income countries, including sub-Saharan Africa. Pregnant women are recommended to take micronutrients like iron or folic acid and deworming medication during pregnancy. Therefore, this study was conducted to assess micronutrient intake and its associated factors among pregnant women in three countries using the most recent demographic and health survey.

Methods

We used data from the most recent demographic and health surveys, which were carried out between 2019 and 2022 in three sub-Saharan African countries. The study included a weighted sample of 13,568 reproductive-age women who had given birth within the five years prior to the survey. Utilizing multilevel logistic regression, the factors associated with the dependent variable were identified. Model comparison and fitness were assessed using the deviance (-2LLR), likelihood ratio test, median odds ratio, and intra-class correlation coefficient. Ultimately, factors were deemed statistically significant if they had a p-value less than 0.05.

Results

The pooled prevalence of micronutrient intake among pregnant women during pregnancy of last birth was 77.56% (95% CI: 76.85%–78.25%). Factors like age [AOR = 1.78; 95% CI (1.14, 2.77)], educational status [AOR = 1.49; 95% CI (1.23, 1.79)], marital status [AOR = 0.66; 95% CI (0.58, 0.75)], working status [AOR = 1.17; 95% CI (1.01, 1.34)], media exposure [AOR = 1.20; 95% CI (1.05, 1.38)], preceding birth interval [AOR = 1.17; 95% CI (1.01, 1.34)], number of ANC visits [AOR = 1.65; 95% CI (1.29, 2.10)], and residence [AOR = 1.19; 95% CI (1.03, 1.37)] were significantly associated with micronutrient intake among pregnant women.

Conclusions

More than three-fourths of the study subjects were micronutrient supplemented during their pregnancy. Improving women's education, disseminating nutrition information through media, providing more attention to young pregnant women who live in rural areas, increasing the number of ANC visits, and women's empowerment are strongly recommended.
Epstein–Barr virus reactivation in pediatric allogeneic stem cell transplant recipients: an 11-year experience on viral load and B lymphocyte monitoring strategy
Authors: Ferrando Giulia , Bagnasco Francesca , Pierri Filomena , Pestarino Sara , Dell’Orso Gianluca , Giardino Stefano , Di Marco Eddi , Santaniello Maria , Castagnola Elio , Faraci Maura
Published: October 2024

Background

Epstein–Barr virus (EBV) reactivation represents a frequent condition after allogeneic hematopoietic stem cell transplantation (allo-HCT) and can cause the development of a severe complication: post-transplant lymphoproliferative disease (PTLD). This retrospective study aims at investigating the incidence of EBV reactivations and analyzing the potential impact of recipient/donor-related transplant-related factors in pediatric patients. The secondary objective was to study the consequences of the approach used at our center regarding the initiation of pre-emptive therapy.

Methods

This study used a retrospective evaluation of patients aged ≤25 years who received an allo-HCT at IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Giannina Gaslini, between 2012 and 2022, with follow-up censored in July 2023. Criteria to start rituximab were as follows: a viral load ≥20,000 copies/105 PBMCs or ≥10,000/105 PBMCs associated with a rise in the proportion of CD 20+ lymphocytes.

Results

Overall, 214 allo-HCTs were performed in 189 patients. A total of 127 (59.3%) procedures were complicated by at least one EBV reactivation, but in only one rituximab was administered. All other reactivations were characterized by viremia below reference ranges and no increase in CD20+ lymphocytes, without clinical consequences. Risk factors for EBV reactivation identified were associated with delayed immune reconstitution.

Conclusion

These results could suggest the effectiveness of the approach used in providing pre-emptive therapy. The strategy adopted differs from that highlighted by other studies and allowed the reduction of the number of children who received rituximab. It has proven effective considering the low incidence rate of PTLD and reduces the risk of rituximab-related adverse events.
Development patterns of the dynamic elastic modulus of saturated coral sand under different drainage conditions
Authors: Zhou Ruirong , Huo Zhilei , Liu Qifei , Yu Qingquan , Wu Qi
Published: October 2024

Long-term cyclic loading can have a significant effect on the modulus of sand, and the influence on saturated coral sand has yet to be established. In this paper, the significant influence of non-plastic fines content (FC) and relative density (Dr) on dynamic elastic modulus (E) of saturated coral sand has been evaluated by a series of cyclic triaxial drainage tests. The results show that the dynamic elastic modulus increases rapidly at the beginning of loading; then the growth slows down and finally stabilizes. In general, the development of E is influenced collectively by FC, Dr and cyclic stress ratio (CSR). The initial dynamic elastic modulus Ed-1 and steady-state dynamic elastic modulus Ed-s increase with the increase of Dr, and decrease as FC increases. The linear fitting equations are given by introducing the equivalent skeleton void ratio esk*. Furthermore, the relative dynamic elastic modulus Er is defined as the ratio of Ed-N to Ed-s, and the prediction equation for Er was developed to provide a basis for the engineering mechanical parameters of coral sands under long-term loads.
Research on the factors affecting the compressive strength of rubber powder modified cement-stabilized crushed stone based on orthogonal experiments
Authors: Xu Feng , Zhu Xuanxuan , Gao Qiju
Published: October 2024

Based on an orthogonal experimental design, this study introduces rubber powder particle size alongside rubber powder content, aggregate gradation, and cement content as factors. A total of 16 mix proportions were formulated. For each mixture, compaction tests and unconfined compressive strength (UCS) tests were conducted. Using Statistical Product and Service Solutions (SPSS) software, a multifactor variance analysis was performed to determine the influence levels of the four factors on maximum dry density and compressive strength. The optimal mix proportion was selected based on compressive strength. The results indicate that aggregate gradation and rubber powder content significantly affect the maximum dry density of the mixture, with aggregate gradation having the greatest impact. Rubber powder content has the most substantial effect on compressive strength, while rubber particle size has the least influence. The optimal formulation is 7% cement content, 30-mesh rubber powder, 0.5% rubber powder content, and a skeletal dense gradation close to the median.
Clinical pharmacist interventions in nutrition-and drug-related problems in critically ill patients with renal dysfunction: a non-randomized controlled study
Authors: Özgan Betül , Ayhan Yunus Emre , Apikoglu Sule , Karakurt Sait
Published: October 2024

Background

Critically ill intensive care unit (ICU) patients often face life-threatening drug-related problems (DRPs) and malnutrition. Clinical pharmacists (CPs) play a crucial role in mitigating these issues and improving outcomes.

Aim

This study was designed to detect, prevent, reduce or resolve nutrition-related problems (NRPs) and DRPs in intensive care patients with renal dysfunction through clinical pharmacy services.

Method

This 9-month, prospective, non-randomized, controlled study was conducted in the ICU. During the intervention period (IP), CP recommendations addressing NRPs and DRPs were provided to the healthcare team. NRPs were evaluated using an expert-developed enteral nutrition consensus protocol, while DRPs were classified according to the Pharmaceutical Care Network Europe (PCNE) Classification for Drug-Related Problems Version 9.1.

Results

The study included 60 patients with a median age of 73 years (IQR: 60.5–80). A total of 504 DRPs (8.4 per patient) were identified across all patients. DRPs were decreased by 50% during the IP compared to the observation period (OP) (p < 0.001). The most common causes of DRPs were ‘too low a drug dose’ (22.2%), ‘drug–drug interactions’ (17%), and ‘too high a drug dose’ (16.4%). Of the recommendations made to the prescribing physician, 140 (97.9%) were accepted. In the IP, targeted calorie and protein supplementation was fully achieved in more patients (p < 0.05). The most common recommendations included ‘changes in the rate of nutrition’ (66.7%), ‘vitamin supplementation’ (16.7%), and ‘changes in enteral nutrition products’ (7.7%).

Conclusion

This study highlights the high incidence of DRPs and malnutrition risk in ICU patients with renal dysfunction, emphasizing the vital role of clinical pharmacists. Their collaboration with healthcare professionals significantly reduced both DRPs and NRPs.
Use of esketamine for tracheoscopic drug injection: a randomized controlled trial
Authors: Zhao Xiaoming , Zhou Zhendong , Li Zhenhua , Hu Zhaolan , Yu Yuanyuan
Published: October 2024

Background

Sufentanil may induce hypotensive bradycardia and other adverse reactions in elderly patients during anesthesia, while esketamine exhibits sedative and analgesic effects with minimal impact on respiration and circulation. The objective of this study was to investigate the impact of these two anesthetics on vital signs in patients undergoing bronchoscopy and lavage under general anesthesia.

Method

This study was a randomized controlled trial with a parallel design. A total of 100 patients aged ≥60 years with ASAI or II who were undergoing bronchoscopy and lavage were randomly assigned to two groups: group A (esketamine, n = 50) and group B (sufentanil, n = 50). During anesthesia induction, both groups received intravenous infusion of propofol at a dose of 1.5 mL/kg and atracurium. In group A, esketamine at a dose of 0.3 mg/kg was injected; in group B, sufentanil at a dose of 0.2 μg/kg was injected intravenously. Subsequently, a laryngeal mask was inserted and connected to an anesthesia machine for mechanical ventilation. Anesthesia maintenance involved continuous intravenous infusion of propofol at a dose of 3 mL/kg. The mean arterial pressure (MAP), heart rate (HR), and blood oxygen saturation (SpO2) were recorded at various time points: before anesthesia injection (T0), after laryngeal mask insertion (T1), 5 min after the operation started (T2), 15 min after the operation started (T3), and before the end of the operation (T4). Additionally, the recovery time was recorded.

Results

The blood pressure of patients in the esketamine group exhibited higher levels compared to those in the sufentanil group at multiple time points during the operation, while maintaining a more stable intraoperative blood pressure and shorter postoperative recovery time than that observed in the sufentanil group. The blood pressure and heart rate of patients in the esketamine group exhibited significant fluctuations after laryngeal mask implantation compared to pre-anesthesia induction, with a statistically significant increase observed. Conversely, no significant changes were observed in the sufentanil group. The heart rate and oxygen saturation showed no significant differences between the two groups, nor did the amount of propofol administered during the procedure.

Conclusion

The utilization of esketamine during the induction phase of bronchoscopy and lavage under general anesthesia can enhance hemodynamic stability and reduce the occurrence of hypotension, thereby facilitating postoperative anesthetic recovery.
Metagenome-based characterization of the gut bacteriome, mycobiome, and virome in patients with chronic hepatitis B-related liver fibrosis
Authors: Chen Wenlin , Liang Fang , Zhang Yue , Zhang Yuncheng , Lv Jinzhen , Jin Xiande , Ran Yun , Li Shenghui , Sun Wen
Published: October 2024

Introduction

The gut microbiota is believed to be directly involved in the etiology and development of chronic liver diseases. However, the holistic characterization of the gut bacteriome, mycobiome, and virome in patients with chronic hepatitis B-related liver fibrosis (CHB-LF) remains unclear.

Methods

In this study, we analyzed the multi-kingdom gut microbiome (i.e., bacteriome, mycobiome, and virome) of 25 CHB-LF patients and 28 healthy individuals through whole-metagenome shotgun sequencing of their stool samples.

Results

We found that the gut bacteriome, mycobiome, and virome of CHB-LF patients were fundamentally altered, characterized by a panel of 110 differentially abundant bacterial species, 16 differential fungal species, and 90 differential viruses. The representative CHB-LF-enriched bacteria included members of Blautia_A (e.g., B. wexlerae, B. massiliensis, and B. obeum), Dorea (e.g., D. longicatena and D. formicigenerans), Streptococcus, Erysipelatoclostridium, while some species of Bacteroides (e.g., B. finegoldii and B. thetaiotaomicron), Faecalibacterium (mainly F. prausnitzii), and Bacteroides_A (e.g., B. plebeius_A and B. coprophilus) were depleted in patients. Fungi such as Malassezia spp. (e.g., M. japonica and M. sympodialis), Candida spp. (e.g., C. parapsilosis), and Mucor circinelloides were more abundant in CHB-LF patients, while Mucor irregularis, Phialophoraverrucosa, Hortaea werneckii, and Aspergillus fumigatus were decreases. The CHB-LF-enriched viruses contained 18 Siphoviridae, 12 Myoviridae, and 1 Podoviridae viruses, while the control-enriched viruses included 16 Siphoviridae, 9 Myoviridae, 2 Quimbyviridae, and 1 Podoviridae_crAss-like members. Moreover, we revealed that the CHB-LF-associated gut multi-kingdom signatures were tightly interconnected, suggesting that they may act together on the disease. Finally, we showed that the microbial signatures were effective in discriminating the patients from healthy controls, suggesting the potential of gut microbiota in the prediction of CHB-LF and related diseases.

Discussion

In conclusion, our findings delineated the fecal bacteriome, mycobiome, and virome landscapes of the CHB-LF microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies.
The impact of pine wilt disease on the endophytic microbial communities structure of Pinus koraiensis
Authors: Li Debin , Yu Yuezhen , Tian Chuan , Lu Shisong , Jiang Shengwei
Published: October 2024

Pine Wilt Disease (PWD) is a devastating pine tree disease characterized by rapid onset, high mortality rate, quick spread, and difficulty in control. Plant microbiome plays a significant role in the development of PWD. However, the endophytic microbial communities of Pinus koraiensis infected by pine wood nematode (PWN) Bursaphelenchus xylophilus remain largely unexplored. In this study, we analyzed the structural changes of endophytic communities of P. koraiensis after infection by the PWN using high-throughput sequencing technology. The results showed that the community structure underwent significant changes as the degree of PWN infection intensified. The diversity and abundance of endophytic fungi in P. koraiensis increased, while those of endophytic bacteria in P. koraiensis decreased during the infection process. Meanwhile, the abundance of some dominant microorganisms has also changed, including species such as Graphilbum and Pseudoalteromonas. Functional prediction analysis showed that the functional composition of endophytic fungi in P. koraiensis was significantly different across the development of PWD, while the composition of endophytic bacteria remained essentially similar. The results indicated that PWN infection had a significant impact on the structure, diversity, abundance, and functional gene composition of endophytic microbial communities in P. koraiensis, and most of the main endophytic microbial groups tended to coordinate with each other. This work provides a better understanding of the changes in endophytic community structure and function caused by PWD infection of P. koraiensis, which may benefit the exploration of potential endophytes for PWN biocontrol.
Mean global field power is reduced in infantile epileptic spasms syndrome after response to vigabatrin
Authors: Nair Arjun , Ewusie Joycelyne , Pentz Rowan , Whitney Robyn , Jones Kevin
Published: October 2024

Purpose

Infantile epileptic spasms syndrome (IESS) is associated with abnormal neuronal networks during a critical period of synaptogenesis and brain plasticity. Hypsarrhythmia is a visual EEG biomarker used to diagnose IESS, assess response to treatment, and monitor relapse. Computational EEG biomarkers hold promise in providing unbiased, reliable, and objective criteria for clinical management. We hypothesized that computational and visual EEG biomarkers of IESS would correlate after treatment with vigabatrin and that these responses might differ between responders and non-responders.

Methods

A retrospective analysis was conducted at a single center, involving children with IESS at initial diagnosis and following first-line treatment with vigabatrin. Visual EEG biomarkers of hypsarrhythmia were compared with computational EEG biomarkers, including spike and spike fast-oscillation source coherence, spectral power, and mean global field power, using retrospective analysis of EEG recorded at initial diagnosis and after vigabatrin treatment. Responders and non-responders were compared based on the characteristics of their follow-up EEGs.

Results

In this pilot study, we observed a reduction in the EEG biomarker of hypsarrhythmia/modified hypsarrhythmia from 20/20 (100%) cases at the initial diagnosis to 9/20 (45%) cases after treatment with vigabatrin, indicating a 55% (11/20) responder rate. No significant difference in spike frequency was observed after treatment (p = 0.104). We observed no significant differences after treatment with vigabatrin in the computational EEG biomarkers that we assessed, including spike source coherence at 90% (p = 0.983), spike source coherence lag range (p > 0.999), spike gamma source coherence at 90% (p = 0.177), spike gamma source coherence lag range (p > 0.999), spectral power (0.642), or mean global field power (0.932). However, when follow-up EEGs were compared, there was a significant difference in mean global field power (p = 0.038) between vigabatrin responders and non-responders. In contrast, no such difference was observed for spike source coherence at 90% (p = 0.285), spike course coherence lag range (p = 0.819), spike gamma source coherence at 90% (p = 0.205), spike gamma source coherence lag range (p > 0.999), or spectral power (p = 0.445). Finally, our treated group did not differ significantly from healthy controls at initial diagnosis or follow-up in terms of spectral power (p = 0.420) or mean global field power (0.127).

Conclusion

In this pilot study, we show that mean global field power is a computational EEG biomarker that is significantly reduced in IESS after treatment with vigabatrin. Although computational EEG biomarkers of network connectivity using spike source coherence appear to be a promising tool, future studies should further explore their potential for assessing treatment responses in IESS.
Therapeutic advances in hepatocellular carcinoma: an update from the 2024 ASCO annual meeting
Authors: Yang Hongyuan , Liu Yanju , Zhang Na , Tao Fengbao , Yin Gaozheng
Published: October 2024

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related deaths worldwide. Recent advances in immunotherapies, targeted therapies, and combination treatments have significantly improved outcomes for many patients with HCC. This review summarizes key findings from the 2024 ASCO Annual Meeting, focusing on emerging therapies, including immune checkpoint inhibitors (ICIs), CAR-T cell therapies, oncolytic viruses, and locoregional treatments like transarterial chemoembolization (TACE) and hepatic arterial infusion chemotherapy (HAIC). ICIs, particularly when combined with other agents, have shown promising efficacy, though challenges such as immune-related adverse events and resistance mechanisms remain. CAR-T cell therapies and oncolytic viruses offer novel therapeutic avenues for advanced HCC, but their long-term efficacy in solid tumors is still under investigation. Locoregional therapies, especially in combination with systemic treatments, continue to play a critical role in managing unresectable HCC and improving conversion rates to surgical resection. Additionally, the potential of biomarkers, such as hypoxia scores and CTNNB1 mutations, is being explored to better personalize treatment and predict patient responses. These biomarkers could pave the way for more targeted and effective therapeutic strategies. Overall, the recent studies presented at the ASCO meeting highlight progress in HCC treatment, underscoring the importance of continued innovation. Future research should focus on overcoming resistance mechanisms, optimizing combination therapies, and integrating biomarker-driven approaches to improve patient outcomes and enhance personalized treatment strategies.
Weight status change during four years and left ventricular hypertrophy in Chinese children
Authors: Liu Qin , Li Cheng , Yang Lili , Gong Zhuo , Zhao Min , Bovet Pascal , Xi Bo
Published: October 2024

Objective

It is well-established that overweight/obesity is a major risk factor for left ventricular hypertrophy (LVH) in childhood. However, it is still unclear if reversing from overweight/obesity to normal weight is associated with decreased LVH in children. This study aimed to examine the association between weight status change during four years and LVH among Chinese children based on a prospective cohort study.

Methods

Data were obtained from the Huantai Childhood Cardiovascular Health Cohort Study in China. A total of 1,178 children without LVH at baseline (mean age: 8.3 years) were included in this study. According to weight status [normal weight or overweight (including obesity)] at baseline (2017) and follow-up (2021), children were divided, based on sex- and age-adjusted body mass index (BMI), into four groups: persistent normal weight (normal weight at both baseline and follow-up), incident overweight (normal weight at baseline but overweight at follow-up), reversal to normal weight (overweight at baseline but normal weight at follow-up), persistent overweight (overweight at both baseline and follow-up).

Results

After adjustment for potential confounding factors, children with incident overweight (n = 114, 30.63 ± 4.74 g/m2.7) and those with persistent overweight (n = 363, 31.56 ± 6.24 g/m2.7) had higher left ventricular mass index (LVMI) at the end of the follow-up period than those with persistent normal weight (n = 632, 28.46 ± 7.64 g/m2.7), while those who reversed from overweight to normal weight had a non-significantly lower LVMI (n = 69, 28.51 ± 4.28 g/m2.7). Compared to children with persistent normal weight, those with persistent overweight [odds ratio (OR) = 5.14, 95% confidence interval (CI) = 3.33–7.95] and those with incident overweight (OR = 3.34, 95% CI = 1.77–6.30) had an increased risk of LVH. The risk of LVH tended to decrease, although not significantly, in those who reversed from overweight to normal weight (OR = 0.76, 95% CI = 0.22–2.55).

Conclusion

Our findings demonstrate a positive association between overweight and left ventricular mass in children and suggest that LVH in childhood could be attenuated by weight loss.
Comprehensive analysis of transcription factor binding sites and expression profiling of rice pathogenesis related genes (OsPR1)
Authors: Kumari Diksha , Prasad Bishun Deo , Dwivedi Padmanabh , Sahni Sangita , Kumar Mankesh , Alamri Saud , Adil Muhammad Faheem , Alakeel Khaled A.
Published: October 2024

Pathogenesis-related (PR) proteins, found in plants, play a crucial role in responding to both biotic and abiotic stresses and are categorized into 17 distinct families based on their properties and functions. We have conducted a phylogenetic analysis of OsPR1 genes (rice PR1 genes) in conjunction with 58 putative PR1 genes identified in Brachypodium distachyon, Hordeum vulgare, Brassica rapa, and Zea mays through BLASTP predictions. We extensively investigated the responses of the remaining 11 rice PR1 genes, using OsPR1a as a reference, under various stress conditions, including phytohormone treatments (salicylic acid and brassinosteroid [BR]), wounding, and heat stress (HS). In rice, of the 32 predicted OsPR1 genes, 12 have been well-characterized for their roles in disease resistance, while the functions of the remaining genes have not been studied extensively. In our study, we selected an additional 11 OsPR1 genes for further analysis and constructed a phylogenetic tree based on the presence of a 10-amino-acid-long conserved motif within these proteins. The phylogenetic analysis revealed that both OsPR1a from earlier studies and OsPR1-74 from our current study belong to the same clade. These genes consistently exhibit upregulation in response to diverse stress treatments such as biotic stress and abiotic stresses such as heat, drought, and salinity, indicating their potential roles in enhancing stress tolerance in rice. Significantly, this study delves into the previously unexplored role of OsPR1 genes in responding to Brassinosteroid (BR) and heat stress (HS) treatments, confirming their involvement in stress responses through qRT-PCR analysis. We found that seven genes were upregulated by EBR treatment. During heat stress (HS), six and seven genes were upregulated at 1hand 4h HS, respectively. The remaining genes OsPR1-22 and OsPR1-75 were upregulated at 1h but downregulated at 4h HS and under EBR treatment. In contrast, OsPR1-76 was upregulated at both 1h and 4h HS, but downregulated under EBR treatment. Promoters of PR1 genes in rice and other crops are rich in transcription factor binding sites (TFBSs) and feature a conserved Cysteine-rich secretory protein (SCP or CAP) motif. This study advances our understanding of PR1 gene regulation and its potential to enhance stress tolerance in rice.
Impacts of long-term different fertilization regimes on microbial utilization of straw-derived carbon in greenhouse vegetable soils: insights from its ecophysiological roles and temperature responses
Authors: Ma Long , Li Ruonan , Luan Haoan , Tang Jiwei , Wang Liying , Guo Tengfei , Huang Shaowen
Published: October 2024

As the largest organic carbon input in the agroecosystems, crop residues can increase soil carbon sequestration and crop production in greenhouse vegetable fields (GVFs). However, the soil microbiological mechanisms driving straw decomposition in GVFs under different incubation temperatures and fertilization treatments are not clear. Thus, soil samples were collected from a long-term field experiment included chemical fertilizer application alone (CF), 2/4 fertilizer N+2/4 organic fertilizer N (CM), 2/4 fertilizer N+1/4 organic fertilizer N+1/4 straw N (CMS), 2/4 fertilizer N+2/4 straw N (CS), and incubated with 13C-labeled straw at different temperatures (15, 25, and 35°C) for 60 days. Organic-amended treatments (CM, CMS, and CS), especially CMS treatment, increased soil bacterial Alpha diversity before and after straw addition. Straw decomposition process was dominated by soil Proteobacteria, Actinobacteria, and Firmicutes for each treatments. The effect of incubation temperature on soil microbial community composition was higher than that of fertilization treatments. Soil Alphaproteobacteria and Actinomycetia were the most predominant class involved in straw decomposition. Gammaproteobacteria (Pseudomonas, Steroidobacter, Acidibacter, and Arenimonas) were the unique and predominant class involved in straw decomposition at medium and high temperatures as well as in the straw-amended treatments. Organic-amended treatments, especially straw-amended treatments, increased the relative abundance of glycosyl transferases (GT) and auxiliary activities (AA). Alphaproteobacteria, Actinomycetia, and Gammaproteobacteria had higher relative contribution to carbohydrase genes. In summary, the long-term organic-amended treatments altered the structure of soil microbial communities and increased soil bacterial diversity, with the CMS having a greater potential to enhance resistance to external environmental changes. Soil Alphaproteobacteria and Actinomycetia were responsible for the dominance of straw decomposition, and Gammaproteobacteria may be responsible for the acceleration of straw decomposition. Fertilization treatments promote straw decomposition by increasing the abundance of indicator bacterial groups involved in straw decomposition, which is important for isolating key microbial species involved in straw decomposition under global warming.
Syntax and the brain: language evolution as the missing link(ing theory)?
Authors: Benítez-Burraco Antonio , Progovac Ljiljana
Published: October 2024

Introduction

This paper provides proof of concept that neurolinguistic research on human language syntax would benefit greatly by expanding its scope to include evolutionary considerations, as well as non-propositional functions of language, including naming/nicknaming and verbal aggression. In particular, an evolutionary approach can help circumvent the so-called granularity problem in studying the processing of syntax in the brain, that is, the apparent mismatch between the abstract postulates of syntax (e.g. Tense Phrase (TP), Determiner Phrase (DP), etc.) and the concrete units of neurobiology (neurons, axons, etc.).

Methods

First, we decompose syntax into its evolutionary primitives, identifying one of the earliest stages as a simple, flat combination of just one verb and one noun. Next, we identify proxies (“living fossils”) of such a stage in present-day languages, including compounds and small clauses, lacking at least some layers of structure, e.g. TPs and DPs. These proxies of ancestral language have been subjected to fMRI neuroimaging experiments.

Results

We discuss the finding that less hierarchical small clauses, in contrast to full sentences with TPs and DPs, show reduced activation in the left Broca’s area (BA) 44 and the right basal ganglia, consistent with the hypothesis that more recent, more elaborate syntax requires more connectivity in the Broca’s-basal ganglia network, whose neuronal density has been significantly enhanced in recent evolution, implicating mutations in FOXP2 and other genes. We also discuss the finding that the processing of ancestral verb-noun compounds, which are typically used for (derogatory) naming and nicknaming, shows enhanced activation in the right fusiform gyrus area (BA 37), the area that is implicated in the processing of metaphoricity and imageability, but also in naming and face recognition, opening up an intriguing possibility that the enhanced face recognition in humans was facilitated by the early emergence of a simple syntactic strategy for naming.

Discussion

The considerations in this paper are consistent with the hypothesis of a gradual gene-culture co-evolution of syntax and the brain, targeting cortico-striatal brain networks. It is also of note that a sound grounding in neurobiology of language should in turn inform syntactic theories themselves.