bluuebunny/crossref_metadata_2025 huggingface dataset:
Antifungal activity of copper oxide nanoparticles derived from Zizyphus spina leaf extract against Fusarium root rot disease in tomato plants
Authors: El-Abeid Sozan E. , Mosa Mohamed A. , El-Tabakh Mohamed A. M. , Saleh Ahmed M. , El-Khateeb Mohamed A. , Haridy Maha S. A.
Published: January 2024

Incorporating green chemistry concepts into nanotechnology is an important focus area in nanoscience. The demand for green metal oxide nanoparticle production has grown in recent years. The beneficial effects of using nanoparticles in agriculture have already been established. Here, we highlight some potential antifungal properties of Zizyphus spina leaf extract-derived copper oxide nanoparticles (CuO-Zs-NPs), produced with a spherical shape and defined a 13–30 nm particle size. Three different dosages of CuO-Zs-NPs were utilized and showed promising antifungal efficacy in vitro and in vivo against the selected fungal strain of F. solani causes tomato root rot disease, which was molecularly identified with accession number (OP824846). In vivo  results indicated that, for all CuO-Zs-NPs concentrations, a significant reduction in Fusarium root rot disease occurred between 72.0 to 88.6% compared to 80.5% disease severity in the infected control. Although treatments with either the chemical fungicide (Kocide 2000) showed a better disease reduction and incidence with (18.33% and 6.67%) values, respectively, than CuO-Zs-NPs at conc. 50 mg/l, however CuO-Zs-NPs at 250 mg/l conc. showed the highest disease reduction (9.17 ± 2.89%) and lowest disease incidence (4.17 ± 3.80%). On the other hand, CuO-Zs-NPs at varied values elevated the beneficial effects of tomato seedling vigor at the initial stages and plant growth development compared to either treatment with the commercial fungicide or Trichoderma Biocide. Additionally, CuO-Zs-NPs treatments introduced beneficial results for tomato seedling development, with a significant increase in chlorophyll pigments and enzymatic activity for CuO-Zs-NPs treatments. Additionally, treatment with low concentrations of CuO-Zs-NPs led to a rise in the number of mature pollen grains compared to the immature ones.  however the data showed that CuO-Zs-NPs have a unique antifungal mechanism against F. solani, they  subsequently imply that CuO-Zs-NPs might be a useful environmentally friendly controlling agent for the Fusarium root rot disease that affects tomato plants.

Graphical Abstract
Transcending frontiers in prostate cancer: the role of oncometabolites on epigenetic regulation, CSCs, and tumor microenvironment to identify new therapeutic strategies
Authors: Ambrosini Giulia , Cordani Marco , Zarrabi Ali , Alcon-Rodriguez Sergio , Sainz Rosa M. , Velasco Guillermo , Gonzalez-Menendez Pedro , Dando Ilaria
Published: January 2024

Prostate cancer, as one of the most prevalent malignancies in males, exhibits an approximate 5-year survival rate of 95% in advanced stages. A myriad of molecular events and mutations, including the accumulation of oncometabolites, underpin the genesis and progression of this cancer type. Despite growing research demonstrating the pivotal role of oncometabolites in supporting various cancers, including prostate cancer, the root causes of their accumulation, especially in the absence of enzymatic mutations, remain elusive. Consequently, identifying a tangible therapeutic target poses a formidable challenge. In this review, we aim to delve deeper into the implications of oncometabolite accumulation in prostate cancer. We center our focus on the consequential epigenetic alterations and impacts on cancer stem cells, with the ultimate goal of outlining novel therapeutic strategies.

Graphical Abstract
Level of attendance at the English National Health Service Diabetes Prevention Programme and risk of progression to type 2 diabetes
Authors: Parkinson Beth , McManus Emma , Meacock Rachel , Sutton Matt
Published: January 2024

Background

We evaluated the dose–response relationship between the level of attendance at the English National Health Service Diabetes Prevention Programme (DPP) and risk of progression to type 2 diabetes amongst individuals participating in the programme.

Methods

We linked data on DPP attendance for 51,803 individuals that were referred to the programme between 1st June 2016 and 31st March 2018 and attended at least one programme session, with primary care records of type 2 diabetes diagnoses from the National Diabetes Audit up to 31st March 2020. Weibull survival regressions were used to estimate the association between the number of programme sessions attended and risk of progression to type 2 diabetes.

Results

Risk of developing type 2 diabetes declined significantly for individuals attending seven of the 13 programme sessions and continued to decline further up to 12 sessions. Attending the full 13 sessions was associated with a 45.5% lower risk (HR: 0.545 95% CI: 0.455 to 0.652). Compared to individuals that only partially attended the programme, attendance at 60% or more of the sessions was associated with a 30.7% lower risk of type 2 diabetes (HR: 0.693 95% CI: 0.645 to 0.745).

Conclusions

Reducing the risk of progression to type 2 diabetes through diabetes prevention programmes requires a minimum attendance level at seven of the 13 programme sessions (54%). Retaining participants beyond this minimum level yields further benefits in diabetes risk reduction. Commissioners may wish to consider altering provider payment schedules to incentivise higher retention levels beyond 60% of programme sessions.
CVD phenotyping in oncologic disorders: cardio-miRNAs as a potential target to improve individual outcomes in revers cardio-oncology
Authors: Yang Ming , Li Tiepeng , Guo Shujin , Song Kangping , Gong Chuhui , Huang Ning , Pang Dejiang , Xiao Hengyi
Published: January 2024

With the increase of aging population and prevalence of obesity, the incidence of cardiovascular disease (CVD) and cancer has also presented an increasing tendency. These two different diseases, which share some common risk factors. Relevant studies in the field of reversing Cardio-Oncology have shown that the phenotype of CVD has a significant adverse effect on tumor prognosis, which is mainly manifested by a positive correlation between CVD and malignant progression of concomitant tumors. This distal crosstalk and the link between different diseases makes us aware of the importance of diagnosis, prediction, management and personalized treatment of systemic diseases. The circulatory system bridges the interaction between CVD and cancer, which suggests that we need to fully consider the systemic and holistic characteristics of these two diseases in the process of clinical treatment. The circulating exosome-miRNAs has been intrinsically associated with CVD -related regulation, which has become one of the focuses on clinical and basic research (as biomarker). The changes in the expression profiles of cardiovascular disease-associated miRNAs (Cardio-miRNAs) may adversely affect concomitant tumors. In this article, we sorted and screened CVD and tumor-related miRNA data based on literature, then summarized their commonalities and characteristics (several important pathways), and further discussed the conclusions of Cardio-Oncology related experimental studies. We take a holistic approach to considering CVD as a risk factor for tumor malignancy, which provides an in-depth analysis of the various regulatory mechanisms or pathways involved in the dual attribute miRNAs (Cardio-/Onco-miRNAs). These mechanisms will be key to revealing the systemic effects of CVD on tumors and highlight the holistic nature of different diseases. Therefore, the Cardio-miRNAs should be given great attention from researchers in the field of CVD and tumors, which might become new targets for tumor treatment. Meanwhile, based on the principles of precision medicine (such as the predictive preventive personalized medicine, 3PM) and reverse Cardio-oncology to better improve individual outcomes, we should consider developing personalized medicine and systemic therapy for cancer from the perspective of protecting cardiovascular function.
Circular RNA hsa_circ_0050386 suppresses non-small cell lung cancer progression via regulating the SRSF3/FN1 axis
Authors: Chen Jinbin , Rao Boqi , Huang Zeqin , Xie Chen , Yu Yonghui , Yang Binyao , Wu Di , Wang Dedong , Qiu Fuman , Zhou Yifeng , Deng Yibin , Lu Jiachun
Published: January 2024

Background

Lung cancer is the most prevalent cancer worldwide, with non-small cell lung cancer (NSCLC) accounting for 85% of all cases. Circular RNAs(circRNA) play crucial roles in regulating the progression of lung cancer. Despite the identification of a large number of circRNAs, their expression patterns, functions, and mechanisms of action in NSCLC development remain unclear.This study aims to investigate the transcriptional expressions, functions, and potential mechanisms of circRNA hsa_circ_0050386 in NSCLC.

Methods

Quantitative real-time polymerase chain reaction (qRT-PCR) was utilized for the analysis of hsa_circ_0050386 expression. Cell proliferation was detected using the IncuCyte Live Cell Analysis System and clone formation assays. Migration and invasion of NSCLC cells were evaluated through Transwell assays. Flow cytometry was performed to assay cell cycle and apoptosis. Western blot was used to investigate protein expression. Protein binding analysis was conducted by employing pull-down assays, RNA immunoprecipitation (RIP), and mass spectrometry. The role of hsa_circ_0050386 in vivo was evaluated through the use of a xenograft model.

Results

The study discovered that hsa_circ_0050386 displayed lower expression levels in NSCLC tissues when compared to adjacent normal tissues. Patients exhibiting lower levels of hsa_circ_0050386 expression exhibited an inverse correlation with the Clinical Stage, T-stage, and M-stage of NSCLC. Functionally, hsa_circ_0050386 suppressed the proliferation and invasion of NSCLC cells both in vitro and in vivo. A comprehensive examination exposed the interaction between hsa_circ_0050386 and RNA binding protein Serine and arginine-rich splicing factor 3 (SRSF3), resulting in the down-regulation of Fibronectin 1 (FN1) expression, which inhibits the progression of NSCLC.

Conclusions

Our study shows that hsa_circ_0050386 suppresses the malignant biological behavior of NSCLC cells by down-regulating the expression of FN1, and may serve as a potential biomarker and therapeutic target for NSCLC treatment.
Growth and longevity modulation through larval environment mediate immunosenescence and immune strategy of Tenebrio molitor
Authors: Crosland Agathe , Rigaud Thierry , Develay Charlène , Moret Yannick
Published: January 2024

Background

The Disposable Soma Theory of aging suggests a trade-off between energy allocation for growth, reproduction and somatic maintenance, including immunity. While trade-offs between reproduction and immunity are well documented, those involving growth remain under-explored. Rapid growth might deplete resources, reducing investment in maintenance, potentially leading to earlier or faster senescence and a shorter lifespan. However, rapid growth could limit exposure to parasitism before reaching adulthood, decreasing immunity needs. The insect immunity’s components (cellular, enzymatic, and antibacterial) vary in cost, effectiveness, and duration. Despite overall immunity decline (immunosenescence), its components seem to age differently. We hypothesize that investment in these immune components is adjusted based on the resource cost of growth, longevity, and the associated risk of parasitism.

Results

We tested this hypothesis using the mealworm beetle, Tenebrio molitor as our experimental subject. By manipulating the larval environment, including three different temperatures and three relative humidity levels, we achieved a wide range of growth durations and longevities. Our main focus was on the relationship between growth duration, longevity, and specific immune components: hemocyte count, phenoloxidase activity, and antibacterial activity. We measured these immune parameters both before and after exposing the individuals to a standard bacterial immune challenge, enabling us to assess immune responses. These measurements were taken in both young and older adult beetles. Upon altering growth duration and longevity by modifying larval temperature, we observed a more pronounced investment in cellular and antibacterial defenses among individuals with slow growth and extended lifespans. Intriguingly, slower-growing and long-lived beetles exhibited reduced enzymatic activity. Similar results were found when manipulating larval growth duration and adult longevity through variations in relative humidity, with a particular focus on antibacterial activity.

Conclusion

The impact of growth manipulation on immune senescence varies by the specific immune parameter under consideration. Yet, in slow-growing T. molitor, a clear decline in cellular and antibacterial immune responses with age was observed. This decline can be linked to their initially stronger immune response in early life. Furthermore, our study suggests an immune strategy favoring enhanced antibacterial activity among slow-growing and long-lived T. molitor individuals.
Role of reactive oxygen species in ultraviolet-induced photodamage of the skin
Authors: Wei Min , He Xin , Liu Na , Deng Hui
Published: January 2024

Reactive oxygen species (ROS), such as superoxides (O2 •−) and hydroxyl groups (OH·), are short-lived molecules containing unpaired electrons. Intracellular ROS are believed to be mainly produced by the mitochondria and NADPH oxidase (NOX) and can be associated with various physiological processes, such as proliferation, cell signaling, and oxygen homeostasis. In recent years, many studies have indicated that ROS play crucial roles in regulating ultraviolet (UV)-induced photodamage of the skin, including exogenous aging, which accounts for 80% of aging. However, to the best of our knowledge, the detailed signaling pathways, especially those related to the mechanisms underlying apoptosis in which ROS are involved have not been reviewed previously. In this review, we elaborate on the biological characteristics of ROS and its role in regulating UV-induced photodamage of the skin.
Optimal analgesic regimen for total shoulder arthroplasty: a randomized controlled trial and network meta-analysis
Authors: Li Shiye , Chen Wenjie , Feng Liang’en , Guo Xu
Published: January 2024

Objective

Clinical approaches to analgesia following total shoulder arthroplasty include liposomal bupivacaine, local infiltration analgesia, single-shot interscalene block, and continuous interscalene block. However, the best method remains contentious. This study conducts a network meta-analysis comparing these four methods, aiming to identify the most effective analgesic approach.

Methods

Randomized controlled trials on analgesic regimens for total shoulder arthroplasty were identified through searches of PUBMED, Cochrane Central Register of Controlled Trials, EMBASE, Web of Science, and Scopus databases, covering their inception through November 2023. Network meta-analysis was performed using STATA 15.1, and the Cochrane Handbook version 5.1.0 risk of bias tool was employed for quality assessment of the literature.

Results

Twelve randomized controlled trials were included, comprising 1537 patients undergoing total shoulder arthroplasty. The interventions compared were ssISB, cISB, LIA, and LB. Regarding the quality of the literature, four studies were deemed low risk, one high risk, and seven moderate risk. The network meta-analysis revealed that in terms of VAS scores in the PACU, the ssISB group was the most effective, followed by cISB and LB, with LIA being the least effective. This pattern continued in VAS scores on the first and second postoperative days. Regarding morphine consumption, the cISB group showed the most significant reduction in the PACU and on the first postoperative day, while the LIA group performed best in total postoperative morphine consumption. The shortest average hospital stay was noted in the cISB group.

Conclusion

The ssISB method excels in controlling early postoperative pain, particularly during the PACU stage and early postoperative period. Additionally, the cISB method is notable for reducing postoperative morphine consumption and shortening average hospital stays. While the LIA method ranks first in reducing total morphine consumption, it is weaker in pain control. The LB method is underwhelming across most assessment parameters. These findings underscore the importance of selecting appropriate analgesic strategies for different postoperative recovery phases and provide valuable insights for clinicians to optimize postoperative pain management. Furthermore, they suggest a need for future research to explore the specific application and effectiveness of these methods in varying clinical contexts.
Correlation between ovarian follicular development and Hippo pathway in polycystic ovary syndrome
Authors: Huang Zichao , Xu Tianyue , Liu Chunling , Wu Honghui , Weng Linglin , Cai Jieyu , Liang Na , Ge Hongshan
Published: January 2024

Background

For women of childbearing age, the biggest problem caused by polycystic ovary syndrome (PCOS) is infertility, which is mainly caused by anovulation, abnormal follicular development, proliferation of small antral follicles, and cystic follicles. The mechanism underlying its occurrence is not clear. The abnormal proliferation and development of follicles in PCOS patients is a complex process, which is affected by many factors. The objective of this study was to investigate the relationship between the Hippo pathway and follicular development in PCOS, and to further explore this relationship by using the YAP inhibitor verteporfin (VP).

Method

30 3-week-old BALB/C female rats were randomly divided into control group (n = 10), DHEA group (n = 10) and DHEA + VP group (n = 10). The morphology of ovary and the degree of follicular development were observed by HE staining, and the expression and location of AMH in ovarian follicles were observed by immunofluorescence. The ovarian reserve function index AMH, cell proliferation index PCNA and the ratio of Hippo pathway related proteins MST, LATS, YAP, P-YAP and P-YAP/YAP were detected by Western blot.

Results

After dividing 30 3-week-old female mice into control, dehydroepiandrosterone (DHEA; model of PCOS), and DHEA + VP groups, we found that the number of small follicles increased in the DHEA group compared to the control group. Additionally, in the DHEA group compared to the control group, anti-müllerian hormone (AMH; ovarian reserve index) increased, proliferating cell nuclear antigen (PCNA; cell proliferation index) decreased, and upstream (MST and LATS) and downstream (YAP and p-YAP) proteins in the Hippo pathway increased, though the p-YAP/YAP ratio decreased. VP ameliorated the increases in AMH, MST, LATS, YAP and p-YAP, but did not ameliorate the decrease in the p-YAP/YAP ratio.

Conclusions

This study indicates that the increased small follicles in the ovaries and changes in ovarian reserve and cell proliferation may be closely related to Hippo pathway activation. This suggests that the Hippo pathway may be an important pathway affecting the proliferation and development of follicles and the occurrence of PCOS.
Driving pressure of respiratory system and lung stress in mechanically ventilated patients with active breathing
Authors: Stamatopoulou Vaia , Akoumianaki Evangelia , Vaporidi Katerina , Stamatopoulos Efstathios , Kondili Eumorfia , Georgopoulos Dimitrios
Published: January 2024

Background

During control mechanical ventilation (CMV), the driving pressure of the respiratory system (ΔPrs) serves as a surrogate of transpulmonary driving pressure (ΔPlung). Expiratory muscle activity that decreases end-expiratory lung volume may impair the validity of ΔPrs to reflect ΔPlung. This prospective observational study in patients with acute respiratory distress syndrome (ARDS) ventilated with proportional assist ventilation (PAV+), aimed to investigate: (1) the prevalence of elevated ΔPlung, (2) the ΔPrs-ΔPlung relationship, and (3) whether dynamic transpulmonary pressure (Plungsw) and effort indices (transdiaphragmatic and respiratory muscle pressure swings) remain within safe limits.

Methods

Thirty-one patients instrumented with esophageal and gastric catheters (n = 22) were switched from CMV to PAV+ and respiratory variables were recorded, over a maximum of 24 h. To decrease the contribution of random breaths with irregular characteristics, a 7-breath moving average technique was applied. In each patient, measurements were also analyzed per deciles of increasing lung elastance (Elung). Patients were divided into Group A, if end-inspiratory transpulmonary pressure (PLEI) increased as Elung increased, and Group B, which showed a decrease or no change in PLEI with Elung increase.

Results

In 44,836 occluded breaths, ΔPlung ≥ 12 cmH2O was infrequently observed [0.0% (0.0–16.9%) of measurements]. End-expiratory lung volume decrease, due to active expiration, was associated with underestimation of ΔPlung by ΔPrs, as suggested by a negative linear relationship between transpulmonary pressure at end-expiration (PLEE) and ΔPlung/ΔPrs. Group A included 17 and Group B 14 patients. As Elung increased, ΔPlung increased mainly due to PLEI increase in Group A, and PLEE decrease in Group B. Although ΔPrs had an area receiver operating characteristic curve (AUC) of 0.87 (95% confidence intervals 0.82–0.92, P < 0.001) for ΔPlung ≥ 12 cmH2O, this was due exclusively to Group A [0.91 (0.86–0.95), P < 0.001]. In Group B, ΔPrs showed no predictive capacity for detecting ΔPlung ≥ 12 cmH2O [0.65 (0.52–0.78), P > 0.05]. Most of the time Plungsw and effort indices remained within safe range.

Conclusion

In patients with ARDS ventilated with PAV+, injurious tidal lung stress and effort were infrequent. In the presence of expiratory muscle activity, ΔPrs underestimated ΔPlung. This phenomenon limits the usefulness of ΔPrs as a surrogate of tidal lung stress, regardless of the mode of support.
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
Authors: Abbas Ahmed , Chandratre Khyati , Gao Yunpeng , Yuan Jiapei , Zhang Michael Q. , Mani Ram S.
Published: January 2024

The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to predict cohesin-mediated chromatin interaction strength between any two loci in the genome. The predictions of ChIPr correlate well with ChIA-PET data in four cell lines. The standard ChIPr model requires three experimental inputs: ChIP-Seq signals for RAD21, H3K27ac, and H3K27me3 but works well with just RAD21 signal. Integrative analysis reveals novel insights into the role of CTCF motif, its orientation, and CTCF binding on cohesin-mediated chromatin interactions.
Efficacy of navigation system-assisted distraction osteogenesis for hemifacial microsomia based on artificial intelligence for 3 to 18 years old: study protocol for a randomized controlled single-blind trial
Authors: Liu Xiangqi , Zhang Ziwei , Han Wenqing , Zhao Zhijie , Kim Byeong Seop , Yan Yingjie , Chen Xiaojun , Wang Xuetong , Li Xin , Yang Xianxian , Wang Bingshun , Xu Haisong , Lin Li , Chai Gang
Published: January 2024

Background

Mandibular distraction osteogenesis (MDO) is a major part of the treatment for hemifacial microsomia patients. Due to the narrow surgical field of the intraoral approach, osteotomy accuracy is highly dependent on the surgeons’ experience. Electromagnetic (EM) tracking systems can achieve satisfying accuracy to provide helpful real-time surgical navigation. Our research team developed an EM navigation system based on artificial intelligence, which has been justified in improving the accuracy of osteotomy in the MDO in animal experiments. This study aims to clarify the effect of the EM navigation system in improving the MDO accuracy for hemifacial microsomia patients.

Methods

This study is designed as a single-centered and randomized controlled trial. Altogether, 22 hemifacial microsomia patients are randomly assigned to the experiment and control groups. All patients receive three-dimensional CT scans and preoperative surgical plans. The EM navigation system will be set up for those in the experiment group, and the control group will undergo traditional surgery. The primary outcome is the surgical precision by comparing the osteotomy position of pre- and postoperative CT scan images through the Geomagic Control software. The secondary outcomes include mandibular symmetry (occlusal plane deviation angle, mandibular ramus height, and body length), pain scale, and complications. Other indications, such as the adverse events of the system and the satisfactory score from patients and their families, will be recorded.

Discussion

This small sample randomized controlled trial intends to explore the application of an EM navigation system in MDO for patients, which has been adopted in other surgeries such as orthognathic procedures. Because of the delicate structures of children and the narrow surgical view, accurate osteotomy and protection of nearby tissue from injury are essential for successful treatment. The EM navigation system based on artificial intelligence adopted in this trial is hypothesized to provide precise real-time navigation for surgeons and optimally improve patient outcomes, including function and aesthetic results. The results of this trial will extend the application of new navigation technology in pediatric plastic surgery.

Trial registration

Chinese Clinical Trial Registry ChiCTR2200061565. Registered on 29 June 2022.
Effectiveness of a blended school-based mindfulness program for the prevention of co-rumination and internalizing problems in Dutch secondary school girls: a cluster randomized controlled trial
Authors: Vuijk Patricia , Bul Kim , Buil Marieke , Rauws Marloes , Curie Keshia , Amesz Charlotte , Weerheijm Ron , Riper Heleen
Published: January 2024

Background

A growing body of literature indicates that adolescent girls who talk with close friends about interpersonal problems or worries in an excessive, speculative way, and with an intense focus on distress (i.e., co-rumination) are at heightened risk for developing internalizing symptoms and disorders as well as reduced friendship quality. However, to date, there are no prevention programs available that target high levels of co-rumination between adolescent girls. As such, we developed the blended school-based mindfulness prevention program Happy Friends, Positive Minds (HFPM) that targets co-rumination at the dyadic level, i.e., between two close female friends. The aim of this trial is to evaluate the effectiveness of HFPM to reduce co-rumination and internalizing problems and to enhance wellbeing and social-emotional behavior in Dutch adolescent girls.

Methods

A cluster Randomized Controlled Trial (cRCT) will be conducted to evaluate HFPM effectiveness. We will recruit 160 female friendship dyads (n = 320 girls) aged 13 to 15 years who will be characterized by high levels of self-reported co-rumination. The cRCT has two arms: (1) an intervention condition in which 160 girls (80 friendship dyads) will receive the 14-week HFPM program in two consecutive cohorts (cohort 1 in academic year 2023/2024 and cohort 2 in academic year 2024/2025, and (2) a control condition in which 160 girls (80 dyads) will receive care-as-usual (CAU) in two consecutive cohorts (cohort 1 in academic year 2023/2024 and cohort 2 in academic year 2024/2025). Data will be collected at baseline (T0), during the program (T1;T2; T3), immediately after the program (T4), and at 1-year follow-up (T5). Participant-level self-reported risk for (early onset) depression and anxiety, self-reported and observed co-rumination, self- and friend-reported friendship quality, self-reported positive and negative affect, self-reported interpersonal responses to positive affect, and self-reported anhedonia symptoms will be the outcome variables.

Discussion

This study will provide insights into the short-term and long-term effects of the HFPM program on girls’ internalizing problems, wellbeing, and social-emotional behavior.

Trial registration

International Standard Randomized Controlled Trials, identifier: ISRCTN54246670. Registered on 27 February 2023.
Unsupervised spatially embedded deep representation of spatial transcriptomics
Authors: Xu Hang , Fu Huazhu , Long Yahui , Ang Kok Siong , Sethi Raman , Chong Kelvin , Li Mengwei , Uddamvathanak Rom , Lee Hong Kai , Ling Jingjing , Chen Ao , Shao Ling , Liu Longqi , Chen Jinmiao
Published: January 2024

Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out inter-cellular communications. We present SEDR, which uses a deep autoencoder coupled with a masked self-supervised learning mechanism to construct a low-dimensional latent representation of gene expression, which is then simultaneously embedded with the corresponding spatial information through a variational graph autoencoder. SEDR achieved higher clustering performance on manually annotated 10 × Visium datasets and better scalability on high-resolution spatial transcriptomics datasets than existing methods. Additionally, we show SEDR’s ability to impute and denoise gene expression (URL: https://github.com/JinmiaoChenLab/SEDR/).
Phenotypic and genotypic assessment of iron acquisition in diverse bovine-associated non-aureus staphylococcal strains
Authors: Reydams Helena , Toledo-Silva Bruno , Mertens Kristien , Piepers Sofie , Vereecke Nick , Souza Fernando Nogueira , Haesebrouck Freddy , De Vliegher Sarne
Published: January 2024

Although the role of iron in bacterial infections has been well described for Staphylococcus (S.) aureus, iron acquisition in (bovine-associated) non-aureus staphylococci and mammaliicocci (NASM) remains insufficiently mapped. This study aimed at elucidating differences between four diverse bovine NASM field strains from two species, namely S. chromogenes and S. equorum, in regards to iron uptake (with ferritin and lactoferrin as an iron source) and siderophore production (staphyloferrin A and staphyloferrin B) by investigating the relationship between the genetic basis of iron acquisition through whole genome sequencing (WGS) with their observed phenotypic behavior. The four field strains were isolated in a previous study from composite cow milk (CCM) and bulk tank milk (BTM) in a Flemish dairy herd. Additionally, two well-studied S. chromogenes isolates originating from a persistent intramammary infection and from a teat apex were included for comparative purpose in all assays. Significant differences between species and strains were identified. In our phenotypical iron acquisition assay, while lactoferrin had no effect on growth recovery for all strains in iron deficient media, we found that ferritin served as an effective source for growth recovery in iron-deficient media for S. chromogenes CCM and BTM strains. This finding was further corroborated by analyzing potential ferritin iron acquisition genes using whole-genome sequencing data, which showed that all S. chromogenes strains contained hits for all three proposed ferritin reductive pathway genes. Furthermore, a qualitative assay indicated siderophore production by all strains, except for S. equorum. This lack of siderophore production in S. equorum was supported by a quantitative assay, which revealed significantly lower or negligible siderophore amounts compared to S. aureus and S. chromogenes. The WGS analysis showed that all tested strains, except for S. equorum, possessed complete staphyloferrin A (SA)-synthesis and export operons, which likely explains the phenotypic absence of siderophore production in S. equorum strains. While analyzing the staphyloferrin A and staphyloferrin B operon landscapes for all strains, we noticed some differences in the proteins responsible for iron acquisition between different species. However, within strains of the same species, the siderophore-related proteins remained conserved. Our findings contribute valuable insights into the genetic elements associated with bovine NASM pathogenesis.
Factors determining fine-scale spatial genetic structure within coexisting populations of common beech (Fagus sylvatica L.), pedunculate oak (Quercus robur L.), and sessile oak (Q. petraea (Matt.) Liebl.)
Authors: Sandurska Elżbieta , Ulaszewski Bartosz , Meyza Katarzyna , Sztupecka Ewa , Burczyk Jarosław
Published: January 2024

Key message

Naturally regenerating populations of common beech, pedunculate, and sessile oaks develop strong spatial genetic structures at adult and seedling stages. Significant genetic relationship occurs between individuals growing up to 60 m apart. This indicates the minimum distance separating trees from which seeds used for reforestation should be harvested to avoid the adverse effects of excessive relatedness among offspring.

Context

Spatial genetic structure is an inherent characteristic of naturally regenerating plant populations and has practical implications in forests for the management of genetic resources.

Aims

We investigated the extent of spatial genetic structure in three broad-leaved forest tree species (common beech—Fagus sylvatica L.; pedunculate oak—Quercus robur L.; and sessile oak—Q. petraea (Matt.) Liebl.) coexisting in the same nature reserve, explored its variation among species and different life stages (adults/offspring), and tested its possible determinants.

Methods

We explored patterns of spatial distribution of individuals, and using microsatellites, we estimated parameters of spatial genetic structure based on kinship relationships, considering possible sources of variation.

Results

In adults, the strongest spatial genetic structure was found for Q. petraea (Sp = 0.0187), followed by F. sylvatica (Sp = 0.0133), and the weakest in Q. robur (Sp = 0.0080). It was uniform across different age classes in pedunculate oak but decreased with age in sessile oak. No apparent relationship between age and spatial genetic structure was found in beech. Offspring exhibited significant spatial genetic structure (ranging from 0.0122 in beech to 0.0188 in sessile oak). The cohorts of seedlings having both parents present within the study site had stronger spatial genetic structures than cohorts of seedlings with only one local parent.

Conclusion

Spatial genetic structure is strong in naturally regenerating populations of heavy-seeded forest trees. Pollen immigration from outside of a local forest stand can significantly decrease the extent of spatial genetic structure in offspring generations.
Psychometric properties of principals’ attitudes toward inclusive education (PATIE) scale: Arabic version
Authors: Aldosari Mubarak S.
Published: January 2024

Background

Inclusive education is critical for the successful integration of students with disabilities into general education schools, and principals’ attitudes play a crucial role in this process. Despite the recognized significance of attitudes, there remains a gap in understanding these attitudes among principals in Arabic-speaking regions concerning inclusive education practices. This study aims to bridge this gap by validating and assessing the reliability of the Arabic version of the Principals’ Attitudes Toward Inclusive Education (PATIE) scale.

Methods

To measure these attitudes in the Arab region, the current study validated and assessed the reliability of the Arabic version of the Principals’ Attitudes Toward Inclusive Education (PATIE) scale using a sample of 391 principals from schools that have in place inclusion programs for students with disabilities. Confirmatory factor analysis (CFA) was employed to validate the scale’s structural, discriminant, and convergent validity, while Cronbach’s alpha and composite reliability (CR) were utilized to evaluate the scale’s reliability.

Results

The results demonstrated the strong validity and reliability of the Arabic version of the PATIE, with all five factors displaying good reliability.

Conclusions

These findings suggest that the scale can effectively measure attitudes toward inclusive education in Arabic-speaking countries. This study’s implications for research and practice are significant, as they underscore the importance of positive attitudes among principals in promoting inclusive education and provide a validated tool for measuring these attitudes.
CNS tumor with CREBBP::BCORL1 Fusion and pathogenic mutations in BCOR and CREBBP: expanding the spectrum of BCOR-altered tumors
Authors: Barresi Valeria , Cardoni Antonello , Miele Evelina , Pedace Lucia , Masotto Barbara , Nardini Claudia , Barresi Sabina , Rossi Sabrina
Published: January 2024

The fifth edition of the World Health Organization (WHO) classification of central nervous system (CNS) tumors introduced the new tumor type CNS tumor with BCOR internal tandem duplication (ITD), characterized by a distinct DNA methylation profile and peculiar histopathological features, including a circumscribed growth pattern, ependymoma-like perivascular pseudorosettes, microcystic pattern, absent or focal GFAP immunostaining, OLIG2 positivity, and BCOR immunoreactivity. We describe a rare case of a CNS tumor in a 45-year-old man with histopathological and immunohistochemical features overlapping the CNS tumor with BCOR internal tandem duplication (ITD) but lacking BCOR immunostaining and BCOR ITD. Instead, the tumor showed CREBBP::BCORL1 fusion and pathogenic mutations in BCOR and CREBBP, along with a DNA methylation profile matching the “CNS tumor with EP300:BCOR(L1) fusion” methylation class. Two CNS tumors with fusions between CREBBP, or its paralog EP300, and BCORL1, and approximately twenty CNS tumors with CREBBP/EP300::BCOR fusions have been reported to date. They exhibited similar ependymoma-like features or a microcystic pattern, along with focal or absent GFAP immunostaining, and shared the same DNA methylation profile. Given their morphological and epigenetic similarities, circumscribed CNS tumors with EP300/CREBBP::BCOR(L1) fusions and CNS tumors with BCOR ITD may represent variants of the same tumor type. The ependymoma-like aspect coupled with the lack of diffuse GFAP immunostaining and the presence of OLIG2 positivity are useful clues for recognizing these tumors in histopathological practice. The diagnosis should be confirmed after testing for BCOR(L1) gene fusions and BCOR ITD.
pH-dependent virucidal effects of weak acids against pathogenic viruses
Authors: Hu Weiyin , Shimoda Hiroshi , Tsuchiya Yoshihiro , Kishi Mikiya , Hayasaka Daisuke
Published: January 2024

Background

Weak acids, such as acetic acid, show virucidal effects against viruses, and disinfectants are considered effective virucidal agents possibly because of their low pH, depending on the proton concentration. This study aimed to evaluate the efficacy of different weak acids (acetic, oxalic, and citric acids) and eligible vinegars under different pH conditions by comparing their inactivation efficacies against enveloped and non-enveloped viruses.

Methods

Acetic, oxalic, and citric acids were adjusted to pH values of 2, 4 and 6, respectively. They were also diluted from 1 M to 0.001 M with distilled water. Enveloped influenza A virus (FulV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and non-enveloped feline calicivirus (FCV) were treated with adjusted weak acids for up to 30 min. These viruses were also reacted with white distilled vinegar (WDV) and grain-flavored distilled vinegar (GV) for up to 30 min. Infectious viral titers after the reactions were expressed as plaque-forming units per mL.

Results

Acetic acid showed virucidal effects against FulV at pH 4, whereas citric and oxalic acids did not. Acetic and citric acids inactivated SARS-CoV-2 at pH 2, whereas oxalic acid did not. All acids showed virucidal effects against FVC at pH 2; however, not at pH 4. The virucidal effects of the serially diluted weak acids were also reflected in the pH-dependent results. WDV and GV significantly reduced FulV titers after 1 min. SARS-CoV-2 was also susceptible to the virucidal effects of WDV and GV; however, the incubation period was extended to 30 min. In contrast, WDV and GV did not significantly inactivate FCV.

Conclusions

The inactivation efficacy of weak acids is different even under the same pH conditions, suggesting that the virucidal effect of weak acids is not simply determined by pH, but that additional factors may also influence these effects. Moreover, eligible vinegars, the main component of which is acetic acid, may be potential sanitizers for some enveloped viruses, such as FulV, in the domestic environment.
A systematic review of gender diversity and its impact on the performance of Microfinance Institutions
Authors: Hossain Md Imran , Mia Md Aslam , Dalla Pellegrina Lucia
Published: January 2024

This study aims to consolidate the available knowledge on gender diversity and its impact on the dual performance (social and financial) of Microfinance Institutions (MFIs). We specifically focus on MFIs due to their distinctive nature compared to other industries, being traditionally women-centered and having a substantial representation of women employees across all levels of the corporate hierarchy. To conduct this comprehensive analysis, we employed a systematic review approach, meticulously selecting 24 relevant papers from the Scopus and Web of Science databases. Our findings revealed that research on gender diversity in MFIs primarily focuses on the board level. However, existing studies present conflicting results, suggesting that the impact of gender diversity on MFI performance is nuanced and complex. This complexity stems largely from the varying roles women play within the organizational structure. Furthermore, our analysis highlights the influence of additional factors, such as the database used, the study's context, and its geographical location, on the reported outcomes. Notably, research on gender diversity at the managerial and loan officer levels remains scarce, presenting a significant gap in the current body of knowledge. To further illuminate this field, this study identifies the most influential papers on the topic of gender diversity in microfinance. Additionally, we provide a co-authorship network analysis, visualizing the connections between existing research. This analysis provides valuable insights and inspiration for future research endeavors in this critical area.
Network analysis uncovers the master role of WRKY transcription factors in
Arabidopsis thaliana
response to
N
-acyl homoserine lactones
Authors: Duan Yongming , Han Min , Grimm Maja , Schikora Adam
Published: January 2024

Background

Plants can perceive bacterial molecules such as the quorum sensing signals
N
-acyl homoserine lactones (AHL), thus modifying their fitness in response to environmental factors. Even though the benefits conferred by AHL depend on various hormone signaling pathways, the understanding of AHL signaling, especially the response to AHL presence, remains largely unknown.

Methods

Weighted gene co-expression network analysis (WGCNA), multi-omics network analysis, and reverse transcription quantitative PCR (RT-qPCR) assays were used to identify key genes in AHL signaling.

Results

To obtain comprehensive insights on AHL signaling, we integrated available transcriptome data from
Arabidopsis thaliana
exposed to different single or multiple AHL molecules and performed a weighted gene co-expression network analysis. We identified several key genes regulated in plants exposed to multiple AHL molecules. Multi-omics network analysis and RT-qPCR assay revealed a potential role of WRKY transcription factors.

Conclusions

Results presented here offer good indications for exploring the mechanism of plants' response to bacterial signaling molecules, which could further support the application of AHL-producing bacteria in sustainable agriculture.
Poor Concordance Between Cancer Antigen-125 and RECIST Assessment for Progression in Patients With Platinum-Sensitive Relapsed Ovarian Cancer on Maintenance Therapy With a Poly(ADP-ribose) Polymerase Inhibitor
Authors: Tjokrowidjaja Angelina , Friedlander M.L. , Ledermann Jonathan A. , Coleman Robert L. , Mirza Mansoor R. , Matulonis Ursula A. , Pujade-Lauraine Eric , Lord Sarah J. , Scott Clare L. , Goble Sandra , York Whitney , Lee Chee K. ,   on behalf of the Gynecologic Cancer Intergroup Meta-Analysis Committee, Khoon Lee Chee , You Benoit , Paoletti Xavier , Glasspool Ros , Friedlander Michael , Scott Clare , Mirza Monsoor , Pujade Lauraine Eric , Ledermann Jonathan , Antill Yoland , Mileshkin Linda , Ethier Josee-Lyne , Bookman Michael , Gourley Charlie
Published: January 2024

PURPOSE

Cancer antigen-125 (CA-125) is recommended by treatment guidelines and widely used to diagnose ovarian cancer recurrence. The value of CA-125 as a surrogate for disease progression (PD) and its concordance with radiologic progression are unclear, particularly for women with platinum-sensitive relapsed ovarian cancer (PSROC) who have responded to chemotherapy and treated with maintenance poly(ADP-ribose) polymerase inhibitor (PARPi).

METHODS

In this pooled analysis of four randomized trials of maintenance PARPi or placebo (Study 19, SOLO2, ARIEL3, and NOVA), we extracted data on CA-125 PD as defined by Gynecologic Cancer InterGroup criteria and RECIST v1.1. We evaluated the concordance between CA-125 and RECIST PD and reported on the negative predictive value (NPV) and positive predictive value (PPV).

RESULTS

Of 1,262 participants (n = 818 PARPi, n = 444 placebo), 403 (32%) had CA-125 PD, and of these, 366 had concordant RECIST PD (PPV, 91% [95% CI, 88 to 93]). However, of 859 (68%) without CA-125 PD, 382 also did not have RECIST PD (NPV, 44% [95% CI, 41 to 48]). Within the treatment arms, PPV remained high (PARPi, 91% [95% CI, 86 to 94]; placebo, 91% [95% CI, 86 to 95]) but NPV was lower on placebo (PARPi, 53% [95% CI, 49 to 57]; placebo, 25% [95% CI, 20 to 31]). Of 477 with RECIST-only PD, most (95%) had a normal CA-125 at the start of maintenance therapy and the majority (n = 304, 64%) had CA-125 that remained within normal range. Solid organ recurrence without peritoneal disease was more common in those with RECIST-only PD than in those with CA-125 and RECIST PD (36% v 24%; P < .001).

CONCLUSION

In patients with PSROC treated with maintenance PARPi, almost half with RECIST PD did not have CA-125 PD, challenging current guidelines. Periodic computed tomography imaging should be considered as part of surveillance, particularly in those with a normal CA-125 at the start of maintenance therapy and on treatment.