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BRCA2 prevents PARPi-mediated PARP1 retention to protect RAD51 filaments

Study on the driving force of seasonal changes of soil erosion in Lulang-Tongmai section of Sichuan-Tibet Highway

In the context of global climate change, the section of the Sichuan-Tibet Highway from Lulang to Tongmai has become a focal point for soil erosion research due to its unique geographical location and complex natural environment. Studies have shown that between 2000 and 2023, soil erosion intensity in this area has decreased. However, erosion intensity increases from southwest to northeast, with particularly severe erosion near the Tongmai Grand Bridge and Polong Gou Grand Bridge. Correlation analysis reveals a significant positive correlation between rainfall and soil erosion, while vegetation cover is positively correlated with erosion in the short term but contributes to reduced erosion over the long term. Geodetector analysis indicates that the main driving factors vary by season. In spring, summer, and autumn, temperature and precipitation are the primary drivers, with driving forces of 0.78 and 0.75, 0.80 and 0.78, and 0.75 and 0.73, respectively. In winter, temperature and elevation are the dominant factors, with driving forces of 0.63 and 0.42. The interaction between temperature, precipitation, and other factors significantly influences soil erosion, particularly in spring and summer, where the interaction driving force exceeds 0.75. These findings provide both theoretical support and decision-making guidance for soil erosion control along the Sichuan-Tibet Highway.

Maturation of human induced pluripotent stem cell-derived cardiomyocytes promoted by Brachyury priming

Definer: A computational method for accurate identification of RNA pseudouridine sites based on deep learning

Pseudouridine is an important modification site, which is widely present in a variety of non-coding RNAs and is involved in a variety of important biological processes. Studies have shown that pseudouridine is important in many biological functions such as gene expression, RNA structural stability, and various diseases. Therefore, accurate identification of pseudouridine sites can effectively explain the functional mechanism of this modification site. Due to the rapid increase of genomics data, traditional biological experimental methods to identify RNA modification sites can no longer meet the practical needs, and it is necessary to accurately identify pseudouridine sites from high-throughput RNA sequence data by computational methods. In this study, we propose a deep learning-based computational method, Definer, to accurately identify RNA pseudouridine loci in three species, Homo sapiens, Saccharomyces cerevisiae and Mus musculus. The method incorporates two sequence coding schemes, including NCP and One-hot, and then feeds the extracted RNA sequence features into a deep learning model constructed from CNN, GRU and Attention. The benchmark dataset contains data from three species, H. sapiens, S. cerevisiae and M. musculus, and the results using 10-fold cross-validation show that Definer significantly outperforms other existing methods. Meanwhile, the data sets of two species, H. sapiens and S. cerevisiae, were tested independently to further demonstrate the predictive ability of the model. In summary, our method, Definer, can accurately identify pseudouridine modification sites in RNA.

Hemosiderin quantification in hemophilic arthropathy using quantitative magnetic resonance imaging

Abstract The goal of this study is to quantify hemosiderin deposition in the knee joint tissues of hemophilic arthropathy (HA) patients using quantitative susceptibility mapping on MRI. Knee synovial tissues from HA patients and controls without hemophilia were included. The tissues underwent ultrashort echo time quantitative susceptibility mapping (UTE-QSM) and clinical MRI. HA tissues were processed histologically with Perl’s Prussian Blue (PPB) staining to identify iron contents. Seven regions of interest were drawn in each tissue, and the susceptibility values were tested. Moreover, the association between the estimated magnetic susceptibility and the iron contents quantified by histology was investigated. Nine synovial tissues were procured from total knee arthroplasty of hemophilia patients (males, 40.8 ± 9.0 years), and three synovial tissues were harvested from cadaveric knee joints of donors without hemophilia as controls (males, 72.0 ± 12.8 years). The estimated susceptibility values (ESVs) showed significant differences between HA and control samples. Accordingly, HA tissues presented a mean ESV of 0.48 ± 1.08 ppm and control tissues of -0.13 ± 0.12 ppm (p < 0.05). A significant linear correlation was found between the iron level quantified by histology (PPB stain) and the ESV estimated by UTE-QSM (R = 0.908, p < 0.01). There was a significant difference in the susceptibility in high load (HL) tissues compared to low load (LL) tissues (ESV = 5.57 ± 1.23 ppm for HL vs. 0.57 ± 0.85 ppm for LL, p < 0.001). Reliable hemosiderin quantification in joint tissues of HA patients can be achieved using MRI based on quantitative susceptibility mapping.

The impact of a school garden program on children’s food literacy, climate change literacy, school motivation, and physical activity: A study protocol

Objective FoodACT aims to investigate how school gardens affect children’s food literacy (FL), climate change literacy (CCL), school motivation (SM), and physical activity (PA). Design It comprises a multimethod, quasi-experimental inquiry into an existing Danish school garden program, Gardens to Bellies (GtB). Data will be collected using surveys, accelerometry, semi-structured and focus-group interviews. The study is preregistered with ClinicalTrials.gov (#NCT05839080). Setting Six GtB school garden locations across Region Zealand and Region of Southern Denmark. Participants Fourth grade pupils attending GtB (approx. 1600) are recruited to the intervention group. Fourth grade pupils from schools not attending GtB (approx. 1600) are recruited to the control group. Intervention Pupils grow, prepare and cook foods for meals in the school garden during eight garden sessions. Main outcome measures FL, CCL and SM are measured using pre- and post-intervention surveys in both groups. Pupils participating in GtB have their PA assessed using accelerometery, and acute SM by text-message-surveys. Semi-structured and focus-groups interviews are held with garden facilitators and pupils focusing on the implementation of GtB and mechanisms related to developing FL and CCL. Analysis The effect on FL, CCL and SM is assessed using linear mixed models. PA and acute SM are assessed by comparing data on days with and without GtB in a subsample of 900 pupils. Qualitative data will be analysed using thematic analysis.

Sustainable subgrade improvement with calcium carbide residue and rice husk ash

Intelligent anti-jamming communication technology with electromagnetic spectrum feature cognition

Against the backdrop of the rapid development of wireless communication technology, the complex signal interference issues in the electromagnetic spectrum environment have become a key factor affecting the quality and reliability of signal transmission. Existing solutions, such as traditional interference suppression techniques that rely on static spectrum allocation and fixed interference patterns, are no longer able to adapt to the rapidly changing electromagnetic environment and face computational complexity challenges when processing large amounts of real-time data. This study proposes an intelligent anti-interference algorithm that combines deep neural networks and game theory, and constructs a model based on near-end strategy optimization. By extracting and processing signal features through deep neural networks, and dynamically adjusting communication strategies with near-end optimization, the model effectively addresses the recognition and prediction of signal transmission feature parameters in target communication systems, generates interference signals with the same feature parameters, and achieves effective interference suppression. Experiments show that the proposed model achieves an accuracy rate of 95.23% in identifying interference signals and an anti-interference accuracy rate of 85.47%, significantly outperforming random forest and deep Q-network models. The study not only clarifies the limitations of existing solutions but also precisely defines the goals of the new model, which are to reduce error rates and improve adaptability in dynamic environments. The results further explain the significance of the used metrics and test conditions, providing new means and strategies for the development of anti-interference communication technology, especially in dealing with new complex electromagnetic spectrum interference.

Phylogeny and evolutionary dynamics of the Rubia genus based on the chloroplast genome of Rubia tibetica

Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with related Alteromonas strains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one-carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous across Alteromonas macleodii strains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole nitrogen source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regarding Alteromonas metabolism. The manually-curated metabolic reconstruction is available as a “Tier-2” database on BioCyc.

Fractional order modeling of hepatitis B virus transmission with imperfect vaccine efficacy

The impact of wide step width on lower limb coordination and its variability in individuals with flat feet

Flat foot is a common condition marked by the collapse of the medial longitudinal arch, leading to altered lower limb biomechanics and increased risk of musculoskeletal injuries. We aimed to investigate if wide step width changes the lower limb inter-joint coordination and its variability in flat feet individuals. Twenty flat-footed individuals participated in this cross-sectional study. Lower limb kinematics were assessed by 3-dimensional motion analysis during walking and running on a treadmill with preferred and wide step widths while receiving visual feedback. Inter-joint coordination was quantified using vector-coding for joint angles in the hip, knee, and ankle. Wide walking showed a shift towards proximal joint motion in sagittal ankle-knee coordination during loading response during LR (p=0.006), an In-phase motion in transverse ankle-hip coordination during push-off (p=0.004), and an In-phase pattern in frontal knee-hip coordination during mid-stance (p=0.027). Frontal ankle and transverse knee coordination during push-off changed to In-phase (p=0.003). Wide running significantly shifted frontal ankle-hip coordination towards proximal joint motion during mid-stance (p=0.05). Transverse ankle-hip coordination showed an in-phase pattern in wide conditions during push-off (p=0.044), during LR (p=0.022). Wide walking, significantly increased coordination variability of the sagittal ankle-knee during LR and decreased transverse ankle-hip during push-off. Wide walking significantly increased coordination variability in ankle-knee in sagittal plane during LR (p<0.001). Wide running significantly decreased the coordination variability in the ankle-knee sagittal during LR (p<0.001) and knee-hip sagittal during LR (p=0.007) and push-off (p=0.016). The results showed that wide step width can affect inter-joint coordination during walking/running in flat-footed individuals at certain points. These results should be considered when using a wide step width as a gait retraining method for managing flat-footed individuals.

Causal association between endocrine diseases and lymphoid malignancies explored through two-sample Mendelian randomization analysis

Optimized CUT&RUN protocol for activated primary mouse B cells

ChIP-seq has long been the standard for study of chromatin-protein interactions. However, development of a new technique, CUT&RUN, showed substantial advantages compared to ChIP-seq including higher quality signal while using substantially less sample. While a powerful technique, the original protocol was designed using cell lines and histones as targets. Due to their fragility, this was unsuitable for obtaining high-quality data from activated primary B lymphocytes. To adapt this protocol for B cells, cells were fixed prior to nuclear isolation, and several critical adjustments were introduced to the procedure and reagents. We measured binding of H3K4me3 histone and RNA Polymerase II, detecting robust peaks with as little as 100k nuclei. Additionally, freeze-thaw of B cells prior to processing did not affect results, emphasizing the flexibility of this modified technique. Using the protocol described here will allow one to quantify non-histone proteins bound to DNA from limited numbers of B cells with more efficiency than can be achieved from the current standard, ChIP-seq.

Novel modified magnetic graphene oxide as an efficient and green catalyst for one-pot synthesis of pyrazoles

CO2 geological storage site selection and long-term potential assessment framework based on TOUGH2/ECO2N

Carbon dioxide capture and storage (CCS) technology is considered a crucial tactic for achieving the “dual carbon” goals. However, current CCS technologies face several challenges, such as the absence of a comprehensive and systematic set of criteria for site selection, coupled with the lack of a universally applicable evaluation framework.To address these issues, this study proposes a regional-scale CO2 geological storage suitability assessment and potential estimation framework that can be adapted to similar regions. Using the Yellow River Delta as a case study, a geological storage site selection indicator system was developed, and a model for assessing site suitability was constructed.The model was employed to evaluate the appropriateness of CO2 geological sequestration sites within the study region, and numerical simulations of CO2 storage were performed utilizing the TOUGH2/ECO2N simulator for prospective target zones. This research examines the migration dynamics of CO2 in saline aquifers, the progression of storage mechanisms, and the carbon sequestration capacity of various storage configurations. The research addresses key questions such as: How can the optimal CO2 geological storage target area be selected? How can the best storage strategy matching the target area be determined? How can the migration and distribution characteristics of CO2 after storage be simulated? Are there potential risks in the future?

Yeast modifies the nonlinear behavior of the electrode electrolyte interface under high voltage stimulation

Pig livers for people: US regulator greenlights first safety trial

Understanding social work’s role in abortion care: A comprehensive scoping review

Background Social workers have played a crucial role in abortion care for decades, addressing clients’ diverse abortion care needs. Social workers have ethical duties to provide unimpeded access to information and supports to clients, in pursuit of social justice. This scoping review comprehensively synthesizes published literature on social work’s role in abortion care. Methods The review adhered to Arksey and O’Malley’s five-stage framework. The following databases were searched for literature published between 1973–2023: PsycINFO, MEDLINE, CINAHL, Social Work Abstracts, Social Services Abstracts, and Scopus. Search results were uploaded to Covidence for de-duplication and screening. Out of 2,980 articles screened in title and abstract review, followed by full-text review, 78 articles were included. Results A majority the 78 studies (n = 67) were set in the United States. The remainder were from the United Kingdom, Australia, Canada, New Zealand, and two studies involved multiple countries. Six themes emerged to summarize the literature base: (1) Social workers’ attitudes regarding abortion and abortion-seekers; (2) Abortion stigma and barriers in social work; (3) Social work and reproductive justice; (4) Social work and ethical considerations regarding abortion; (5) Social work and abortion policy and advocacy; and (6) Social work and family planning: roles, approaches, and practice frameworks. Discussion Social workers have long played intrinsic roles in abortion care, including counseling, providing access to concrete supports and mitigating barriers to abortion care, and abortion rights advocacy. Social justice and professional ethical commitments underpin social work’s role in abortion care. However, existing gaps in abortion education, training, and practice frameworks are impeded by the dynamic legal landscape and stigma attached to people seeking abortion care. Reproductive justice offers a framework, that overlaps with the field’s social justice tenets, to raise consciousness among social work students, professionals, and researchers, and to address gaps in abortion education, training, and scholarship.

Author Correction: Osthole induces accumulation of impaired autophagosome against pancreatic cancer cells