Transcription profiles of boron-deficiency-responsive genes in citrus rootstock root by suppression subtractive hybridization and cDNA microarray

Boron (B) deficiency has seriously negative effect on citrus production. Carrizo citrange (CC) has been reported as a B-deficiency tolerant rootstock. However, the molecular mechanism of its B-deficiency tolerance remained not well-explored. To understand the molecular basis of citrus rootstock to B-deficiency, suppression subtractive hybridization (SSH) and microarray approaches were combined to identify the potential important or novel genes responsive to B-deficiency. Firstly four SSH libraries were constructed for the root tissue of two citrus rootstocks CC and Trifoliate orange (TO) to compare B-deficiency treated and non-treated plants. Then 7680 clones from these SSH libraries were used to construct a cDNA array and microarray analysis was carried out to verify the expression changes of these clones upon B-deficiency treatment at various time points compared to the corresponding controls. A total of 139 unigenes that were differentially expressed upon B-deficiency stress either in CC or TO were identified from microarray analysis, some of these genes have not previously been reported to be associated with B-deficiency stress. In this work, several genes involved in cell wall metabolism and transmembrane transport were identified to be highly regulated under B-deficiency stress, and a total of 23 metabolic pathways were affected by B-deficiency, especially the lignin biosynthesis pathway, nitrogen metabolism, and glycolytic pathway. All these results indicated that CC was more tolerant than TO to B-deficiency stress. The B-deficiency responsive genes identified in this study could provide further information for understanding the mechanisms of B-deficiency tolerance in citrus

Dense matter with eXTP

In this White Paper we present the potential of the Enhanced X-ray Timing and Polarimetry (eXTP) mission for determining the nature of dense matter; neutron star cores host an extreme density regime which cannot be replicated in a terrestrial laboratory. The tightest statistical constraints on the dense matter equation of state will come from pulse profile modelling of accretion-powered pulsars, burst oscillation sources, and rotation-powered pulsars. Additional constraints will derive from spin measurements, burst spectra, and properties of the accretion flows in the vicinity of the neutron star. Under development by an international Consortium led by the Institute of High Energy Physics of the Chinese Academy of Science, the eXTP mission is expected to be launched in the mid 2020s.Comment: Accepted for publication on Sci. China Phys. Mech. Astron. (2019

A cost-effectiveness analysis evaluating endoscopic surveillance for gastric cancer for populations with low to intermediate risk

10.1371/journal.pone.0083959PLoS ONE812-POLN

A Unified Intracellular pH Landscape with SITE-pHorin: a Quantum-Entanglement-Enhanced pH Probe

An accurate map of intracellular organelle pH is crucial for comprehending cellular metabolism and organellar functions. However, a unified intracellular pH spectrum using a single probe is still lack. Here, we developed a novel quantum entanglement-enhanced pH-sensitive probe called SITE-pHorin, which featured a wide pH-sensitive range and ratiometric quantitative measurement capabilities. Subsequently, we measured the pH of various organelles and their sub-compartments, including mitochondrial sub-spaces, Golgi stacks, endoplasmic reticulum, lysosomes, peroxisomes, and endosomes in COS-7 cells. For the long-standing debate on mitochondrial compartments pH, we measured the pH of mitochondrial cristae as 6.60 \pm 0.40, the pH of mitochondrial intermembrane space as 6.95 \pm 0.30, and two populations of mitochondrial matrix pH at approximately 7.20 \pm 0.27 and 7.50 \pm 0.16, respectively. Notably, the lysosome pH exhibited a single, narrow Gaussian distribution centered at 4.79 \pm 0.17. Furthermore, quantum chemistry computations revealed that both the deprotonation of the residue Y182 and the discrete curvature of deformed benzene ring in chromophore are both necessary for the quantum entanglement mechanism of SITE-pHorin. Intriguingly, our findings reveal an accurate pH gradient (0.6-0.9 pH unit) between mitochondrial cristae and matrix, suggesting prior knowledge about \Delta pH (0.4-0.6) and mitochondrial proton motive force (pmf) are underestimated.Comment: 64 pages, 7 figures, the supplemental material contains 13 supplemental figures and 4 supplemental table

Performance of Foundation Models vs Physicians in Textual and Multimodal Ophthalmological Questions

Importance: There is an increasing amount of literature evaluating the clinical knowledge and reasoning performance of large language models (LLMs) in ophthalmology, but to date, investigations into its multimodal abilities clinically—such as interpreting images and tables—have been limited. Objective: To evaluate the multimodal performance of the following 7 foundation models (FMs): GPT-4o (OpenAI), Gemini 1.5 Pro (Google), Claude 3.5 Sonnet (Anthropic), Llama-3.2-11B (Meta), DeepSeek V3 (High-Flyer), Qwen2.5-Max (Alibaba Cloud), and Qwen2.5-VL-72B (Alibaba Cloud) in answering offline Fellowship of the Royal College of Ophthalmologists part 2 written multiple-choice textual and multimodal questions, with head-to-head comparisons with physicians. Design, Setting, and Participants: This cross-sectional study was conducted between September 2024 and March 2025 using questions sourced from a textbook used as an examination preparation resource for the Fellowship of the Royal College of Ophthalmologists part 2 written examination. Exposure: FM performance. Main Outcomes and Measures: The primary outcome measure was FM accuracy, defined as the proportion of answers generated by the model matching the textbook’s labeled letter answer. Results: For textual questions, Claude 3.5 Sonnet (accuracy, 77.7%) outperformed all other FMs (followed by GPT-4o [accuracy, 69.9%], Qwen2.5-Max [accuracy, 69.3%], DeepSeek V3 [accuracy, 63.2%], Gemini Advanced [accuracy, 62.6%], Qwen2.5-VL-72B [accuracy, 58.3%], and Llama-3.2-11B [accuracy, 50.7%]), ophthalmology trainees (difference, 9.0%; 95% CI, 2.4%-15.6%; P = .01) and junior physicians (difference, 35.2%; 95% CI, 28.3%-41.9%; P < .001), with comparable performance with expert ophthalmologists (difference, 1.3%; 95% CI, −5.1% to 7.4%; P = .72). GPT-4o (accuracy, 69.9%) outperformed GPT-4 (OpenAI; difference, 8.5%; 95% CI, 1.1%-15.8%; P = .02) and GPT-3.5 (OpenAI; difference, 21.8%; 95% CI, 14.3%-29.2%; P < .001). For multimodal questions, GPT-4o (accuracy, 57.5%) outperformed all other FMs (Claude 3.5 Sonnet [accuracy, 47.5%], Qwen2.5-VL-72B [accuracy, 45%], Gemini Advanced [accuracy, 35%], and Llama-3.2-11B [accuracy, 25%]) and the junior physician (difference, 15%; 95% CI, −6.7% to 36.7%; P = .18) but was weaker than expert ophthalmologists (accuracy range, 70.0%-85.0%; P = .16) and trainees (accuracy range, 62.5%-80%; P = .35). Conclusions and Relevance: Results of this cross-sectional study suggest that for textual questions, current FMs exhibited notable improvements in ophthalmological knowledge reasoning when compared with older LLMs and ophthalmology trainees, with performance comparable with that of expert ophthalmologists. These models demonstrated potential for medical assistance for answering ophthalmological textual queries, but their multimodal abilities remain limited. Further research or fine-tuning models with diverse ophthalmic multimodal data may lead to more capable applications with multimodal functionalities

Observation of γγ → ττ in proton-proton collisions and limits on the anomalous electromagnetic moments of the τ lepton

The production of a pair of τ leptons via photon–photon fusion, γγ → ττ, is observed for the f irst time in proton–proton collisions, with a significance of 5.3 standard deviations. This observation is based on a data set recorded with the CMS detector at the LHC at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 138 fb−1. Events with a pair of τ leptons produced via photon–photon fusion are selected by requiring them to be back-to-back in the azimuthal direction and to have a minimum number of charged hadrons associated with their production vertex. The τ leptons are reconstructed in their leptonic and hadronic decay modes. The measured fiducial cross section of γγ → ττ is σfid obs = 12.4+3.8 −3.1 fb. Constraints are set on the contributions to the anomalous magnetic moment (aτ) and electric dipole moments (dτ) of the τ lepton originating from potential effects of new physics on the γττ vertex: aτ = 0.0009+0.0032 −0.0031 and |dτ| &lt; 2.9×10−17ecm (95% confidence level), consistent with the standard model

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe