CitySpec with Shield: A Secure Intelligent Assistant for Requirement Formalization

An increasing number of monitoring systems have been developed in smart cities to ensure that the real-time operations of a city satisfy safety and performance requirements. However, many existing city requirements are written in English with missing, inaccurate, or ambiguous information. There is a high demand for assisting city policymakers in converting human-specified requirements to machine-understandable formal specifications for monitoring systems. To tackle this limitation, we build CitySpec, the first intelligent assistant system for requirement specification in smart cities. To create CitySpec, we first collect over 1,500 real-world city requirements across different domains (e.g., transportation and energy) from over 100 cities and extract city-specific knowledge to generate a dataset of city vocabulary with 3,061 words. We also build a translation model and enhance it through requirement synthesis and develop a novel online learning framework with shielded validation. The evaluation results on real-world city requirements show that CitySpec increases the sentence-level accuracy of requirement specification from 59.02% to 86.64%, and has strong adaptability to a new city and a new domain (e.g., the F1 score for requirements in Seattle increases from 77.6% to 93.75% with online learning). After the enhancement from the shield function, CitySpec is now immune to most known textual adversarial inputs (e.g., the attack success rate of DeepWordBug after the shield function is reduced to 0% from 82.73%). We test the CitySpec with 18 participants from different domains. CitySpec shows its strong usability and adaptability to different domains, and also its robustness to malicious inputs.Comment: arXiv admin note: substantial text overlap with arXiv:2206.0313

GlanceSeg: Real-time microaneurysm lesion segmentation with gaze-map-guided foundation model for early detection of diabetic retinopathy

Early-stage diabetic retinopathy (DR) presents challenges in clinical diagnosis due to inconspicuous and minute microangioma lesions, resulting in limited research in this area. Additionally, the potential of emerging foundation models, such as the segment anything model (SAM), in medical scenarios remains rarely explored. In this work, we propose a human-in-the-loop, label-free early DR diagnosis framework called GlanceSeg, based on SAM. GlanceSeg enables real-time segmentation of microangioma lesions as ophthalmologists review fundus images. Our human-in-the-loop framework integrates the ophthalmologist's gaze map, allowing for rough localization of minute lesions in fundus images. Subsequently, a saliency map is generated based on the located region of interest, which provides prompt points to assist the foundation model in efficiently segmenting microangioma lesions. Finally, a domain knowledge filter refines the segmentation of minute lesions. We conducted experiments on two newly-built public datasets, i.e., IDRiD and Retinal-Lesions, and validated the feasibility and superiority of GlanceSeg through visualized illustrations and quantitative measures. Additionally, we demonstrated that GlanceSeg improves annotation efficiency for clinicians and enhances segmentation performance through fine-tuning using annotations. This study highlights the potential of GlanceSeg-based annotations for self-model optimization, leading to enduring performance advancements through continual learning.Comment: 12 pages, 10 figure

The Nematic Energy Scale and the Missing Electron Pocket in FeSe

Superconductivity emerges in proximity to a nematic phase in most iron-based superconductors. It is therefore important to understand the impact of nematicity on the electronic structure. Orbital assignment and tracking across the nematic phase transition prove to be challenging due to the multiband nature of iron-based superconductors and twinning effects. Here, we report a detailed study of the electronic structure of fully detwinned FeSe across the nematic phase transition using angle-resolved photoemission spectroscopy. We clearly observe a nematicity-driven band reconstruction involving dxz, dyz, and dxy orbitals. The nematic energy scale between dxz and dyz bands reaches a maximum of 50 meV at the Brillouin zone corner. We are also able to track the dxz electron pocket across the nematic transition and explain its absence in the nematic state. Our comprehensive data of the electronic structure provide an accurate basis for theoretical models of the superconducting pairing in FeSe

Molecular characterization of sub-frontal recurrent medulloblastomas reveals potential clinical relevance

BackgroundSingle recurrence in the sub-frontal region after cerebellar medulloblastoma (MB) resection is rare and the underlying molecular characteristics have not been specifically addressed.MethodsWe summarized two such cases in our center. All five samples were molecularly profiled for their genome and transcriptome signatures.ResultsThe recurrent tumors displayed genomic and transcriptomic divergence. Pathway analysis of recurrent tumors showed functional convergence in metabolism, cancer, neuroactive ligand–receptor interaction, and PI3K-AKT signaling pathways. Notably, the sub-frontal recurrent tumors had a much higher proportion (50–86%) of acquired driver mutations than that reported in other recurrent locations. The acquired putative driver genes in the sub-frontal recurrent tumors functionally enriched for chromatin remodeler-associated genes, such as KDM6B, SPEN, CHD4, and CHD7. Furthermore, the germline mutations of our cases showed a significant functional convergence in focal adhesion, cell adhesion molecules, and ECM–receptor interaction. Evolutionary analysis showed that the recurrence could be derived from a single primary tumor lineage or had an intermediate phylogenetic similarity to the matched primary one.ConclusionRare single sub-frontal recurrent MBs presented specific mutation signatures that might be related to the under-dose radiation. Particular attention should be paid to optimally covering the sub-frontal cribriform plate during postoperative radiotherapy targeting

The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases

Reports on bacteria detected in maternal fluids during pregnancy are typically associated with adverse consequences, and whether the female reproductive tract harbours distinct microbial communities beyond the vagina has been a matter of debate. Here we systematically sample the microbiota within the female reproductive tract in 110 women of reproductive age, and examine the nature of colonisation by 16S rRNA gene amplicon sequencing and cultivation. We find distinct microbial communities in cervical canal, uterus, fallopian tubes and peritoneal fluid, differing from that of the vagina. The results reflect a microbiota continuum along the female reproductive tract, indicative of a non-sterile environment. We also identify microbial taxa and potential functions that correlate with the menstrual cycle or are over-represented in subjects with adenomyosis or infertility due to endometriosis. The study provides insight into the nature of the vagino-uterine microbiome, and suggests that surveying the vaginal or cervical microbiota might be useful for detection of common diseases in the upper reproductive tract.Shenzhen Municipal Government of China [JCYJ20160229172757249, JCYJ20150601090833370]; Danish Strategic Research Council [2106-07-0021]; Ole Romer grant from Danish Natural Science Research Council; Solexa project [272-07-0196]SCI(E)ARTICLE

cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth

The LKB1 tumor suppressor gene is frequently mutated and inactivated in non–small cell lung cancer (NSCLC). Loss of LKB1 promotes cancer progression and influences therapeutic responses in preclinical studies; however, specific targeted therapies for lung cancer with LKB1 inactivation are currently unavailable. Here, we have identified a long noncoding RNA (lncRNA) signature that is associated with the loss of LKB1 function. We discovered that LINC00473 is consistently the most highly induced gene in LKB1-inactivated human primary NSCLC samples and derived cell lines. Elevated LINC00473 expression correlated with poor prognosis, and sustained LINC00473 expression was required for the growth and survival of LKB1-inactivated NSCLC cells. Mechanistically, LINC00473 was induced by LKB1 inactivation and subsequent cyclic AMP–responsive element–binding protein (CREB)/CREB-regulated transcription coactivator (CRTC) activation. We determined that LINC00473 is a nuclear lncRNA and interacts with NONO, a component of the cAMP signaling pathway, thereby facilitating CRTC/CREB-mediated transcription. Collectively, our study demonstrates that LINC00473 expression potentially serves as a robust biomarker for tumor LKB1 functional status that can be integrated into clinical trials for patient selection and treatment evaluation, and implicates LINC00473 as a therapeutic target for LKB1-inactivated NSCLC

The metagenome of the female upper reproductive tract

publishedVersio

Associations of HLA-DP Variants with Hepatitis B Virus Infection in Southern and Northern Han Chinese Populations: A Multicenter Case-Control Study

) locus has been reported to be associated with hepatitis B virus (HBV) infection in populations of Japan and Thailand. We aimed to examine whether the association can be replicated in Han Chinese populations. = 0.097∼0.697 and 0.198∼0.615 in northern Chinese population, respectively). loci were strongly associated with HBV infection in southern and northern Han Chinese populations, but not with HBV progression