Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling.

The detection of mitochondrial DNA (mtDNA) mutations in single cells holds considerable potential to define clonal relationships coupled with information on cell state in humans. Previous methods focused on higher heteroplasmy mutations that are limited in number and can be influenced by functional selection, introducing biases for lineage tracing. Although more challenging to detect, intermediate to low heteroplasmy mtDNA mutations are valuable due to their high diversity, abundance, and lower propensity to selection. To enhance mtDNA mutation detection and facilitate fine-scale lineage tracing, we developed the single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling (ReDeeM) approach, an integrated experimental and computational framework. Recently, some concerns have been raised about the analytical workflow in the ReDeeM framework. Specifically, it was noted that the mutations detected in a single molecule per cell are enriched on edges of mtDNA molecules, suggesting they resemble artifacts reported in other sequencing approaches. It was then proposed that all mutations found in one molecule per cell should be removed. We detail our error correction method, demonstrating that the observed edge mutations are distinct from previously reported sequencing artifacts. We further show that the proposed removal leads to massive elimination of bona fide and informative mutations. Indeed, mutations accumulating on edges impact a minority of all mutation calls (for example, in hematopoietic stem cells, the excess mutations on the edge account for only 4.3%-7.6% of the total). Recognizing the value of addressing edge mutations even after applying consensus correction, we provide an additional filtering option in the ReDeeM-R package. This approach effectively eliminates the position biases, leads to a mutational signature indistinguishable from bona fide mitochondrial mutations, and removes excess low molecule high connectedness mutations. Importantly, this option preserves the large majority of unique mutations identified by ReDeeM, maintaining the ability of ReDeeM to provide a more than 10-fold increase in variant detection compared to previous methods. Additionally, the cells remain well-connected. While there is room for further refinement in mutation calling strategies, the significant advances and biological insights provided by the ReDeeM framework are unique and remain intact. We hope that this detailed discussion and analysis enables the community to employ this approach and contribute to its further development.

Dose escalation in radical radio(chemo)therapy for cervical and upper thoracic esophageal cancer with 3DCRT/IMRT (ChC&UES): a multicenter retrospective study.

BACKGROUND: Cervical and upper thoracic esophageal cancer (ESCA) presents treatment challenges due to limited clinical evidence. This multi-center study (ChC&UES) explores radical radio(chemo)therapy efficacy and safety, especially focusing on radiation dose. METHOD: We retrospectively analyzed clinical data from 1,422 cases across 8 medical centers. According to the radiation dose for primary gross tumor, patients were divided into standard dose radiotherapy (SD, 50-55 Gy) or high dose (HD, > 55 Gy) radiotherapy. HD was further subdivided into conventional- high-dose group (HD-conventional, 55-63 Gy) and ultra-high-dose group (HD-ultra, ≥ 63 Gy). Primary outcome was Overall Survival (OS). RESULTS: The median OS was 33.0 months (95% CI: 29.401-36.521) in the whole cohort. Compared with SD, HD shown significant improved survival in cervical ESCA in Kaplan-Meier (P = 0.029) and cox multivariate regression analysis (P = 0.024) while shown comparable survival in upper thoracic ESCA (P = 0.735). No significant difference existed between HD-conventional and HD-ultra in cervical (P = 0.976) and upper thoracic (P = 0.610) ESCA. Incidences of radiation esophagitis and pneumonia from HD were comparable to SD (P = 0.097, 0.240), while myosuppression risk was higher(P = 0.039). The Bonferroni method revealed that, for both cervical and upper thoracic ESCA, HD-ultra enhance the objective response rate (ORR) compared to SD (P < 0.05). CONCLUSION: HD radiotherapy benefits cervical but not upper thoracic ESCA, while increasing bone marrow suppression risk. Further dose escalating (≥ 63 Gy) doesn't improve survival but enhances ORR.

Evaluating the embryotoxicity of benzophenone-based photoinitiators in stem cells and zebrafish embryos.

Benzophenones (BPs) are widely used as photoinitiators (PIs) or printing inks in food packaging, which may migrate into foods. However, the toxicity information of some BP analogues, such as 4,4'-bis(diethylamino)-benzophenone (DEAB), 4-phenylbenzophenone (4-PBP), 4 (hydroxymethyl)benzophenone (4-HMBP), those are used as PIs is lacking. Developmental toxicity is a health concern associated with PIs exposure. Recently, alternative non-in vivo methods have been proposed to evaluate the concerned chemicals or better understand the modes of action of certain toxicological endpoints. In this study, using in silico methods, we predicted that BP, DEAB, 4-PBP and 4-HMBP might exhibit developmental toxicity. However, we found that only DEAB is strong embryotoxic and disturbs the early differentiation of mouse embryonic stem cells into three germ layers and cardiomyocytes. DEAB treatment also prevented cardiomyocyte differentiation in human induced pluripotent stem cells (hiPSCs) on day 10. However, BP, 4-PBP and 4-HMBP had no similar effects on cardiomyocyte differentiation on day 10. Transcriptomic analysis revealed that treatment with DEAB significantly decreased the mRNA levels of differentiation-related transcription factors SOX17 and FOXA1, in hiPSCs on day 4. Furthermore, DEAB treatment caused tail malformations and yolk sac edema in zebrafish embryos. To conclude, DEAB may be embryotoxic because it disturbs the early differentiation of stem cells. Further studies are warranted to better understand the health effects of DEAB exposure.

Experimental quantum Byzantine agreement on a three-user quantum network with integrated photonics.

Quantum communication networks are crucial for both secure communication and cryptographic networked tasks. Building quantum communication networks in a scalable and cost-effective way is essential for their widespread adoption. Here, we establish a complete polarization entanglement-based fully connected network, which features an ultrabright integrated Bragg reflection waveguide quantum source, managed by an untrusted service provider, and a streamlined polarization analysis module, which requires only one single-photon detector for each user. We perform a continuously working quantum entanglement distribution and create correlated bit strings between users. Within the framework of one-time universal hashing, we provide the experimental implementation of source-independent quantum digital signatures using imperfect keys circumventing the necessity for private amplification. We further beat the 1/3 fault tolerance bound in the Byzantine agreement, achieving unconditional security without relying on sophisticated techniques. Our results offer an affordable and practical route for addressing consensus challenges within the emerging quantum network landscape.

Clinical study of camrelizumab combined with docetaxel and carboplatin as a neoadjuvant treatment for locally advanced oesophageal squamous cell carcinoma.

Herein, we aimed to evaluate the efficacy and safety of camrelizumab combined with docetaxel and carboplatin as a neoadjuvant treatment for locally advanced oesophageal squamous cell carcinoma (OSCC). Fifty-one patients with OSCC, treated from July 2020 to October 2022, were analyzed. Of them, 41 patients underwent surgery 4-8 weeks after undergoing two cycles of camrelizumab (200 mg IV Q3W) combined with docetaxel (75 mg/m2 IV Q3W) and carboplatin (area under the curve = 5-6 IV Q3W). The primary endpoint was the pathological complete response rate. All 51 patients (100%) experienced treatment-related grades 1-2 adverse events, and 2 patients (3.9%) experienced grade 4 events (including elevated alanine transaminase/aspartate transferase levels and Guillain-Barre syndrome). Fifty patients were evaluated for the treatment efficacy. Of them, 13 achieved complete response, and the objective response rate was 74%. Only 41 patients underwent surgical treatment. The pathological complete response rate was 17.1%, the major pathological response rate was 63.4%, and the R0 resection rate was 100%. Approximately 22% of the patients had tumor regression grades 0. Eight patients (19.5%) developed surgery-related complications. The median follow-up time was 18 months (range: 3-29 months). Four patients experienced disease progression, while four died. The median disease-free survival and overall survival were not reached. Camrelizumab combined with docetaxel and carboplatin is an effective and safe neoadjuvant treatment for locally advanced OSCC. This regimen may afford a potential strategy to treat patients with locally advanced OSCC.

Deciphering cell states and genealogies of human haematopoiesis.

The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.

Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution.

Mitochondria (MT) participate in most metabolic activities of mammalian cells. A near-unidirectional mitochondrial transfer from T cells to cancer cells was recently observed to "metabolically empower" cancer cells while "depleting immune cells," providing new insights into tumor-T cell interaction and immune evasion. Here, we leverage single-cell RNA-seq technology and introduce MERCI, a statistical deconvolution method for tracing and quantifying mitochondrial trafficking between cancer and T cells. Through rigorous benchmarking and validation, MERCI accurately predicts the recipient cells and their relative mitochondrial compositions. Application of MERCI to human cancer samples identifies a reproducible MT transfer phenotype, with its signature genes involved in cytoskeleton remodeling, energy production, and TNF-α signaling pathways. Moreover, MT transfer is associated with increased cell cycle activity and poor clinical outcome across different cancer types. In summary, MERCI enables systematic investigation of an understudied aspect of tumor-T cell interactions that may lead to the development of therapeutic opportunities.

The microstructural change of the brain and its clinical severity association in pediatric Tourette syndrome patients.

BACKGROUND: Gilles de la Tourette syndrome (GTS) is a prevalent pediatric neurological disorder. Most studies point to abnormalities in the cortico-striato-thalamocortical (CSTC) circuits. Neuroimaging studies have shown GTS's extensive impact on the entire brain. However, due to participant variability and potential drug and comorbidity impact, the results are inconsistent. To mitigate the potential impact of participant heterogeneity, we excluded individuals with comorbidities or those currently undergoing medication treatments. Based on the hypothesis of abnormality within the CSTC circuit, we investigated microstructural changes in white matter using diffusion spectrum imaging (DSI). This study offers the first examination of microstructural changes in treatment-naïve pediatric patients with pure GTS using diffusion spectrum imaging. METHODS: This single-center prospective study involved 30 patients and 30 age- and gender-matched healthy volunteers who underwent sagittal T1-weighted MRI and DSI. We analyzed generalized fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity. RESULTS: No significant differences were observed in mean diffusivity and axial diffusivity values between the two groups. However, the patient group exhibited significantly higher generalized fractional anisotropy values in the right frontostriatal tract of the dorsolateral prefrontal cortex, the right frontostriatal tract of the precentral gyrus, and bilateral thalamic radiation of the dorsolateral prefrontal cortex. Additionally, the generalized fractional anisotropy value of the right frontostriatal tract of the precentral gyrus is inversely correlated with the total tic severity scores at the most severe condition. CONCLUSION: Treatment-naïve pediatric GTS patients demonstrated increased connectivity within the CSTC circuit as per diffusion spectrum imaging, indicating possible CSTC circuit dysregulation. This finding could also suggest a compensatory change. It thus underscores the necessity of further investigation into the fundamental pathological changes in GTS. Nevertheless, the observed altered connectivity in GTS patients might serve as a potential target for therapeutic intervention.

Single cell multiomic analysis reveals diabetes-associated ß-cell heterogeneity driven by HNF1A.

Broad heterogeneity in pancreatic ß-cell function and morphology has been widely reported. However, determining which components of this cellular heterogeneity serve a diabetes-relevant function remains challenging. Here, we integrate single-cell transcriptome, single-nuclei chromatin accessibility, and cell-type specific 3D genome profiles from human islets and identify Type II Diabetes (T2D)-associated ß-cell heterogeneity at both transcriptomic and epigenomic levels. We develop a computational method to explicitly dissect the intra-donor and inter-donor heterogeneity between single ß-cells, which reflect distinct mechanisms of T2D pathogenesis. Integrative transcriptomic and epigenomic analysis identifies HNF1A as a principal driver of intra-donor heterogeneity between ß-cells from the same donors; HNF1A expression is also reduced in ß-cells from T2D donors. Interestingly, HNF1A activity in single ß-cells is significantly associated with lower Na+ currents and we nominate a HNF1A target, FXYD2, as the primary mitigator. Our study demonstrates the value of investigating disease-associated single-cell heterogeneity and provides new insights into the pathogenesis of T2D.

Massively parallel base editing to map variant effects in human hematopoiesis.

Systematic evaluation of the impact of genetic variants is critical for the study and treatment of human physiology and disease. While specific mutations can be introduced by genome engineering, we still lack scalable approaches that are applicable to the important setting of primary cells, such as blood and immune cells. Here, we describe the development of massively parallel base-editing screens in human hematopoietic stem and progenitor cells. Such approaches enable functional screens for variant effects across any hematopoietic differentiation state. Moreover, they allow for rich phenotyping through single-cell RNA sequencing readouts and separately for characterization of editing outcomes through pooled single-cell genotyping. We efficiently design improved leukemia immunotherapy approaches, comprehensively identify non-coding variants modulating fetal hemoglobin expression, define mechanisms regulating hematopoietic differentiation, and probe the pathogenicity of uncharacterized disease-associated variants. These strategies will advance effective and high-throughput variant-to-function mapping in human hematopoiesis to identify the causes of diverse diseases.

Experimental quantum secure network with digital signatures and encryption.

Cryptography promises four information security objectives, namely, confidentiality, integrity, authenticity and non-repudiation, to support trillions of transactions annually in the digital economy. Efficient digital signatures, ensuring integrity, authenticity and non-repudiation of data with information-theoretical security are highly urgent and intractable open problems in cryptography. Here, we propose a high-efficiency quantum digital signature (QDS) protocol using asymmetric quantum keys acquired via secret sharing, one-time universal2 hashing and a one-time pad. We just need to use a 384-bit key to sign documents of lengths up to 264 with a security bound of 10-19. If a one-megabit document is signed, the signature efficiency is improved by more than 108 times compared with previous QDS protocols. Furthermore, we build the first all-in-one quantum secure network integrating information-theoretically secure communication, digital signatures, secret sharing and conference key agreement and experimentally demonstrate this signature efficiency advantage. Our work completes the cryptography toolbox of the four information security objectives.

Multiple-State Nonvolatile Memory Based on Ultrathin Indium Oxide Film via Liquid Metal Printing.

In this work, the ultrathin two-dimensional (2D) indium oxide (InOx) with a large area of more than 100 µm2 and a high degree of uniformity was automatically peeled off from indium by the liquid-metal printing technique. Raman and optical measurements revealed that 2D-InOx has a polycrystalline cubic structure. By altering the printing temperature which affects the crystallinity of 2D-InOx, the mechanism of the existence and disappearance of memristive characteristics was established. The tunable characteristics of the 2D-InOx memristor with reproducible one-order switching was manifest from the electrical measurements. Further adjustable multistate characteristics of the 2D-InOx memristor and its resistance switching mechanism were evaluated. A detailed examination of the memristive process demonstrated the Ca2+ mimic dynamic in 2D-InOx memristors as well as the fundamental principles underlying biological and artificial synapses. These surveys allow us to comprehend a 2D-InOx memristor using the liquid-metal printing technique and could be applied to future neuromorphic applications and in the field of revolutionary 2D material exploration.

Environmental damage compensation for illegal solid waste dumping in China.

China aims to improve its system for pursuing environmental damage compensation environmental violation cases. To hold violators accountable, China has an effective system for the identification and assessment (I&A) of environmental damage. This study selected a typical case of the illegal dumping of solid waste (IDSW) in China to analyze the causes, the degree, and characteristics of environmental damage, focusing on components such as the physical quantification and valuation of damage. The findings were as follows: (1) Compensation claimants and obligors consider baseline damage confirmation and causality analysis key components of I&A. (2) The I&A process for a specific case needs to focus on key nodes such as the type, location, and duration of IDSW. (3) Restraining IDSW requires accurately quantifying the physical and value-related losses caused by solid waste dumping. (4) In the selected case study, the damage from environmental contamination caused by the IDSW incident amounted to 3938,990 yuan, including an environmental damage value of 3651,990 yuan and a transaction cost of 287,000 yuan. Both parties accepted the I&A calculation process in this case, and the desired punishment effect was achieved. Hence, the case study demonstrated that accurate I&A is the technical basis for environmental damage compensation. Thus, in the future, more attention should be paid to the role of scientific and technological means and knowledge reserves in the I&A of environmental damage.

Lipid rafts may affect the coalescence of milk fat globules through phase transition after thermal treatment.

This study aimed to investigate changes of fat globules and their membranes, and further analyze evolution of lipid profile of lipid rafts in membranes during heat processing of cow milk. Size of fat globules increased from 3.16 µm to 3.70 µm and ζ-potential decreased from -0.53 mV to -0.38 mV after thermal treatment, suggesting that fat globule membrane was destroyed and fat globule occurred coalescence. Glycerophospholipids and cholesterol in fat globule membrane decreased while sphingomyelin increased after thermal treatment. Results of lipidomics show that total of 38 species of 5 lipids molecule showed ability to differentiate the samples. At high temperatures, highly unsaturated glycerophospholipids and sterol lipids were lost from rafts, meanwhile, sphingomyelin and ceramide increased in this region. Significant change of lipid profile in the raft region during thermal treatment suggested a potential relationship between lipid rafts and fat globule coalescence behavior.

What Constitutes the High-Quality Soundscape in Human Habitats? Utilizing a Random Forest Model to Explore Soundscape and Its Geospatial Factors Behind.

Soundscape is the production of sounds and the acoustic environment, and it emphasizes peoples' perceiving and experiencing process in the context. To this end, this paper focuses on the Pearl River Delta in China, and implements an empirical study based on the soundscape evaluation data from the Participatory Soundscape Sensing (PSS) system, and the geospatial data from multiple sources. The optimal variable set with 24 features are successfully used to establish a random forest model to predict the soundscape comfort of a new site (F1 = 0.61). Results show that the acoustic factors are most important to successfully classify soundscape comfort (averaged relative importance of 17.45), subsequently ranking by built environment elements (11.28), temporal factors (9.59), and demographic factors (9.14), while landscape index (8.60) and land cover type (7.71) seem to have unclear importance. Furthermore, the partial dependence analysis provides the answers about the appropriate threshold or category of various variables to quantitatively or qualitatively specify the necessary management and control metrics for maintaining soundscape quality. These findings suggest that mainstreaming the soundscape in the coupled natural-human systems and clarifying the mechanisms between soundscape perception and geospatial factors can be beneficial to create a high-quality soundscape in human habitats.

Simple security proof of coherent-one-way quantum key distribution.

Coherent-one-way quantum key distribution (COW-QKD), which requires a simple experimental setup and has the ability to withstand photon-number-splitting attacks, has been not only experimentally implemented but also commercially applied. However, recent studies have shown that the current COW-QKD system is insecure and can only distribute secret keys safely within 20 km of the optical fiber length. In this study, we propose a practical implementation of COW-QKD by adding a two-pulse vacuum state as a new decoy sequence. This proposal maintains the original experimental setup as well as the simplicity of its implementation. Utilizing detailed observations on the monitoring line to provide an analytical upper bound on the phase error rate, we provide a high-performance COW-QKD asymptotically secure against coherent attacks. This ensures the availability of COW-QKD within 100 km and establishes theoretical foundations for further applications.

A full-face mask for protection against respiratory infections.

BACKGROUND: Aerosols and droplets are the transmission routes of many respiratory infectious diseases. The COVID-19 management guidance recommends against the use of nebulized inhalation therapy directly in the emergency room or in an ambulance to prevent possible viral transmission. The three-dimensional printing method was used to develop an aerosol inhalation treatment mask that can potentially prevent aerosol dispersion. We conducted this utility validation study to understand the practicability of this new nebulizer mask system. RESULTS: The fit test confirmed that the filter can efficiently remove small particles. The different locations of the mask had an excellent fit with a high pressure making a proper face seal usability. The full-face mask appeared to optimize filtration with pressure and is an example of materials that perform well for improvised respiratory protection using this design. The filtering effect test confirmed that the contamination of designated locations could be protected when using the mask with filters. As in the clinical safety test, a total of 18 participants (10 [55.6%] females; aged 33.1 ± 0.6 years) were included in the final analysis. There were no significant changes in SPO2, EtCO2, HR, SBP, DBP, and RR at the beginning, 20th, 40th, or 60th minutes of the test (all p >.05). The discomfort of wearing a mask increased slightly after time but remained within the tolerable range. The vision clarity score did not significantly change during the test. The mask also passed the breathability test. CONCLUSION: The results of our study showed that this mask performed adequately in the fit test, the filtering test, and the clinical safety test. The application of a full-face mask with antiviral properties, together with the newly designed shape of a respirator that respects the natural curves of a human face, will facilitate the production of personal protective equipment with a highly efficient filtration system. METHODS: We conducted three independent tests in this validation study: (1) a fit test to calculate the particle number concentration and its association with potential leakage; (2) a filtering effect test to verify the mask's ability to contain aerosol spread; and (3) a clinical safety test to examine the clinical safety, comfortableness, and visual clarity of the mask.

Inferring gene regulation from stochastic transcriptional variation across single cells at steady state.

Regulatory relationships between transcription factors (TFs) and their target genes lie at the heart of cellular identity and function; however, uncovering these relationships is often labor-intensive and requires perturbations. Here, we propose a principled framework to systematically infer gene regulation for all TFs simultaneously in cells at steady state by leveraging the intrinsic variation in the transcriptional abundance across single cells. Through modeling and simulations, we characterize how transcriptional bursts of a TF gene are propagated to its target genes, including the expected ranges of time delay and magnitude of maximum covariation. We distinguish these temporal trends from the time-invariant covariation arising from cell states, and we delineate the experimental and technical requirements for leveraging these small but meaningful cofluctuations in the presence of measurement noise. While current technology does not yet allow adequate power for definitively detecting regulatory relationships for all TFs simultaneously in cells at steady state, we investigate a small-scale dataset to inform future experimental design. This study supports the potential value of mapping regulatory connections through stochastic variation, and it motivates further technological development to achieve its full potential.

Evaluation of alkaline activated sodium persulfate sustained release rod for the removal of dissolved trichloroethylene.

The presence of trichloroethylene (TCE) dense non-aqueous phase liquid (DNAPL) in the subsurface can generate a dissolved phase plume in groundwater. This study developed an alkaline activated sodium persulfate (SPS) sustained release oxidation rod (alkaline SPS SR-Rod) for long-term in situ chemical oxidation accelerated treatment of TCE dissolved from TCE DNAPL, by creating a greater concentration gradient at the TCE DNPL boundary. The dissolution of TCE DNAPL (1 mL) in water (280 mL) generated ~700 mg L-1, with a volumetric mass transfer coefficient (kLa) of 0.0187 d-1. The alkaline SPS SR-Rod system had a kLa of 0.013 d-1 for TCE dissolution at early stage, and thereafter aqueous TCE concentration remained below ~10 mg L-1 over 60 d of reaction. An SPS SR-Rod life-span of 186 d, for 90% of SPS released from the rod, was estimated. In the soil-water system, aqueous TCE was maintained < 3 mg L- 1 throughout the reaction and the soil oxidant demand was determined to be ~4 g-SPS/kg-soil in the alkaline SPS SR-Rod system. These results revealed that the use of the alkaline SPS SR-Rod can be effective as a method of treating dissolved TCE released from DNAPL contamination, and thereby accelerating TCE DNAPL removal.