Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic association of toxin production in the dinoflagellate Alexandrium minutum

Dinoflagellates of the genus Alexandrium are responsible for harmful algal blooms and produce paralytic shellfish toxins (PSTs). Their very large and complex genomes make it challenging to identify the genes responsible for toxin synthesis. A family-based genomic association study was developed to determine the inheritance of toxin production in Alexandrium minutum and identify genomic regions linked to this production. We show that the ability to produce toxins is inheritable in a Mendelian way, while the heritability of the toxin profile is more complex. We developed the first dinoflagellate genetic linkage map. Using this map, several major results were obtained: 1. A genomic region related to the ability to produce toxins was identified. 2. This region does not contain any polymorphic sxt genes, known to be involved in toxin production in cyanobacteria. 3. The sxt genes, known to be present in a single cluster in cyanobacteria, are scattered on different linkage groups in A. minutum. 4. The expression of two sxt genes not assigned to any linkage group, sxtI and sxtG, may be regulated by the genomic region related to the ability to produce toxins. Our results provide new insights into the organization of toxicity-related genes in A. minutum, suggesting a dissociated genetic mechanism for the production of the different analogues and the ability to produce toxins. However, most of the newly identified genes remain unannotated. This study therefore proposes new candidate genes to be further explored to understand how dinoflagellates synthesize their toxins.
Emerging metal doped carbon dots for promising theranostic applications

As a bridge between organic fluorophores and inorganic quantum dots, carbon dots (CDs) have been recognized as emerging nanotheranostics for biomedical applications owing to their distinctive merits such as superior optical properties, flexible modification, adjustable functionalities, and remarkable photoactive therapeutic outcome, etc. Compared to metal free CDs, the introduction of metal ion in CDs endowed metal-doped CDs (MCDs) with tunable optical properties and new intrinsic properties, thereby illustrating its different capabilities from metal-free CDs for bioimaging and therapy. This review aims to summarize the recent progress of photonic MCDs as emerging nanoagent for theranostic application such as disease-related diagnostic (involving biosensing and bioimaging) and cancer therapy. The challenges and potential development of MCDs in nanotheranostic fields are also discussed.
Low-Rank Tensor Completion Based on Self-Adaptive Learnable Transforms.

The tensor nuclear norm (TNN), defined as the sum of nuclear norms of frontal slices of the tensor in a frequency domain, has been found useful in solving low-rank tensor recovery problems. Existing TNN-based methods use either fixed or data-independent transformations, which may not be the optimal choices for the given tensors. As the consequence, these methods cannot exploit the potential low-rank structure of tensor data adaptively. In this article, we propose a framework called self-adaptive learnable transform (SALT) to learn a transformation matrix from the given tensor. Specifically, SALT aims to learn a lossless transformation that induces a lower average-rank tensor, where the Schatten- p quasi-norm is used as the rank proxy. Then, because SALT is less sensitive to the orientation, we generalize SALT to other dimensions of tensor (SALTS), namely, learning three self-adaptive transformation matrices simultaneously from given tensor. SALTS is able to adaptively exploit the potential low-rank structures in all directions. We provide a unified optimization framework based on alternating direction multiplier method for SALTS model and theoretically prove the weak convergence property of the proposed algorithm. Experimental results in hyperspectral image (HSI), color video, magnetic resonance imaging (MRI), and COIL-20 datasets show that SALTS is much more accurate in tensor completion than existing methods. The demo code can be found at https://faculty.uestc. edu.cn/gaobin/zh_ CN/lwcg/153392/list/index.htm.
Protocol for a mobile laboratory study of co-administration of cannabis concentrates with a standard alcohol dose in humans

Cannabis is commonly used among people who drink alcohol, yet evidence on acute effects of co-use is conflicting. Two important variables that may influence the effects of cannabis and alcohol are cannabinoid content (i.e., the ratio of cannabidiol [CBD] and 9-tetrahydrocannabinol [THC]) as well as the order of use (i.e., cannabis before alcohol vs. alcohol before cannabis). Research is mixed regarding the acute imapct of cannabis on alcohol consumption and intoxication, with some studies suggesting additive effects of alcohol and cannabis, and others demonstrating negligible effects of combining these substances. Further complicating this, high-THC-content cannabis concentrates are increasingly popular on the legal-market, but to our knowledge, no studies have explored concentrate and alcohol co-use. In addition to cannabinoid content, order of use may influence intoxication and other acute effects, but is also understudied. Co-use studies typically administer a fixed dose of alcohol before cannabis, and there is a lack of data on the acute effects of cannabis before alcohol. Thus, there is a need for experimental co-use studies exploring the impact of cannabinoid content (particularly of highly potent cannabis concentrates) and order effects on intoxication. This study uses a federally-compliant mobile laboratory procedure to explore the effects of co-administration of legal-market cannabis concentrates with a moderate alcohol dose (.8g/kg) in a sample of community participants who regularly use alcohol and cannabis. The study will also explore alcohol and cannabis order effects (cannabis before alcohol vs. alcohol before cannabis). Outcomes are objective intoxication (measured using blood cannabinoid level, heart rate, psychomotor performance and breath alcohol level [BrAC]) and subjective intoxication (assessed via self-report measures). Overall, this study may influence harm-reduction recommendations for individuals who drink alcohol and use cannabis.
Shear wave elastography evaluation of cats with chronic kidney disease.

Chronic kidney disease (CKD) is a major health condition in cats that can lead to poor quality of life and financial implications for therapy. Currently staging and identification of CKD is limited by diagnostic testing such as creatinine and urine-specific gravity, which do not change until late in the disease course. Other methods to evaluate CKD would be valuable in the clinical setting. Shear wave elastography is one novel ultrasound method, which has shown promise in identifying increases in tissue stiffness and identifying CKD in people. As CKD is often histologically characterized by tubulointerstitial fibrosis, shear wave elastography has the potential to identify CKD and differentiate between stages of CKD in cats. This prospective observational case-control study with 78 cats found no difference in shear wave velocities between groups (P = 0.33), a contradictory finding to one prior publication. There was no effect of weight (P = 0.65), nor the presence of mineralization (P = 0.31) or infarction (P = 0.52) on cortical shear wave velocities. There was a significant effect of age on shear wave velocity (P = 0.018) where velocities increased with age. The intraclass correlation coefficient was only moderate (0.62). Possible reasons for the difference in results between our work and that published prior, include differences in methodology and differences in instrumentation. Variability in measurements in our population may be due to the effects of respiratory motion or limitations in shear wave elastography software. As such, shear wave elastography is not currently recommended as a tool to evaluate CKD in cats and further work is necessary.
SCF-SKP2 E3 ubiquitin ligase links mTORC1/ER stress/ISR with YAP activation in murine renal cystogenesis

The Hippo pathway nuclear effector Yes-associated protein (YAP) potentiates the progression of polycystic kidney disease (PKD) arising from ciliopathies. The mechanisms underlying the increase in YAP expression and transcriptional activity in PKD remain obscure. We observed that in kidneys from mice with juvenile cystic kidney (jck) ciliopathy, the aberrant hyperactivity of mechanistic target of rapamycin complex 1 (mTORC1), driven by ERK1/2 and PI3K/AKT cascades, induced ER proteotoxic stress. To reduce this stress by reprogramming translation, the protein kinase R–like ER kinase–eukaryotic initiation factor 2α (PERK/eIF2α) arm of the integrated stress response (ISR) was activated. PERK-mediated phosphorylation of eIF2α drove the selective translation of activating transcription factor 4 (ATF4), potentiating YAP expression. In parallel, YAP underwent K63-linked polyubiquitination by SCF S-phase kinase-associated protein 2 (SKP2) E3 ubiquitin ligase, a Hippo-independent, nonproteolytic ubiquitination that enhances YAP nuclear trafficking and transcriptional activity in cancer cells. Defective ISR cellular adaptation to ER stress in eIF2α phosphorylation–deficient jck mice further augmented YAP-mediated transcriptional activity and renal cyst growth. Conversely, pharmacological tuning down of ER stress/ISR activity and SKP2 expression in jck mice by administration of tauroursodeoxycholic acid (TUDCA) or tolvaptan impeded these processes. Restoring ER homeostasis and/or interfering with the SKP2-YAP interaction represent potential therapeutic avenues for stemming the progression of renal cystogenesis.
Oropharyngeal samples versus lesion specimens at diagnosis in patients infected with monkeypox virus in Northern France

The ongoing outbreak of monkeypox virus (MPXV) is the largest one in historically non‐endemic countries. Early reports described atypical epidemiological and clinical presentations. We investigated MPXV DNA detection in oropharyngeal samples (OPS), and compared the viral load to that in lesion samples at diagnosis in patients infected with MPXV. We retrospectively included patients suspected to have monkeypox in Northern France, who underwent a MPXV PCR in the Virology Laboratory, University Hospital of Lille, from May 23 to August 18, 2022. Overall, a total of 228 patients (376 samples) were included. A positive result in at least one sample was found in 138 patients (60.5%). We compared PCR results between OPS and lesion samples (i.e., cutaneous or anal/rectal samples) in patients with both samples. A positive result in OPS was observed in 54 out of 60 patients (90%). The viral load in OPS (median Ct value = 29.5; interquartile range [IQR] = 24.7−34) was significantly lower than that in lesion samples (median Ct value = 17.8; IQR = 16.3 and 19.7) (p < 0.0001). This report shows that pharyngeal sampling does not bring additional information for the initial diagnosis in patients presenting with typical lesions.
Efficacy and safety of electroacupuncture for oxaliplatin-induced peripheral neuropathy in colorectal cancer patients: a single-blinded, randomized, sham-controlled trial

Background: Oxaliplatin-based chemotherapy is a major first-line conventional therapy for advanced and metastatic colorectal cancer (CRC). However, oxaliplatin causes chemotherapy-induced peripheral neuropathy (CIPN). Acupuncture has long been used to alleviate limb numbness in Chinese medicine practice. Aim: The aim of this study was to examine the efficacy and safety of electroacupuncture (EA) for the alleviation of CIPN in CRC patients. Design: This was a pilot single-blinded, randomized, sham-controlled trial. Setting/participants: Sixty eligible patients, who had been diagnosed with CRC and were undergoing oxaliplatin-based chemotherapy, were randomized in a ratio of 1:1 to the EA intervention group or sham acupuncture (SA) control group. During a 12-week treatment period, patients in the EA group received EA once a week, while patients in the SA group received SA; both groups were followed up for 12 weeks. Results: Compared with the SA group, the EA group exhibited significant alleviation of CIPN severity during chemotherapy. Moreover, EA also improved the physical function, role function, and social function of CRC patients. However, there were no significant differences in tests of vibration or light touch sensation. In addition, EA appeared to be a safe treatment for CIPN and was both feasible and acceptable to CRC patients during chemotherapy. Conclusion: This study showed preliminary evidence for the efficacy and safety of EA in acute CIPN among CRC patients, although further studies are needed to verify these effects and to further explore the potential role of EA in chronic CIPN (effects on which remain unclear). Trial registration number: NCT03582423 (ClinicalTrials.gov)
Interplay between particle microstructure, network topology and sample shape in magnetic gels -- A molecular dynamics simulation study

Ferrogels, i.e., hydrogels loaded with magnetic nanoparticles, have the ability to deform in external magnetic fields. The precise shape of deformation and the alignment of the gel in the field, however, depend on the interplay of several factors. In this paper, we introduce a coarse-grained simulation model, which takes into account the configuration of magnetic particles in the gel, the sample shape, and aspects of the polymer network topology. We use this model to show that in gels with an isotropic microstructure, an external magnetic field reduces clustering, while this is not the case for uniaxial gels, in which the particle configuration is anisotropic due to the presence of a magnetic field during cross-linking. For ellipsoidal gels, we find that a uniaxial microstructure additionally can override the deformation and alignment expected as indicated the demagnetization energy. Finally, we examine to what degree gels with different network topologies maintain the particle microstructure ``frozen in`` during the cross-linking process.
Relative validity of the online Meal-based Diet History Questionnaire for evaluating the overall diet quality and quality of each meal type in Japanese adults

Abstract The aim of this study was to examine the relative validity of the online Meal-based Diet History Questionnaire (MDHQ) for assessing the overall diet quality and quality of each meal type (breakfast, lunch, dinner and snacks). In total, 222 Japanese adults (111 for each sex) aged 30–76 years completed the online MDHQ and then the 4-non-consecutive-day weighed dietary record (DR). The diet quality was assessed using the Healthy Eating Index-2015 (HEI-2015) and Nutrient-Rich Food Index 9.3 (NRF9.3). For the HEI-2015, compared with the DR, the MDHQ provided high median values for breakfast (in women only) and dinner and low median values for snacks. There were no significant differences observed for overall diet and lunch. For the NRF9.3, the MDHQ provided higher median values for breakfast and dinner and a lower median value for overall diet than the DR in women, with no significant differences for lunch and snacks. In men, no significant difference was observed, except for overall diet (the MDHQ providing a lower median value). For the HEI-2015, median Spearman correlation coefficient was 0·43, with a range from 0·12 (snacks in women) to 0·68 (breakfast in men). For the NRF9.3, median Spearman correlation coefficient was 0·47, with a range from 0·26 (snacks in men) to 0·65 (breakfast in men). Bland–Altman plots showed wide limits of agreement and, in some cases, proportional bias. In conclusion, the online MDHQ showed an acceptable ability for ranking individuals according to the quality of overall diet, breakfast, lunch and dinner, but not snacks.
Reproductive coercion as a form of family violence against immigrant and refugee women in Australia

Reproductive coercion (RC), generally considered a form of intimate partner violence (IPV), refers to perpetrator behaviours and actions that are intended to interfere with and control the autonomous decision-making of a person regarding their reproductive health. To date there are few studies that document RC as experienced by immigrant and refugee women. In this article, we explore cases of RC as described by women who were part of a larger qualitative study investigating violence against immigrant and refugee women in southern Australia. The study aimed to identify the types of RC detailed in immigrant and refugee women’s narratives, and to illustrate the contexts in which these experiences occurred. Analysis followed Baxter and Jack’s (2008) case study methodology; whereby particular “cases” are used to describe a phenomenon in context. Thirteen women from seven countries described experiences that fit definitions of RC. The cases describe various types of RC including violence during pregnancy with the intent of causing miscarriage, forced abortion, contraception sabotage and forced pregnancy. As well as intimate partners, some women described multiple perpetrators being complicit in their experience of RC, especially in regard to controlling women’s access to, and interactions with health services. More information is needed about immigrant and refugee women’s experiences of RC, and how vulnerability to multi-perpetrator violence affects health service access. In particular knowledge about how multi-perpetrator RC can affect consent processes for women who already face barriers to health care requires attention. Further research is required to address knowledge gaps about appropriate prevention and advocacy work about RC in refugee and migrant communities, and what training is needed for professionals in the family violence sector, women’s health services, women’s organisations, multicultural and ethno-specific services.
Thermodynamic limits for optomechanical systems with conservative potentials

The mechanical force from light -- radiation pressure -- provides an intrinsic nonlinear interaction. Consequently, optomechanical systems near their steady state, such as the canonical optical spring, can display non-analytic behavior as a function of external parameters. This non-analyticity, a key feature of thermodynamic phase transitions, suggests that there could be an effective thermodynamic description of optomechanical systems. Here we explicitly define the thermodynamic limit for optomechanical systems and derive a set of sufficient constraints on the system parameters as the mechanical system grows large. As an example, we show how these constraints can be satisfied in a system with $\mathbb{Z}_2$ symmetry and derive a free energy, allowing us to characterize this as an equilibrium phase transition.
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli

Most bacteria can form biofilms, which typically have a life cycle from cells initially attaching to a surface before aggregation and growth produces biomass and an extracellular matrix before finally cells disperse. To maximize fitness at each stage of this life cycle and given the different events taking place within a biofilm, temporal regulation of gene expression is essential. We recently described the genes required for optimal fitness over time during biofilm formation in Escherichia coli using a massively parallel transposon mutagenesis approach called TraDIS-Xpress. We have now repeated this study in Salmonella enterica serovar Typhimurium to determine the similarities and differences in biofilm formation through time between these species. A core set of pathways involved in biofilm formation in both species included matrix production, nucleotide biosynthesis, flagella assembly and LPS biosynthesis. We also identified several differences between the species, including a divergent impact of the antitoxin TomB on biofilm formation in each species. We observed deletion of tomB to be detrimental throughout the development of the E. coli biofilms but increased biofilm biomass in S. Typhimurium. We also found a more pronounced role for genes involved in respiration, specifically the electron transport chain, on the fitness of mature biofilms in S. Typhimurium than in E. coli and this was linked to matrix production. This work deepens understanding of the core requirements for biofilm formation in the Enterobacteriaceae whilst also identifying some genes with specialised roles in biofilm formation in each species.
Transformed Flux-Form Semi-Lagrangian Scheme

Abstract : Transformed flux-form semi-Lagrangian (TFSL) scheme provides stable and accurate algorithm to solve the advection-diffusion equation. Different from the existing flux-form semi- Lagrangian schemes, the flux at boundary of grid cell is treated as the temporal mean between present and next time steps. After the temporal-spatial transformation using the characteristic-line concept, the temporal integration of the flux from present to next time step becomes the spatial integration of the flux at the present time step. This scheme is always stable even for large Courant numbers (> 20) with the second order accuracy in both time and space. For the Courant number not larger than 0.5, the TFSL scheme reduces to the Lax-Wendroff scheme. The capability of the TFSL scheme is demonstrated by the simulation of the equatorial Rossby-soliton propagation.
Insights into symbiotic interactions from metatranscriptome analysis of deep‐sea mussel Gigantidas platifrons under long‐term laboratory maintenance

Symbioses between invertebrates and chemosynthetic bacteria are of fundamental importance in deep‐sea ecosystems, but the mechanisms that enable their symbiont associations are still largely undescribed, owing to the culturable difficulties of deep‐sea lives. Bathymodiolinae mussels are remarkable in their ability to overcome decompression and can be maintained successfully for an extended period under atmospheric pressure, thus providing a model for investigating the molecular basis of symbiotic interactions. Herein, we conducted metatranscriptome sequencing and gene co‐expression network analysis of Gigantidas platifrons under laboratory maintenance with gradual loss of symbionts. The results revealed that one‐day short‐term maintenance triggered global transcriptional perturbation in symbionts, but little gene expression changes in mussel hosts, which were mainly involved in responses to environmental changes. Long‐term maintenance with depleted symbionts induced a metabolic shift in the mussel host. The most notable changes were the suppression of sterol biosynthesis and the complementary activation of terpenoid backbone synthesis in response to the reduction of bacteria‐derived terpenoid sources. In addition, we detected the upregulation of host proteasomes responsible for amino acid deprivation caused by symbiont depletion. Additionally, a significant correlation between host microtubule motor activity and symbiont abundance was revealed, suggesting the possible function of microtubule‐based intracellular trafficking in the nutritional interaction of symbiosis. Overall, by analyzing the dynamic transcriptomic changes during the loss of symbionts, our study highlights the nutritional importance of symbionts in supplementing terpenoid compounds and essential amino acids and provides insight into the molecular mechanisms and strategies underlying the symbiotic interactions in deep‐sea ecosystems.