Miracle-dz/UniFAR-FTUs huggingface dataset:
A Mechanism of the MJO Invoking Scale Interactions

This chapter distinguishes the mechanism of tropical convective disturbances, such as a hurricane, from that of the Madden–Julian oscillation (MJO). The hurricane is maintained by organized convection around the azimuth. In a hurricane the organization of convection, the generation of eddy available potential energy, and the transformation of eddy available potential energy into eddy kinetic energy all occur on the scale of the hurricane and these are called “in-scale processes,” which invoke quadratic nonlinearity. The MJO is not a hurricane type of disturbance; organized convection simply does not drive an MJO in the same manner. The maintenance of the MJO is more akin to a multibody problem where the convection is indeed organized on scales of tropical synoptic disturbances that carry a similar organization of convection and carry similar roles for the generation of eddy available potential energy and its conversion to the eddy kinetic energy for their maintenance. The maintenance of the MJO is a scale.
The Msh5 complex shows homeostatic localization in response to DNA double-strand breaks in yeast meiosis

Meiotic crossing over is essential for the segregation of homologous chromosomes. The formation and distribution of meiotic crossovers (COs), which are initiated by the formation of double-strand break (DSB), are tightly regulated to ensure at least one CO per bivalent. One type of CO control, CO homeostasis, maintains a consistent level of COs despite fluctuations in DSB numbers. Here, we analyzed the localization of proteins involved in meiotic recombination in budding yeast xrs2 hypomorphic mutants which show different levels of DSBs. The number of cytological foci with recombinases, Rad51 and Dmc1, which mark single-stranded DNAs at DSB sites is proportional to the DSB numbers. Among the pro-CO factor, ZMM/SIC proteins, the focus number of Zip3, Mer3, or Spo22/Zip4, was linearly proportional to reduced DSBs in the xrs2 mutant. In contrast, foci of Msh5, a component of the MutSγ complex, showed a non-linear response to reduced DSBs. We also confirmed the homeostatic response of COs by genetic analysis of meiotic recombination in the xrs2 mutants and found a chromosome-specific homeostatic response of COs. Our study suggests that the homeostatic response of the Msh5 assembly to reduced DSBs was genetically distinct from that of the Zip3 assembly for CO control.
Can lamina fresh mass be used to represent lamina dry mass? Evidence from Photinia serratifolia

Lamina dry mass (LDM) per unit area is an important plant functional trait. However, it is time-consuming to dry leaves in practice. Previous studies have demonstrated that lamina fresh mass (LFM) is approximately proportional to LDM for some broad-leaved plants. However, those studies largely overlooked the influence of leaf age on the proportional relationship, and leaves were sampled without distinguishing age. In the present study, we used eight leaf-age groups of Photinia serratifolia to test whether LDM is proportional to LFM. And we also compared the two linear equations (y = a + bx, and y = a + x, where x = ln LFM, y = ln LDM, a and b are constants to be estimated) to test whether the introduction of parameter b is worthwhile based on the percent error of the goodness-of-fit between the two equations. There were four of eight leaf-age groups whose 95% confidence intervals (CIs) for b included unity, and for the other four leaf-age groups the difference between the lower limit of the 95% CI and unity was smaller than 0.03, supporting the validity of the LDM vs. LFM proportional relationship. Additionally, the percent errors between the two equations for the eight leaf-age groups were all smaller than 5%, which further supports the hypothesis of a proportional relationship at the individual leaf-age group level. However, the LDM/LFM ratio exhibited a non-linear (quadratic) function of time, which indicates that the intercept, a, depends upon leaf age.
A proposal to analyze the progression of non-dialytic chronic kidney disease by surrogate endpoints: introducing parametric survival models

Introduction Chronic kidney disease (CDK) progression studies increasingly use surrogate endpoints based on the estimated glomerular filtration rate. The clinical characteristics of these endpoints bring new challenges in comparing groups of patients, as traditional Cox models may lead to biased estimates mainly because they do not assume a hazard function. Objective This study proposes the use of parametric survival analysis models with the three most commonly used endpoints in nephrology based on a case study. Estimated glomerular filtration rate (eGFR) decay > 5 mL/year, eGFR decline > 30%, and change in CKD stage were evaluated. Method The case study is a 5-year retrospective cohort study that enrolled 778 patients in the predialysis stage. Exponential, Weibull, Gompertz, lognormal, and logistic models were compared, and proportional hazard and accelerated failure time (AFT) models were evaluated. Results The endpoints had quite different hazard functions, demonstrating the importance of choosing appropriate models for each. AFT models were more suitable for the clinical interpretation of the effects of covariates on these endpoints. Conclusion Surrogate endpoints have different hazard distributions over time, which is already recognized by nephrologists. More flexible analysis techniques that capture these relevant clinical characteristics in decision-making should be encouraged and disseminated in nephrology research.
Unraveling the genetic potential of native rice (Oryza sativa L.) landraces for tolerance to early-stage submergence

Direct-seeded rice (DSR) is a promising alternative to the traditional puddled rice system. It has become more popular among rice growers as a result of socioeconomic shifts and global climate change. Although DSR offers advantages, rice plants experience greater anaerobic stress at sowing from unpredicted rainfall. Rice is unique among cereals in its ability to germinate under anaerobiosis. The coleoptile of rice rapidly elongates above the water surface to obtain more oxygen and enhance vigorous seedling growth. A panel of 115 landraces and four check varieties were subjected to anaerobic stress with a water level of 10 cm for up to 15 days. The present study observed significant variation in anaerobic germination percentage (AGP) (10%–100%) and anaerobic vigor index (AVI) (150–4,433). Landraces Karuthakar, Poovan samba, Mattaikar, Edakkal, Manvilayan, and Varappu kudainchan were identified as genotypes tolerant to early water submergence. The shoot and root length of susceptible landraces were significantly lower than the tolerant landraces under hypoxia condition, implying that landraces with longer shoots and roots had a higher survival rate. The response index substantiated this. The results clearly show that tolerant and moderately tolerant landraces possessed higher mean values for root and shoot lengths than susceptible landraces. The landraces grouped under the long–bold category had superior AGP and AVI scores to other grain type groups. This raises the possibility that differences in kernel breadth, which is linked to grain type, could affect anaerobic germination potential. Molecular confirmation using gene-specific markers, viz., DFR, TTP_G4, RM478, RM208, and RM24161, for which the polymorphic information content (PIC) value ranged from 0.36 (RM478) to 0.68 (RM206) suggests that this diverse panel of landraces must be assessed further using advanced molecular tools to precisely clarify the genetic mechanism behind this phenomenon. The tolerant landraces thus identified may become donors in breeding programs. The introduction of these traits would contribute to the development of rice varieties tolerant to anaerobic stress, resulting in sustainable yields. This solution could promote the DSR system across the world.
MicroRNA-146a-5p induces cell cycle arrest and enhances apoptosis in gastric cancer via targeting CDC14A

Objective: The present study was designed to investigate the expression of miRNA-146a-5p in gastric cancer (GC) tissues and the paired nonmalignant counterparts, to explore the influences of miRNA-146a-5p on the cell biological behavior of MKN-28 cells (highly metastatic human gastric cancer cells), and to identify the function of abnormal expression of its target gene cell division cycle 14 homolog A (CDC14A) in GC. Methods: We detected the expression of miRNA-146a-5p in formalin-fixed and paraffin-embedded (FFPE) GC tissues through microarray and quantitative real-time polymerase chain reaction (qRT-PCR). Then, we employed cell counting kit-8 (CCK-8) assays, cell cycle assays, and apoptosis analysis to uncover the latent function of miRNA-146a-5p in MKN-28 human GC cells. We also validated the target of miRNA-146a-5p via luciferase reporter assays. Results: miRNA-146a-5p levels were examined in the majority of primary GC tissues and several GC cell lines. As a result, miRNA-146a-5p levels were significantly declined in the GC tissues and cells. In addition, miRNA-146a-5p demonstrated a straight act on its 3′-untranslated region (3′-UTR) of CDC14A mRNA, accordingly decreasing the contents of CDC14A mRNA as well as its protein expression. An inverse correlation between CDC14A and miRNA-146a-5p was observed. Conclusion: The data suggest miRNA-146a-5p may contribute to inducing cell cycle arrest as well as prompting GC cell apoptosis via directly targeting CDC14A. Therefore, miRNA-146a-5p may be a potential indicator of the occurrence and development of GC.
Epilepsy in a mouse model of GNB1 encephalopathy arises from altered potassium (GIRK) channel signaling and is alleviated by a GIRK inhibitor

De novo mutations in GNB1, encoding the Gβ1 subunit of G proteins, cause a neurodevelopmental disorder with global developmental delay and epilepsy, GNB1 encephalopathy. Here, we show that mice carrying a pathogenic mutation, K78R, recapitulate aspects of the disorder, including developmental delay and generalized seizures. Cultured mutant cortical neurons also display aberrant bursting activity on multi-electrode arrays. Strikingly, the antiepileptic drug ethosuximide (ETX) restores normal neuronal network behavior in vitro and suppresses spike-and-wave discharges (SWD) in vivo. ETX is a known blocker of T-type voltage-gated Ca2+ channels and G protein-coupled potassium (GIRK) channels. Accordingly, we present evidence that K78R results in a gain-of-function (GoF) effect by increasing the activation of GIRK channels in cultured neurons and a heterologous model (Xenopus oocytes)—an effect we show can be potently inhibited by ETX. This work implicates a GoF mechanism for GIRK channels in epilepsy, identifies a new mechanism of action for ETX in preventing seizures, and establishes this mouse model as a pre-clinical tool for translational research with predicative value for GNB1 encephalopathy.
Oxygen metabolism analysis of a single organoid for non-invasive discrimination of cancer subpopulations with different growth capabilities

Heterogeneous nature is a pivotal aspect of cancer, rendering treatment problematic and frequently resulting in recurrence. Therefore, advanced techniques for identifying subpopulations of a tumour in an intact state are essential to develop novel screening platforms that can reveal differences in treatment response among subpopulations. Herein, we conducted a non-invasive analysis of oxygen metabolism on multiple subpopulations of patient-derived organoids, examining its potential utility for non-destructive identification of subpopulations. We utilised scanning electrochemical microscopy (SECM) for non-invasive analysis of oxygen metabolism. As models of tumours with heterogeneous subpopulations, we used patient-derived cancer organoids with a distinct growth potential established using the cancer tissue-originated spheroid methodology. Scanning electrochemical microscopy measurements enabled the analysis of the oxygen consumption rate (OCR) for individual organoids as small as 100 µm in diameter and could detect the heterogeneity amongst studied subpopulations, which was not observed in conventional colorectal cancer cell lines. Furthermore, our oxygen metabolism analysis of pre-isolated subpopulations with a slow growth potential revealed that oxygen consumption rate may reflect differences in the growth rate of organoids. Although the proposed technique currently lacks single-cell level sensitivity, the variability of oxygen metabolism across tumour subpopulations is expected to serve as an important indicator for the discrimination of tumour subpopulations and construction of novel drug screening platforms in the future.
Evidence of vascular involvement in myopia: a review

The benign public perception of myopia (nearsightedness) as a visual inconvenience masks the severity of its sight-threatening consequences. Myopia is a significant risk factor for posterior pole conditions such as maculopathy, choroidal neovascularization and glaucoma, all of which have a vascular component. These associations strongly suggest that myopic eyes might experience vascular alterations prior to the development of complications. Myopic eyes are out of focus because they are larger in size, which in turn affects their overall structure and function, including those of the vascular beds. By reviewing the vascular changes that characterize myopia, this review aims to provide an understanding of the gross, cellular and molecular alterations identified at the structural and functional levels with the goal to provide an understanding of the latest evidence in the field of experimental and clinical myopia vascular research. From the evidence presented, we hypothesize that the interaction between excessive myopic eye growth and vascular alterations are tipping-points for the development of sight-threatening changes.
A lncRNA-disease association prediction tool development based on bridge heterogeneous information network via graph representation learning for family medicine and primary care

Identification of long non-coding RNAs (lncRNAs) associated with common diseases is crucial for patient self-diagnosis and monitoring of health conditions using artificial intelligence (AI) technology at home. LncRNAs have gained significant attention due to their crucial roles in the pathogenesis of complex human diseases and identifying their associations with diseases can aid in developing diagnostic biomarkers at the molecular level. Computational methods for predicting lncRNA-disease associations (LDAs) have become necessary due to the time-consuming and labor-intensive nature of wet biological experiments in hospitals, enabling patients to access LDAs through their AI terminal devices at any time. Here, we have developed a predictive tool, LDAGRL, for identifying potential LDAs using a bridge heterogeneous information network (BHnet) constructed via Structural Deep Network Embedding (SDNE). The BHnet consists of three types of molecules as bridge nodes to implicitly link the lncRNA with disease nodes and the SDNE is used to learn high-quality node representations and make LDA predictions in a unified graph space. To assess the feasibility and performance of LDAGRL, extensive experiments, including 5-fold cross-validation, comparison with state-of-the-art methods, comparison on different classifiers and comparison of different node feature combinations, were conducted, and the results showed that LDAGRL achieved satisfactory prediction performance, indicating its potential as an effective LDAs prediction tool for family medicine and primary care.
The role of self-efficacy beliefs in dealing with misinformation among adolescents

The present study aims to understand the processes involved in misinformation among adolescents by examining the role of self-efficacy beliefs in dealing with misleading news. Specifically, we argue that the perceived capability to analyze and reflect critically on the reliability of online information sources should be stayed with the perceived self-regulatory capability to resist online social pressures to share unverifiable news. Moreover, we posited that specific online self-efficacies beliefs can be promoted by the capabilities related to regulating emotions and reflecting on new problems. In a sample of 273, we tested a path analysis model. The results attest that self-efficacy beliefs in dealing with online misinformation refer to specific capabilities: an active one, related to checking the sources of the news in order to validate their content, and an inhibitory one, related to the capability to refrain from sharing the news that seems unreliable. Moreover, self-efficacy beliefs in self-control during online interaction spreading misleading news are supported by cognitive reflective capability and self-efficacy in regulating negative emotion. The relationship between active self-efficacy related to fact-checking and sharing misleading news is not significant. The role of regulation in sharing misinformation during activated online dynamics is discussed.
Escherichia coli multilocus sequence type 38 from humans and broiler production represent distinct monophyletic groups

Escherichia coli belonging to multilocus sequence type 38 (ST38) is a well-known cause of extra-intestinal infections in humans, and are frequently associated with resistance to extended-spectrum cephalosporins (ESCs). Resistance to carbapenems, mediated by blaOXA-genes has also been reported in this ST. Recently, the European Centre for Disease Prevention and Control (ECDC) released a rapid risk assessment on the increased detection of OXA-244 producing E. coli ST38 in humans, requesting further knowledge to determine the source. ST38 is also one of the most common STs among ESC-resistant E. coli from broiler production. Our aim was to investigate the genetic characteristics and relationship between E. coli ST38 from broiler production and humans, and to investigate if there has been a potential spillover between these sources. A total of 288 E. coli ST38 genomes isolated from humans in Europe (collected 2009–2019) and from Nordic broiler production (collected 2011–2014) were analyzed. The results showed distinct monophyletic clades associated to humans and broiler production. Furthermore, there were differences in the ESC resistance genes present in E. coli ST38 from the two sources. The blaOXA-244 gene was not present in E. coli from broiler production. Our results show that ST38 from humans and broiler production belong to well-separated clades, and suggest that the increased detection of OXA-244-producing E. coli ST38 in humans is not associated with spillover from broiler production.
Expanding hyperspectral imaging applications to the clinical scene: non-invasive, label-free approaches for early diagnostics and precision medicine

Non-invasive, label-free hyperspectral imaging technologies are powerful tools that can provide critical insights into the spatiotemporal dynamics of evolving systems. They are already integrated into autonomous adaptive surveillance workflows for precision agriculture, remote sensing, environmental monitoring, and food analysis. However, these technologies are not yet routinely used in medicine. With these technologies applied to the biomedical sciences, we anticipate landmark advances in the physicochemical behavioral refinement of high signal-to-noise probes and in the rapid screening of patient exosome populations. To implement label-free spatiochemical imaging techniques while meeting the practical needs of clinicians, technology, workflow design and development must be tailored to the specific medical field while considering existing visualization modalities. This perspective merges basic, translational, and clinical views of label-free, non-invasive hyperspectral imaging. We explore its potential role in positively impacting cancer-related precision medicine and early diagnostics to support clinically implemented point-of-care technologies.
Longitudinal assessment and determinants of short-term and longer-term psychological distress in a sample of healthcare workers during the COVID-19 pandemic in Quebec, Canada

Introduction Previous research has demonstrated the negative impact of the COVID-19 pandemic emergency on the wellbeing of healthcare workers. However, few research contributions reported a longitudinal evaluation of psychological distress and examined determinants of its duration and course over time. The present study aims to explore the impact of the pandemic emergency on HCWs mental health by adopting a longitudinal design and assessing mental health as combination of overlapping clinical symptoms (post-traumatic stress disorder, depression and anxiety). Methods Data were collected weekly through a mobile application during and after the first wave of COVID-19 in the province of Quebec, Canada, in 2020. Analysis was conducted on a final sample of 382 participants. Participants were grouped into “resilient” (RES) if they did not manifest clinical-level psychological distress during monitoring, “short-term distress” (STD) if distress exceeded the clinical threshold for 1–3 weeks, and longer-term distress (LTD) if it occurred for four or more weeks, even if not consecutively. Descriptive statistics for all variables were computed for each subgroup (RES, STD and LTD), and pairwise comparisons between each group for every descriptive variable were made using chi square statistics for categorical variables and t-test for continuous variables. Predictors of distress groups (STD and LTD vs RES) were assessed running multinomial hierarchical logistic regression models. Results In our sample, almost two third (59.4%) HCWs did not manifest moderate or severe distress during the monitoring time. Short-term distress, mostly post-traumatic symptoms that lasted for less than 4 weeks, were the most common distress response, affecting almost one third of participants. Longer psychological distress occurred only in a smaller percentage (12.6%) of cases, as a combination of severe posttraumatic, depressive and anxiety symptoms. Perceived occupational stress was the most significant risk factor; moreover individual, peritraumatic work and family risk and protective factors, were likely to significantly affect the stress response. Discussion Results tend to provide a more complex and resiliency-oriented representation of psychological distress compared to previous cross-sectional studies, but are in line with stress response studies. Findings allow us to better describe the profiles of distress response in STD and LTD groups. Participants that manifest short term distress experience acute stress reaction in which the interplay between personal, family and professional life events is associated with the stress response. Conversely, longer term distress response in HCWs presents a more complex mental health condition with an higher level of impairment and support needs compared to participants with short-term distress.