transitive inference

The significant heterogeneity of Wilms' tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms' tumors using a publicly available RNAseq dataset of high-risk Wilms' tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or "archetypes", resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney...

Cardiovascular diseases (CVDs) represent a major concern for global health, whose mechanistic understanding is complicated by a complex interplay between genetic predisposition and environmental factors. Specifically, heart failure (HF), encompassing dilated cardiomyopathy (DC), ischemic cardiomyopathy (ICM), and hypertrophic cardiomyopathy (HCM), is a topic of substantial interest in basic and clinical research. Here, we used a Partial Correlation Coefficient-based algorithm (PCC) within the context of a meta-analysis framework to construct a Gene Regulatory Network (GRN) that identifies key regulators whose activity is perturbed in Heart Failure...

Systematic studies of numerical dynamo simulations reveal that the transition from dipole-dominated non-reversing fields to models that exhibit reversals occurs when inertial effects become strong enough. However, the inertial force is expected to play a secondary role in the force balance in Earth's outer core. Here we show that reversals in numerical dynamo models with heterogeneous outer boundary heat flux inferred from lower mantle seismic anomalies appear when the amplitude of heat flux heterogeneity is increased...

Archaeological evidence supports sporadic seafaring visits to the Eastern Mediterranean island of Cyprus by Epipaleolithic hunter-gatherers over 12,000 years ago, followed by permanent settlements during the early Neolithic. The geographical origins of these early seafarers have so far remained elusive. By systematically analysing all available genomes from the late Pleistocene to early Holocene Near East (c. 14,000-7000 cal BCE), we provide a comprehensive overview of the genetic landscape of the early Neolithic Fertile Crescent and Anatolia and infer the likely origins of three recently published genomes from Kissonerga-Mylouthkia (Cypriot Late Pre-Pottery Neolithic B, c...

BACKGROUND: Smartphone apps may help to prevent the transition from minor to severe mental health problems. We compared a free self-help smartphone app (COGITO; www.uke.de/cogito_app) against a wait-list condition for the improvement of self-esteem and depression. METHODS: The Rosenberg Self-Esteem Scale represented the primary outcome in this controlled trial. The final sample (n = 213) was randomly assigned to either the app or to the control condition...

RNA velocity estimation is a potentially powerful tool to reveal the directionality of transcriptional changes in single-cell RNA-sequencing data, but it lacks accuracy, absent advanced metabolic labeling techniques. We developed an approach, TopicVelo , that disentangles simultaneous, yet distinct, dynamics by using a probabilistic topic model, a highly interpretable form of latent space factorization, to infer cells and genes associated with individual processes, thereby capturing cellular pluripotency or multifaceted functionality...

Pigs are the most important source of meat and valuable biomedical models. However, the porcine immune system, especially the heterogeneity of CD8 T cell subtypes, has not been fully characterized. Here, using single-cell RNA sequencing, we identified 14 major cell types from peripheral blood circulating cells of pigs and observed remarkable heterogeneity among CD8 T cell types. Upon re-clustering of CD8+ T cells, we defined four CD8 T cell subtypes and revealed their potential differentiation trajectories and transcriptomic differences among them...

Relational cognition-the ability to infer relationships that generalize to novel combinations of objects-is fundamental to human and animal intelligence. Despite this importance, it remains unclear how relational cognition is implemented in the brain due in part to a lack of hypotheses and predictions at the levels of collective neural activity and behavior. Here we discovered, analyzed, and experimentally tested neural networks (NNs) that perform transitive inference (TI), a classic relational task (if A > B and B > C, then A > C)...

Studies in atomic-scale modeling of surface phase equilibria often focus on temperatures near zero Kelvin due to the challenges in calculating the free energy of surfaces at finite temperatures. The Bayesian-inference-based nested sampling (NS) algorithm allows for modeling phase equilibria at arbitrary temperatures by directly and efficiently calculating the partition function, whose relationship with free energy is well known. This work extends NS to calculate adsorbate phase diagrams, incorporating all relevant configurational contributions to the free energy...

Perovskite materials that aren't stable during the oxygen evolution reaction (OER) are unsuitable for anion-exchange membrane water electrolyzers (AEMWE). But through manipulating their electronic structures, their performance can further increase. Among the first-row transition metals, nickel and iron are widely recognized as prominent electrocatalysts; thus, the researchers are looking into how combining them can improve the OER. Recent research has actively explored the design and study of heterostructures in this field, showcasing the dynamic exploration of innovative catalyst configurations...

The anadromous Atlantic salmon undergo a preparatory physiological transformation before seawater entry, referred to as smoltification. Key molecular developmental processes involved in this life stage transition, such as remodeling of gill functions, are known to be synchronized and modulated by environmental cues like photoperiod. However, little is known about the photoperiod influence and genome regulatory processes driving other canonical aspects of smoltification such as the large-scale changes in lipid metabolism and energy homeostasis in the developing smolt liver...

Second sphere coordination effects ubiquitous in enzymatic catalysis occur through direct interactions, either covalent or non-covalent, with reaction intermediates and transition states. We present herein evidence of indirect second sphere coordination effects in which ligation of water/alkanols far removed from the primary coordination sphere of the active site nevertheless alter energetic landscapes within catalytic redox cycles in the absence of direct physicochemical interactions with surface species mediating catalytic turnovers...

Monolayers of transition metal dichalcogenides (TMDCs) are direct-gap semiconductors with strong light-matter interactions featuring tightly bound excitons, while plasmonic crystals (PCs), consisting of metal nanoparticles that act as meta-atoms, exhibit collective plasmon modes and allow one to tailor electric fields on the nanoscale. Recent experiments show that TMDC-PC hybrids can reach the strong-coupling limit between excitons and plasmons, forming new quasiparticles, so-called plexcitons. To describe this coupling theoretically, we develop a self-consistent Maxwell-Bloch theory for TMDC-PC hybrid structures, which allows us to compute the scattered light in the near- and far-fields explicitly and provide guidance for experimental studies...

Titanium dioxide (TiO2 ) is an important industrial chemical, and studies suggest its major production route - the chloride process could lead to the generation of unintentional dl-POPs. However, no relevant studies assessed the occurrence of dl-POPs associated with TiO2 production in the industrial zones, which is mostly due to the ultra-trace level distribution of these compounds in environmental compartments. The present study explored the novel possibility of utilising foraging animal-origin foods as sensitive indicators for addressing this challenge and generated a globally beneficial dataset by assessing the background levels of dl-POPs in the vicinity of a TiO2 production house in Southern India...

Climatic and geomorphological changes during the Quaternary period impacted global patterns of speciation and diversification across a wide range of taxa, but few studies have examined these effects on African riverine fishes. The lower Congo River is an excellent natural laboratory for understanding complex speciation and population diversification processes as it is hydrologically extremely dynamic and recognized as a continental hotspot of diversity harboring many narrowly endemic species. A previous study using genome-wide SNP data highlighted the importance of dynamic hydrological regimes to the diversification and speciation in lower Congo River cichlids...

Breast cancer is still the largest cause of cancer death in women, and around 70% of primary breast cancer patients are estrogen receptor (ER)-positive, which is the most frequent kind of breast cancer. The lemur tyrosine kinase-3 (LMTK3) receptor has been linked to estrogen responsiveness in breast cancer. However, the function of LMTK3 in reaction to cytotoxic chemotherapy has yet to be studied. Breast cancer therapy research remains tricky due to a paucity of structural investigations on LMTK3. We performed structural investigations on LMTK3 using molecular docking and molecular dynamics (MD) simulations of the LMTK3 receptor in complex with the top three inhibitor molecules along with a control inhibitor...

In this research work, a novel fuzzy data transformation technique has been proposed and applied to the hormonal imbalance dataset. Hormonal imbalance is ubiquitously found principally in females of reproductive age which ultimately leads to numerous related medical conditions. Polycystic Ovary Syndrome (PCOS) is one of them. Treatment along with adopting a healthy lifestyle is advised to mitigate its consequences on the quality of life. The biological dataset of hormonal imbalance "PCOS" provides limited results that is whether the syndrome is present or not...

In many fields, accurate prediction of cascade outbreaks during their early stages of propagation is of paramount importance. Based on percolation theory, we propose a global propagation probability algorithm that effectively estimates the probability of information spreading from source nodes to the giant component. Building on this, we further introduce an early prediction method for cascade outbreaks, which provides quantitative predictions of both the probability and scope of cascade outbreaks by fully considering the network structure data and propagation dynamics...

Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model and 124 years of unsuccessfully sampling the fossil record for transitions...

Organic-inorganic hybrid iodide systems, which can form highly ordered chromophores and uniformly oriented transition dipole moments, serve as optimal host-guest systems for the fabrication of micrometer-scale optical devices. In particular, those with low-dimensional structures can exhibit strong quantum-limited and highly localized charges, enabling the generation of high exciton energies and stable excitation emission. In this study, we report a novel instance of an organic-inorganic hybrid iodate, (C13 H11 N2 )(IO3 ), which was synthesized by incorporating the optically active organic compound, 9-aminoacridine...