Machine learning promises to revolutionize clinical decision making and diagnosis. In medical diagnosis a doctor aims to explain a patient's symptoms by determining the diseases causing them. ...However, existing machine learning approaches to diagnosis are purely associative, identifying diseases that are strongly correlated with a patients symptoms. We show that this inability to disentangle correlation from causation can result in sub-optimal or dangerous diagnoses. To overcome this, we reformulate diagnosis as a counterfactual inference task and derive counterfactual diagnostic algorithms. We compare our counterfactual algorithms to the standard associative algorithm and 44 doctors using a test set of clinical vignettes. While the associative algorithm achieves an accuracy placing in the top 48% of doctors in our cohort, our counterfactual algorithm places in the top 25% of doctors, achieving expert clinical accuracy. Our results show that causal reasoning is a vital missing ingredient for applying machine learning to medical diagnosis.
Cancer cells are typically subject to profound metabolic alterations, including the Warburg effect wherein cancer cells oxidize a decreased fraction of the pyruvate generated from glycolysis. We show ...herein that the mitochondrial pyruvate carrier (MPC), composed of the products of the MPC1 and MPC2 genes, modulates fractional pyruvate oxidation. MPC1 is deleted or underexpressed in multiple cancers and correlates with poor prognosis. Cancer cells re-expressing MPC1 and MPC2 display increased mitochondrial pyruvate oxidation, with no changes in cell growth in adherent culture. MPC re-expression exerted profound effects in anchorage-independent growth conditions, however, including impaired colony formation in soft agar, spheroid formation, and xenograft growth. We also observed a decrease in markers of stemness and traced the growth effects of MPC expression to the stem cell compartment. We propose that reduced MPC activity is an important aspect of cancer metabolism, perhaps through altering the maintenance and fate of stem cells.
Display omitted
•MPC1 downregulation/deletion in many cancers correlates with poor survival•The MPC complex is a node by which cancer cells regulate pyruvate metabolism•Re-expressing MPC1+2 in colon cancer cells reduces growth in 3D and xenografts•The deleterious effects of MPC re-expression manifest in the stem cell compartment
Cancer cells enforce the metabolic perturbation known as the Warburg effect by reducing pyruvate utilization via loss of the mitochondrial pyruvate carrier (MPC). Re-expression of the MPC restores mitochondrial pyruvate oxidation and limits colon cancer cell growth in anchorage-independent culture and xenografts due to defects in the proliferating cell population.
Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first ...plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
The canonical role of the hemostatic and fibrinolytic systems is to maintain vascular integrity. Perturbations in either system can prompt primary pathological end points of hemorrhage or thrombosis ...with vessel occlusion. However, fibrin(ogen) and proteases controlling its deposition and clearance, including (pro)thrombin and plasmin(ogen), have powerful roles in driving acute and reparative inflammatory pathways that affect the spectrum of tissue injury, remodeling, and repair. Indeed, fibrin(ogen) deposits are a near-universal feature of tissue injury, regardless of the nature of the inciting event, including injuries driven by mechanical insult, infection, or immunological derangements. Fibrin can modify multiple aspects of inflammatory cell function by engaging leukocytes through a variety of cellular receptors and mechanisms. Studies on the role of coagulation system activation and fibrin(ogen) deposition in models of inflammatory disease and tissue injury have revealed points of commonality, as well as context-dependent contributions of coagulation and fibrinolytic factors. However, there remains a critical need to define the precise temporal and spatial mechanisms by which fibrinogen-directed inflammatory events may dictate the severity of tissue injury and coordinate the remodeling and repair events essential to restore normal organ function. Current research trends suggest that future studies will give way to the identification of novel hemostatic factor-targeted therapies for a range of tissue injuries and disease.
Multicellular eukaryotes coevolve with microbial pathogens, which exert strong selective pressure on the immune systems of their hosts. Plants and animals use intracellular proteins of the ...nucleotide-binding domain, leucine-rich repeat (NLR) superfamily to detect many types of microbial pathogens. The NLR domain architecture likely evolved independently and convergently in each kingdom, and the molecular mechanisms of pathogen detection by plant and animal NLRs have long been considered to be distinct. However, microbial recognition mechanisms overlap, and it is now possible to discern important key trans-kingdom principles of NLR-dependent immune function. Here, we attempt to articulate these principles. We propose that the NLR architecture has evolved for pathogen-sensing in diverse organisms because of its utility as a tightly folded "hair trigger" device into which a virtually limitless number of microbial detection platforms can be integrated. Recent findings suggest means to rationally design novel recognition capabilities to counter disease.
The plant immune system involves cell-surface receptors that detect intercellular pathogen-derived molecules, and intracellular receptors that activate immunity upon detection of pathogen-secreted ...effector proteins that act inside the plant cell. Immunity mediated by surface receptors has been extensively studied
, but that mediated by intracellular receptors has rarely been investigated in the absence of surface-receptor-mediated immunity. Furthermore, interactions between these two immune pathways are poorly understood. Here, by activating intracellular receptors without inducing surface-receptor-mediated immunity, we analyse interactions between these two distinct immune systems in Arabidopsis. Pathogen recognition by surface receptors activates multiple protein kinases and NADPH oxidases, and we find that intracellular receptors primarily potentiate the activation of these proteins by increasing their abundance through several mechanisms. Likewise, the hypersensitive response that depends on intracellular receptors is strongly enhanced by the activation of surface receptors. Activation of either immune system alone is insufficient to provide effective resistance against the bacterial pathogen Pseudomonas syringae. Thus, immune pathways activated by cell-surface and intracellular receptors in plants mutually potentiate to activate strong defences against pathogens. These findings reshape our understanding of plant immunity and have broad implications for crop improvement.
Spectrally resolved photoluminescence (PL) decays were measured for samples of colloidal, ligand-passivated silicon nanocrystals. These samples have PL emission energies with peak positions in the ...range ∼1.4–1.8 eV and quantum yields of ∼30–70%. Their ensemble PL decays are characterized by a stretched-exponential decay with a dispersion factor of ∼0.8, which changes to an almost monoexponential character at fixed detection energies. The dispersion factors and decay rates for various detection energies were extracted from spectrally resolved curves using a mathematical approach that excluded the effect of homogeneous line width broadening. Since nonradiative recombination would introduce a random lifetime variation, leading to a stretched-exponential decay for an ensemble, we conclude that the observed monoexponential decay in size-selected ensembles signifies negligible nonradiative transitions of a similar strength to the radiative one. This conjecture is further supported as extracted decay rates agree with radiative rates reported in the literature, suggesting 100% internal quantum efficiency over a broad range of emission wavelengths. The apparent differences in the quantum yields can then be explained by a varying fraction of “dark” or blinking nanocrystals.
The syntheses of colloidal silicon nanocrystals (Si-NCs) with dimensions in the 3–4 nm size regime as well as effective methodologies for their functionalization with alkyl, amine, phosphine, and ...acetal functional groups are reported. Through rational variation in the surface moieties we demonstrate that the photoluminescence of Si-NCs can be effectively tuned across the entire visible spectral region without changing particle size. The surface-state dependent emission exhibited short-lived excited-states and higher relative photoluminescence quantum yields compared to Si-NCs of equivalent size exhibiting emission originating from the band gap transition. The Si-NCs were exhaustively characterized using transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and Fourier transformed infrared spectroscopy (FTIR), and their optical properties were thoroughly investigated using fluorescence spectroscopy, excited-state lifetime measurements, photobleaching experiments, and solvatochromism studies.
Despite decades of bile acid research, diverse biological roles for bile acids have been discovered recently due to developments in understanding the human microbiota. As additional bacterial enzymes ...are characterized, and the tools used for identifying new bile acids become increasingly more sensitive, the repertoire of bile acids metabolized and/or synthesized by bacteria continues to grow. Additionally, bile acids impact microbiome community structure and function. In this Review, we highlight how the bile acid pool is manipulated by the gut microbiota, how it is dependent on the metabolic capacity of the bacterial community and how external factors, such as antibiotics and diet, shape bile acid composition. It is increasingly important to understand how bile acid signalling networks are affected in distinct organs where the bile acid composition differs, and how these networks impact infectious, metabolic and neoplastic diseases. These advances have enabled the development of therapeutics that target imbalances in microbiota-associated bile acid profiles.
Early researchers of radiocarbon levels in Southern Hemisphere tree rings identified a variable North-South hemispheric offset, necessitating construction of a separate radiocarbon calibration curve ...for the South. We present here SHCal20, a revised calibration curve from 0–55,000 cal BP, based upon SHCal13 and fortified by the addition of 14 new tree-ring data sets in the 2140–0, 3520–3453, 3608–3590 and 13,140–11,375 cal BP time intervals. We detail the statistical approaches used for curve construction and present recommendations for the use of the Northern Hemisphere curve (IntCal20), the Southern Hemisphere curve (SHCal20) and suggest where application of an equal mixture of the curves might be more appropriate. Using our Bayesian spline with errors-in-variables methodology, and based upon a comparison of Southern Hemisphere tree-ring data compared with contemporaneous Northern Hemisphere data, we estimate the mean Southern Hemisphere offset to be 36 ± 27 14C yrs older.
PDF
