Miracle-dz/UniFAR-FTUs huggingface dataset:
OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer

In many real-world applications, such as those based on patient electronic health records, prognostic prediction of patient survival is based on heterogeneous sets of clinical laboratory measurements. To address the trade-off between the predictive accuracy of a prognostic model and the costs related to its clinical implementation, we propose an optimized L0-pseudonorm approach to learn sparse solutions in multivariable regression. The model sparsity is maintained by restricting the number of nonzero coefficients in the model with a cardinality constraint, which makes the optimization problem NP-hard. In addition, we generalize the cardinality constraint for grouped feature selection, hence making it possible to identify key sets of predictors that may be measured together in a kit in clinical practice. We demonstrate the operation of our cardinality constraint-based feature subset selection method, named OSCAR, in the context of prognostic modelling of prostate cancer, where it enabled one to determine the key explanatory predictors at different levels of model sparsity, and to explore how the model sparsity affects the model accuracy and implementation cost. Author summary Feature selection has become a crucial part in building biomedical models, due to the abundance of available predictors in many applications, yet there remains an uncertainty of their importance and generalization ability. Regularized regression methods have become popular approaches to tackle this challenge by balancing the model goodness-of-fit against the increasing complexity of the model in terms of coefficients that deviate from zero. Regularization norms are pivotal in formulating the model complexity, and currently L1 (LASSO), L2 (Ridge Regression) and their hybrid (Elastic Net) norms dominate the field. In this paper, we present a novel methodology using the L0-pseudonorm, also known as the best subset selection, which has largely gone overlooked due to its challenging discrete nature. Our methodology makes use of a continuous transformation of the discrete optimization problem, and provides effective solvers implemented in a user friendly R software package. We exemplify the use of oscar-package in the context of prostate cancer prognostic prediction using both real-world hospital registry and clinical cohort data. By benchmarking the methodology against related regularization methods, we illustrate the advantages of the L0-pseudonorm for better clinical applicability and selection of grouped features.
Dimensionality reduction and statistical modeling of scGET-seq data

Single cell multiomics approaches are innovative techniques with the ability to profile orthogonal features in the same single cell, giving the opportunity to dig more deeply into the stochastic nature of individual cells. We recently developed scGET-seq, a technique that exploits a Hybrid Transposase (tnH) along with the canonical enzyme (tn5), which is able to profile altogether closed and open chromatin in a single experiment. This technique adds an important feature to the classic scATAC-seq assays. In fact, the lack of a closed chromatin signal in scATAC: (i) restricts sampling of DNA sequence to a very small portion of the chromosomal landscapes, substantially reducing the ability to investigate copy number alteration and sequence variations, and (ii) hampers the opportunity to identify regions of closed chromatin, that cannot be distinguished between non-sampled open regions and truly closed. scGET-seq overcomes these issues in the context of single cells. In this work, we describe the latest advances in the statistical analysis and modeling of scGET-seq data, touching several aspects of the computational framework: from dimensionality reduction, to statistical modeling, and trajectory analysis.
Circadian regulation of dentate gyrus excitability mediated by G-protein signaling

The central circadian regulator within the suprachiasmatic nucleus transmits time of day information by a diurnal spiking rhythm that is driven by intrinsic activity of molecular clock genes controlling membrane excitability. Most brain regions, including the hippocampus, harbor similar intrinsic circadian transcriptional machinery but whether these molecular programs generate oscillations of membrane properties is unexplored. Here, we show that intrinsic excitability of mouse dentate granule neurons exhibits a 24-hour oscillation that controls spiking probability. Diurnal changes in excitability are mediated by antiphase G-protein regulation of potassium and sodium conductances to reduce excitability during the light phase. Disruption of the circadian transcriptional machinery by conditional deletion of Bmal1 enhances excitability selectively during the light phase, increasing engram recruitment and spatial discrimination memory. These results reveal that circadian transcriptional machinery regulates intrinsic excitability, highlighting the role of cell-autonomous oscillations in hippocampal function and behavior. Highlights Dentate neurons exhibit a 24-hour oscillation of excitability with low excitability during the Light phase Reduced excitability results from G-protein regulation of passive and active properties Bmal1 deletion disrupts G-protein regulation to enhance excitability during the Light Bmal1 deletion enhances the size of memory engrams and spatial discrimination
A conserved role of Hippo signaling in initiation of the first lineage specification event across mammals

Our understanding of the molecular events driving cell specification in early mammalian development relies mainly on mouse studies, and it remains unclear whether these mechanisms are conserved across mammals, including humans. We have recently shown that the establishment of cell polarity via aPKC is a conserved event in the initiation of the trophectoderm (TE) placental program in mouse, cow, and human embryos. However, the molecular mechanisms transducing cell polarity into cell fate in cow and human embryos is unknown. Here, we have examined the evolutionary conservation of the molecular cascade downstream of aPKC in four different mammalian species: mouse, rat, cow, and human. Surprisingly, by morphokinetic and immunofluorescence analyses, we observe that rat embryos more closely recapitulate human and cow developmental dynamics, in comparison to the mouse. Nevertheless, in all four species, inhibition of the Hippo pathway by targeting LATS kinases is sufficient to drive ectopic TE initiation and downregulation of SOX2, a marker of the inner cell mass. Our comparative embryology approach uncovered intriguing differences as well as similarities in a fundamental developmental process among mammals, reinforcing the importance of cross-species investigations.
AAV Vector Transduction Restriction and Attenuated Toxicity in hESCs via a Rationally Designed Inverted Terminal Repeat

Recombinant adeno-associated virus (rAAV) inverted terminal repeats (ITRs) induce p53-dependent apoptosis in human embryonic stem cells (hESCs). To interrogate this phenomenon, a rationally designed ITR (SynITR), deleted for p53 binding sites was evaluated for vector production and gene delivery. While SynITR genomes were decreased for transgenic genome replication compared to wtITRs, similar production titers indicated that replication is not rate-limiting. Packaged in the AAV2 capsid, wtITR and SynITR vectors demonstrated similar transduction efficiencies of human cell lines with no differences in reporter kinetics. Following rAAV2-wtITR infection of hESCs, rapid apoptosis was observed, in contrast, rAAV2-SynITR infection resulted in attenuated hESC toxicity with cells retaining their differentiation potential. While hESC particle entry and double stranded circular episomes was similar for the ITR contexts, reporter expression was significantly inhibited from transduced SynITR genomes. Infection of hESCs induced γH2AX in an ITR-independent manner, however, canonical activation of p53α was uncoupled using rAAV-SynITR. Further hESC investigations revealed 2 additional novel findings: i) p53β is uniquely and constitutively active, and ii) rAAV infection, independent of the ITR sequence, induces activation of p53ψ. The data herein reveal an ITR-dependent rAAV transduction restriction specific to hESCs and manipulation of the DNA damage response via ITR engineering.
Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations

Metabolic flexibility is a central component of any organism’s ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. ABSTRACT Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (ΔrG′), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism’s ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.
Promotion of Healthy Eating: Among New Immigrant Women in Ontario

Little attention has been given to the dietary patterns of new immigrant women in Canada. Research suggests that before migration, many immigrants, especially those from non-Western countries, consume a healthy diet, but this changes on migration. This paper presents information from a recently completed literature review conducted for the Women's Health Council of the Ontario Ministry of Health and Long-Term Care. The paper includes a review of the major determinants of food choice and health promotion strategies appropriate to new immigrant women. Our findings suggest that nutrition intervention for new immigrant women must consider the social context of these women's lives, address cultural, linguistic, economic and informational barriers and consider how these change over time. Recommendations are also made on how to best promote healthy eating in this group.
Odd-even oddball task: Evaluating event-related potentials during word discrimination compared to speech-token and tone discrimination

The use of tonal and speech token auditory oddball tasks has been used abundantly in past literature; however, it has been argued that tasks using non-word sounds fail to capture the higher-level ability to interpret and discriminate stimuli based on meaning which are critical to language comprehension. As such this study aims to examine how neural signals associated with discrimination and evaluation-processes (P3b) from semantic stimuli compare with those elicited by pure tones and speech tokens. This study comprises of two experiments, both containing thirteen adults (Exp 1: (Mean(SD)age = 25.20(3.89) years and Exp 2: Mean(SD)age = 25.3(3.79) years) with normal hearing in both ears (PTA ≤ 20dB HL). Scalp electroencephalography and auditory event related potentials was recorded in free field whilst they completed three different oddball tasks: 1) Tones, 2) Speech tokens and 3) Odd/Even numbers. In experiment two, the duration of each stimulus was the same. P3b peak latency was significantly different between all three tasks, in both experiments. P3b amplitude was identified to be sensitive to reaction time, with tasks that have a large reaction time variability resulting in the P3b amplitude to be smeared out, thereby reducing the amplitude size. The findings from this study highlight the need to take into consideration all factors of the task before attributing any effects to any additional process such as semantic processing and mental effort. Furthermore, it highlights the need for more cautious interpretation of P3b results in auditory oddball tasks.
Ion-channel degeneracy and heterogeneities in the emergence of complex spike bursts in CA3 pyramidal neurons

Complex spike bursting (CSB) is a characteristic electrophysiological signature exhibited by several neurons and has been implicated in neural plasticity, learning, perception, anesthesia, and active sensing. Here, we address the question of how pronounced intrinsic and synaptic heterogeneities affect CSB, with hippocampal CA3 pyramidal neurons (CA3PN) as a substrate where CSB emergence and heterogeneities are well-characterized. We randomly generated 12,000 unique models and found 236 valid models that satisfied 11 characteristic CA3PN measurements. These morphologically and biophysically realistic valid models accounted for gating kinetics and somato-dendritic expression profiles of 10 active ion channels. This heterogeneous population of valid models was endowed with broad distributions of underlying parameters showing weak pair-wise correlations. We found two functional subclasses of valid models, intrinsically bursting and regular spiking, with significant differences in the expression of calcium and calcium-activated potassium conductances. We triggered CSB in all 236 models through different intrinsic or synaptic protocols and observed considerable heterogeneity in CSB propensity and properties spanning models and protocols. Finally, we employed virtual knockout analyses and showed that synergistic interactions between intrinsic and synaptic mechanisms regulated CSB emergence and dynamics. Specifically, although there was a dominance of calcium and calcium-activated potassium channels in the emergence of CSB, individual deletion of none of the several ion channels or N-methyl-D-aspartate receptors resulted in the complete elimination of CSB across all models. Together, our analyses critically implicate ion-channel degeneracy in the robust emergence of CSB and other characteristic signatures of CA3PNs, despite pronounced heterogeneities in underlying intrinsic and synaptic properties.
A novel homeostatic mechanism tunes PI(4,5)P2-dependent signaling at the plasma membrane

The lipid molecule phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2) controls all aspects of plasma membrane (PM) function in animal cells, from its selective permeability to the attachment of the cytoskeleton. Although disruption of PI(4,5)P2 is associated with a wide range of diseases, it remains unclear how cells sense and maintain PI(4,5)P2 levels to support various cell functions. Here, we show that the PIP4K family of enzymes that synthesize PI(4,5)P2 via a minor pathway, also function as sensors of tonic PI(4,5)P2 levels. PIP4Ks are recruited to the PM by elevated PI(4,5)P2 levels, where they inhibit the major PI(4,5)P2-synthesizing PIP5Ks. Perturbation of this simple homeostatic mechanism reveals differential sensitivity of PI(4,5)P2-dependent signaling to elevated PI(4,5)P2 levels. These findings reveal that a subset of PI(4,5)P2-driven functions may drive disease associated with disrupted PI(4,5)P2 homeostasis. One-Sentence Summary The enzyme PIP4K functions as both a sensor and negative regulator of PI(4,5)P2 synthesis by the closely related PIP5K enzymes, tuning the activity of numerous membrane functions.
Functional and compositional changes in the fecal microbiome of a shorebird during pre-migratory weight gain

Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA. Using 16S rRNA sequencing on 90 of these samples and metatranscriptomic sequencing on 22, we show that taxonomic composition of the microbiome shifts during weight gain, as do functional aspects of the metatranscriptome. We identified ten genes that are associated with weight class and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds.
The Genomic Basis of Evolutionary Novelties in a Leafhopper

Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the Glassy-Winged Sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS, then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.
The impact of ants and vertebrate predators on arthropods and plants: a meta-analysis

The trophic interactions between plants, insect herbivores and their predators are complex and prone to trophic cascades. Theory predicts that predators increase plant biomass by feeding on herbivores. However, it remains unclear whether different types of predators regulate herbivores to the same degree, and how intraguild predation impacts these trophic interactions. Specifically, we lack a more comprehensive look at the effects of various groups of predators on a global scale. Here we report a meta-analysis of 486 experiments gathered from 157 publications reporting the effect of insectivorous vertebrates (birds and bats) and ants on abundances of predatory (spiders, ants, others) and herbivorous (chewers and others) arthropods; on arthropod richness and plant damage. Generally, the absence of vertebrate predators led to the increase of predatory arthropods by 18%, herbivorous arthropods by 75%, and plant damage by 47%. In contrast, after the removal of ants, the increase in the abundances of other predatory arthropods did not compensate for missing ants, herbivore arthropods increased their abundances by 53%, and plant damage increased by 146%. The effects of ant exclosures were stronger in communities at lower elevations and latitudes, while we did not detect any clear geographical patterns in the effect of vertebrate exclosures. Neither precipitation nor NDVI had a significant impact on most of the measured effects, and the effect of exclosures was robust for both plant growth forms and different habitat types. We found vertebrate insectivores to be the more dominant predators of arthropods, but we detected that the strength of their trophic cascades was weakened by intraguild predation. On the other hand, we found that although ants were relatively less dominant as predators, and their influence was detectable only in the most productive sites, the effect of trophic cascades on plants they caused was stronger than that of vertebrate insectivores.
Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice

YAP1 is a transcriptional co-activator regulated by the Hippo Signaling Pathway, including NF2. Meningiomas are the most common primary brain tumors, a large percentage exhibit heterozygous loss of chromosome 22 (harboring the NF2 gene) and functional inactivation of the remaining NF2 copy, implicating oncogenic YAP activity in these tumors. Recently, fusions between YAP1 and MAML2 have been identified in a subset of pediatric NF2-wild type meningiomas. Here, we show that human YAP1-MAML2-positive meningiomas resemble NF2-mutant meningiomas by global and YAP-related gene expression signatures. We then show that expression of YAP1-MAML2 in mice induces tumors that resemble human YAP1 fusion-positive and NF2-mutant meningiomas by gene expression. We demonstrate that YAP1-MAML2 primarily functions by exerting TEAD-dependent YAP activity that is resistant to Hippo signaling. Treatment with YAP-TEAD inhibitors is sufficient to inhibit the viability of YAP1-MAML2-driven mouse tumors ex vivo. Finally, we show that expression of constitutively active YAP1 (S127/397A-YAP1) is sufficient to induce similar tumors suggesting that the YAP component of the gene fusion is the critical driver of these tumors. In summary, our results implicate YAP1-MAML2 as a causal oncogenic driver and highlight TEAD-dependent YAP activity as an oncogenic driver in YAP1-MAML2-fusion meningioma as well as NF2-mutant meningioma in general.