Almond Grafting for Plum Pox Virus Resistance Triggers Significant Transcriptomic and Epigenetic Shifts in Peaches.

Sharka disease, caused by the plum pox virus (PPV), negatively impacts stone fruit production, resulting in economic losses. It has been demonstrated that grafting the almond ( (Miller) D.A.

Persistence and neutrality in interacting replicator dynamics.

We study the large-time behavior of an ensemble of entities obeying replicator-like stochastic dynamics with mean-field interactions as a model for a primordial ecology. We prove the propagation-of-chaos property and establish conditions for the strong persistence of the N-replicator system and the existence of invariant distributions for a class of associated McKean-Vlasov dynamics. In particular, our results show that, unlike typical models of neutral ecology, fitness equivalence does not need to be assumed but emerges as a condition for the persistence of the system.

The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR.

Transcription factor binding sites (TFBSs) are important sources of evolutionary innovations. Understanding how evolution navigates the sequence space of such sites can be achieved by mapping TFBS adaptive landscapes. In such a landscape, an individual location corresponds to a TFBS bound by a transcription factor.

The emergence and evolution of gene expression in genome regions replete with regulatory motifs.

Gene regulation is essential for life and controlled by regulatory DNA. Mutations can modify the activity of regulatory DNA, and also create new regulatory DNA, a process called regulatory emergence. Non-regulatory and regulatory DNA contain motifs to which transcription factors may bind.

Dynamical theory of complex systems with two-way micro-macro causation.

In many complex systems encountered in the natural and social sciences, mechanisms governing system dynamics at a microscale depend upon the values of state variables characterizing the system at coarse-grained, macroscale (Goldenfeld and Woese, 2011, Noble et al., 2019, and Chater and Loewenstein, 2023). State variables, in turn, are averages over relevant probability distributions of the microscale variables.

The metaphors of artificial intelligence.

A few months after ChatGPT was released, the neural network pioneer Terrence Sejnowski wrote about coming to grips with the shock of what large language models (LLMs) could do: "Something is beginning to happen that was not expected even a few years ago. A threshold was reached, as if a space alien suddenly appeared that could communicate with us in an eerily human way.…Some aspects of their behavior appear to be intelligent, but if it's not human intelligence, what is the nature of their intelligence?"

Variable and dynamic associations between hot weather, thermal comfort, and individuals' emotional states during summertime.

The effects of heat exposure on negative affect are thought to be central to the observed relationships between hot summer days and deleterious outcomes, such as violent crime or mental health crises. As these relationships are likely to be magnified by the effects of climate change, a better understanding of how consistent or variable the effects of hot weather on affective states is required. The current work combines data gathered from an ecological momentary assessment (EMA) study on individuals' thermal perceptions, comfort, and affective states in outdoor environments during their daily lives with high spatiotemporal resolution climate-modeled weather variables.

The refinement paradox and cumulative cultural evolution: Complex products of collective improvement favor conformist outcomes, blind copying, and hyper-credulity.

Social learning is common in nature, yet cumulative culture (where knowledge and technology increase in complexity and diversity over time) appears restricted to humans. To understand why, we organized a computer tournament in which programmed entries specified when to learn new knowledge and when to refine (i.e.

Small populations of Palaeolithic humans in Cyprus hunted endemic megafauna to extinction.

The hypothesized main drivers of megafauna extinctions in the late Quaternary have wavered between over-exploitation by humans and environmental change, with recent investigations demonstrating more nuanced synergies between these drivers depending on taxon, spatial scale, and region. However, most studies still rely on comparing archaeologically based chronologies of timing of initial human arrival into naïve ecosystems and palaeontologically inferred dates of megafauna extinctions. Conclusions arising from comparing chronologies also depend on the reliability of dated evidence, dating uncertainties, and correcting for the low probability of preservation (Signor-Lipps effect).

Code sharing in ecology and evolution increases citation rates but remains uncommon.

Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here, we conduct a literature review estimating temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation rate. We find that code is rarely published (only 6% of papers), with little improvement over time.

The role of funding in the performance of Latin America's protected areas.

Conservationists have long argued that inadequate funding for managing protected areas (PAs) jeopardizes their ability to achieve conservation goals. However, this claim has rarely been substantiated by quantitative evaluations. To address this, we examined the impact of funding on PA effectiveness both at the scale of 17 national PA systems across Latin America and within a PA system (Ecuador), for which we had precise historical financial data.

The Turing Test and our shifting conceptions of intelligence.

"Can machines think?" So asked Alan Turing in his 1950 paper, "Computing Machinery and Intelligence." Turing quickly noted that, given the difficulty of defining , the question is "too meaningless to deserve discussion." As is often done in philosophical debates, he proposed replacing it with a different question.

Non-Biochemical Gradient Sequence-Controlled Polymers with Tuned Kinetics and Self-Assembled Morphologies.

Two key challenges in the multidisciplinary field of sequence-controlled polymers are their efficient synthesis and the establishment of correlation with polymer properties. In this context, in this paper, gradient architecture in the hydrophobic tail of an amphiphile is implemented and synthesized for a fixed hydrophilic unit (polyethylene glycol, PEG), by means of two monomers (2-hydroxypropyl methacrylate, HPMA, and diacetone acrylamide, DAAM) of contrasting reactivities. The resulting non-biochemical gradient sequence-controlled polymers are generated from a one-pot, homogeneous mixture through a PET-RAFT-PISA (photoinduced electron/energy transfer-reversible addition-fragmentation chain transfer-polymerization-induced self-assembly) method.

The Kinematics of 3D Arm Movements in Sub-Acute Stroke: Impaired Inter-Joint Coordination is Attributable to Both Weakness and Flexor Synergy Intrusion.

Background: It has long been of interest to characterize the components of the motor abnormality in the arm after stroke. One approach has been to decompose the hemiparesis phenotype into negative signs, such as weakness, and positive signs, such as intrusion of synergies. We sought to identify the contributions of weakness and flexor synergy to motor deficits in sub-acute stroke.

Adaptation of turnip mosaic virus to involves rewiring of VPg-host proteome interactions.

The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study, we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron.

Exploiting relationship directionality to enhance statistical modeling of peer-influence across social networks.

Risky-prescribing is the excessive or inappropriate prescription of drugs that singly or in combination pose significant risks of adverse health outcomes. In the United States, prescribing of opioids and other "risky" drugs is a national public health concern. We use a novel data framework-a directed network connecting physicians who encounter the same patients in a sequence of visits-to investigate if risky-prescribing diffuses across physicians through a process of peer-influence.

Influential individuals can promote prosocial practices in heterogeneous societies: a mathematical and agent-based model.

In this paper, we examine how different governance types impact prosocial behaviors in a heterogenous society. We construct a general theoretical framework to examine a game-theoretic model to assess the ease of achieving a cooperative outcome. We then build a dynamic agent-based model to examine three distinct governance types in a heterogenous population: monitoring one's neighbors, despotic leadership, and influencing one's neighbors to adapt strategies that lead to better fitness.

An efficient plasmid-based system for the recovery of recombinant vesicular stomatitis virus encoding foreign glycoproteins.

Viral glycoproteins mediate entry into host cells, thereby dictating host range and pathogenesis. In addition, they constitute the principal target of neutralizing antibody responses, making them important antigens in vaccine development. Recombinant vesicular stomatitis virus (VSV) encoding foreign glycoproteins can provide a convenient and safe surrogate system to interrogate the function, evolution, and antigenicity of viral glycoproteins from viruses that are difficult to manipulate or those requiring high biosafety level containment.

A sensorimotor-association axis of thalamocortical connection development.

Human cortical development follows a sensorimotor-to-association sequence during childhood and adolescence. The brain's capacity to enact this sequence over decades indicates that it relies on intrinsic mechanisms to regulate inter-regional differences in the timing of cortical maturation, yet regulators of human developmental chronology are not well understood. Given evidence from animal models that thalamic axons modulate windows of cortical plasticity, here we evaluate the overarching hypothesis that structural connections between the thalamus and cortex help to coordinate cortical maturational heterochronicity during youth.

Reversion to sensitivity explains limited transmission of resistance in a hospital pathogen.

Bacterial pathogens that are successful in hospital environments must survive times of intense antibiotic exposure and times of no antibiotic exposure. When these organisms are closely associated with human hosts, they must also transmit from one patient to another for the resistance to spread. The resulting evolutionary dynamics have, in some settings, led to rising levels of resistance in hospitals.