ClimSim: A large multi-scale dataset for hybrid physics-ML climate emulation

Modern climate projections lack adequate spatial and temporal resolution due to computational constraints. A consequence is inaccurate and imprecise predictions of critical processes such as storms. Hybrid methods that combine physics with machine learning (ML) have introduced a new generation of higher fidelity climate simulators that can sidestep Moore's Law by outsourcing compute-hungry, short, high-resolution simulations to ML emulators. However, this hybrid ML-physics simulation approach requires domain-specific treatment and has been inaccessible to ML experts because of lack of training data and relevant, easy-to-use workflows. We present ClimSim, the largest-ever dataset designed for hybrid ML-physics research. It comprises multi-scale climate simulations, developed by a consortium of climate scientists and ML researchers. It consists of 5.7 billion pairs of multivariate input and output vectors that isolate the influence of locally-nested, high-resolution, high-fidelity physics on a host climate simulator's macro-scale physical state.The dataset is global in coverage, spans multiple years at high sampling frequency, and is designed such that resulting emulators are compatible with downstream coupling into operational climate simulators. We implement a range of deterministic and stochastic regression baselines to highlight the ML challenges and their scoring. The data (https://huggingface.co/datasets/LEAP/ClimSim_high-res) and code (https://leap-stc.github.io/ClimSim) are released openly to support the development of hybrid ML-physics and high-fidelity climate simulations for the benefit of science and society

Review TRENDS in Ecology and Evolution Vol.20 No.3 March 2005 Functional aspects of song learning in songbirds

The oscine passerines, or ‘songbirds’, are one of the few animal taxa in which individuals learn their vocal signals. Recent comparative studies reveal a remarkable diversity of song-learning strategies in the songbirds. Here, we discuss recent studies that shed light on the possible functional basis of different song-learning programs. We argue that further insights into the evolution and ecology of song learning will require that comparative data and functional hypotheses be analyzed in a phylogenetic context, and we review recent studies that we feel might be the first steps in this process. Songs are complex species-specific signals given by animals of many taxa in mating and intrasexual contexts, most commonly by males to attract females and to repel rival males [1]. In most animal taxa, these species-specifi

Evolutionary and biophysical relationships among the papillomavirus E2 proteins

Infection by a human papillomavirus (HPV) may result in a variety of clinical conditions ranging from benign warts to invasive cancer depending on the viral type. The HPV E2 protein represses transcription of the E6 and E7 genes in integrated papillomavirus genomes and together with the E1 protein is required for viral replication. E2 proteins bind with high affinity to palindromic DNA sequences consisting of two highly conserved four base pair sequences flanking a variable ‘spacer’ of identical length. The E2 proteins directly contact the conserved DNA but not the spacer DNA. However, variation in naturally occurring spacer sequences results in differential protein binding affinity. This discrimination in binding is dependent on their sensitivity to the unique conformational and/or dynamic properties of the spacer DNA in a process termed ‘indirect readout’. This article explores the structure of the E2 proteins and their interaction with DNA and other proteins, the effects of ions on affinity and specificity, and the phylogenetic and biophysical nature of this core viral protein. We have analyzed the sequence conservation and electrostatic features of three-dimensional models of the DNA binding domains of 146 papillomavirus types and variants with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, three-dimensional structure, and the electrostatic features of E2 protein DNA binding domain showed high conservation among all papillomavirus types. This indicates that the specific interactions between the E2 protein and its binding sites on DNA have been conserved throughout PV evolution. Analysis of the E2 protein’s transactivation domain showed that unlike the DNA binding domain, the transactivation domain does not have extensive surfaces of highly conserved residues. Rather, the regions of high conservation are localized to small surface patches. The invariance of the E2 DNA binding domain structure, electrostatics and sequence suggests that it may be a suitable target for the development of vaccines effective against a broad spectrum of HPV types

Immediate and long-term effects of testosterone on song plasticity and learning in juvenile song sparrows

Steroid sex hormones play critical roles in the development of brain regions used for vocal learning. It has been suggested that puberty-induced increases in circulating testosterone (T) levels crystallize a bird's repertoire and inhibit future song learning. Previous studies show that early administration of T crystallizes song repertoires but have not addressed whether new songs can be learned after this premature crystallization. We brought 8 juvenile song sparrows (Melospiza melodia) into the laboratory in the late summer and implanted half of them with subcutaneous T pellets for a two week period in October. Birds treated with T tripled their singing rates and crystallized normal songs in 2 weeks. After T removal, subjects were tutored by 4 new adults. Birds previously treated with T tended toward learning fewer new songs post T, consistent with the hypothesis that T helps to close the song learning phase. However, one T-treated bird proceeded to learn several new songs in the spring, despite singing perfectly crystallized songs in the fall. His small crystallized fall repertoire and initial lag behind other subjects in song development suggest that this individual may have had limited early song learning experience. We conclude that an exposure to testosterone sufficient for crystallization of a normal song repertoire does not necessarily prevent future song learning and suggest that early social experiences might override the effects of hormones in closing song learning. (c) 2012 Elsevier B.V. All rights reserved.</p

Life Course Biopsychosocial Effects of Retrospective Childhood Social Support and Later-Life Cognition

Social support during childhood lays the foundation for social relationships throughout the life course and has been shown to predict a wide range of mental and physical health outcomes. Social support measured in late life is prospectively associated with better cognitive aging, but few studies have evaluated social support received earlier in the life course. We quantified the effects of childhood social support, reported retrospectively, on later-life cognitive trajectories and investigated biopsychosocial mechanisms underlying these associations. Latent growth curve models estimated 10-year cognitive trajectories in 8,538 participants (baseline ages 45-93; Mage = 63) in the REasons for Geographic And Racial Differences in Stroke (REGARDS) project. Independent of sociodemographics, childhood socioeconomic status, and household size, greater retrospective childhood social support was associated with better initial episodic memory, but not verbal fluency or cognitive change, in later adulthood. Associations with initial memory level were mediated by sociodemographic and psychosocial variables; specifically, those who reported greater childhood social support reported higher educational attainment and had better physical and emotional health in adulthood, which were each associated with better memory. These results provide support for broad and enduring effects of childhood social support on mental, physical, and cognitive health decades later. (PsycINFO Database Record (c) 2019 APA, all rights reserved)