A powerful framework for differential co-expression analysis of general risk factors.

Differential co-expression analysis (DCA) aims to identify genes in a pathway whose shared expression depends on a risk factor. While DCA provides insights into the biological activity of diseases, existing methods are limited to categorical risk factors and/or suffer from bias due to batch and variance-specific effects. We propose a new framework, Kernel-based Differential Co-expression Analysis (KDCA), that harnesses correlation patterns between genes in a pathway to detect differential co-expression arising from general (i.

SCAMPI: A scalable statistical framework for genome-wide interaction testing harnessing cross-trait correlations.

Family-based heritability estimates of complex traits are often considerably larger than their single-nucleotide polymorphism (SNP) heritability estimates. This discrepancy may be due to non-additive effects of genetic variation, including variation that interacts with other genes or environmental factors to influence the trait. Variance-based procedures provide a computationally efficient strategy to screen for SNPs with potential interaction effects without requiring the specification of the interacting variable.

Binding energies of CD4 and fragment species to Pt(111): Implications for measurements of anion electron stimulated desorption.

We consider the electron stimulated desorption, via dissociative electron attachment, of anionic species from thin condensed CD4 films deposited on a Pt substrate and compare experimentally observed desorption yields with density functional theory calculations of the binding energies of various anionic and neutral moieties to Pt(111). Certain species (which can be considered chemisorbed) exhibit very high binding energies and large charge transfer with the substrate. Other "physisorbed" species have much lower binding energies.

Identifying latent genetic interactions in genome-wide association studies using multiple traits.

The "missing" heritability of complex traits may be partly explained by genetic variants interacting with other genes or environments that are difficult to specify, observe, and detect. We propose a new kernel-based method called Latent Interaction Testing (LIT) to screen for genetic interactions that leverages pleiotropy from multiple related traits without requiring the interacting variable to be specified or observed. Using simulated data, we demonstrate that LIT increases power to detect latent genetic interactions compared to univariate methods.

Label-free, whole-brain in vivo mapping in an adult vertebrate with third harmonic generation microscopy.

Comprehensive understanding of interconnected networks within the brain requires access to high resolution information within large field of views and over time. Currently, methods that enable mapping structural changes of the entire brain in vivo are extremely limited. Third harmonic generation (THG) can resolve myelinated structures, blood vessels, and cell bodies throughout the brain without the need for any exogenous labeling.

A tale of two males: Behavioral and neural mechanisms of alternative reproductive tactics in midshipman fish.

An amalgam of investigations at the interface of neuroethology and behavioral neuroendocrinology first established the most basic behavioral, neuroanatomical, and neurophysiological characters of vocal-acoustic communication morphs in the plainfin midshipman fish, Porichthys notatus Girard. This foundation has led, in turn, to the repeated demonstration that neuro-behavioral mechanisms driving reproductive-related, vocal-acoustic behaviors can be uncoupled from gonadal state for two adult male phenotypes that follow alternative reproductive tactics (ARTs).

Electron-Induced Damage by UV Photolysis of DNA Attached to Gold Nanoparticles.

Photolysis of DNA attached to gold nanoparticles (AuNPs) with ultraviolet (UV) photons induces DNA damage. The release of nucleobases (Cyt, Gua, Ade, and Thy) from DNA was the major reaction (99%) with an approximately equal release of pyrimidines and purines. This reaction contributes to the formation of abasic sites in DNA.

Midbrain node for context-specific vocalisation in fish.

Vocalizations communicate information indicative of behavioural state across divergent social contexts. Yet, how brain regions actively pattern the acoustic features of context-specific vocal signals remains largely unexplored. The midbrain periaqueductal gray (PAG) is a major site for initiating vocalization among mammals, including primates.

Sound production biomechanics in three-spined toadfish and potential functional consequences of swim bladder morphology in the Batrachoididaea).

The relationship between sound complexity and the underlying morphology and physiology of the vocal organ anatomy is a fundamental component in the evolution of acoustic communication, particularly for fishes. Among vertebrates, the mammalian larynx and avian syrinx are the best-studied vocal organs, and their ability to produce complex vocalizations has been modeled. The range and complexity of the sounds in mammalian lineages have been attributed, in part, to the bilateral nature of the vocal anatomy.

Identifying latent genetic interactions in genome-wide association studies using multiple traits.

Genome-wide association studies of complex traits frequently find that SNP-based estimates of heritability are considerably smaller than estimates from classic family-based studies. This 'missing' heritability may be partly explained by genetic variants interacting with other genes or environments that are difficult to specify, observe, and detect. To circumvent these challenges, we propose a new method to detect genetic interactions that leverages pleiotropy from multiple related traits without requiring the interacting variable to be specified or observed.

The Quantitative Genetics of Human Disease: 1 Foundations.

In this the first of an anticipated four paper series, fundamental results of quantitative genetics are presented from a first principles approach. While none of these results are in any sense new, they are presented in extended detail to precisely distinguish between definition and assumption, with a further emphasis on distinguishing quantities from their usual approximations. Terminology frequently encountered in the field of human genetic disease studies will be defined in terms of their quantitive genetics form.

California singing fish.

Bass describes the fascinating life history, behavior, and neurobiology of the California singing fish, including its remarkable vocal abilities.

Acoustic and postural displays in a miniature and transparent teleost fish, Danionella dracula.

Acoustic behavior is widespread across vertebrates, including fishes. We report robust acoustic displays during aggressive interactions for a laboratory colony of Danionella dracula, a miniature and transparent species of teleost fish closely related to zebrafish (Danio rerio), which are hypothesized to be sonic based on the presence of a hypertrophied muscle associated with the male swim bladder. Males produce bursts of pulsatile sounds and a distinct postural display - extension of a hypertrophied lower jaw, a morphological trait not present in other Danionella species - during aggressive but not courtship interactions.

Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity.

The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions.

Shape Resonances in DNA: Nucleobase Release, Reduction, and Dideoxynucleoside Products Induced by 1.3 to 2.3 eV Electrons.

Understanding the details of DNA damage caused by high-energy particles or photons is complicated by the multitude of reactive species, arising from the ionization and dissociation of HO, DNA, and protein. In this work, oligonucleotides (ODNs) are irradiated with a beam of low-energy electrons of 1.3 to 2.

Common risk variants for epilepsy are enriched in families previously targeted for rare monogenic variant discovery.

Background: The epilepsies are highly heritable conditions that commonly follow complex inheritance. While monogenic causes have been identified in rare familial epilepsies, most familial epilepsies remain unsolved. We aimed to determine (1) whether common genetic variation contributes to familial epilepsy risk, and (2) whether that genetic risk is enriched in familial compared with non-familial (sporadic) epilepsies.

Noise-induced hearing loss correlates with inner ear hair cell decrease in larval zebrafish.

Anthropogenic noise can be hazardous for the auditory system and wellbeing of animals, including humans. However, very limited information is known on how this global environmental pollutant affects auditory function and inner ear sensory receptors in early ontogeny. The zebrafish (Danio rerio) is a valuable model in hearing research, including investigations of developmental processes of the vertebrate inner ear.

Oxytocin-like receptor expression in evolutionarily conserved nodes of a vocal network associated with male courtship in a teleost fish.

Neuropeptides, including oxytocin-like peptides, are a conserved group of hormones that regulate a wide range of social behaviors, including vocal communication. In the current study, we evaluate whether putative brain sites for the actions of isotocin (IT), the oxytocin (OT) homolog of teleost fishes are associated with vocal courtship and circuitry in the plainfin midshipman fish (Porichthys notatus). During the breeding season, nesting males produce advertisement calls known as "hums" to acoustically court females at night and attract them to nests.

Chemical transformation of molecular ices containing NO and CD by low energy electrons: New chemical species of astronomical interest.

We have employed electron stimulated desorption (ESD) and x-ray photoelectron spectroscopy (XPS) to study the chemical species generated from multilayer films of NO, CD, and mixtures thereof (i.e., NO/CD) by the impact of low energy electrons with energies between 30 and 70 eV.

To hum or not to hum: Neural transcriptome signature of male courtship vocalization in a teleost fish.

For many animal species, vocal communication is a critical social behavior and often a necessary component of reproductive success. Additionally, vocalizations are often demanding motor acts. Wanting to know whether a specific molecular toolkit might be required for vocalization, we used RNA-sequencing to investigate neural gene expression underlying the performance of an extreme vocal behavior, the courtship hum of the plainfin midshipman fish (Porichthys notatus).