The rockefeller university

Solids are distinguished from fluids by their ability to resist shear. In equilibrium systems, the resistance to shear is associated with the emergence of broken translational symmetry as exhibited by a nonuniform density pattern that is persistent, which in turn results from minimizing the free energy. In this work, we focus on a class of systems where this paradigm is challenged. We show that shear-driven jamming in dry granular materials is a collective process controlled by the constraints of mechanical equilibrium. We argue that these constraints can lead to a persistent pattern in a dual space that encodes the statistics of contact forces and the topology of the contact network. The shear-jamming transition is marked by the appearance of this persistent pattern. We investigate the structure and behavior of patterns both in real space and the dual space as the system evolves through the rigidity transition for a range of packing fractions and in two different shear protocols. We show that, in the protocol that creates homogeneous jammed states without shear bands, measures of shear jamming do not depend on strain and packing fraction independently but obey a scaling form with a packing-fraction-dependent characteristic strain that goes to zero at the isotropic jamming point phi(J). We demonstrate that it is possible to define a protocol-independent order parameter in this dual space, which provides a quantitative measure of the rigidity of shear-jammed states.

A skewness of the probability for instantaneous current fluctuations, in a nonequilibrium steady state, is observed experimentally in a dusty plasma. This skewness is attributed to the spatial asymmetry, which is imminent to the nonequilibrium systems due to the external hydrodynamic gradient. Using the modern framework of the large deviation theory, we extend the Onsager-Machlup ansatz for equilibrium fluctuations to systems with a preferred spatial direction, and provide a modulated Gaussian probability distribution, which is tested by simulations. This probability distribution is also of potential interest for other statistical disciplines. Connections with the principles of statistical mechanics, due to Boltzmann and Gibbs, are discussed as well.

The choice of stochasticity distribution for modeling the noise distribution is a fundamental assumption for the analysis of sequencing data and consequently is critical for the accurate assessment of biological heterogeneity and differential expression. The stochasticity of RNA sequencing has been assumed to follow Poisson distributions. We collected microRNA sequencing data and observed that its stochasticity is better approximated by gamma distributions, likely because of the stochastic nature of exponential PCR amplification. We validated our findings with two independent datasets, one for microRNA sequencing and another for RNA sequencing. Motivated by the gamma distributed stochasticity, we provided a simple method for the analysis of RNA sequencing data and showed its superiority to three existing methods for differential expression analysis using three data examples of technical replicate data and biological replicate data.

The signaling molecule cAMP regulates functions ranging from bacterial transcription to mammalian memory. In mammals, cAMP is synthesized by nine transmembrane adenylyl cyclases (ACs) and one soluble AC (sAC). Despite similarities in their catalytic domains, these ACs differ in regulation. Transmembrane ACs respond to G proteins, whereas sAC is uniquely activated by bicarbonate. Via bicarbonate regulation, sAC acts as a physiological sensor for pH/bicarbonate/CO2, and it has been implicated as a therapeutic target, e.g. for diabetes, glaucoma, and a male contraceptive. Here we identify the bisphenols bithionol and hexachlorophene as potent, sAC-specific inhibitors. Inhibition appears mostly non-competitive with the substrate ATP, indicating that they act via an allosteric site. To analyze the interaction details, we solved a crystal structure of an sAC.bithionol complex. The structure reveals that the compounds are selective for sAC because they bind to the sAC-specific, allosteric binding site for the physiological activator bicarbonate. Structural comparison of the bithionol complex with apo-sAC and other sAC.ligand complexes along with mutagenesis experiments reveals an allosteric mechanism of inhibition; the compound induces rearrangements of substrate binding residues and of Arg(176), a trigger between the active site and allosteric site. Our results thus provide 1) novel insights into the communication between allosteric regulatory and active sites, 2) a novel mechanism for sAC inhibition, and 3) pharmacological compounds targeting this allosteric site and utilizing this mode of inhibition. These studies provide support for the future development of sAC-modulating drugs.

The common marmoset (Callithrix jacchus) has garnered interest recently as a powerful model for the future of neuroscience research. Much of this excitement has centered on the species' reproductive biology and compatibility with gene editing techniques, which together have provided a path for transgenic marmosets to contribute to the study of disease as well as basic brain mechanisms. In step with technical advances is the need to establish experimental paradigms that optimally tap into the marmosets' behavioral and cognitive capacities. While conditioned task performance of a marmoset can compare unfavorably with rhesus monkey performance on conventional testing paradigms, marmosets' social behavior and cognition are more similar to that of humans. For example, marmosets are among only a handful of primates that, like humans, routinely pair bond and care cooperatively for their young. They are also notably pro-social and exhibit social cognitive abilities, such as imitation, that are rare outside of the Apes. In this Primer, we describe key facets of marmoset natural social behavior and demonstrate that emerging behavioral paradigms are well suited to isolate components of marmoset cognition that are highly relevant to humans. These approaches generally embrace natural behavior, which has been rare in conventional primate testing, and thus allow for a new consideration of neural mechanisms underlying primate social cognition and signaling. We anticipate that through parallel technical and paradigmatic advances, marmosets will become an essential model of human social behavior, including its dysfunction in neuropsychiatric disorders.

Testosterone has in recent years been proven essential for normal growth and maturation of small growing follicles. Concomitantly, low functional ovarian reserve (LFOR), characterized by a small growing follicle pool, has been associated with low testosterone levels, which can be of ovarian and/or adrenal origin. In this study we, therefore, investigated whether peripheral sex steroid precursors and testosterone levels potentially reflect on adrenal function. In a retrospective cohort study of 355 consecutive infertile women, who presented to an academically affiliated fertility center in New York City, we investigated in a series of statistical models whether low peripheral sex steroid precursors and testosterone are associated with peripheral cortisol (C) levels, reflecting adrenal function. To determine potential correlations, we investigated the dehydroepiandrosterone (DHEA), DHEA sulfate (DHEAS), androstenedione (AD), total testosterone (TT), free testosterone (FT); sex hormone binding globulin (SHBG), anti-Mullerian hormone (AMH), thyroid stimulating hormone (TSH) and C in a series of multivariate and logistic regression analyses, utilizing C either as a continuous variable or with cut off <5.0 mu g/dL, and TT only as a continuous variable. Practically all models demonstrated significant predictability of peripheral sex hormone precursors for C levels, with DHEA demonstrating the strongest and most consistent predictability as an individual parameter and as part of the DHEAS/DHEA ratio. We conclude that in infertile women peripheral sex hormone precursors, especially DHEA, reflect C levels and, therefore, adrenal function. In infertile women, at all ages low levels of sex hormone precursors, therefore, should be considered indications for further adrenal assessments. (C) 2016 Elsevier Ltd. All rights reserved.

Background: Caregiver burden associated with caring for women with ovarian cancer has received limited focus. However, these patients often have complex needs, requiring a high level of care at home and imposing substantial burdens on caregivers. Objectives: This pilot study assessed the level of caregiver burden experienced by the primary caregivers of patients with end-stage ovarian cancer and identified variables associated with caregiver burden. Methods: Caregiver burden was assessed using the Caregiver Reaction Assessment. Fifty caregivers completed an anonymous and voluntary survey. Pearson correlations and independent samples t tests were used to analyze data. Findings: Most participants were Caucasian, married or living with a partner, and college graduates, with an annual household income of less than $90,000. Caregiver ages ranged from 29-81 years. Participants agreed most with the self-esteem scale, indicating they had pride in caring for their loved ones. Disrupted schedules and financial problems were the most burdensome factors in providing care. Because financial issues affected caregiver burden, nurses should facilitate interdisciplinary support. Future research is needed to determine the impact of nurse-led interventions to reduce caregiver burden.

G protein gated inward rectifier K+ (GIRK) channels open and thereby silence cellular electrical activity when inhibitory G protein coupled receptors (GPCRs) are stimulated. Here we describe an assay to measure neuronal GIRK2 activity as a function of membrane-anchored G protein concentration. Using this assay we show that four G beta gamma subunits bind cooperatively to open GIRK2, and that intracellular Na+ which enters neurons during action potentials further amplifies opening mostly by increasing G beta gamma affinity. A Na+ amplification function is characterized and used to estimate the concentration of G beta gamma subunits that appear in the membrane of mouse dopamine neurons when GABreceptors are stimulated. We conclude that GIRK2, through its dual responsiveness to G beta gamma and Na+, mediates a form of neuronal inhibition that is amplifiable in the setting of excess electrical activity.

Due to their central role in essential physiological processes, potassium channels are common targets for animal toxins. These toxins in turn are of great value as tools for studying channel function and as lead compounds for drug development. Here, we used a direct toxin pull-down assay with immobilised KcsA potassium channel to isolate a novel KcsA-binding toxin (called Tx7335) from eastern green mamba snake (Dendroaspis angusticeps) venom. Sequencing of the toxin by Edman degradation and mass spectrometry revealed a 63 amino acid residue peptide with 4 disulphide bonds that belongs to the three-finger toxin family, but with a unique modification of its disulphide-bridge scaffold. The toxin induces a dose-dependent increase in both open probabilities and mean open times on KcsA in artificial bilayers. Thus, it unexpectedly behaves as a channel activator rather than an inhibitor. A charybdotoxin-sensitive mutant of KcsA exhibits similar susceptibility to Tx7335 as wild-type, indicating that the binding site for Tx7335 is distinct from that of canonical pore-blocker toxins. Based on the extracellular location of the toxin binding site (far away from the intracellular pH gate), we propose that Tx7335 increases potassium flow through KcsA by allosterically reducing inactivation of the channel.