Universal inference.

We propose a general method for constructing confidence sets and hypothesis tests that have finite-sample guarantees without regularity conditions. We refer to such procedures as "universal." The method is very simple and is based on a modified version of the usual likelihood-ratio statistic that we call "the split likelihood-ratio test" (split LRT) statistic.

Magnetically-responsive, multifunctional drug delivery nanoparticles for elastic matrix regenerative repair.

Unlabelled: Arresting or regressing growth of abdominal aortic aneurysms (AAAs), localized expansions of the abdominal aorta are contingent on inhibiting chronically overexpressed matrix metalloproteases (MMPs)-2 and -9 that disrupt elastic matrix within the aortic wall, concurrent with providing a stimulus to augmenting inherently poor auto-regeneration of these matrix structures. In a recent study we demonstrated that localized, controlled and sustained delivery of doxycycline (DOX; a tetracycline-based antibiotic) from poly(lactic-co-glycolic acid) nanoparticles (PLGA NPs), enhances elastic matrix deposition and MMP-inhibition at a fraction of the therapeutically effective oral dose. The surface functionalization of these NPs with cationic amphiphiles, which enhances their arterial uptake, was also shown to have pro-matrix regenerative and anti-MMP effects independent of the DOX.

Magnetically Responsive Bone Marrow Mesenchymal Stem Cell-Derived Smooth Muscle Cells Maintain Their Benefits to Augmenting Elastic Matrix Neoassembly.

Abdominal aortic aneurysms (AAA) represent abnormal aortal expansions that result from chronic proteolytic breakdown of elastin and collagen fibers by matrix metalloproteases. Poor elastogenesis by adult vascular smooth muscle cells (SMCs) limits regenerative repair of elastic fibers, critical for AAA growth arrest. Toward overcoming these limitations, we recently demonstrated significant elastogenesis by bone marrow mesenchymal stem cell-derived SMCs (BM-SMCs) and their proelastogenesis and antiproteolytic effects on rat aneurysmal SMCs (EaRASMCs).

Fibrinolytic PLGA nanoparticles for slow clot lysis within abdominal aortic aneurysms attenuate proteolytic loss of vascular elastic matrix.

Abdominal aortic aneurysms (AAAs) involve chronic overexpression of proteases in the aortic wall that result in disruption of elastic fibers and consequent loss of vessel elasticity. Nearly 75% of AAAs contain flow-obstructing, fibrin-rich intraluminal thrombi (ILT), which act as a) a bioinert shield, protecting the underlying AAA wall from high hemodynamic stresses, and b) a reservoir of inflammatory cells and proteases that cause matrix breakdown. For these reasons, restoring flow through the aorta lumen and facilitating transmural diffusion of therapeutics from circulation to the AAA wall must be achieved by slow thrombolysis of the ILT to render it porous without rapid breakdown.

Nanoparticulate delivery of agents for induced elastogenesis in three-dimensional collagenous matrices.

The degradation of elastic matrix in the infrarenal aortic wall is a critical parameter underlying the formation and progression of abdominal aortic aneurysms. It is mediated by the chronic overexpression of matrix metalloprotease (MMP)-2 and MMP-9, leading to a progressive loss of elasticity and weakening of the aortic wall. Delivery of therapeutic agents to inhibit MMPs, while concurrently coaxing cell-based regenerative repair of the elastic matrix represents a potential strategy for slowing or arresting abdominal aortic aneurysm growth.

Nanoparticles for localized delivery of hyaluronan oligomers towards regenerative repair of elastic matrix.

Abdominal aortic aneurysms (AAAs) are rupture-prone progressive dilations of the infrarenal aorta due to a loss of elastic matrix that lead to weakening of the aortic wall. Therapies to coax biomimetic regenerative repair of the elastic matrix by resident, diseased vascular cells may thus be useful to slow, arrest or regress AAA growth. Hyaluronan oligomers (HA-o) have been shown to induce elastic matrix synthesis by healthy and aneurysmal rat aortic smooth muscle cells (SMCs) in vitro but only via exogenous dosing, which potentially has side-effects and limitations to in vivo delivery towards therapy.

Multifunctional nanoparticles for doxycycline delivery towards localized elastic matrix stabilization and regenerative repair.

Abdominal aortic aneurysms (AAAs) are abnormal expansions of the aortic wall, typically characterized by chronic up-regulation of matrix metalloproteases (MMPs)-2 and -9. These MMPs degrade elastin and elastic matrix within the aortic wall, leading to a progressive loss of elasticity of the abdominal aorta as the condition progresses. Doxycycline (DOX) is a tetracycline-based antibiotic which has shown significant promise in delaying and slowing the growth of AAAs in both clinical studies and animal models.

Advances in biomimetic regeneration of elastic matrix structures.

Elastin is a vital component of the extracellular matrix, providing soft connective tissues with the property of elastic recoil following deformation and regulating the cellular response via biomechanical transduction to maintain tissue homeostasis. The limited ability of most adult cells to synthesize elastin precursors and assemble them into mature crosslinked structures has hindered the development of functional tissue-engineered constructs that exhibit the structure and biomechanics of normal native elastic tissues in the body. In diseased tissues, the chronic overexpression of proteolytic enzymes can cause significant matrix degradation, to further limit the accumulation and quality (e.

Time-dependent conformational changes in adsorbed albumin and its effect on platelet adhesion.

Recent studies have shown that platelets can adhere to adsorbed albumin (Alb) through a receptor-mediated mechanism, but only if the Alb undergoes more than a critical degree of adsorption-induced unfolding. The objectives of this research were to investigate whether Alb that was initially adsorbed in a manner that induced unfolding that was less than this critical level would undergo further unfolding with time and, if so, whether this would induce the onset of platelet adhesion once this critical level was exceeded. To address these questions, CD spectropolarimetry was used to monitor the structure of Alb on OH- and CH(3)-functionalized alkanethiol self-assembled monolayer surfaces, with the Alb initially adsorbed under conditions resulting in degrees of unfolding that were below this critical level, and then the adsorbed Alb layers were aged over 6 months in sterile physiological saline at 37 °C.

Delineating the roles of the GPIIb/IIIa and GP-Ib-IX-V platelet receptors in mediating platelet adhesion to adsorbed fibrinogen and albumin.

Platelet adhesion to adsorbed plasma proteins, such as fibrinogen (Fg), has been conventionally thought to be mediated by the GPIIb/IIIa receptor binding to Arg-Gly-Asp (RGD)-like motifs in the adsorbed protein. In previous studies, we showed that platelet adhesion response to adsorbed Fg and Alb was strongly influenced by the degree of adsorption-induced protein unfolding and that platelet adhesion was only partially blocked by soluble RGD, with RGD-blocked platelets adhering without activation. Based on these results, we hypothesized that in addition to the RGD-specific GPIIb/IIIa receptor, which mediates both adhesion and activation, a non-RGD-specific receptor set likely also plays a role in platelet adhesion (but not activation) to both Fg and albumin (Alb).

Learning generative models for protein fold families.

We introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN (Generative REgularized ModeLs of proteINs), learns an undirected probabilistic graphical model of the amino acid composition within the MSA. The resulting model encodes both the position-specific conservation statistics and the correlated mutation statistics between sequential and long-range pairs of residues.

Alternative paths in HIV-1 targeted human signal transduction pathways.

Background: Human immunodeficiency virus-1 (HIV-1) has a minimal genome of only 9 genes, which encode 15 proteins. HIV-1 thus depends on the human host for virtually every aspect of its life cycle. The universal language of communication in biological systems, including between pathogen and host, is via signal transduction pathways.

The adherence of platelets to adsorbed albumin by receptor-mediated recognition of binding sites exposed by adsorption-induced unfolding.

Although albumin (Alb) is the most abundant plasma protein, it is considered to be non-adhesive to platelets, as it lacks any known amino acid sequences for binding platelet receptors. Recent studies have suggested that platelets adhere to adsorbed Alb by mechanisms linked to its conformational state. To definitively address this issue we used circular dichroism (CD) spectropolarimetry to characterize the conformation of Alb adsorbed on a broad range of surface chemistries from a wide range of Alb solution concentrations, with platelet adhesion examined using a lactate dehydrogenase (LDH) assay and scanning electron microscopy (SEM).

The relationship between platelet adhesion on surfaces and the structure versus the amount of adsorbed fibrinogen.

While platelet adhesion to biomaterial surfaces is widely recognized to be related to adsorbed fibrinogen (Fg), it has remained controversial whether platelet adhesion is in response to the adsorbed amount or the adsorbed conformation of this protein. To address this issue, we designed a series of platelet adhesion studies to clearly separate these two factors, thus enabling us to definitively determine whether it is the amount or the conformation of adsorbed Fg that mediates platelet response. Fg was adsorbed to a broad range of surface chemistries from a wide range of solution concentrations, with the amount and conformation of adsorbed Fg determined by absorbance and circular dichroism (CD) spectropolarimetry, respectively.

Probing the conformation and orientation of adsorbed enzymes using side-chain modification.

The bioactivity of enzymes that are adsorbed on surfaces can be substantially influenced by the orientation of the enzyme on the surface and adsorption-induced changes in the enzyme's structure. Circular dichroism (CD) is a powerful method for observing the secondary structure of proteins; however, it provides little information regarding the tertiary structure of a protein or its adsorbed orientation. In this study, we developed methods using side-chain-specific chemical modification of solvent-exposed tryptophan residues to complement CD spectroscopy and bioactivity assays to provide greater detail regarding whether changes in enzyme bioactivity following adsorption are due to adsorbed orientation and/or adsorption-induced changes in the overall structure.

Investigation of the effects of surface chemistry and solution concentration on the conformation of adsorbed proteins using an improved circular dichroism method.

In this paper we present the development of methods using circular dichroism spectropolarimetry with a custom-designed cuvette to increase the signal-to-noise ratio for the measurement of the secondary structure of adsorbed proteins, thus providing enhanced sensitivity and reproducibility. These methods were then applied to investigate how surface chemistry and solution concentration influence both the amount of adsorbed proteins and their secondary structure. Human fibrinogen and albumin were adsorbed onto alkanethiol self-assembled monolayers (SAMs) on gold with CH3, OCH2-CF3, NH2, COOH, and OH terminal groups from both dilute (0.