Profiting From Purpose: Profiles of Success and Challenge in Eight Social Purpose Businesses

Offers an in-depth analysis of eight community-based human service and youth-serving nonprofit organizations that received assistance from Seedco's Nonprofit Venture Network to develop their capacity to launch social purpose businesses

Purification and structural characterization of the Na⁺-translocating ferredoxin: NAD⁺ reductase (Rnf) complex of Clostridium tetanomorphum

Various microbial metabolisms use H+/Na+-translocating ferredoxin:NAD+ reductase (Rnf) either to exergonically oxidize reduced ferredoxin by NAD+ for generating a transmembrane electrochemical potential or reversely to exploit the latter for producing reduced ferredoxin. For cryo-EM structural analysis, we elaborated a quick four-step purification protocol for the Rnf complex from Clostridium tetanomorphum and integrated the homogeneous and active enzyme into a nanodisc. The obtained 4.27 Å density map largely allows chain tracing and redox cofactor identification complemented by biochemical data from entire Rnf and single subunits RnfB, RnfC and RnfG. On this basis, we postulated an electron transfer route between ferredoxin and NAD via eight [4Fe-4S] clusters, one Fe ion and four flavins crossing the cell membrane twice related to the pathway of NADH:ubiquinone reductase. Redox-coupled Na+ translocation is provided by orchestrating Na+ uptake/release, electrostatic effects of the assumed membrane-integrated FMN semiquinone anion and accompanied polypeptide rearrangements mediated by different redox steps

Ligand binding and conformational dynamics of the E. coli nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry

Nicotinamide nucleotide transhydrogenases are integral membrane proteins that utilizes the proton motive force to reduce NADP+ to NADPH while converting NADH to NAD+. Atomic structures of various transhydrogenases in different ligand-bound states have become available, and it is clear that the molecular mechanism involves major conformational changes. Here we utilized hydrogen/deuterium exchange mass spectrometry (HDX-MS) to map ligand binding sites and analyzed the structural dynamics of E. coli transhydrogenase. We found different allosteric effects on the protein depending on the bound ligand (NAD+, NADH, NADP+, NADPH). The binding of either NADP+ or NADPH to domain III had pronounced effects on the transmembrane helices comprising the proton-conducting channel in domain II. We also made use of cyclic ion mobility separation mass spectrometry (cyclic IMS-MS) to maximize coverage and sensitivity in the transmembrane domain, showing for the first time that this technique can be used for HDX-MS studies. Using cyclic IMS-MS, we increased sequence coverage from 68 % to 73 % in the transmembrane segments. Taken together, our results provide important new insights into the transhydrogenase reaction cycle and demonstrate the benefit of this new technique for HDX-MS to study ligand binding and conformational dynamics in membrane proteins

On the Sets of Real Numbers Recognized by Finite Automata in Multiple Bases

This article studies the expressive power of finite automata recognizing sets of real numbers encoded in positional notation. We consider Muller automata as well as the restricted class of weak deterministic automata, used as symbolic set representations in actual applications. In previous work, it has been established that the sets of numbers that are recognizable by weak deterministic automata in two bases that do not share the same set of prime factors are exactly those that are definable in the first order additive theory of real and integer numbers. This result extends Cobham's theorem, which characterizes the sets of integer numbers that are recognizable by finite automata in multiple bases. In this article, we first generalize this result to multiplicatively independent bases, which brings it closer to the original statement of Cobham's theorem. Then, we study the sets of reals recognizable by Muller automata in two bases. We show with a counterexample that, in this setting, Cobham's theorem does not generalize to multiplicatively independent bases. Finally, we prove that the sets of reals that are recognizable by Muller automata in two bases that do not share the same set of prime factors are exactly those definable in the first order additive theory of real and integer numbers. These sets are thus also recognizable by weak deterministic automata. This result leads to a precise characterization of the sets of real numbers that are recognizable in multiple bases, and provides a theoretical justification to the use of weak automata as symbolic representations of sets.Comment: 17 page

Radio-Frequency Spectroscopy

Contains reports on three research projects

Glassy timescale divergence and anomalous coarsening in a kinetically constrained spin chain

We analyse the out of equilibrium behavior of an Ising spin chain with an asymmetric kinetic constraint after a quench to a low temperature T. In the limit T\to 0, we provide an exact solution of the resulting coarsening process. The equilibration time exhibits a `glassy' divergence \teq=\exp(const/T^2) (popular as an alternative to the Vogel-Fulcher law), while the average domain length grows with a temperature dependent exponent, \dbar ~ t^{T\ln 2}. We show that the equilibration time \teq also sets the timescale for the linear response of the system at low temperatures.Comment: 4 pages, revtex, includes two eps figures. Proof of energy barrier hierarchy added. Version to be published in Phys Rev Let

Obesity and STING1 genotype associate with 23-valent pneumococcal vaccination efficacy

© 2020, Sebastian etal. BACKGROUND. Obesity has been associated with attenuated vaccine responses and an increased risk of contracting pneumococcal pneumonia, but no study to our knowledge has assessed the impact of obesity and genetics on 23-valent pneumococcal vaccine (PPSV23) efficacy. We assessed the relationship of obesity (primary analysis) and stimulator of interferon genes (STING1) genotype (secondary analysis) on PPSV23 efficacy. METHODS. Nonobese (BMI 22-25 kg/m2) and obese participants (BMI ≥30 kg/m2) were given a single dose of PPSV23. Blood was drawn immediately prior to and 4-6 weeks after vaccination. Serum samples were used to assess PPSV23-specific antibodies. STING1 genotypes were identified using PCR on DNA extracted from peripheral blood samples. RESULTS. Forty-six participants were categorized as nonobese (n = 23; 56.5% women; mean BMI 23.3 kg/m2) or obese (n = 23; 65.2% women; mean BMI 36.3 kg/m2). Obese participants had an elevated fold change in vaccine-specific responses compared with nonobese participants (P \u3c 0.0001). The WT STING1 group (R232/R232) had a significantly higher PPSV23 response than individuals with a single copy of HAQ-STING1 regardless of BMI (P = 0.0025). When WT was assessed alone, obese participants had a higher fold serotype-specific response compared with nonobese participants (P \u3c 0.0001), but no difference was observed between obese and nonobese individuals with 1 HAQ allele (P = 0.693). CONCLUSIONS. These observations demonstrate a positive association between obesity and PPSV23 efficacy specifically in participants with the WT STING1 genotype. TRIAL REGISTRATION. ClinicalTrials.gov NCT02471014. FUNDING. This research was supported by the NIH and the University of Florida MD-PhD Training Program

User-definable resource bounds analysis for logic programs

We present a static analysis that infers both upper and lower bounds on the usage that a logic program makes of a set of user-definable resources. The inferred bounds will in general be functions of input data sizes. A resource in our approach is a quite general, user-defined notion which associates a basic cost function with elementary operations. The analysis then derives the related (upper- and lower-bound) resource usage functions for all predicates in the program. We also present an assertion language which is used to define both such resources and resourcerelated properties that the system can then check based on the results of the analysis. We have performed some preliminary experiments with some concrete resources such as execution steps, bytes sent or received by an application, number of files left open, number of accesses to a datábase, number of calis to a procedure, number of asserts/retracts, etc. Applications of our analysis include resource consumption verification and debugging (including for mobile code), resource control in parallel/distributed computing, and resource-oriented specialization

Dynamics of the frustrated Ising lattice gas

The dynamical properties of a three dimensional model glass, the frustrated Ising lattice gas (FILG) are studied by Monte Carlo simulations. We present results of compression experiments, where the chemical potential is either slowly or abruptly changed, as well as simulations at constant density. One time quantities like density and two time ones like correlations, responses and mean square displacements are measured, and the departure from equilibrium clearly characterized. The aging scenario, particularly in the case of density autocorrelations is reminiscent of spin glass phenomenology with violations of the Fluctuation-dissipation theorem, typical of systems with one replica symmetry breaking. The FILG, as a valid on-lattice model of structural glasses can be described with tools developed in spin glass theory and, being a finite dimensional model, can open the way for a systematic study of activated processes in glasses.Comment: to appear in Phys. Rev. E, november (2000

Breast tumors: an overview

Review on Breast tumors: an overview, with data on clinics, and the genes involved