Cluster Computing and the Power of Edge Recognition

We study the robustness--the invariance under definition changes--of the cluster class CL#P [HHKW05]. This class contains each #P function that is computed by a balanced Turing machine whose accepting paths always form a cluster with respect to some length-respecting total order with efficient adjacency checks. The definition of CL#P is heavily influenced by the defining paper's focus on (global) orders. In contrast, we define a cluster class, CLU#P, to capture what seems to us a more natural model of cluster computing. We prove that the naturalness is costless: CL#P = CLU#P. Then we exploit the more natural, flexible features of CLU#P to prove new robustness results for CL#P and to expand what is known about the closure properties of CL#P. The complexity of recognizing edges--of an ordered collection of computation paths or of a cluster of accepting computation paths--is central to this study. Most particularly, our proofs exploit the power of unique discovery of edges--the ability of nondeterministic functions to, in certain settings, discover on exactly one (in some cases, on at most one) computation path a critical piece of information regarding edges of orderings or clusters

Guarantees for the Success Frequency of an Algorithm for Finding Dodgson-Election Winners

In the year 1876 the mathematician Charles Dodgson, who wrote fiction under the now more famous name of Lewis Carroll, devised a beautiful voting system that has long fascinated political scientists. However, determining the winner of a Dodgson election is known to be complete for the p 2 level of the polynomial hierarchy. This implies that unless P = NP no polynomial-time solution to this problem exists, and unless the polynomial hierarchy collapses to NP the problem is not even in NP. Nonetheless, we prove that when the number of voters is much greater than the number of candidates— although the number of voters may still be polynomial in the number of candidates—a simple greedy algorithm very frequently finds the Dodgson winners in such a way that it “knows” that it has found them, and furthermore the algorithm never incorrectly declares a nonwinner to be a winner

The Complexity of Computing the Size of an Interval

Given a p-order A over a universe of strings (i.e., a transitive, reflexive, antisymmetric relation such that if (x, y) is an element of A then |x| is polynomially bounded by |y|), an interval size function of A returns, for each string x in the universe, the number of strings in the interval between strings b(x) and t(x) (with respect to A), where b(x) and t(x) are functions that are polynomial-time computable in the length of x. By choosing sets of interval size functions based on feasibility requirements for their underlying p-orders, we obtain new characterizations of complexity classes. We prove that the set of all interval size functions whose underlying p-orders are polynomial-time decidable is exactly #P. We show that the interval size functions for orders with polynomial-time adjacency checks are closely related to the class FPSPACE(poly). Indeed, FPSPACE(poly) is exactly the class of all nonnegative functions that are an interval size function minus a polynomial-time computable function. We study two important functions in relation to interval size functions. The function #DIV maps each natural number n to the number of nontrivial divisors of n. We show that #DIV is an interval size function of a polynomial-time decidable partial p-order with polynomial-time adjacency checks. The function #MONSAT maps each monotone boolean formula F to the number of satisfying assignments of F. We show that #MONSAT is an interval size function of a polynomial-time decidable total p-order with polynomial-time adjacency checks. Finally, we explore the related notion of cluster computation.Comment: This revision fixes a problem in the proof of Theorem 9.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have \u3e21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph

Asymmetric magnetic proximity interactions in MoSe2_{2}/CrBr3_{3} van der Waals heterostructures

Magnetic proximity interactions (MPIs) between atomically-thin semiconductors and two-dimensional magnets provide a means to manipulate spin and valley degrees of freedom in nonmagnetic monolayers, without the use of applied magnetic fields. In such van der Waals (vdW) heterostructures, MPIs originate in the nanometer-scale coupling between the spin-dependent electronic wavefunctions in the two materials, and typically their overall effect is regarded as an effective magnetic field acting on the semiconductor monolayer. Here we demonstrate that this picture, while appealing, is incomplete: The effects of MPIs in vdW heterostructures can be markedly asymmetric, in contrast to that from an applied magnetic field. Valley-resolved optical reflection spectroscopy of MoSe$_{2}$/CrBr$_{3}$ vdW structures reveals strikingly different energy shifts in the $K$ and $K'$ valleys of the MoSe$_2$, due to ferromagnetism in the CrBr$_3$ layer. Strong asymmetry is observed at both the A- and B-exciton resonances. Density-functional calculations indicate that valley-asymmetric MPIs depend sensitively on the spin-dependent hybridization of overlapping bands, and as such are likely a general feature of such hybrid vdW structures. These studies suggest routes to selectively control \textit{specific} spin and valley states in monolayer semiconductors.Comment: 12 pages total (including 4 figures + 7 Supplemental Figures

The Secreted Proteins of \u3cem\u3eAchlya hypogyna\u3c/em\u3e and \u3cem\u3eThraustotheca clavata\u3c/em\u3e Identify the Ancestral Oomycete Secretome and Reveal Gene Acquisitions by Horizontal Gene Transfer

Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the “secretome” and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here,we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle

Novel use Of Hydroxyurea in an African Region with Malaria (NOHARM): a trial for children with sickle cell anemia

Hydroxyurea treatment is recommended for children with sickle cell anemia (SCA) living in high-resource malaria-free regions, but its safety and efficacy in malaria-endemic sub-Saharan Africa, where the greatest sickle-cell burden exists, remain unknown. In vitro studies suggest hydroxyurea could increase malaria severity, and hydroxyurea-associated neutropenia could worsen infections. NOHARM (Novel use Of Hydroxyurea in an African Region with Malaria) was a randomized, double-blinded, placebo-controlled trial conducted in malaria-endemic Uganda, comparing hydroxyurea to placebo at 20 ± 2.5 mg/kg per day for 12 months. The primary outcome was incidence of clinical malaria. Secondary outcomes included SCA-related adverse events (AEs), clinical and laboratory effects, and hematological toxicities. Children received either hydroxyurea (N = 104) or placebo (N = 103). Malaria incidence did not differ between children on hydroxyurea (0.05 episodes per child per year; 95% confidence interval [0.02, 0.13]) vs placebo (0.07 episodes per child per year [0.03, 0.16]); the hydroxyurea/placebo malaria incidence rate ratio was 0.7 ([0.2, 2.7]; P = .61). Time to infection also did not differ significantly between treatment arms. A composite SCA-related clinical outcome (vaso-occlusive painful crisis, dactylitis, acute chest syndrome, splenic sequestration, or blood transfusion) was less frequent with hydroxyurea (45%) than placebo (69%; P = .001). Children receiving hydroxyurea had significantly increased hemoglobin concentration and fetal hemoglobin, with decreased leukocytes and reticulocytes. Serious AEs, sepsis episodes, and dose-limiting toxicities were similar between treatment arms. Three deaths occurred (2 hydroxyurea, 1 placebo, and none from malaria). Hydroxyurea treatment appears safe for children with SCA living in malaria-endemic sub-Saharan Africa, without increased severe malaria, infections, or AEs. Hydroxyurea provides SCA-related laboratory and clinical efficacy, but optimal dosing and monitoring regimens for Africa remain undefined. This trial was registered at www.clinicaltrials.gov as #NCT01976416

The RESET tephra database and associated analytical tools

An open-access database has been set up to support the research project study- ing the ‘Response of Humans to Abrupt Environmental Transitions’ (RESET). The main methodology underlying this project was to use tephra layers to tie together and synchronise the chronologies of stratigraphic records at archaeological and envi- ronmental sites. The database has information on occurrences, and chemical compo- sitions, of glass shards from tephra and cryptotephra deposits found across Europe. The data includes both information from the RESET project itself and from the published literature. With over 12,000 major element analyses and over 3000 trace element analyses on glass shards, relevant to 80 late Quaternary eruptions, the RESET project has generated an important archive of data. When added to the published information, the database described here has a total of more than 22,000 major element analyses and nearly 4000 trace element analyses on glass from over 240 eruptions. In addition to the database and its associated data, new methods of data analysis for assessing correlations have been developed as part of the project. In particular an approach using multi-dimensional kernel density estimates to evaluate the likelihood of tephra compositions matching is described here and tested on data generated as part of the RESET project.</p