Precise Measures of Orbital Period, Before and After Nova Eruption for QZ Aurigae

For the ordinary classical nova QZ Aurigae (which erupted in 1964), we report 1317 magnitudes from 1912--2016, including four eclipses detected on archival photographic plates from long before the eruption. We have accurate and robust measures of the orbital period both pre-eruption and post-eruption, and we find that the orbital period decreased, with a fractional change of -290.71+-0.28 parts-per-million across the eruption, with the orbit necessarily getting smaller. Further, we find that the light curve outside of eclipses and eruption is flat at near B=17.14 from 1912--1981, whereupon the average light curve starts fading down to B=17.49 with large variability. QZ Aur is a robust counter-example against the Hibernation model for the evolution of cataclysmic variables, where the model requires that all novae have their period increase across eruptions. Large period decreases across eruptions can easily arise from mass imbalances in the ejecta, as are commonly seen in asymmetric nova shells.Comment: MNRAS in press, 24 pages, 5 tables, 6 figure

Inference of population splits and mixtures from genome-wide allele frequency data

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.comComment: 28 pages, 6 figures in main text. Attached supplement is 22 pages, 15 figures. This is an updated version of the preprint available at http://precedings.nature.com/documents/6956/version/

Testing for the Dual-Route Cascade Reading Model in the Brain: An fMRI Effective Connectivity Account of an Efficient Reading Style

Neuropsychological data about the forms of acquired reading impairment provide a strong basis for the theoretical framework of the dual-route cascade (DRC) model which is predictive of reading performance. However, lesions are often extensive and heterogeneous, thus making it difficult to establish precise functional anatomical correlates. Here, we provide a connective neural account in the aim of accommodating the main principles of the DRC framework and to make predictions on reading skill. We located prominent reading areas using fMRI and applied structural equation modeling to pinpoint distinct neural pathways. Functionality of regions together with neural network dissociations between words and pseudowords corroborate the existing neuroanatomical view on the DRC and provide a novel outlook on the sub-regions involved. In a similar vein, congruent (or incongruent) reliance of pathways, that is reliance on the word (or pseudoword) pathway during word reading and on the pseudoword (or word) pathway during pseudoword reading predicted good (or poor) reading performance as assessed by out-of-magnet reading tests. Finally, inter-individual analysis unraveled an efficient reading style mirroring pathway reliance as a function of the fingerprint of the stimulus to be read, suggesting an optimal pattern of cerebral information trafficking which leads to high reading performance

The complete genome sequence of a Neandertal from the Altai Mountains

We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans

A Search for TeV Gamma-ray Emission from the PSR B1259-63/SS2883 Binary System with the CANGAROO-II 10-m Telescope

Observations of the PSR B1259-63/SS2883 binary system using the CANGAROO-II Cherenkov telescope are reported. This nearby binary consists of a 48msec radio pulsar in a highly eccentric orbit around a Be star, and offers a unique laboratory to investigate the interactions between the outflows of the pulsar and Be star at various distances. It has been pointed out that the relativistic pulsar wind and the dense mass outflow of the Be star may result in the emission of gamma rays up to TeV energies. We have observed the binary in 2000 and 2001, 47 and 157 days after the October 2000 periastron. Upper limits at the 0.13--0.54 Crab level are obtained. A new model calculation for high-energy gamma-ray emission from the Be star outflow is introduced and the estimated gamma-ray flux considering Bremsstrahlung, inverse Compton scattering, and the decay of neutral pions produced in proton-proton interactions, is found to be comparable to the upper limits of these observations. Comparing our results with these model calculations, the mass-outflow parameters of the Be star are constrained.Comment: 29 pages, 10 figures, accepted by Ap

Pulsations, Boundary Layers, and Period Bounce in the Cataclysmic Variable RE J1255+266

We report time-series photometry of the quiescent optical counterpart of the EUV transient RE J1255+266. The star appears as a DA white dwarf with bright emission lines and a complex spectrum of periodic signals in its light curve. A signal at 0.0829 d is likely to be the orbital period of the underlying cataclysmic binary (probably a dwarf nova). Characteristic periods of 1344, 1236, and 668 s are seen, and a host of weaker signals. We interpret these noncommensurate signals as (nonradial) pulsation periods of the white dwarf. The donor star is unseen at all wavelengths, and the accretion rate is very low. We estimate a distance of 180+-50 pc, and M_v=14.6+-1.3 for the accretion light. The binary probably represents a very late stage of evolution, with the donor star whittled down to M_2<0.05 M_sol. Such binaries stubbornly resist discovery due to their faintness and reluctance to erupt, but are probably a very common type of cataclysmic variable. If the signal at 0.0829 d is indeed the orbital period, then the binary is an excellent candidate as a "period bouncer". Plausible colleagues in this club include four dwarf novae and the (so far) noneruptive stars GD 552 and 1RXS J105010.3-140431 (hereafter RX 1050). The 1994 EUV eruption implies a soft X-ray/EUV luminosity of 10^(34-35) erg/s, greater than that of any other dwarf nova. We attribute that to a favorable blend of properties: a high-mass white dwarf; a very transparent line of sight (the "Local Chimney"); and a low binary inclination. The first maximizes the expected temperature and luminosity of boundary-layer emission; the other two increase the likelihood that soft X-rays can survive their perilous passage through an accretion-disk wind and the interstellar medium.Comment: PDF, 43 pages, 5 tables, 10 figures, 1 appendix; accepted, in press, to appear May 2005, PASP; more info at http://cba.phys.columbia.edu

Substrate Specifity Profiling of the Aspergillus fumigatus Proteolytic Secretome Reveals Consensus Motifs with Predominance of Ile/Leu and Phe/Tyr

The filamentous fungus Aspergillus fumigatus (AF) can cause devastating infections in immunocompromised individuals. Early diagnosis improves patient outcomes but remains challenging because of the limitations of current methods. To augment the clinician's toolkit for rapid diagnosis of AF infections, we are investigating AF secreted proteases as novel diagnostic targets. The AF genome encodes up to 100 secreted proteases, but fewer than 15 of these enzymes have been characterized thus far. Given the large number of proteases in the genome, studies focused on individual enzymes may overlook potential diagnostic biomarkers.As an alternative, we employed a combinatorial library of internally quenched fluorogenic probes (IQFPs) to profile the global proteolytic secretome of an AF clinical isolate in vitro. Comparative protease activity profiling revealed 212 substrate sequences that were cleaved by AF secreted proteases but not by normal human serum. A central finding was that isoleucine, leucine, phenylalanine, and tyrosine predominated at each of the three variable positions of the library (44.1%, 59.1%, and 57.0%, respectively) among substrate sequences cleaved by AF secreted proteases. In contrast, fewer than 10% of the residues at each position of cleaved sequences were cationic or anionic. Consensus substrate motifs were cleaved by thermostable serine proteases that retained activity up to 50°C. Precise proteolytic cleavage sites were reliably determined by a simple, rapid mass spectrometry-based method, revealing predominantly non-prime side specificity. A comparison of the secreted protease activities of three AF clinical isolates revealed consistent protease substrate specificity fingerprints. However, secreted proteases of A. flavus, A. nidulans, and A. terreus strains exhibited striking differences in their proteolytic signatures.This report provides proof-of-principle for the use of protease substrate specificity profiling to define the proteolytic secretome of Aspergillus fumigatus. Expansion of this technique to protease secretion during infection could lead to development of novel approaches to fungal diagnosis

Adenovirus-5-Vectored P. falciparum Vaccine Expressing CSP and AMA1. Part B: Safety, Immunogenicity and Protective Efficacy of the CSP Component

Background: A protective malaria vaccine will likely need to elicit both cell-mediated and antibody responses. As adenovirus vaccine vectors induce both these responses in humans, a Phase 1/2a clinical trial was conducted to evaluate the efficacy of an adenovirus serotype 5-vectored malaria vaccine against sporozoite challenge.\ud \ud Methodology/Principal Findings: NMRC-MV-Ad-PfC is an adenovirus vector encoding the Plasmodium falciparum 3D7 circumsporozoite protein (CSP). It is one component of a two-component vaccine NMRC-M3V-Ad-PfCA consisting of one adenovector encoding CSP and one encoding apical membrane antigen-1 (AMA1) that was evaluated for safety and immunogenicity in an earlier study (see companion paper, Sedegah et al). Fourteen Ad5 seropositive or negative adults received two doses of NMRC-MV-Ad-PfC sixteen weeks apart, at 1x1010 particle units per dose. The vaccine was safe and well tolerated. All volunteers developed positive ELISpot responses by 28 days after the first immunization (geometric mean 272 spot forming cells/million[sfc/m]) that declined during the following 16 weeks and increased after the second dose to levels that in most cases were less than the initial peak (geometric mean 119 sfc/m). CD8+ predominated over CD4+ responses, as in the first clinical trial. Antibody responses were poor and like ELISpot responses increased after the second immunization but did not exceed the initial peak. Pre-existing neutralizing antibodies (NAb) to Ad5 did not affect the immunogenicity of the first dose, but the fold increase in NAb induced by the first dose was significantly associated with poorer antibody responses after the second dose, while ELISpot responses remained unaffected. When challenged by the bite of P. falciparum-infected mosquitoes, two of 11 volunteers showed a delay in the time to patency compared to infectivity controls, but no volunteers were sterilely protected.\ud \ud Significance: The NMRC-MV-Ad-PfC vaccine expressing CSP was safe and well tolerated given as two doses, but did not provide sterile protection