ASU Scholarship Showcase

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

For more than 80 years, Proconsul has held a pivotal position in interpretations of catarrhine evolution in East Africa. From early hypotheses of phyletic relationships with modern apes to more recent debates over their position within Hominoidea, the well-preserved fossils of this genus have been a foundation for most evolutionary scenarios regarding the early diversification of hominoids. The majority of what we "know" about Proconsul, however, derives from abundant younger fossils found at the Kisingiri localities on Rusinga and Mfangano Islands rather than from the smaller samples found at Koru – the locality of the type species, Proconsul africanus – and other Tinderet deposits. One outcome of this is seen in recent attempts to expand the genus "Ugandapithecus" (considered here a junior subjective synonym of Proconsul), wherein much of the Tinderet sample was referred to that genus based primarily on differentiating it from the Kisingiri specimens rather than from the type species, P. africanus. This and other recent taxonomic revisions to Proconsul prompted us to undertake a systematic review of dentognathic specimens attributed to this taxon. Results of our study underscore and extend the substantive distinction of Tinderet and Ugandan Proconsul (i.e., Proconsul sensu stricto) from the Kisingiri fossils, the latter recognized here as a new genus. Specimens of the new genus are readily distinguished from Proconsul sensu stricto by morphology preserved in the P. africanus holotype, M 14084, but also in I1s, lower incisors, upper and lower canines, and especially mandibular characteristics. A number of these differences are more advanced among Kisingiri specimens in the direction of crown hominoids. Proconsul sensu stricto is characterized by a suite of unique features that strongly unite the included species as a clade. There have been decades of contentious debate over the phylogenetic placement of Proconsul (sensu lato), due in part to there being a mixture of primitive and more advanced morphology within the single genus. By recognizing two distinct clades that, in large part, segregate these character states, we believe that better phylogenetic resolution can be achieved.

Background: Ebola is one of the most virulent human viral diseases, with a case fatality ratio between 25% to 90%. The 2014 West African outbreaks are the largest and worst in history. There is no specific treatment or effective/safe vaccine against the disease. Hence, control efforts are restricted to basic public health preventive (non-pharmaceutical) measures. Such efforts are undermined by traditional/cultural belief systems and customs, characterized by general mistrust and skepticism against government efforts to combat the disease. This study assesses the roles of traditional customs and public healthcare systems on the disease spread.

Methods: A mathematical model is designed and used to assess population-level impact of basic non-pharmaceutical control measures on the 2014 Ebola outbreaks. The model incorporates the effects of traditional belief systems and customs, along with disease transmission within health-care settings and by Ebola-deceased individuals. A sensitivity analysis is performed to determine model parameters that most affect disease transmission. The model is parameterized using data from Guinea, one of the three Ebola-stricken countries. Numerical simulations are performed and the parameters that drive disease transmission, with or without basic public health control measures, determined. Three effectiveness levels of such basic measures are considered.

Results: The distribution of the basic reproduction number (R_0) for Guinea (in the absence of basic control measures) is such that R_ 0 ∈ [0.77,1.35], for the case when the belief systems do not result in more unreported Ebola cases. When such systems inhibit control efforts, the distribution increases to R_ 0 ∈ [1.15,2.05]. The total Ebola cases are contributed by Ebola-deceased individuals (22%), symptomatic individuals in the early (33%) and latter (45%) infection stages. A significant reduction of new Ebola cases can be achieved by increasing health-care workers’ daily shifts from 8 to 24 hours, limiting hospital visitation to 1 hour and educating the populace to abandon detrimental traditional/cultural belief systems.

Conclusions: The 2014 outbreaks are controllable using a moderately-effective basic public health intervention strategy alone. A much higher (>50%) disease burden would have been recorded in the absence of such intervention.

Background:
Pandemic influenza is said to 'shift mortality' to younger age groups; but also to spare a subpopulation of the elderly population. Does one of these effects dominate? Might this have important ramifications?

Methods: We estimated age-specific excess mortality rates for all-years for which data were available in the 20th century for Australia, Canada, France, Japan, the UK, and the USA for people older than 44 years of age. We modeled variation with age, and standardized estimates to allow direct comparison across age groups and countries. Attack rate data for four pandemics were assembled.

Results: For nearly all seasons, an exponential model characterized mortality data extremely well. For seasons of emergence and a variable number of seasons following, however, a subpopulation above a threshold age invariably enjoyed reduced mortality. 'Immune escape', a stepwise increase in mortality among the oldest elderly, was observed a number of seasons after both the A(H2N2) and A(H3N2) pandemics. The number of seasons from emergence to escape varied by country. For the latter pandemic, mortality rates in four countries increased for younger age groups but only in the season following that of emergence. Adaptation to both emergent viruses was apparent as a progressive decrease in mortality rates, which, with two exceptions, was seen only in younger age groups. Pandemic attack rate variation with age was estimated to be similar across four pandemics with very different mortality impact.

Conclusions: In all influenza pandemics of the 20th century, emergent viruses resembled those that had circulated previously within the lifespan of then-living people. Such individuals were relatively immune to the emergent strain, but this immunity waned with mutation of the emergent virus. An immune subpopulation complicates and may invalidate vaccine trials. Pandemic influenza does not 'shift' mortality to younger age groups; rather, the mortality level is reset by the virulence of the emerging virus and is moderated by immunity of past experience. In this study, we found that after immune escape, older age groups showed no further mortality reduction, despite their being the principal target of conventional influenza vaccines. Vaccines incorporating variants of pandemic viruses seem to provide little benefit to those previously immune. If attack rates truly are similar across pandemics, it must be the case that immunity to the pandemic virus does not prevent infection, but only mitigates the consequences.

One argument used by detractors of human embryonic stem cell research (hESCR) invokes Kant's formula of humanity, which proscribes treating persons solely as a means to an end, rather than as ends in themselves. According to Fuat S. Oduncu, for example, adhering to this imperative entails that human embryos should not be disaggregated to obtain pluripotent stem cells for hESCR. Given that human embryos are Kantian persons from the time of their conception, killing them to obtain their cells for research fails to treat them as ends in themselves.

This argument assumes two points that are rather contentious given a Kantian framework. First, the argument assumes that when Kant maintains that humanity must be treated as an end in itself, he means to argue that all members of the species Homo sapiens must be treated as ends in themselves; that is, that Kant regards personhood as co-extensive with belonging to the species Homo sapiens. Second, the argument assumes that the event of conception is causally responsible for the genesis of a Kantian person and that, therefore, an embryo is a Kantian person from the time of its conception.

In this paper, I will present challenges against these two assumptions by engaging in an exegetical study of some of Kant's works. First, I will illustrate that Kant did not use the term "humanity" to denote a biological species, but rather the capacity to set ends according to reason. Second, I will illustrate that it is difficult given a Kantian framework to denote conception (indeed any biological event) as causally responsible for the creation of a person. Kant ascribed to a dualistic view of human agency, and personhood, according to him, was derived from the supersensible capacity for reason. To argue that a Kantian person is generated due to the event of conception ignores Kant's insistence in various aspects of his work that it is not possible to understand the generation of a person qua a physical operation. Finally, I will end the paper by drawing from Allen Wood's work in Kantian philosophy in order to generate an argument in favor of hESCR.

The per-capita growth rate of a species is influenced by density-independent, positive and negative density-dependent factors. These factors can lead to nonlinearity with a consequence that species may process multiple nontrivial equilibria in its single state (e.g., Allee effects). This makes the study of permanence of discrete-time multi-species population models very challenging due to the complex boundary dynamics. In this paper, we explore the permanence of a general discrete-time two-species-interaction model with nonlinear per-capita growth rates for the first time. We find a simple sufficient condition for guaranteeing the permanence of the system by applying and extending the ecological concept of the relative nonlinearity to estimate systems' external Lyapunov exponents. Our method allows us to fully characterize the effects of nonlinearities in the per-capita growth functions and implies that the fluctuated populations may devastate the permanence of systems and lead to multiple attractors. These results are illustrated with specific two species competition and predator-prey models with generic nonlinear per-capita growth functions. Finally, we discuss the potential biological implications of our results.

We calculate the electron self-energy in a magnetized QED plasma to the leading perturbative order in the coupling constant and to the linear order in an external magnetic field. We find that the chiral asymmetry of the normal ground state of the system is characterized by two new Dirac structures. One of them is the familiar chiral shift previously discussed in the Nambu-Jona-Lasinio model. The other structure is new. It formally looks like that of the chiral chemical potential but is an odd function of the longitudinal component of the momentum, directed along the magnetic field. The origin of this new parity-even chiral structure is directly connected with the long-range character of the QED interaction. The form of the Fermi surface in the weak magnetic field is determined.

We calculate the leading radiative corrections to the axial current in the chiral separation effect in dense QED in a magnetic field. Contrary to the conventional wisdom suggesting that the axial current should be exactly fixed by the chiral anomaly relation and is described by the topological contribution on the lowest Landau level in the free theory, we find in fact that the axial current receives nontrivial radiative corrections. The direct calculations performed to the linear order in the external magnetic field show that the nontrivial radiative corrections to the axial current are provided by the Fermi surface singularity in the fermion propagator at nonzero fermion density.

Recently fabricated two-dimensional phosphorene crystal structures have demonstrated great potential in applications of electronics. In this paper, strain effect on the electronic band structure of phosphorene was studied using first-principles methods including density functional theory (DFT) and hybrid functionals. It was found that phosphorene can withstand a tensile stress and strain up to 10 N/m and 30%, respectively. The band gap of phosphorene experiences a direct-indirect-direct transition when axial strain is applied. A moderate −2% compression in the zigzag direction can trigger this gap transition. With sufficient expansion (+11.3%) or compression (−10.2% strains), the gap can be tuned from indirect to direct again. Five strain zones with distinct electronic band structure were identified, and the critical strains for the zone boundaries were determined. Although the DFT method is known to underestimate band gap of semiconductors, it was proven to correctly predict the strain effect on the electronic properties with validation from a hybrid functional method in this work. The origin of the gap transition was revealed, and a general mechanism was developed to explain energy shifts with strain according to the bond nature of near-band-edge electronic orbitals. Effective masses of carriers in the armchair direction are an order of magnitude smaller than that of the zigzag axis, indicating that the armchair direction is favored for carrier transport. In addition, the effective masses can be dramatically tuned by strain, in which its sharp jump/drop occurs at the zone boundaries of the direct-indirect gap transition.