Is the number of species on earth increasing or decreasing? Time, chaos and the origin of species

Darwin's On the Origin of Species has led to a theory of evolution with a mass of empirical detail on population genetics below species level, together with heated debate on the details of macroevolutionary patterns above species level. Most of the main principles are clear and generally accepted, notably that life originated once and has evolved over time by descent with modification. Here, I review the fossil and molecular phylogenetic records of the response of life on Earth to Quaternary climatic changes. I suggest that the record can be best understood in terms of the nonlinear dynamics of the relationship between genotype and phenotype, and between climate and environments. 'The origin of species' is essentially unpredictable, but is nevertheless an inevitable consequence of the way that organisms reproduce through time. The process is 'chaotic', but not 'random'. I suggest that biodiversity is best considered as continuously branching systems of lineages, where 'species' are the branch tips. The Earth's biodiversity should thus (1) be in a state of continuous increase and (2) show continuous discrepancies between genetic and morphological data in time and space. © The Palaeontological Association.

Glycation, glycoxidation, and cross-linking of collagen by glucose. Kinetics, mechanisms, and inhibition of late stages of the Maillard reaction

The Maillard or browning reaction between sugar and protein contributes to the increased chemical modification and cross-linking of long-lived tissue proteins in diabetes. To evaluate the role of glycation and oxidation in these reactions, we have studied the effects of oxidative and antioxidative conditions and various types of inhibitors on the reaction of glucose with rat tail tendon collagen in phosphate buffer at physiological pH and temperature. The chemical modifications of collagen that were measured included fructoselysine, the glycoxidation products N epsilon-(carboxymethyl)lysine and pentosidine and fluorescence. Collagen cross-linking was evaluated by analysis of cyanogen bromide peptides using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by changes in collagen solubilization on treatment with pepsin or sodium dodecylsulfate. Although glycation was unaffected, formation of glycoxidation products and cross-linking of collagen were inhibited by antioxidative conditions. The kinetics of formation of glycoxidation products proceeded with a short lag phase and were independent of the amount of Amadori adduct on the protein, suggesting that autoxidative degradation of glucose was a major contributor to glycoxidation and cross-linking reactions. Chelators, sulfhydryl compounds, antioxidants, and aminoguanidine also inhibited formation of glycoxidation products, generation of fluorescence, and cross-linking of collagen without significant effect on the extent of glycation of the protein. We conclude that autoxidation of glucose or Amadori compounds on protein plays a major role in the formation of glycoxidation products and cross-liking of collagen by glucose in vitro and that chelators, sulfhydryl compounds, antioxidants, and aminoguanidine act as uncouplers of glycation from subsequent glycoxidation and cross-linking reactions.

Multi-epoch high-resolution spectroscopy of SN2011fe - Linking the progenitor to its environment

This study attempts to establish a link between the reasonably well known nature of the progenitor of SN2011fe and its surrounding environment. This is done with the aim of enabling the identification of similar systems in the vast majority of the cases, when distance and epoch of discovery do not allow a direct approach. To study the circumstellar environment of SN2011fe we have obtained high-resolution spectroscopy of SN2011fe on 12 epochs, from 8 to 86 days after the estimated date of explosion, targeting in particular at the time evolution of CaII and NaI. Three main absorption systems are identified from CaII and NaI, one associated to the Milky Way, one probably arising within a high-velocity cloud, and one most likely associated to the halo of M101. The Galactic and host galaxy reddening, deduced from the integrated equivalent widths (EW) of the NaI lines are E(B-V)=0.011+/-0.002 and E(B-V)=0.014+/-0.002 mag, respectively. The host galaxy absorption is dominated by a component detected at the same velocity measured from the 21-cm HI line at the projected SN position (~180 km/s). During the ~3 months covered by our observations, its EW changed by 15.6+/-6.5 mA. This small variation is shown to be compatible with the geometric effects produced by therapid SN photosphere expansion coupled to the patchy fractal structure of the ISM. The observed behavior is fully consistent with ISM properties similar to those derived for our own Galaxy, with evidences for structures on scales

Clicking Well-Defined Biodegradable Nanoparticles and Nanocapsules by UV-Induced Thiol-Ene Cross-Linking in Transparent Miniemulsions

A novel approach for the preparation of nanomaterials is developed by tuning miniemulsion reaction systems to be transparent in order to enable highly efficient photoreactions. Biodegradable nanoparticles and nanocapsules are obtained by UV-induced thiol-ene cross-linking of polylactide (PLA)-based precursor polymers preassembled in transparent miniemulsions. These well-defined nanomaterials may potentially serve as ideal scaffolds for drug delivery.

Modification of the formation of high-Mach number electrostatic shock-like structures by the ion acoustic instability

The formation of unmagnetized electrostatic shock-like structures with a high Mach number is examined with one- and two-dimensional particle-in-cell (PIC) simulations. The structures are generated through the collision of two identical plasma clouds, which consist of equally hot electrons and ions with a mass ratio of 250. The Mach number of the collision speed with respect to the initial ion acoustic speed of the plasma is set to 4.6. This high Mach number delays the formation of such structures by tens of inverse ion plasma frequencies. A pair of stable shock-like structures is observed after this time in the 1D simulation, which gradually evolve into electrostatic shocks. The ion acoustic instability, which can develop in the 2D simulation but not in the 1D one, competes with the nonlinear process that gives rise to these structures. The oblique ion acoustic waves fragment their electric field. The transition layer, across which the bulk of the ions change their speed, widens and their speed change is reduced. Double layer-shock hybrid structures develop.

Impact of the number of users on error probabilities in multiuser diversity systems

Multiuser diversity gain has been investigated well in terms of a system capacity formulation in the literature. In practice, however, designs on multiuser systems with nonzero error rates require a relationship between the error rates and the number of users within a cell. Considering a best-user scheduling, where the user with the best channel condition is scheduled to transmit per scheduling interval, our focus is on the uplink. We assume that each user communicates with the base station through a single-input multiple-output channel. We derive a closed-form expression for the average BER, and analyze how the average BER goes to zero asymptotically as the number of users increases for a given SNR. Note that the analysis of average BER even in SI SO multiuser diversity systems has not been done with respect to the number of users for a given SNR. Our analysis can be applied to multiuser diversity systems with any number of antennas.

Dynamical symmetry breaking with optimal control: Reducing the number of pieces

We analyze the production of defects during the dynamical crossing of a mean-field phase transition with a real order parameter. When the parameter that brings the system across the critical point changes in time according to a power-law schedule, we recover the predictions dictated by the well-known Kibble-Zurek theory. For a fixed duration of the evolution, we show that the average number of defects can be drastically reduced for a very large but finite system, by optimizing the time dependence of the driving using optimal control techniques. Furthermore, the optimized protocol is robust against small fluctuations.

Prior Autoimmune Disease and Risk of Monoclonal Gammopathy of Undetermined Significance and Multiple Myeloma:A Systematic Review

Background: Several observational studies have investigated autoimmune disease and subsequent risk of monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma. Findings have been largely inconsistent and hindered by the rarity and heterogeneity of the autoimmune disorders investigated. A systematic review of the literature was undertaken to evaluate the strength of the evidence linking prior autoimmune disease and risk of MGUS/multiple myeloma.

Methods: A broad search strategy using key terms for MGUS, multiple myeloma, and 50 autoimmune diseases was used to search four electronic databases (PubMed, Medline, Embase, and Web of Science) from inception through November 2011.

Results: A total of 52 studies met the inclusion criteria, of which 32 were suitably comparable to perform a meta-analysis. “Any autoimmune disorder” was associated with an increased risk of both MGUS [n = 760 patients; pooled relative risk (RR) 1.42; 95% confidence interval (CI), 1.14–1.75] and multiple myeloma (n>2,530 patients; RR 1.13, 95% CI, 1.04–1.22). This risk was disease dependent with only pernicious anemia showing an increased risk of both MGUS (RR 1.67; 95% CI, 1.21–2.31) and multiple myeloma (RR 1.50; 95% CI, 1.25–1.80).

Conclusions: Our findings, based on the largest number of autoimmune disorders and patients with MGUS/multiple myeloma reported to date, suggest that autoimmune diseases and/or their treatment may be important in the etiology of MGUS/multiple myeloma. The strong associations observed for pernicious anemia suggest that anemia seen in plasma cell dyscrasias may be of autoimmune origin.

Impact: Underlying mechanisms of autoimmune diseases, general immune dysfunction, and/or treatment of autoimmune diseases may be important in the pathogenesis of MGUS/multiple myeloma. Cancer Epidemiol Biomarkers Prev; 23(2); 332–42. ©2014 AACR.

Linking response strategies adopted by construction firms during the 2007 economic recession to Porter’s generic strategies

The time period bridging the years 2007 to 2012 will be remembered as one characterised by dramatic changes in the Irish and UK construction industries. Construction companies witnessed unprecedented changes in the environment, namely the coincidence of a sharp economic downturn, the significant decline of public works, a reduction in lending, increased competition, and structural changes in the marketplace. Nevertheless, little has been documented on what response strategies construction companies adopt as a result of an economic recession. Based on four exploratory case studies, a taxonomy framework of the response strategies adopted by Irish and UK construction companies during the 2007 economic recession was developed relative to Porter’s (1980) generic strategies of cost leadership, differentiation, and focus. Porter’s model (1980) is a well known theoretical framework among business strategists and industrial economists worldwide. The analysis provides strong support for the adoption of cost leadership strategies as a means to surviving the 2007 economic recession. The case studies further suggest that cost control initiatives are one of the most important attributes in companies’ responses to the 2007 recession. The findings provide valuable assistance for construction contractors in developing effective strategies and thus reducing business failures during recessionary periods.

SN 2009N: linking normal and subluminous Type II-P Sne

We present ultraviolet, optical, near-infrared photometry and spectroscopy of SN 2009N in NGC 4487. This object is a Type II-P supernova with spectra resembling those of subluminous II-P supernovae, while its bolometric luminosity is similar to that of the intermediate-luminosity SN 2008in. We created SYNOW models of the plateau phase spectra for line identification and to measure the expansion velocity. In the near-infrared spectra we find signs indicating possible weak interaction between the supernova ejecta and the pre-existing circumstellar material. These signs are also present in the previously unpublished near-infrared spectra of SN 2008in. The distance to SN 2009N is determined via the expanding photosphere method and the standard candle method as D = 21.6 ± 1.1 Mpc. The produced nickel-mass is estimated to be ∼0.020 ± 0.004 M⊙. We infer the physical properties of the progenitor at the explosion through hydrodynamical modelling of the observables. We find the values of the total energy as ∼0.48 × 1051 erg, the ejected mass as ∼11.5 M⊙, and the initial radius as ∼287 R⊙.

Linking watershed terrain and hydrology to soil chemical properties, microbial communities and impacts on soil organic C in a humid mid-latitude forested watershed

Understanding the response of humid mid-latitude forests to changes in precipitation, temperature, nutrient cycling, and disturbance is critical to improving our predictive understanding of changes in the surface-subsurface energy balance due to climate change. Mechanistic understanding of the effects of long-term and transient moisture conditions are needed to quantify
linkages between changing redox conditions, microbial activity, and soil mineral and nutrient interactions on C cycling and greenhouse gas releases. To illuminate relationships between the soil chemistry, microbial communities and organic C we established transects across hydraulic and topographic gradients in a small watershed with transient moisture conditions. Valley bottoms tend to be more frequently saturated than ridge tops and side slopes which generally are only saturated when shallow storm flow zones are active. Fifty shallow (~36”) soil cores were collected during timeframes representative of low CO2, soil winter conditions and high CO2, soil summer conditions. Cores were subdivided into 240 samples based on pedology and analyses of the geochemical (moisture content, metals, pH, Fe species, N, C, CEC, AEC) and microbial (16S rRNA gene
amplification with Illumina MiSeq sequencing) characteristics were conducted and correlated to watershed terrain and hydrology. To associate microbial metabolic activity with greenhouse gas emissions we installed 17 soil gas probes, collected gas samples for 16 months and analyzed them for CO2 and other fixed and greenhouse gasses. Parallel to the experimental efforts our data is being used to support hydrobiogeochemical process modeling by coupling the Community Land Model (CLM) with a subsurface process model (PFLOTRAN) to simulate processes and interactions from the molecular to watershed scales. Including above ground processes (biogeophysics, hydrology, and vegetation dynamics), CLM provides mechanistic water, energy, and organic matter inputs to the surface/subsurface models, in which coupled biogeochemical reaction
networks are used to improve the representation of below-ground processes. Preliminary results suggest that inclusion of above ground processes from CLM greatly improves the prediction of moisture response and water cycle at the watershed scale.