So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity

System identification algorithms for the analysis of dielectric responses from broadband spectroscopies

We discuss the modeling of dielectric responses for an electromagnetically excited network of capacitors and resistors using a systems identification framework. Standard models that assume integral order dynamics are augmented to incorporate fractional order dynamics. This enables us to relate more faithfully the modeled responses to those reported in the Dielectrics literature

Estimated workload intensity during volunteer aquarium dives

Background: This study aimed to characterize the physiological demands of working dives on volunteer divers at a public aquarium in the USA. Aims: To estimate the workloads associated with volunteer dives in a US aquarium. Methods: Participants completed a medical and diving history questionnaire. Measurements included blood pressure before and after diving and continuous ECG (Holter) monitoring during diving. Dive profiles were recorded using loggers. Mean workload was estimated from total air consumption. Results Twenty-seven divers recorded 49 air dives over 5 days. Two-thirds were male and ages ranged from 40 to 78 years. Typically, each diver made two dives with a 30-60 min surface interval. Mean heart rate while diving was 100 beats per minute (bpm). Mean estimated workload during the dives recorded during this study was 5.8 metabolic equivalents (METS), with a range from 4.1 to 10.5. The highest mean recorded heart rate was 120 bpm over 40 min, vacuuming the floor in the shark exhibit. Conclusions: Given the mean age of this sample and the prevalence of cardiovascular risk factors (body mass index, high cholesterol and hypertension), it may be prudent for aquariums to regularly monitor SAC/kg and heart rate in volunteer divers, to identify which tasks require the highest workload intensity. Divers with existing cardiovascular risk factors might then be employed in dives with lighter workloads. In conclusion, volunteer dives at this aquarium required a mean workload intensity that was described by recreational divers as moderate. The highest workload, at 10 METS for 23 min, would be considered by many recreational divers as exhausting

Premature mortality in refractory partial epilepsy: does surgical treatment make a difference?

Background: Epilepsy carries an increased risk of premature death. For some people with intractable focal epilepsy, surgery offers hope for a seizure-free life. The authors aimed to see whether epilepsy surgery influenced mortality in people with intractable epilepsy. Methods: The authors audited survival status in two cohorts (those who had surgery and those who had presurgical assessment but did not have surgery). Results: There were 40 known deaths in the non-surgical group (3365 person years of follow-up) and 19 in the surgical group (3905 person-years of follow-up). Non-operated patients were 2.4 times (95% CI 1.4 to 4.2) as likely to die as those who had surgery. They were 4.5 times (95% CI 1.9 to 10.9) as likely to die a probable epilepsy-related death. In the surgical group, those with ongoing seizures 1 year after surgery were 4.0 (95% CI 1.2 to 13.7) times as likely to die as those who were seizure-free or who had only simple partial seizures. Time-dependent Cox analysis showed that the yearly outcome group did not significantly affect mortality (HR 1.3, 95% CI 0.9 to 1.8). Conclusion: Successful epilepsy surgery was associated with a reduced risk of premature mortality, compared with those with refractory focal epilepsy who did not have surgical treatment. To some extent, the reduced mortality is likely to be conferred by inducing freedom from seizures. It is not certain whether better survival is attributable only to surgery, as treatment decisions were not randomised, and there may be inherent differences between the groups.<br/

High signal to noise ratio THz spectroscopy with ASOPS and signal processing schemes for mapping and controlling molecular and bulk relaxation processes

Asynchronous Optical Sampling has the potential to improve signal to noise ratio in THz transient sperctrometry. The design of an inexpensive control scheme for synchronising two femtosecond pulse frequency comb generators at an offset frequency of 20 kHz is discussed. The suitability of a range of signal processing schemes adopted from the Systems Identification and Control Theory community for further processing recorded THz transients in the time and frequency domain are outlined. Finally, possibilities for femtosecond pulse shaping using genetic algorithms are mentioned

The potential impact of orange-fleshed sweetpotatoes on vitamin A intake in Sub-Saharan Africa.

A recent ex ante impact assessment indicates that orangefleshed sweetpotatoes can make a major contribution to alleviating vitamin A malnutrition in Sub-Saharan Africa. Replacing the white-fleshed varieties now grown by farmers with new high ß-carotene cultivars that meet local preferences would benefit an estimated 50 million children under age 6 who are currently at risk. The majority of children in Burundi, Rwanda and Uganda would benefit, as would about half of the children in Tanzania. Children in Ethiopia, Kenya and South Africa would also be affected, though to a lesser degree. The study did not take into account the benefits of the new cultivars to pregnant and lactating women, a population whose health is also likely to improve from the availability of the new plant types. Vitamin A deficiency is a major public health problem throughout the region and is responsible for tens of thousands of deaths annually among young children

Lockin to Weak Ferromagnetism in TbNi2B2C and ErNi2B2C

This article describes a model in which ferromagnetism necessarily accompanies a spin-density-wave lockin transition in the borocarbide structure provided the commensurate phase wave vector satisfies Q = (m/n)a* with m even and n odd. The results account for the magnetic properties of TbNi2B2C, and are also possibly relevant also for those of ErNi2B2C.Comment: 4 page

Etching of random solids: hardening dynamics and self-organized fractality

When a finite volume of an etching solution comes in contact with a disordered solid, a complex dynamics of the solid-solution interface develops. Since only the weak parts are corroded, the solid surface hardens progressively. If the etchant is consumed in the chemical reaction, the corrosion dynamics slows down and stops spontaneously leaving a fractal solid surface, which reveals the latent percolation criticality hidden in any random system. Here we introduce and study, both analytically and numerically, a simple model for this phenomenon. In this way we obtain a detailed description of the process in terms of percolation theory. In particular we explain the mechanism of hardening of the surface and connect it to Gradient Percolation.Comment: Latex, aipproc, 6 pages, 3 figures, Proceedings of 6th Granada Seminar on Computational Physic