The early expansion and evolutionary dynamics of POU class genes.

The POU genes represent a diverse class of animal-specific transcription factors that play important roles in neurogenesis, pluripotency, and cell-type specification. Although previous attempts have been made to reconstruct the evolution of the POU class, these studies have been limited by a small number of representative taxa, and a lack of sequences from basally branching organisms. In this study, we performed comparative analyses on available genomes and sequences recovered through "gene fishing" to better resolve the topology of the POU gene tree. We then used ancestral state reconstruction to map the most likely changes in amino acid evolution for the conserved domains. Our work suggests that four of the six POU families evolved before the last common ancestor of living animals-doubling previous estimates-and were followed by extensive clade-specific gene loss. Amino acid changes are distributed unequally across the gene tree, consistent with a neofunctionalization model of protein evolution. We consider our results in the context of early animal evolution, and the role of POU5 genes in maintaining stem cell pluripotency

State Space Methods in Stata

We illustrate how to estimate parameters of linear state-space models using the Stata program sspace. We provide examples of how to use sspace to estimate the parameters of unobserved-component models, vector autoregressive moving-average models, and dynamic-factor models. We also show how to compute one-step, filtered, and smoothed estimates of the series and the states; dynamic forecasts and their confidence intervals; and residuals.

State Space Methods in Stata

We illustrate how to estimate parameters of linear state-space models using the Stata program sspace. We provide examples of how to use sspace to estimate the parameters of unobserved-component models, vector autoregressive moving-average models, and dynamic-factor models. We also show how to compute one-step, filtered, and smoothed estimates of the series and the states; dynamic forecasts and their confidence intervals; and residuals

Transcriptional and environmental control of bacterial denitrification and N2O emissions

In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3−) respiration in which the NO3− is sequentially reduced via nitrite (NO2−), nitric oxide (NO) and nitrous oxide (N2O) to dinitrogen (N2). However, atmospheric N2O continues to rise, a significant proportion of which is microbial in origin. This implies that the enzyme responsible for N2O reduction, nitrous oxide reductase (NosZ), does not always carry out the final step of denitrification either efficiently, or in synchrony with the rest of the pathway. Despite a solid understanding of the biochemistry underpinning denitrification, there is a relatively poor understanding of how environmental signals and respective transcriptional regulators control expression of the denitrification apparatus. This mini-review will describe the current picture for transcriptional regulation of denitrification in the model bacterium, Paracoccus denitrificans, highlighting differences in other denitrifying bacteria where appropriate, as well as gaps in our understanding. Alongside this, the emerging role of small regulatory RNAs (sRNAs) in regulation of denitrification will be discussed. We will conclude by speculating how this information, aside from providing a better understanding of the denitrification process, can be translated into development of novel greenhouse gas mitigation strategies

An Instrumentation System for Studying Feeding and Drinking Behavior of Individual Poultry

This article describes an instrumentation system that was developed to study the dynamic feeding and drinking behavior of individual birds. The system, consisting of 24 feeding and drinking stations interfaced via an RS 485 communication network to a central PC, provides continuous recording of feeding and drinking events. Each feeding/drinking station includes a precision electronic balance (1210–g capacity and 0.1–g resolution) for the feeder and a temperature–controlled drinking water reservoir (1500–mL capacity and 1000– to 1500–mL operating range) whose height and thus volume was sensed with a differential pressure transducer (0 – 2.5 VDC output). The system was tested using growing broiler chickens subjected to constant or cyclic thermal conditions. Sample data are presented to demonstrate how researchers can use the system to examine and understand the effects of environmental modification on feeding and drinking behavior of individual birds. A series of subsequent studies have been planned that will use the system to investigate the interactive effects of environmental and dietary nutrition manipulations on ingestion behavior and poultry performance.total P

Adinkras From Ordered Quartets of BC4{}_4 Coxeter Group Elements and Regarding 1,358,954,496 Matrix Elements of the Gadget

We examine values of the Adinkra Holoraumy-induced Gadget representation space metric over all possible four-color, four-open node, and four-closed node adinkras. Of the 1,358,954,496 gadget matrix elements, only 226,492,416 are non-vanishing and take on one of three values: $-1/3$, $1/3$, or $1$ and thus a subspace isomorphic to a description of a body-centered tetrahedral molecule emerges.Comment: LaTeX twice, 56pp, 30 tables, 5 figures, latest version includes link to updated code, minor corrections, and additional support about inequivalent representations and tetrahedral geometry comments added along with observations about similarity with results previously found by Nekraso

Identification of important error fields in stellarators using Hessian matrix method

Error fields are predominantly attributed to inevitable coil imperfections. Controlling error fields during coil fabrication and assembly is crucial for stellarators. Excessively tight coil tolerance increases time and cost, and, in part, led to the cancellation of NCSX and delay of W7-X. In this paper, we improve the recently proposed Hessian matrix method to rapidly identify important coil deviations. Two of the most common figures of merit, magnetic island size and quasi-symmetry, are analytically differentiated over coil parameters. By extracting the eigenvectors of the Hessian matrix, we can directly identify sensitive coil deviations in the order of the eigenvalues. The new method is applied to the upcoming CFQS configuration. Important perturbations that enlarge n/m=4/11 islands and deteriorate quasi-axisymmetry of the magnetic field are successfully determined. The results suggest each modular coil should have separate tolerance and some certain perturbation combinations will produce significant error fields. By relaxing unnecessary coil tolerance, this method will hopefully lead to a substantial reduction in time and cost.Comment: Accepted by Nuclear Fusio

Air Quality and Emissions from Livestock and Poultry Production/Waste Management Systems

The objective of this paper is to summarize the available literature on the concentrations and emissions of odor, ammonia, nitrous oxide, hydrogen sulfide, methane, non-methane volatile organic carbon, dust, and microbial and endotoxin aerosols from livestock and poultry buildings and manure management systems (storage and treatment units).Animal production operations are a source of numerous airborne contaminants including gases, odor, dust, and microorganisms. Gases and odors are generated from livestock and poultry manure decomposition (1) shortly after it is produced, (2) during storage and treatment, and (3) during land application. Particulate matter and dust are primarily composed of feed and animal matter including hair, feathers, and feces. Microorganisms that populate the gastro-intestinal systems of animals are present in freshly excreted manure. Other types of microorganisms colonize the manure during the storage and treatment processes. The generation rates of odor, manure gases, microorganisms, particulates, and other constituents vary with weather, time, species, housing, manure handling system, feed type, and management system. Therefore, predicting the concentrations and emissions of these constituents is extremely difficult.Numerous control strategies are being investigated to reduce the generation of airborne materials. However, airborne contaminants will continue to be generated from livestock and poultry operations even when best management systems and/or mitigation techniques are employed.Livestock and poultry buildings may contain concentrations of contaminants that negatively affect human and animal health. Most of these health concerns are associated with chronic or longterm exposure to gases, dust, or microorganisms. However, acute or short-term exposures to high concentrations of certain constituents can also have a negative effect on both human and animal health. For example, the agitation and pumping of liquid manure inside a livestock building can generate concentrations of hydrogen sulfide that are lethal to humans and animals.Once airborne contaminants are generated they can be emitted from the sources (building, manure storage, manure treatment unit, or cropland) through ventilation systems or by natural (weather) forces. The quantification of emissions or emission rates for gases, odor, dust, and microorganisms from both point sources (buildings) and area sources (beef and dairy cattle feedlot surfaces, manure storage and treatment units and manure applied on cropland) is being intensely researched in the U.S., in many European countries, Japan, and Australia. However, the accurate quantification of emissions is difficult since so many factors (time of year and day, temperature, humidity, wind speed, solar intensity and other weather conditions, ventilation rates, housing type, manure properties or characteristics, and animal species, stocking density, and age) are involved in the generation and dispersion of airborne materials. Furthermore, there are no standardized methods for the collection, measurement and calculation of such constituents, resulting in significant variability and large ranges in the published literature. In fact, emission rates of only a few airborne contaminants have been investigated. Ammonia, hydrogen sulfide, and methane emissions have been more thoroughly studied than other gases and compounds because of the negative environmental impacts or human health concerns associated with them. Unfortunately, there is very little emission data for other contaminants such as odor, nitrous oxide, non-methane volatile organic compounds, dust, and endotoxins. The long-term impacts of these constituents on the environment and on human health are also not known

Engineering: Cornell Quarterly, Vol.02, No.1 (Spring 1967): Improving Man's Environment

In this Issue: "Engineering for Human Needs" by William McGuire ... "New Concept in Nuclear Reactor Housing" by Richard N. White ... "Land Resource Utilization and Planning" by David J. Henkel ... "Water Shortage, No ... Sound Managemen, Yes" by Charles D. Gates ... "Systems Engineering and Human Environment" by Gordon P. Fisher ... Faculty Publications ... Editorial

A haloarchaeal ferredoxin electron donor that plays an essential role in nitrate assimilation

In the absence of ammonium, many organisms, including the halophilic archaeon Haloferax volcanii DS2 (DM3757), may assimilate inorganic nitrogen from nitrate or nitrite, using a ferredoxin-dependent assimilatory NO3-/NO2- reductase pathway. The small acidic ferredoxin Hv-Fd plays an essential role in the electron transfer cascade required for assimilatory nitrate and nitrite reduction by the cytoplasmic NarB- and NirA-type reductases respectively. UV–visible absorbance and EPR spectroscopic characterization of purified Hv-Fd demonstrate that this protein binds a single [2Fe–2S] cluster, and potentiometric titration reveals that the cluster shares similar redox properties with those present in plant-type ferredoxins