Signal extraction and estimation of a trend: a Monte Carlo study

Several authors (King and Rebelo, 1993; Cogley and Nason, 1995) have questioned the use of exponentially weighted moving average filters such as the Hodrick–Prescott filter in decomposing a series into a trend and cycle, claiming that they lead to the observation of spurious or induced cycles and to misinterpretation of stylized facts. However, little has been done to propose different methods of estimation or other ways of defining trend extraction. This paper has two main contributions. First, we suggest that the decomposition between the trend and cycle has not been done in an appropriate way. Second, we argue for a general to specific approach based on a more general filter, the stochastic trend model, that allows us to estimate all the parameters of the model rather than fixing them arbitrarily, as is done with mainly of the commonly used filters. We illustrate the properties of the proposed technique relative to the conventional ones by employing a Monte Carlo study. Copyright © 1999 John Wiley & Sons, Ltd.     

Resculpting the binding pocket of APC superfamily LeuT-fold amino acid transporters

Amino acid transporters are essential components of prokaryote and eukaryote cells, possess distinct physiological functions, and differ markedly in substrate specificity. Amino acid transporters can be both drug targets and drug transporters (bioavailability, targeting) with many monogenic disorders resulting from dysfunctional membrane transport. The largest collection of amino acid transporters (including the mammalian SLC6, SLC7, SLC32, SLC36, and SLC38 families), across all kingdoms of life, is within the Amino acid-Polyamine-organoCation (APC) superfamily. The LeuT-fold is a paradigm structure for APC superfamily amino acid transporters and carriers of sugars, neurotransmitters, electrolytes, osmolytes, vitamins, micronutrients, signalling molecules, and organic and fatty acids. Each transporter is specific for a unique sub-set of solutes, specificity being determined by how well a substrate fits into each binding pocket. However, the molecular basis of substrate selectivity remains, by and large, elusive. Using an integrated computational and experimental approach, we demonstrate that a single position within the LeuT-fold can play a crucial role in determining substrate specificity in mammalian and arthropod amino acid transporters within the APC superfamily. Systematic mutation of the amino acid residue occupying the equivalent position to LeuT V104 titrates binding pocket space resulting in dramatic changes in substrate selectivity in exemplar APC amino acid transporters including PAT2 (SLC36A2) and SNAT5 (SLC38A5). Our work demonstrates how a single residue/site within an archetypal structural motif can alter substrate affinity and selectivity within this important superfamily of diverse membrane transporters.     

Decision‐Based Forecast Evaluation of UK Interest Rate Predictability

This paper illustrates the importance of density forecasting and forecast evaluation in portfolio decision making. The decision‐making environment is fully described for an investor seeking to optimally allocate her portfolio between long and short Treasury bills, over investment horizons of up to 2 years. We examine the impact of parameter uncertainty and predictability in bond returns on the investor's allocation and we describe how the forecasts are computed and used in this context. Both statistical and decision‐based criteria are used to assess the predictability of returns. Our results show sensitivity to the evaluation criterion used and, in the context of investment decision making under an economic value criterion, we find some potential gain for the investor from assuming predictability. Copyright © 2015 John Wiley & Sons, Ltd.     

Recommendations of the 2006 Human Variome Project meeting

Lists of variations in genomic DNA and their effects have been kept for some time and have been used in diagnostics and research. Although these lists have been carefully gathered and curated, there has been little standardization and coordination, complicating their use. Given the myriad possible variations in the estimated 24,000 genes in the human genome, it would be useful to have standard criteria for databases of variation. Incomplete collection and ascertainment of variants demonstrates a need for a universally accessible system. These and other problems led to the World Heath Organization-cosponsored meeting on June 20-23, 2006 in Melbourne, Australia, which launched the Human Variome Project. This meeting addressed all areas of human genetics relevant to collection of information on variation and its effects. Members of each of eight sessions (the clinic and phenotype, the diagnostic laboratory, the research laboratory, curation and collection, informatics, relevance to the emerging world, integration and federation and funding and sustainability) developed a number of recommendations that were then organized into a total of 96 recommendations to act as a foundation for future work worldwide. Here we summarize the background of the project, the meeting and its recommendations.     

Whole-genome sequence of Schistosoma haematobium

Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide. No vaccines are available, and treatment relies on one drug, praziquantel. Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer and as a predisposing factor for HIV/AIDS. The parasite is transmitted to humans from freshwater snails. Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease and induce squamous cell carcinoma. Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites. We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.     

Short-term effects of wildfire on montane stream ecosystems in the southern Rocky Mountains: one and two years post-burn

The frequency and intensity of wildfire in the western United States has increased over the last century, creating a heterogeneous mosaic of landscapes in various stages of recovery. The 2002 Hayman Fire was one of the largest wildfires in Colorado history and was unprecedented for its speed and intensity, with over 50%–70% of the burn area classified as moderate to high severity where much of the canopy crown was consumed. We evaluated the short-term impact of the Hayman Fire on ecological properties in montane stream ecosystems in the summers of 2003 and 2004, one and two years post-fire. Fire significantly altered surface temperature, dissolved oxygen concentration, and the chemical composition of stream water, including concentrations of nitrate, phosphate, and mineral salts. However, fire did not have significant impacts on stream conductivity, pH, or total concentrations of cations or anions during our study period. Streams in the burn area contained fewer benthic macroinvertebrate taxa compared to unburned streams during the year after fire and contained lower invertebrate densities and biomass compared to reference streams 2 years post-fire. Average C:N ratio of the benthic macroinvertebrate community was significantly and negatively related to stream nitrate concentration, possibly due to a shift in community composition or invertebrate nitrogen acquisition in fire-affected streams.     

Somatostatin immunoneutralization overcomes the inhibitory effects of quipazine and pargyline on growth hormone secretion in domestic fowl

The inhibitory effects of pargyline and quipazine on chicken growth hormone secretion were overcome by passive immunoneutralization of endogenous somatostatin (SRIF)-14 or SRIF-28(1-14)-like immunoreactivity. Administration of the specific antisera to control birds pretreated with 0.9% NaCl elevated the basal plasma GH concentrations. These results suggest that peptides with SRIF-14 or SRIF-28(1-14)-like immunoreactivity tonically inhibit GH secretion and are at least partially responsible for the inhibitory effects of pargyline and quipazine on GH release in immature domestic fowl.