Behavioural Differences between Single Scandinavian Brown Bears (Ursus arctos) and Females with Dependent Young When Experimentally Approached by Humans

PubMed Central

Sahlén, Veronica; Ordiz, Andrés; Swenson, Jon E.; Støen, Ole Gunnar

2015-01-01

Carnivore-human encounters that result in human injury present a conservation and management challenge and it is therefore important to understand under what conditions such incidents occur. Females with cubs are often involved when humans are injured by brown bears Ursus arctos. In Scandinavia, this is particularly true for unarmed recreational forest users. Our aim was to document behavioural differences between single bears and females with cubs in order to develop recommendations to minimize the risk of injuries to recreational forest users. We documented the reactions of GPS-collared females with cubs and single brown bears to experimental approaches by humans to 50 m from the bear on 42 and 108 occasions, respectively. The majority of females with cubs (95%) and single bears (89%) left when approached. Bears that left were passed at shorter distances and were in more open areas than those that stayed. Both groups had similar flight initiation distances, which were longer for bears that were active at the time of the disturbance. Females with cubs selected more open habitat than single bears, also for the new site they selected following disturbance. Females with cubs, particularly active females with cubs of the year, moved greater distances and spent more time active following the approach. Females with cubs and single bears were seen or heard in 26% and 14% of the approaches, respectively. None of the bears displayed any aggressive behaviour during the approaches. Females with cubs selected more open habitat, perhaps predisposing them to encountering people that are not involved in hunting activities, which might be the primary explanation why females with cubs are most frequently involved when unarmed people are injured by bears in Scandinavia. To mitigate injury risks, one must consider factors that bring bears closer to human activity in the first place. PMID:25830333

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

PubMed Central

Wald, Naama; Alroy, Maya; Botzman, Maya; Margalit, Hanah

2012-01-01

Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation. PMID:22581775

Species Based Synonymous Codon Usage in Fusion Protein Gene of Newcastle Disease Virus

PubMed Central

Kumar, Chandra Shekhar; Kumar, Sachin

2014-01-01

Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species. PMID:25479071

MicroCub Subscale Aircraft

NASA Image and Video Library

2018-01-18

The MicroCub is the newest addition to NASA Armstrong's fleet of subscale research aircraft. The aircraft is a modified a Bill Hempel 60-percent-scale super cub, designed with a 21-foot wingspan, a Piccolo Autopilot guidance system and a JetCat SPT-15 Turboprop.

Modes of Thermal Protection in Polar Bear Cubs - at Birth and upon Emergence from the Den,

DTIC Science & Technology

1978-01-01

Morphological characteristics potentially relevant to temperature regulation were visually examined. Fat and skeletal muscle (m. psoas and m. latissimus dorsi ... latissimus dorsi ) were excised and processed for electron microscopical examination as described for the newborn cubs. In order to investigate the...circles o 0 ). The weight of the cub as 12.5 kg. 21 Fig. 6 Two micrographs of the latissimus dorsi muscle of a polar bear A and B. cub aged approximately

Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions.

PubMed

Subramanian, Abhishek; Sarkar, Ram Rup

2015-10-01

Understanding the variations in gene organization and its effect on the phenotype across different Leishmania species, and to study differential clinical manifestations of parasite within the host, we performed large scale analysis of codon usage patterns between Leishmania and other known Trypanosomatid species. We present the causes and consequences of codon usage bias in Leishmania genomes with respect to mutational pressure, translational selection and amino acid composition bias. We establish GC bias at wobble position that governs codon usage bias across Leishmania species, rather than amino acid composition bias. We found that, within Leishmania, homogenous codon context coding for less frequent amino acid pairs and codons avoiding formation of folding structures in mRNA are essentially chosen. We predicted putative differences in global expression between genes belonging to specific pathways across Leishmania. This explains the role of evolution in shaping the otherwise conserved genome to demonstrate species-specific function-level differences for efficient survival. Copyright © 2015 Elsevier Inc. All rights reserved.

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

PubMed

Behura, Susanta K; Severson, David W

2013-02-01

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Cucurbitacin B and SCH772984 exhibit synergistic anti-pancreatic cancer activities by suppressing EGFR, PI3K/Akt/mTOR, STAT3 and ERK signaling

PubMed Central

Zhou, Jingkai; Zhao, Tiangang; Ma, Linfeng; Liang, Min; Guo, Ying-Jie; Zhao, Li-Mei

2017-01-01

Cucurbitacin B (CuB) is a natural tetracyclic triterpene product and displays antitumor activity across a wide array of cancers. In this study, we explored the anti-pancreatic cancer activity of CuB alone and in combination with SCH772984, an ERK inhibitor, in vitro and in vivo. CuB inhibited proliferation of pancreatic cancer cells by arresting them in the G2/M cell cycle phase. This was associated with inhibition of EGFR expression and activity and downstream signaling, including PI3K/Akt/mTOR and STAT3. Interestingly, ERK activity was markedly enhanced by activating AMPK signaling after 12 h of CuB treatment. SCH772984 potentiates the cytotoxic effect of CuB on pancreatic cancer cells through complementary inhibition of EGFR, PI3K/Akt/mTOR, STAT3 and ERK signaling, followed by an increase in the pro-apoptotic protein Bim and a decrease in the anti-apoptotic proteins Mcl-1, Bcl-2, Bcl-xl and survivin. Furthermore, combined therapy with CuB and SCH772984 resulted in highly significant growth inhibition of pancreatic cancer xenografts. These results may provide a basis for further development of combining CuB and ERK inhibitors to treat pancreatic cancer. PMID:29262554

The Dynamics of Cuba Anticyclones (CubANs) and Interaction With the Loop Current/Florida Current System

NASA Astrophysics Data System (ADS)

Kourafalou, Vassiliki; Androulidakis, Yannis; Le Hénaff, Matthieu; Kang, HeeSook

2017-10-01

Mesoscale anticyclonic eddies along the northern Cuban coast (CubANs) have been identified in the Straits of Florida, associated with the northward shift of the Florida Current (FC) and the anticyclonic curvature of the Loop Current (LC) at the western entrance of the Straits. The dynamics of CubAN eddies and their interaction with the LC/FC system are described for the first time using satellite, drifter and buoy data, and a high-resolution model. It is shown that the evolution of CubANs to the south of the FC front complements the evolution of cyclonic eddies to the north of the FC, advancing previous studies on synergy between FC meandering and eddy activity. Two types of CubAN eddies are characterized: (a) a main anticyclonic cell (type "A") within the core of the LC during retracted phase conditions, associated with the process of LC Eddy (LCE) shedding from an extended LC, and (b) an individual, distinct anticyclonic eddy that is released from the main LC core and is advected eastward, along the northern Cuban coast (type "B"). There are also mixed cases, when the process of LCE shedding has started, so a type "A" CubAN is being formed, in the presence of one or more eastward progressing type "B" eddies. CubAN evolution is associated with an increased mixed layer and weaker stratification of the upper ocean along the eddy's track. The cyclonic activity along the Cuban coast and wind-induced upwelling events also contribute to the evolution and fate of the CubAN eddies.

Cataracts and strabismus associated with hand rearing using artificial milk formulas in Bengal tiger (Panthera tigris spp tigris) cubs

PubMed Central

Lange, Rogério Ribas; Lima, Leandro; Frühvald, Erika; da Silva, Vera Sônia Nunes; de Souza, Aparecida Sônia; Montiani-Ferreira, Fabiano

2017-01-01

The aim of this investigation is to describe the potential contributing nutritional factors involved in the development of ophthalmic and dermatologic changes in four Bengal tiger (Panthera tigris spp tigris) cubs fed an artificial milk formula. The affected animals were compared with two other tiger cubs that had been nursed by their dam naturally. After the first clinical signs appeared, the tiger cubs underwent ophthalmic evaluation. Severe symmetric generalized alopecia over the trunk, sparing the head and distal portion of the front and rear limbs, bilateral cataracts and strabismus were noticed. Milk and blood from the mother, as well as blood from the healthy and affected cubs were collected in order to evaluate complete blood counts, serum chemistry values, and amino acid levels. The amino acid concentrations in the artificial formula were also evaluated for comparison to the milk from the dam. The concentration of taurine, arginine, phenylalanine, tryptophan and histidine were very low in the artificial formulas as compared to the dam´s milk. The tiger cubs that received the artificial formula had lower levels of the amino acids listed previously as compared to those that nursed from the dam naturally. Taurine, as well as arginine, phenylalanine, tryptophan and histidine deficiency appeared to be possible causes of the development of skin problems, cataracts and strabismus in the tiger cubs fed with these particular artificial milk replacers. In the future, special attention should be given in order to make sure that adequate levels of these amino acids are present in artificial milk for tiger cubs. PMID:28210544

Analysis of the synonymous codon usage bias in recently emerged enterovirus D68 strains.

PubMed

Karniychuk, Uladzimir U

2016-09-02

Understanding the codon usage pattern of a pathogen and relationship between pathogen and host's codon usage patterns has fundamental and applied interests. Enterovirus D68 (EV-D68) is an emerging pathogen with a potentially high public health significance. In the present study, the synonymous codon usage bias of 27 recently emerged, and historical EV-D68 strains was analyzed. In contrast to previously studied enteroviruses (enterovirus 71 and poliovirus), EV-D68 and human host have a high discrepancy between favored codons. Analysis of viral synonymous codon usage bias metrics, viral nucleotide/dinucleotide compositional parameters, and viral protein properties showed that mutational pressure is more involved in shaping the synonymous codon usage bias of EV-D68 than translation selection. Computation of codon adaptation indices allowed to estimate expression potential of the EV-D68 genome in several commonly used laboratory animals. This approach requires experimental validation and may provide an auxiliary tool for the rational selection of laboratory animals to model emerging viral diseases. Enterovirus D68 genome compositional and codon usage data can be useful for further pathogenesis, animal model, and vaccine design studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Curiosity driven reinforcement learning for motion planning on humanoids

PubMed Central

Frank, Mikhail; Leitner, Jürgen; Stollenga, Marijn; Förster, Alexander; Schmidhuber, Jürgen

2014-01-01

Most previous work on artificial curiosity (AC) and intrinsic motivation focuses on basic concepts and theory. Experimental results are generally limited to toy scenarios, such as navigation in a simulated maze, or control of a simple mechanical system with one or two degrees of freedom. To study AC in a more realistic setting, we embody a curious agent in the complex iCub humanoid robot. Our novel reinforcement learning (RL) framework consists of a state-of-the-art, low-level, reactive control layer, which controls the iCub while respecting constraints, and a high-level curious agent, which explores the iCub's state-action space through information gain maximization, learning a world model from experience, controlling the actual iCub hardware in real-time. To the best of our knowledge, this is the first ever embodied, curious agent for real-time motion planning on a humanoid. We demonstrate that it can learn compact Markov models to represent large regions of the iCub's configuration space, and that the iCub explores intelligently, showing interest in its physical constraints as well as in objects it finds in its environment. PMID:24432001

A biotransformation process for the production of cucurbitacin B from its glycoside using a selected Streptomyces sp.

PubMed

Mei, Jianfeng; Li, Sha; Jin, Hang; Tang, Lan; Yi, Yu; Wang, Hong; Ying, Guoqing

2016-09-01

Cucurbitacin B (CuB) and its glycoside, cucurbitacin B 2-o-β-D-glucoside (CuBg), abundantly occur in the pedicels of Cucumis melo. Compared with CuB, CuBg is not efficiently extracted from the pedicels. Furthermore, the anticancer activity of CuBg is lower than that of the aglycone. A process for CuBg biotransformation to CuB was developed for the first time. A strain of Streptomyces species that converts CuBg into CuB was isolated from an enrichment culture of C. melo pedicels. After optimization of conditions for enzyme production and biotransformation, a maximum conversion rate of 92.6 % was obtained at a CuBg concentration of 0.25 g/L. When biotransformation was performed on C. melo pedicel extracts, the CuB concentration in the extracts increased from 1.50 to 3.27 g/L. The conversion rate was almost 100 %. The developed process may be an effective biotransformation method for industrial production CuB from C. melo pedicels for pharmaceuticals.

Milk composition in free-ranging polar bears (Ursus maritimus) as a model for captive rearing milk formula.

PubMed

Hedberg, Gail E; Derocher, Andrew E; Andersen, Magnus; Rogers, Quinton R; DePeters, Edward J; Lönnerdal, Bo; Mazzaro, Lisa; Chesney, Russell W; Hollis, Bruce

2011-01-01

The goals of this study were to have an improved understanding of milk composition and to help create a suitable milk formula for cubs raised in captivity. Milk samples were evaluated for fat, fatty acids, carbohydrate, vitamin D(3), 25(OH)D(3), vitamin A (retinol), vitamin E (α-tocopherol), protein, and amino acids. Total lipids in milk did not differ for cubs (mean ± SEM = 26.60 ± 1.88 g/100 ml vs. yearlings 27.80 ± 2.20 g/100 ml). Milk lipids were of 23.6% saturated fatty acid for cubs and 22.4% for yearlings. Milk consumed by cubs and yearlings contained 43.8 and 42.0% mono-unsaturated fatty acids and 23.4 and 21.9% polyunsaturated fatty acids, respectively. Carbohydrate content was higher in milk for cubs (4.60 ± 0.64 g/100 ml) than for yearlings (2.60 ± 0.40 g/100 ml). Vitamin D(3) concentration of milk was 18.40 ± 5.00 ng/ml in early lactation compared with 7.60 ± 2.00 ng/ml for mid-lactation. 25(OH)D(3) was lower in milk consumed by cubs (162.00 ± 6.70 pg/ml) than in milk consumed by yearlings (205.00 ± 45.70 pg/ml). Vitamin A concentrations were 0.06 ± 0.01 and 0.03 ± 0.01 µg/ml for cubs and yearlings, respectively. Vitamin E was higher in milk consumed by cubs (20.16 ± 4.46 µg/ml) than by yearlings (7.30 ± 1.50 µg/ml). Protein content did not differ in milk available to cubs (11.40 ± 0.80 g/100 ml compared with milk for yearlings 11.80 ± 0.40 g/100 ml). Taurine was the most abundant free amino acid at 3,165.90 ± 192.90 nmol/ml (0.04% as fed basis). © 2011 Wiley Periodicals, Inc.

Growth rates and energy intake of hand-reared cheetah cubs (Acinonyx jubatus) in South Africa.

PubMed

Bell, K M; Rutherfurd, S M; Morton, R H

2012-04-01

Growth rate is an important factor in neonatal survival. The aim of this study was to determine growth rates in hand-reared cheetah cubs in South Africa fed a prescribed energy intake, calculated for growth in the domestic cat. Growth was then compared with previously published data from hand-reared cubs in North America and the relationship between growth and energy intake explored. Daily body weight (BW) gain, feed and energy intake data was collected from 18 hand-reared cheetah cubs up to 120 days of age. The average pre-weaning growth rate was 32 g/day, which is lower than reported in mother-reared cubs and hand-reared cubs in North American facilities. However, post-weaning growth increased to an average of 55 g/day. Growth was approximately linear prior to weaning, but over the entire age range it exhibited a sigmoidal shape with an asymptotic plateau averaging 57 kg. Energy intake associated with pre-weaning growth was 481 kJ ME/kg BW(0.75). Regression analysis described the relationship between metabolic BW, metabolisable energy (ME) intake, and hence daily weight gain. This relationship may be useful in predicting energy intake required to achieve growth rates in hand-reared cheetah cubs similar to those observed for their mother-reared counterparts. © 2011 Blackwell Verlag GmbH.

Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance.

PubMed

Das, Shibsankar; Roymondal, Uttam; Sahoo, Satyabrata

2009-08-15

Based on the hypothesis that highly expressed genes are often characterized by strong compositional bias in terms of codon usage, there are a number of measures currently in use that quantify codon usage bias in genes, and hence provide numerical indices to predict the expression levels of genes. With the recent advent of expression measure from the score of the relative codon usage bias (RCBS), we have explicitly tested the performance of this numerical measure to predict the gene expression level and illustrate this with an analysis of Yeast genomes. In contradiction with previous other studies, we observe a weak correlations between GC content and RCBS, but a selective pressure on the codon preferences in highly expressed genes. The assertion that the expression of a given gene depends on the score of relative codon usage bias (RCBS) is supported by the data. We further observe a strong correlation between RCBS and protein length indicating natural selection in favour of shorter genes to be expressed at higher level. We also attempt a statistical analysis to assess the strength of relative codon bias in genes as a guide to their likely expression level, suggesting a decrease of the informational entropy in the highly expressed genes.

Quantifying lion (Panthera leo) demographic response following a three-year moratorium on trophy hunting

PubMed Central

Becker, Matt; Creel, Scott; Rosenblatt, Elias; Merkle, Johnathan; Dröge, Egil; Mwape, Henry; Masonde, Jones; Simpamba, Twakundine

2018-01-01

Factors that limit African lion populations are manifold and well-recognized, but their relative demographic effects remain poorly understood, particularly trophy hunting near protected areas. We identified and monitored 386 individual lions within and around South Luangwa National Park, Zambia, for five years (2008–2012) with trophy hunting and for three additional years (2013–2015) during a hunting moratorium. We used these data with mark-resight models to estimate the effects of hunting on lion survival, recruitment, and abundance. The best survival models, accounting for imperfect detection, revealed strong positive effects of the moratorium, with survival increasing by 17.1 and 14.0 percentage points in subadult and adult males, respectively. Smaller effects on adult female survival and positive effects on cub survival were also detected. The sex-ratio of cubs shifted from unbiased during trophy-hunting to female-biased during the moratorium. Closed mark-recapture models revealed a large increase in lion abundance during the hunting moratorium, from 116 lions in 2012 immediately preceding the moratorium to 209 lions in the last year of the moratorium. More cubs were produced each year of the moratorium than in any year with trophy hunting. Lion demographics shifted from a male-depleted population consisting mostly of adult (≥4 years) females to a younger population with more (>29%) adult males. These data show that the three-year moratorium was effective at growing the Luangwa lion population and increasing the number of adult males. The results suggest that moratoria may be an effective tool for improving the sustainability of lion trophy hunting, particularly where systematic monitoring, conservative quotas, and age-based harvesting are difficult to enforce. PMID:29782514

Quantifying lion (Panthera leo) demographic response following a three-year moratorium on trophy hunting.

PubMed

Mweetwa, Thandiwe; Christianson, David; Becker, Matt; Creel, Scott; Rosenblatt, Elias; Merkle, Johnathan; Dröge, Egil; Mwape, Henry; Masonde, Jones; Simpamba, Twakundine

2018-01-01

Factors that limit African lion populations are manifold and well-recognized, but their relative demographic effects remain poorly understood, particularly trophy hunting near protected areas. We identified and monitored 386 individual lions within and around South Luangwa National Park, Zambia, for five years (2008-2012) with trophy hunting and for three additional years (2013-2015) during a hunting moratorium. We used these data with mark-resight models to estimate the effects of hunting on lion survival, recruitment, and abundance. The best survival models, accounting for imperfect detection, revealed strong positive effects of the moratorium, with survival increasing by 17.1 and 14.0 percentage points in subadult and adult males, respectively. Smaller effects on adult female survival and positive effects on cub survival were also detected. The sex-ratio of cubs shifted from unbiased during trophy-hunting to female-biased during the moratorium. Closed mark-recapture models revealed a large increase in lion abundance during the hunting moratorium, from 116 lions in 2012 immediately preceding the moratorium to 209 lions in the last year of the moratorium. More cubs were produced each year of the moratorium than in any year with trophy hunting. Lion demographics shifted from a male-depleted population consisting mostly of adult (≥4 years) females to a younger population with more (>29%) adult males. These data show that the three-year moratorium was effective at growing the Luangwa lion population and increasing the number of adult males. The results suggest that moratoria may be an effective tool for improving the sustainability of lion trophy hunting, particularly where systematic monitoring, conservative quotas, and age-based harvesting are difficult to enforce.

Comparison of shoulder internal rotation test with the elbow flexion test in the diagnosis of cubital tunnel syndrome.

PubMed

Ochi, Kensuke; Horiuchi, Yukio; Tanabe, Aya; Morita, Kozo; Takeda, Kentaro; Ninomiya, Ken

2011-05-01

To compare the shoulder internal rotation test-a new, provocative test-with the elbow flexion test in the diagnosis of cubital tunnel syndrome (CubTS). Twenty-five patients with CubTS were examined before and after surgery with 10 seconds each of the elbow flexion and shoulder internal rotation tests. Fifty-four asymptomatic individuals and 14 neuropathy patients with a diagnosis other than CubTS were also examined as control cases. For the shoulder internal rotation test, the patient's upper extremity was kept at 90° abduction, maximum internal rotation, and 10° flexion at the shoulder, with 90° elbow flexion and neutral position of the forearm and wrist, with finger extension. Test results were considered positive if any slight symptom attributable to CubTS occurred within 10 seconds. Extraneural pressure inside the cubital tunnel was intraoperatively measured with the positions of both the elbow flexion and shoulder internal rotation tests, in 15 of the CubTS cases. Statistical analyses were performed using Student's t-test with a confidence level of 95%. The preoperative sensitivity in CubTS cases was 80% in the 10-second shoulder internal rotation test and 36% in the 10-second elbow flexion test, and these differences were significant. None of the control cases had positive results in either test. All the CubTS cases improved with surgery; after surgery, neither test provoked symptoms in any surgical patient. The extraneural pressure increased in both provocative positions with no significant difference. Positive results for the 10-second shoulder internal rotation test were more sensitive than that for the elbow flexion test of the same duration and seemed specific to CubTS. Copyright © 2011 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Early Induction of NRF2 Antioxidant Pathway by RHBDF2 Mediates Rapid Cutaneous Wound Healing

PubMed Central

Hosur, Vishnu; Burzenski, Lisa M.; Stearns, Timothy M.; Farley, Michelle L.; Sundberg, John P.; Wiles, Michael V.; Shultz, Leonard D.

2017-01-01

Rhomboid family protein RHBDF2, an upstream regulator of the epidermal growth factor (EGF) receptor signaling, has been implicated in cutaneous wound healing. However, the underlying molecular mechanisms are still emerging. In humans, a gain-of-function mutation in the RHBDF2 gene accelerates cutaneous wound healing in an EGFR-dependent manner. Likewise, a gain-of-function mutation in the mouse Rhbdf2 gene (Rhbdf2cub/cub) shows a regenerative phenotype (rapid ear-hole closure) resulting from constitutive activation of the EGFR pathway. Because the RHBDF2-regulated EGFR pathway is relevant to cutaneous wound healing in humans, we used Rhbdf2cub/cub mice to investigate the biological networks and pathways leading to accelerated ear-hole closure, with the goal of identifying therapeutic targets potentially effective in promoting wound healing in humans. Comparative transcriptome analysis of ear pinna tissue from Rhbdf2cub/cub and Rhbdf2+/+ mice at 0h, 15 min, 2h, and 24h post-wounding revealed an early induction of the nuclear factor E2-related factor 2 (NRF2)-mediated anti-oxidative pathway (0h and 15 min), followed by the integrin-receptor aggregation pathway (2h) as early-stage events immediately and shortly after wounding in Rhbdf2cub/cub mice. Additionally, we observed genes enriched for the Fc fragment of the IgG receptor IIIa (FCGR3A)-mediated phagocytosis pathway 24h post-wounding. Although cutaneous wound repair in healthy individuals is generally non-problematic, it can be severely impaired due to aging, diabetes, and chronic inflammation. This study suggests that activation of the NRF2-antioxidant pathway by rhomboid protein RHBDF2 might be beneficial in treating chronic non-healing wounds. PMID:28268192

Early induction of NRF2 antioxidant pathway by RHBDF2 mediates rapid cutaneous wound healing.

PubMed

Hosur, Vishnu; Burzenski, Lisa M; Stearns, Timothy M; Farley, Michelle L; Sundberg, John P; Wiles, Michael V; Shultz, Leonard D

2017-04-01

Rhomboid family protein RHBDF2, an upstream regulator of the epidermal growth factor (EGF) receptor signaling, has been implicated in cutaneous wound healing. However, the underlying molecular mechanisms are still emerging. In humans, a gain-of-function mutation in the RHBDF2 gene accelerates cutaneous wound healing in an EGFR-dependent manner. Likewise, a gain-of-function mutation in the mouse Rhbdf2 gene (Rhbdf2 cub/cub ) shows a regenerative phenotype (rapid ear-hole closure) resulting from constitutive activation of the EGFR pathway. Because the RHBDF2-regulated EGFR pathway is relevant to cutaneous wound healing in humans, we used Rhbdf2 cub/cub mice to investigate the biological networks and pathways leading to accelerated ear-hole closure, with the goal of identifying therapeutic targets potentially effective in promoting wound healing in humans. Comparative transcriptome analysis of ear pinna tissue from Rhbdf2 cub/cub and Rhbdf2 +/+ mice at 0h, 15min, 2h, and 24h post-wounding revealed an early induction of the nuclear factor E2-related factor 2 (NRF2)-mediated anti-oxidative pathway (0h and 15min), followed by the integrin-receptor aggregation pathway (2h) as early-stage events immediately and shortly after wounding in Rhbdf2 cub/cub mice. Additionally, we observed genes enriched for the Fc fragment of the IgG receptor IIIa (FCGR3A)-mediated phagocytosis pathway 24h post-wounding. Although cutaneous wound repair in healthy individuals is generally non-problematic, it can be severely impaired due to aging, diabetes, and chronic inflammation. This study suggests that activation of the NRF2-antioxidant pathway by rhomboid protein RHBDF2 might be beneficial in treating chronic non-healing wounds. Copyright © 2017 Elsevier Inc. All rights reserved.

Bilateral carpal valgus deformity in hand-reared cheetah cubs (Acinonyx jubatus).

PubMed

Bell, Katherine M; van Zyl, Malan; Ugarte, Claudia E; Hartman, Angela

2011-01-01

Four hand-reared cheetah cubs (Acinonyx jubatus) exhibited progressively severe bilateral valgus deformity of the carpi (CV) during the weaning period. Radiographs of the thoracic limbs suggested normal bone ossification, and serum chemistry was unremarkable. All affected cubs developed CV shortly after the onset of gastroenteritis, which was treated medically, and included use of a prescription diet. A sudden decrease in growth rate was associated with gastrointestinal disease. Before gastroenteritis and CV, affected cubs had higher growth rates than unaffected cubs, despite similar mean daily energy intake. Return to normal thoracic limb conformation was consequent to dietary manipulation (including a reduction in energy intake and vitamin and mineral supplementation), as well as decreased growth rates and recovery from gastroenteritis. The cause of the CV is likely to have been multi-factorial with potentially complex physiological interactions involved. © 2010 Wiley-Liss, Inc.

"Reversed" intraguild predation: red fox cubs killed by pine marten.

PubMed

Brzeziński, Marcin; Rodak, Lukasz; Zalewski, Andrzej

2014-01-01

Camera traps deployed at a badger Meles meles set in mixed pine forest in north-eastern Poland recorded interspecific killing of red fox Vulpes vulpes cubs by pine marten Martes martes . The vixen and her cubs settled in the set at the beginning of May 2013, and it was abandoned by the badgers shortly afterwards. Five fox cubs were recorded playing in front of the den each night. Ten days after the first recording of the foxes, a pine marten was filmed at the set; it arrived in the morning, made a reconnaissance and returned at night when the vixen was away from the set. The pine marten entered the den several times and killed at least two fox cubs. It was active at the set for about 2 h. This observation proves that red foxes are not completely safe from predation by smaller carnivores, even those considered to be subordinate species in interspecific competition.

Design Report Final - CUB Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Armijo, Kenneth Miguel; Monda, Mark J.; Brunson, Gregory Paul

CUB (Critical Utility Base), Fig. 1.0, are individual portable energy and utility units utilizing renewable energy technologies integrated with high efficient conventional components to provide electricity, battery storage, heat, potable water, waste water treatment, cooling, liquid fuels, to name some of the primary utilities. Typically, these units were designed to provide power / utilities to any remote location or facility like forward operating bases, disaster relief centers, and Native American communities or to energize African villages. Although some CUB models have already been designed to date, the main unit, the CUB-E (electricity), lacks a critical component included in its design.more » It is the integral portion that automates solar electric panel racking deployment and retraction. This racking system will enable the CUB-E to rapidly deploy its utility within minutes, a feature not available in any form currently on the market.« less

Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes.

PubMed

Prabha, Ratna; Singh, Dhananjaya P; Sinha, Swati; Ahmad, Khurshid; Rai, Anil

2017-04-01

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

Discovery of a Metal-Poor Little Cub

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2017-09-01

The discovery of an extremely metal-poor star-forming galaxy in our local universe, dubbed Little Cub, is providing astronomers with front-row seats to the quenching of a near-pristine galaxy.SDSS image of NGC 3359 (left) and Little Cub (right), with overlying contours displaying the location of hydrogen gas. Little Cubs (also shown in the inset) stellar mass lies in the blue contour of the right-hand side. The outer white contours show the extended gas of the galaxy, likely dragged out as a tidal tail by Little Cubs interaction with NGC 3359. [Hsyu et al. 2017]The Hunt for Metal-Poor GalaxiesLow-metallicity, star-forming galaxies can show us the conditions under which the first stars formed. The galaxies with the lowest metallicities, however, also tend to be those with the lowest luminosities making them difficult to detect. Though we know that there should be many low-mass, low-luminosity, low-metallicity galaxies in the universe, weve detected very few of them nearby.In an effort to track down more of these metal-poor galaxies, a team of scientists led by Tiffany Hsyu (University of California Santa Cruz) searched through Sloan Digital Sky Survey data, looking for small galaxies with the correct photometric color to qualify a candidate blue compact dwarfs, a type of small, low-luminosity, star-forming galaxy that is often low-metallicity.Hsyu and collaborators identified more than 2,500 candidate blue compact dwarfs, and next set about obtaining follow-up spectroscopy for many of the candidates from the Keck and Lick Observatories. Though this project is still underway, around 100 new blue compact dwarfs have already been identified via the spectroscopy, including one of particular interest: the Little Cub.Little CubThis tiny star-forming galaxy gained its nickname from its location in the constellation Ursa Major. Little Cub is perhaps 50 or 60 million light-years away, and Hsyu and collaborators find it to be one of the lowest-metallicity star-forming galaxies in our local universe. The galaxy contains 100,000 solar masses of stars and it is notably gas-rich with nearly 100 times the stellar mass in neutral gas.The environment of Little Cub is also interesting: it appears to be just a couple hundred thousand light-years away from the grand design spiral galaxy NGC 3359. The galaxies proximity and kinematics suggest that Little Cub may be a companion of NGC 3359, and Little Cubs morphology indicates that the larger galaxy may be tidally stripping gas from it.Emission-line spectra of Little Cub from Keck Observatory. [Hsyu et al. 2017]A First Passage?If Little Cub is indeed being tidally stripped by NGC 3359, then its surprising that the small galaxy still contains so much hot, star-forming gas; timescales for tidal stripping of this sort are thought to be very short. Hsyu and collaborators therefore speculate that we may have caught Little Cub in the early stages of its first passage around NGC 3359, allowing us to witness the quenching of a near-pristine satellite by a Milky-Way-like galaxy.This quenching process is thought to commonly happen around other massive host galaxies in the universe including around our own Milky Way, where nearly all satellite galaxies within roughly a million light-years are already quiescent and contain little neutral gas. Little Cub provides us with a rare opportunity to watch this process in action in our nearby universe, and it will be an intriguing laboratory for testing our understanding of dwarf satellite galaxy evolution.CitationTiffany Hsyu et al 2017 ApJL 845 L22. doi:10.3847/2041-8213/aa821f

PCBs and OH-PCBs in polar bear mother-cub pairs: a comparative study based on plasma levels in 1998 and 2008.

PubMed

Bytingsvik, Jenny; Lie, Elisabeth; Aars, Jon; Derocher, Andrew E; Wiig, Øystein; Jenssen, Bjørn M

2012-02-15

The aim of this study was to examine the plasma concentrations and prevalence of polychlorinated biphenyls (PCBs) and hydroxylated PCB-metabolites (OH-PCBs) in polar bear (Ursus maritimus) mothers (n=26) and their 4 months old cubs-of-the-year (n=38) from Svalbard to gain insight into the mother-cub transfer, biotransformation and to evaluate the health risk associated with the exposure to these contaminants. As samplings were performed in 1997/1998 and 2008, we further investigated the differences in levels and pattern of PCBs between the two sampling years. The plasma concentrations of Σ(21)PCBs (1997/1998: 5710 ± 3090 ng/g lipid weight [lw], 2008: 2560 ± 1500 ng/g lw) and Σ(6)OH-PCBs (1997/1998: 228 ± 60 ng/g wet weight [ww], 2008: 80 ± 38 ng/g ww) in mothers were significantly lower in 2008 compared to in 1997/1998. In cubs, the plasma concentrations of Σ(21)PCBs (1997/1998: 14680 ± 5350 ng/g lw, 2008: 6070 ± 2590 ng/g lw) and Σ(6)OH-PCBs (1997/1998: 98 ± 23 ng/g ww, 2008: 49 ± 21 ng/g ww) were also significantly lower in 2008 than in 1997/1998. Σ(21)PCBs in cubs was 2.7 ± 0.7 times higher than in their mothers. This is due to a significant maternal transfer of these contaminants. In contrast, Σ(6)OH-PCBs in cubs were approximately 0.53 ± 0.16 times the concentration in their mothers. This indicates a lower maternal transfer of OH-PCBs compared to PCBs. The majority of the metabolite/precursor-ratios were lower in cubs compared to mothers. This may indicate that cubs have a lower endogenous capacity to biotransform PCBs to OH-PCBs than polar bear mothers. Exposure to PCBs and OH-PCBs is a potential health risk for polar bears, and the levels of PCBs and OH-PCBs in cubs from 2008 were still above levels associated with health effects in humans and wildlife. Copyright © 2012 Elsevier B.V. All rights reserved.

Codon usage bias in phylum Actinobacteria: relevance to environmental adaptation and host pathogenicity.

PubMed

Lal, Devi; Verma, Mansi; Behura, Susanta K; Lal, Rup

2016-10-01

Actinobacteria are Gram-positive bacteria commonly found in soil, freshwater and marine ecosystems. In this investigation, bias in codon usages of ninety actinobacterial genomes was analyzed by estimating different indices of codon bias such as Nc (effective number of codons), SCUO (synonymous codon usage order), RSCU (relative synonymous codon usage), as well as sequence patterns of codon contexts. The results revealed several characteristic features of codon usage in Actinobacteria, as follows: 1) C- or G-ending codons are used frequently in comparison with A- and U ending codons; 2) there is a direct relationship of GC content with use of specific amino acids such as alanine, proline and glycine; 3) there is an inverse relationship between GC content and Nc estimates, 4) there is low SCUO value (<0.5) for most genes; and 5) GCC-GCC, GCC-GGC, GCC-GAG and CUC-GAC are the frequent context sequences among codons. This study highlights the fact that: 1) in Actinobacteria, extreme GC content and codon bias are driven by mutation rather than natural selection; (2) traits like aerobicity are associated with effective natural selection and therefore low GC content and low codon bias, demonstrating the role of both mutational bias and translational selection in shaping the habitat and phenotype of actinobacterial species. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Genome-wide analysis of codon usage bias in Ebolavirus.

PubMed

Cristina, Juan; Moreno, Pilar; Moratorio, Gonzalo; Musto, Héctor

2015-01-22

Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species. The interplay of codon usage among viruses and their hosts is expected to affect overall viral survival, fitness, evasion from host's immune system and evolution. In the present study, we performed comprehensive analyses of codon usage and composition of ZEBOV. Effective number of codons (ENC) indicates that the overall codon usage among ZEBOV strains is slightly biased. Different codon preferences in ZEBOV genes in relation to codon usage of human genes were found. Highly preferred codons are all A-ending triplets, which strongly suggests that mutational bias is a main force shaping codon usage in ZEBOV. Dinucleotide composition also plays a role in the overall pattern of ZEBOV codon usage. ZEBOV does not seem to use the most abundant tRNAs present in the human cells for most of their preferred codons. Copyright © 2014 Elsevier B.V. All rights reserved.

The Checklist of Unit Behaviours (CUB): Validation within a Canadian outpatient day hospital programme.

PubMed

Taube-Schiff, M; El Morr, C; Counsell, A; Mehak, Adrienne; Gollan, J

2018-05-01

WHAT IS KNOWN ON THE SUBJECT?: The psychometrics of the CUB measure have been tested within an inpatient psychiatric setting. Results show that the CUB has two factors that reflect patients' approach and avoidance of dimensions of the treatment milieu, and that an increase of approach and decrease of avoidance are correlated with discharge. No empirical research has examined the validity of the CUB in a day hospital programme. WHAT THIS ARTICLE ADDS TO EXISTING KNOWLEDGE?: This study was the first to address the validity of this questionnaire within a psychiatric day hospital setting. This now allows other mental health service providers to use this questionnaire following administration of patient engagement interventions (such as behavioural activation), which are routinely used within this type of a setting. WHAT ARE THE IMPLICATIONS FOR PRACTICE?: Our results can enable healthcare providers to employ an effective and psychometrically validated tool in a day hospital setting to measure treatment outcomes and provide reflections of patients' approach behaviours and avoidance behaviours. Introduction We evaluated the Checklist of Unit Behaviours (CUBs) questionnaire in a novel mental health setting: a day hospital within a large acute care general hospital. No empirical evidence exists, as of yet, to look at the validity of this measure in this type of a treatment setting. The CUB measures two factors, avoidance or approach, of the patients' engagement with the treatment milieu within the previous 24 hr. Aim A confirmatory factor analysis (CFA) was conducted to validate the CUB's original two factor structure in an outpatient day programme. Methods Psychiatric outpatients (n = 163) completed the CUB daily while participating in a day hospital programme in Toronto, Canada. Results A CFA was used to confirm the CUB factors but resulted in a poor fitting model for our sample, χ 2 (103) = 278.59, p < .001, CFI = 0.80, RMSEA = 0.10, SRMR = 0.10. Questions 5, 8 and 10 had higher loadings on a third factor revealed through exploratory factor analysis. We believe this factor, "Group Engagement," reflects the construct of group-related issues. Discussion The CUB was a practical and useful tool in our psychiatric day hospital setting at a large acute care general hospital. Implications for practice Our analysis identified group engagement, a critical variable in day programmes, as patients have autonomy regarding staying or leaving the programme. © 2017 John Wiley & Sons Ltd.

Tetralogy of Fallot and atrial septal defect in a white Bengal Tiger cub (Panthera tigris tigris)

PubMed Central

2014-01-01

A 3-week-old female white Bengal Tiger cub (Panthera tigris tigris) presented with acute onset tachypnoea, cyanosis and hypothermia. The cub was severely hypoxaemic with a mixed acid–base disturbance. Echocardiography revealed severe pulmonic stenosis, right ventricular hypertrophy, high membranous ventricular septal defect and an overriding aorta. Additionally, an atrial septal defect was found on necropsy, resulting in the final diagnosis of Tetralogy of Fallot with an atrial septal defect (a subclass of Pentalogy of Fallot). This report is the first to encompass arterial blood gas analysis, thoracic radiographs, echocardiography and necropsy findings in a white Bengal Tiger cub diagnosed with Tetralogy of Fallot with an atrial septal defect. PMID:24594084

Body mass dynamics in hand reared clouded leopard (Neofelis nebulosa) cubs from birth to weaning.

PubMed

Nájera, Fernando; Brown, Janine; Wildt, David E; Virolle, Laurie; Kongprom, Urarikha; Revuelta, Luis; Goodrowe-Beck, Karen

2015-01-01

To study the dynamics of body mass changes in hand reared clouded leopards, we analyzed 3,697 weight data points during the first 3 months of life in 49 cubs from 24 zoo-born litters from 2003 through 2012. All cubs were fed the same formula mixture after a similar weaning protocol. The hand rearing process was divided into three periods based on feeding protocols: Stage 1: formula only (Days 1-28; Day 0 = day of birth); Stage 2, formula supplemented with protein (e.g., turkey baby food; Days 29-42); Stage 3, formula in decreasing amounts supplemented with meat (chicken and/or beef; Days 43-90). Weights at birth were 11.2% higher (P < 0.001) for males (n = 29) than females (n = 20). Daily weight gain was slowest (P < 0.05) during Stage 1 when cubs were fed straight formula only and fastest during Stage 3 when provided a mixture of formula and meat. Mean growth rate (± SD) during hand rearing differed (P < 0.05) by gender, being 34.6 ± 1.4 g/day for male and 30.0 ± 1.2 g/day for female cubs. Eighteen cubs (37%) exhibited mild to severe diarrhea during the study; however, palliative treatment resulted in similar (P > 0.05) growth and weaning weights compared to healthy counterparts. These are the first data documenting, on a large scale, the growth patterns for zoo born, hand reared clouded leopard cubs. Findings are valuable as an aid in managing this rare species, including for helping identify early onset of medical issues and further determining key factors regulating the first 3 months of development. © 2015 Wiley Periodicals, Inc.

Codon usage bias and phylogenetic analysis of mitochondrial ND1 gene in pisces, aves, and mammals.

PubMed

Uddin, Arif; Choudhury, Monisha Nath; Chakraborty, Supriyo

2018-01-01

The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subunit of the respiratory chain complex I and involved in the first step of the electron transport chain of oxidative phosphorylation (OXPHOS). To understand the pattern of compositional properties, codon usage and expression level of mitochondrial ND1 genes in pisces, aves, and mammals, we used bioinformatic approaches as no work was reported earlier. In this study, a perl script was used for calculating nucleotide contents and different codon usage bias parameters. The codon usage bias of MT-ND1 was low but the expression level was high as revealed from high ENC and CAI value. Correspondence analysis (COA) suggests that the pattern of codon usage for MT-ND1 gene is not same across species and that compositional constraint played an important role in codon usage pattern of this gene among pisces, aves, and mammals. From the regression equation of GC12 on GC3, it can be inferred that the natural selection might have played a dominant role while mutation pressure played a minor role in influencing the codon usage patterns. Further, ND1 gene has a discrepancy with cytochrome B (CYB) gene in preference of codons as evident from COA. The codon usage bias was low. It is influenced by nucleotide composition, natural selection, mutation pressure, length (number) of amino acids, and relative dinucleotide composition. This study helps in understanding the molecular biology, genetics, evolution of MT-ND1 gene, and also for designing a synthetic gene.

Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses

PubMed Central

Bhatia, Sandeep; Sood, Richa; Selvaraj, Pavulraj

2016-01-01

Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts. PMID:27119730

Reaction of cyanide with cytochrome ba3 from Thermus thermophilus: spectroscopic characterization of the Fe(II)a3-CN.Cu(II)B-CN complex suggests four 14N atoms are coordinated to CuB.

PubMed Central

Surerus, K K; Oertling, W A; Fan, C; Gurbiel, R J; Einarsdóttir, O; Antholine, W E; Dyer, R B; Hoffman, B M; Woodruff, W H; Fee, J A

1992-01-01

Cytochrome ba3 from Thermus thermophilus reacts slowly with excess HCN at pH 7.4 to create a form of the enzyme in which CuA, cytochrome b, and CuB remain oxidized, while cytochrome a3 is reduced by one electron, presumably with the formation of cyanogen. We have examined this form of the enzyme by UV-visible, resonance Raman, EPR, and electron nuclear double resonance spectroscopies in conjunction with permutations of 13C- and 15N-labeled cyanide. The results support a model in which one CN- binds through the carbon atom to ferrous a3, supporting a low-spin (S = 0) configuration on the Fe; bridging by this cyanide to the CuB is weak or absent. Four 14N atoms, presumably donated by histidine residues of the protein, provide a strong equatorial ligand field about CuB; a second CN- is coordinated through the carbon atom to CuB in an axial position. PMID:1314380

Systemic calicivirus epidemic in captive exotic felids.

PubMed

Harrison, Tara M; Sikarskie, James; Kruger, John; Wise, Annabel; Mullaney, Thomas P; Kiupel, Matti; Maes, Roger K

2007-06-01

A 5-day-old, mother-raised, Amur tiger cub (Panthera tigris altaica) presented with tongue ulcerations. Identical lesions appeared and progressed to sloughing of the tongue in the three littermates of this cub the following day. The lesions progressed in all cubs to include sloughing of the carpal, tarsal, metacarpal, and metatarsal foot pad epithelium. Oral ulcerations were also noted in adult African lions (Panthera leo) and Amur tigers (Panthera tigris altaica), but not in two adult snow leopards (Panthera uncia) housed in the same building. All adult cats had been previously vaccinated for common feline diseases including feline calicivirus (FCV). Detection of FCV RNA in oral secretions by a real-time reverse transcription polymerase chain reaction assay (RRT-PCR) confirmed FCV infection in the tiger cubs and one lion. A male lion and a male tiger cub died during the disease outbreak. RRT-PCR confirmed FCV in multiple tissues in both of these animals. A stray cat live-trapped outside the feline building during the epidemic was found to be positive for FCV by virus isolation and was thought to be the source of infection.

Estimating numbers of females with cubs-of-the-year in the Yellowstone grizzly bear population

USGS Publications Warehouse

Keating, K.A.; Schwartz, C.C.; Haroldson, M.A.; Moody, D.

2001-01-01

For grizzly bears (Ursus arctos horribilis) in the Greater Yellowstone Ecosystem (GYE), minimum population size and allowable numbers of human-caused mortalities have been calculated as a function of the number of unique females with cubs-of-the-year (FCUB) seen during a 3- year period. This approach underestimates the total number of FCUB, thereby biasing estimates of population size and sustainable mortality. Also, it does not permit calculation of valid confidence bounds. Many statistical methods can resolve or mitigate these problems, but there is no universal best method. Instead, relative performances of different methods can vary with population size, sample size, and degree of heterogeneity among sighting probabilities for individual animals. We compared 7 nonparametric estimators, using Monte Carlo techniques to assess performances over the range of sampling conditions deemed plausible for the Yellowstone population. Our goal was to estimate the number of FCUB present in the population each year. Our evaluation differed from previous comparisons of such estimators by including sample coverage methods and by treating individual sightings, rather than sample periods, as the sample unit. Consequently, our conclusions also differ from earlier studies. Recommendations regarding estimators and necessary sample sizes are presented, together with estimates of annual numbers of FCUB in the Yellowstone population with bootstrap confidence bounds.

Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations

PubMed Central

Porto, Markus; Bastolla, Ugo

2010-01-01

Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction. PMID:20463869

The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana

PubMed Central

Camiolo, Salvatore; Farina, Lorenzo; Porceddu, Andrea

2012-01-01

The codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both regionally and transcriptionally associated mutational biases were associated significantly with codon bias, they could not explain the observed differences fully. Similarly, given that transcript abundances did not account for the differences in codon usage, it is unlikely that selection for translational efficiency can account exclusively for the observed codon bias. Thus, we considered the possible evolution of codon bias as an adaptive response to the different abundances of tRNAs in different tissues. Our analysis demonstrated that in some cases, codon usage in genes that were expressed in a broad range of tissues was influenced primarily by the tissue in which the gene was expressed maximally. On the basis of this finding we propose that genes that are expressed in certain tissues might show a tissue-specific compositional signature in relation to codon usage. These findings might have implications for the design of transgenes in relation to optimizing their expression. PMID:22865738

Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome.

PubMed

Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

2016-02-24

Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts.

Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome

PubMed Central

Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

2016-01-01

Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts. PMID:26927064

Modes of thermal protection in polar bear cubs--at birth and on emergence from the den.

PubMed

Blix, A S; Lentfer, J W

1979-01-01

At birth in late December the polar bear is small (700 g), uninsulated, and helpless. It probably has a modest capacity for metabolic heat production and depends on the female and a snow den in which it is born for thermal protection. The microclimate of an artificial polar bear den was investigated at Point Barrow, AK, and the temperature therein found to stay around 0 degrees C provided a heat source (200 W) equivalent to an adult polar bear was introduced. When the bears desert the den in early April the cub has grown to about 10 kg and has a well-developed fur insulation, but almost no subcutaneous fat. The cub has a high resting metabolic rate (4.6 W.kg-1), which is supported by the fat polar bear milk. Its lower critical temperature is about -30 degrees C, and an ambient temperature of -45 degrees C results in only a 33% increase in metabolism. The cub can tolerate a wind chill of 2.3 kW.m2 without apparent stress of drop in rectal temperature. If the cub is immersed in ice water rectal temperature drops 11 degrees C in 30 min. It is concluded that the cub can tolerate extremely low temperatures in air due to fur insulation and high metabolic heat production, but is unable to cope with the chill of ice water for any prolonged period of time.

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species.

PubMed

Dass, J Febin Prabhu; Sudandiradoss, C

2012-07-15

5-HT (5-Hydroxy-tryptamine) or serotonin receptors are found both in central and peripheral nervous system as well as in non-neuronal tissues. In the animal and human nervous system, serotonin produces various functional effects through a variety of membrane bound receptors. In this study, we focus on 5-HT receptor family from different mammals and examined the factors that account for codon and nucleotide usage variation. A total of 110 homologous coding sequences from 11 different mammalian species were analyzed using relative synonymous codon usage (RSCU), correspondence analysis (COA) and hierarchical cluster analysis together with nucleotide base usage frequency of chemically similar amino acid codons. The mean effective number of codon (ENc) value of 37.06 for 5-HT(6) shows very high codon bias within the family and may be due to high selective translational efficiency. The COA and Spearman's rank correlation reveals that the nucleotide compositional mutation bias as the major factors influencing the codon usage in serotonin receptor genes. The hierarchical cluster analysis suggests that gene function is another dominant factor that affects the codon usage bias, while species is a minor factor. Nucleotide base usage was reported using Goldman, Engelman, Stietz (GES) scale reveals the presence of high uracil (>45%) content at functionally important hydrophobic regions. Our in silico approach will certainly help for further investigations on critical inference on evolution, structure, function and gene expression aspects of 5-HT receptors family which are potential antipsychotic drug targets. Copyright © 2012 Elsevier B.V. All rights reserved.

Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution.

PubMed

Nasrullah, Izza; Butt, Azeem M; Tahir, Shifa; Idrees, Muhammad; Tong, Yigang

2015-08-26

The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.

The Little Cub: Discovery of an Extremely Metal-poor Star-forming Galaxy in the Local Universe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsyu, Tiffany; Prochaska, J. Xavier; Bolte, Michael

We report the discovery of the Little Cub, an extremely metal-poor star-forming galaxy in the local universe, found in the constellation Ursa Major (a.k.a. the Great Bear). We first identified the Little Cub as a candidate metal-poor galaxy based on its Sloan Digital Sky Survey photometric colors, combined with spectroscopy using the Kast spectrograph on the Shane 3 m telescope at Lick Observatory. In this Letter, we present high-quality spectroscopic data taken with the Low Resolution Imaging Spectrometer at Keck Observatory, which confirm the extremely metal-poor nature of this galaxy. Based on the weak [O iii] λ 4363 Å emissionmore » line, we estimate a direct oxygen abundance of 12 + log(O/H) = 7.13 ± 0.08, making the Little Cub one of the lowest-metallicity star-forming galaxies currently known in the local universe. The Little Cub appears to be a companion of the spiral galaxy NGC 3359 and shows evidence of gas stripping. We may therefore be witnessing the quenching of a near-pristine galaxy as it makes its first passage about a Milky Way–like galaxy.« less

The Little Cub: Discovery of an Extremely Metal-poor Star-forming Galaxy in the Local Universe

NASA Astrophysics Data System (ADS)

Hsyu, Tiffany; Cooke, Ryan J.; Prochaska, J. Xavier; Bolte, Michael

2017-08-01

We report the discovery of the Little Cub, an extremely metal-poor star-forming galaxy in the local universe, found in the constellation Ursa Major (a.k.a. the Great Bear). We first identified the Little Cub as a candidate metal-poor galaxy based on its Sloan Digital Sky Survey photometric colors, combined with spectroscopy using the Kast spectrograph on the Shane 3 m telescope at Lick Observatory. In this Letter, we present high-quality spectroscopic data taken with the Low Resolution Imaging Spectrometer at Keck Observatory, which confirm the extremely metal-poor nature of this galaxy. Based on the weak [O III] λ4363 Å emission line, we estimate a direct oxygen abundance of 12 + log(O/H) = 7.13 ± 0.08, making the Little Cub one of the lowest-metallicity star-forming galaxies currently known in the local universe. The Little Cub appears to be a companion of the spiral galaxy NGC 3359 and shows evidence of gas stripping. We may therefore be witnessing the quenching of a near-pristine galaxy as it makes its first passage about a Milky Way-like galaxy.

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

PubMed Central

Wang, Hongju; Liu, Siqing; Zhang, Bo

2016-01-01

Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts. PMID:27893824

Molecular dynamics study of the diffusivity of a hydrophobic drug Cucurbitacin B in pseudo-poly(ethylene oxide-b-caprolactone) micelle environments.

PubMed

Razavilar, Negin; Choi, Phillip

2014-07-08

Isobaric-isothermal molecular dynamics simulation was used to study the diffusion of a hydrophobic drug Cucurbitacin B (CuB) in pseudomicelle environments consisting of poly(ethylene oxide-b-caprolactone) (PEO-b-PCL) swollen by various amounts of water. Two PEO-b-PCL configurations, linear and branched, with the same total molecular weight were used. For the branched configuration, the block copolymer contained one linear block of PEO with the same molecular weight as that of the PEO block used in the linear configuration but with one end connecting to three PCL blocks with the same chain length, hereafter denoted PEO-b-3PCL. Regardless of the configuration, the simulation results showed that the diffusivity of CuB was insensitive to the water concentration up to ∼8 wt % while that of water decreased with an increasing water concentration. The diffusivity of CuB (10(-8) cm(2)/s) was 3 orders of magnitude lower than that of water (10(-5) cm(2)/s). This is attributed to the fact that CuB relied on the wiggling motion of the block copolymers to diffuse while water molecules diffused via a hopping mechanism. The rates at which CuB and water diffused into PEO-b-PCL were twice those in PEO-b-3PCL because the chain mobility and the degree of swelling are higher and there are fewer intermolecular hydrogen bonds in the case of PEO-b-PCL. The velocity autocorrelation functions of CuB show that the free volume holes formed by PEO-b-3PCL are more rigid than those formed by PEO-b-PCL, making CuB exhibit higher-frequency collision motion in PEO-b-3PCL than in PEO-b-PCL, and the difference in frequency is insensitive to water concentration.

Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects.

PubMed

Selva Kumar, C; Nair, Rahul R; Sivaramakrishnan, K G; Ganesh, D; Janarthanan, S; Arunachalam, M; Sivaruban, T

2012-12-01

Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages.

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.

PubMed

Bera, Bidhan Ch; Virmani, Nitin; Kumar, Naveen; Anand, Taruna; Pavulraj, S; Rash, Adam; Elton, Debra; Rash, Nicola; Bhatia, Sandeep; Sood, Richa; Singh, Raj Kumar; Tripathi, Bhupendra Nath

2017-08-23

Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2. Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the codon usage patterns and evolution of polymerase genes of EIVs.

Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum

PubMed Central

Charles, Hubert; Calevro, Federica; Vinuelas, José; Fayard, Jean-Michel; Rahbe, Yvan

2006-01-01

Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in Buchnera: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon–anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of Buchnera. PMID:16963497

Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum.

PubMed

Charles, Hubert; Calevro, Federica; Vinuelas, José; Fayard, Jean-Michel; Rahbe, Yvan

2006-01-01

Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in Buchnera: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon-anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of Buchnera.

Double aortic arch and persistent left vena cava in a white lion cub (Panthera leo).

PubMed

Goldin, J P; Lambrechts, N E

1999-03-01

A 4-mo-old female white lion (Panthera leo) cub was presented with a 2-wk history of persistent postprandial regurgitation, mild dyspnea, and poor weight gain. The cub was weak and thin but otherwise alert. Survey and contrast radiography revealed a large dilated esophagus cranial to the heart base, with an esophageal filling defect present at the level of the fourth thoracic vertebra. A vascular ring anomaly was tentatively diagnosed. Exploratory thoracotomy revealed a double aortic arch and a persistent left vena cava. The left aortic arch was ligated and divided, and recovery was uneventful. A single episode of regurgitation occurred within the first postoperative month, and the cub gained 5.5 kg in weight during the same time period. Neither double aortic arch nor persistent left vena cava has been reported in a nondomestic felid.

B cell Variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions

PubMed Central

Saini, Jasmine; Hershberg, Uri

2015-01-01

The exceptional ability of B cells to diversify through somatic mutation and improve affinity of the repertoire towards the antigens is the cornerstone of adaptive immunity. Somatic mutation is not evenly distributed and exhibits certain micro-sequence specificities. We show here that the combination of somatic mutation targeting and the codon usage in human B cell receptor (BCR) Variable (V) genes create expected patterns of mutation and post mutation changes that are focused on their complementarity determining regions (CDR). T cell V genes are also skewed in targeting mutations but to a lesser extent and are lacking the codon usage bias observed in BCRs. This suggests that the observed skew in T cell receptors is due to their amino acid usage, which is similar to that of BCRs. The mutation targeting and the codon bias allow B cell CDRs to diversify by specifically accumulating nonconservative changes. We counted the distribution of mutations to CDR in 4 different human datasets. In all four cases we found that the number of actual mutations in the CDR correlated significantly with the V gene mutation biases to the CDR predicted by our models. Finally, it appears that the mutation bias in V genes indeed relates to their long-term survival in actual human repertoires. We observed that resting repertoires of B cells overexpressed V genes that were especially biased towards focused mutation and change in the CDR. This bias in V gene usage was somewhat relaxed at the height of the immune response to a vaccine, presumably because of the need for a wider diversity in a primary response. However, older patients did not retain this flexibility and were biased towards using only highly skewed V genes at all stages of their response. PMID:25660968

B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions.

PubMed

Saini, Jasmine; Hershberg, Uri

2015-05-01

The exceptional ability of B cells to diversify through somatic mutation and improve affinity of the repertoire toward the antigens is the cornerstone of adaptive immunity. Somatic mutation is not evenly distributed and exhibits certain micro-sequence specificities. We show here that the combination of somatic mutation targeting and the codon usage in human B cell receptor (BCR) Variable (V) genes create expected patterns of mutation and post mutation changes that are focused on their complementarity determining regions (CDR). T cell V genes are also skewed in targeting mutations but to a lesser extent and are lacking the codon usage bias observed in BCRs. This suggests that the observed skew in T cell receptors is due to their amino acid usage, which is similar to that of BCRs. The mutation targeting and the codon bias allow B cell CDRs to diversify by specifically accumulating nonconservative changes. We counted the distribution of mutations to CDR in 4 different human datasets. In all four cases we found that the number of actual mutations in the CDR correlated significantly with the V gene mutation biases to the CDR predicted by our models. Finally, it appears that the mutation bias in V genes indeed relates to their long-term survival in actual human repertoires. We observed that resting repertoires of B cells overexpressed V genes that were especially biased toward focused mutation and change in the CDR. This bias in V gene usage was somewhat relaxed at the height of the immune response to a vaccine, presumably because of the need for a wider diversity in a primary response. However, older patients did not retain this flexibility and were biased toward using only highly skewed V genes at all stages of their response. Copyright © 2015 Elsevier Ltd. All rights reserved.

Observations of mixed-aged litters in brown bears

USGS Publications Warehouse

Swenson, J.E.; Haroldson, M.A.

2008-01-01

We report on 3 cases of mixed-aged litters (young born in different years) in brown bears (Ursus arctos); in 1 instance the cub-of-the-year (hereafter called cubs) died in the den. Two cases occurred in Sweden after mothers were separated from their young during the breeding season. In one, the mother was separated from the accompanying cub for at least 12.5 hours and possibly up to 3.3 days, and later possibly separated for 4 days. In the other, the mother was separated from her yearling at least 3 times for 1-14, 1-6 and 1-6 days. She was with a male during the first separation. Specific events that produced the mixed-aged litter observed in Greater Yellowstone Ecosystem were unknown and our interpretation is based on estimates of ages of accompanying young from photographs. The observation of only 2 mixed-aged litters, after den emergence, from a sample of 406 observed cub litters accompanying radiomarked females confirms the rarity of this phenomenon. The mechanism apparently includes a short separation of mother and young, and, in the case of cubs, the mother must mate while lactating. Better understanding of the physiological mechanisms that allow mixed-age litters would help us in the debate about the occurrence of sexually selected infanticide in bears.

Effects of Angiotensin Inhibitor Valsartan on the Expression of the Angiotensin II 1 Receptor, Matrix Metalloproteinases -2 and -9 in Human Bladder Cancer Cell Lines.

PubMed

Yang, Delin; Huo, Qian; Luan, Ting; Wang, Jiansong; Tang, Zhaoran; Wang, Haifeng

2016-08-01

In order to investigate how valsartan-the angiotensin II 1 receptor (AT1R) antagonist-affects the expressions of AT1R antigen, matrix metalloproteinases (MMPs) -2 and -9 in carcinoma of urinary bladder (CUB) cell lines with different invasive abilities. Three cell lines, EJ-M3, EJ, and BIU-87, with different invasive abilities were cultured and treated with valsartan. Cell proliferation states were determined by the methyl thiazolyl tetrazolium (MTT) method. The expressions at protein level and gene level were determined by Western blot and real-time fluorescence reverse transcription polymerase chain reaction (RT-PCR), respectively. The invasive abilities and migratory abilities of the three cell lines were determined by Transwell in vitro cell invasion assay and wound healing assay, respectively. MTT results show that valsartan can inhibit the proliferation of CUB cells, and the inhibition effect is enhanced with the increase of concentration. AngII promotes the MMP2 and MMP9 expressions (both protein and gene levels) in CUB cells through AT1R, but their expressions can be effectively inhibited by valsartan, the AngII inhibitor. AngII inhibitor may become a novel drug that can inhibit CUB metastasis and prolong the survival of CUB patients.

Characterization of codon usage pattern and influencing factors in Japanese encephalitis virus.

PubMed

Singh, Niraj K; Tyagi, Anuj; Kaur, Rajinder; Verma, Ramneek; Gupta, Praveen K

2016-08-02

Recently, several outbreaks of Japanese encephalitis (JE), caused by Japanese encephalitis virus (JEV), have been reported and it has become cause of concern across the world. In this study, detailed analysis of JEV codon usage pattern was performed. The relative synonymous codon usage (RSCU) values along with mean effective number of codons (ENC) value of 55.30 indicated the presence of low codon usages bias in JEV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations of A3s, U3s, G3s, C3s, GC3s, ENC values, with overall nucleotide contents (A%, U%, G%, C%, and GC%). The correlation analysis of A3s, U3s, G3s, C3s, GC3s, with axis values of correspondence analysis (CoA) further confirmed the role of mutational pressure. However, the correlation analysis of Gravy values and Aroma values with A3s, U3s, G3s, C3s, and GC3s, indicated the presence of natural selection on codon usage bias in addition to mutational pressure. The natural selection was further confirmed by codon adaptation index (CAI) analysis. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern to some extent. Copyright © 2016 Elsevier B.V. All rights reserved.

Simultaneous determination of cucurbitacin B and cucurbitacin E in rat plasma by UHPLC-MS/MS: A pharmacokinetics study after oral administration of cucurbitacin tablets.

PubMed

Wang, Zhibin; Zhu, Wenbo; Gao, Mingjie; Wu, Chengcui; Yang, Chunjuan; Yang, Jing; Wu, Gaosong; Yang, Bingyou; Kuang, Haixue

2017-10-15

Cucurbitacin B (CuB) and cucurbitacin E (CuE) are tetracyclic triterpene compounds from Cucurbitaceae, and the main bioactive compounds of cucurbitacins tablets that used to treatment of chronic hepatitis. Pharmacological research has been very comprehensive, and there are few studies on pharmacokinetics, especially about CuE. An Ultra High Performance Liquid Chromatography-tandem Mass Spectrometry (UHPLC-MS/MS) method with high selectivity, simplicity and sensitivity has been used for quantitative analysis of Cucurbitacin B (CuB) and cucurbitacin E (CuE). Plasma samples were pretreatment by Liquid-liquid extraction (LLE) method with dichloromethane. The chromatographic separation was achieved on a C 18 column (Agilent Eclipse Plus, 1.8μm, 50×2.1mm) using gradient elution with water - methanol at a flow rate of 0.3mL/min and the column temperature was set at 30°C. The method was validated according to FDA guidelines. Lower limit of quantification (LLOQ) was 1.60ng/mL for CuB and 1.58ng/mL for CuE. Correlation coefficients of CuB and CuE were more than 0.99 in rat plasma. All values of intra-day and inter-day precision (RSD%) were not exceeded 15%, the accuracy (RE%) were within -5.57 to 5.20% for CuB and -3.33 to 7.37% for CuE. The mean extraction recoveries were more than 80%. Pharmacokinetic parameters were also evaluated by UHPLC-MS/MS method. The results suggestion that this method was successfully applied to pharmacokinetic study of CuB and CuE in rat plasma after oral administration cucurbitacin tablets. Published by Elsevier B.V.

Cucurbitacin B inhibits breast cancer metastasis and angiogenesis through VEGF-mediated suppression of FAK/MMP-9 signaling axis.

PubMed

Sinha, Sonam; Khan, Sajid; Shukla, Samriddhi; Lakra, Amar Deep; Kumar, Sudhir; Das, Gunjan; Maurya, Rakesh; Meeran, Syed Musthapa

2016-08-01

Available breast cancer therapeutic strategies largely target the primary tumor but are ineffective against tumor metastasis and angiogenesis. In our current study, we determined the effect of Cucurbitacin B (CuB), a plant triterpenoid, on the metastatic and angiogenic potential of breast cancer cells. CuB was found to inhibit cellular proliferation and induce apoptosis in breast cancer cells in a time- and dose-dependent manner. Further, CuB-treatment significantly inhibited the migratory and invasive potential of highly metastatic breast cancer MDA-MB-231 and 4T1 cells at sub-IC50 concentrations, where no significant apoptosis was observed. CuB was also found to inhibit migratory, invasive and tube-forming capacities of HUVECs in vitro. In addition, inhibition of pre-existing vasculature in chick embryo chorioallantoic membrane ex vivo further supports the anti-angiogenic effect of CuB. CuB-mediated anti-metastatic and anti-angiogenic effects were associated with the downregulation of VEGF/FAK/MMP-9 signaling, which has been validated by using FAK-inhibitor (FI-14). CuB-treatment resulted in a significant inhibition of VEGF-induced phosphorylation of FAK and MMP-9 expressions similar to the action of FI-14. CuB was also found to decrease the micro-vessel density as evidenced by the decreased expression of CD31, a marker for neovasculature. Further, CuB-treatment inhibited tumor growth, lung metastasis and angiogenesis in a highly metastatic 4T1-syngeneic mouse mammary cancer. Collectively, our findings suggest that CuB inhibited breast cancer metastasis and angiogenesis, at least in part, through the downregulation of VEGF/FAK/MMP-9 signaling. Copyright © 2016 Elsevier Ltd. All rights reserved.

SURGICAL CORRECTION OF BILATERAL PATELLAR LUXATION IN AN AMERICAN BLACK BEAR CUB (URSUS AMERICANUS).

PubMed

Bennett, Katarina R; Desmarchelier, Marion R; Bailey, Trina R

2015-06-01

A wild orphaned male American black bear cub ( Ursus americanus ) presented with hind limb gait abnormalities and was found to have bilateral grade 3 laterally luxating patellas. There were no other significant abnormalities detected on neurologic, radiographic, or hematologic examinations. The trochlear grooves were deepened with a chondroplasty, and the redundant soft tissues imbricated. There was a marked improvement in the bear's gait postoperatively, with an apparent full return to function. To the authors' knowledge, patellar luxation has not been reported in the Ursidae family, and the success in this case suggests that this technique may be used in large wild or captive carnivore cubs.

The world of tomorrow: Aerospace activities for 8- to 10-year olds. A guide for leaders of children's groups and teachers of the lower grades

NASA Technical Reports Server (NTRS)

1978-01-01

During January 1977, NASA helped the Cub Scout Division of the Boy Scouts of America in the conduct of its The World of Tomorrow monthly theme. In this period, 249 Cub Scout packs participated in a nationwide aerospace activities project, a pilot project in which den leaders and Cubmasters conducted local programs for their Cub Scouts and Webelos Scouts. The products of these local programs are presented with the written accounts submitted by adult leaders and written compositions, pictures, and photographs of models submitted by the youngsters.

Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica.

PubMed

Romero, H; Zavala, A; Musto, H

2000-01-25

It is widely accepted that the compositional pressure is the only factor shaping codon usage in unicellular species displaying extremely biased genomic compositions. This seems to be the case in the prokaryotes Mycoplasma capricolum, Rickettsia prowasekii and Borrelia burgdorferi (GC-poor), and in Micrococcus luteus (GC-rich). However, in the GC-poor unicellular eukaryotes Dictyostelium discoideum and Plasmodium falciparum, there is evidence that selection, acting at the level of translation, influences codon choices. This is a twofold intriguing finding, since (1) the genomic GC levels of the above mentioned eukaryotes are lower than the GC% of any studied bacteria, and (2) bacteria usually have larger effective population sizes than eukaryotes, and hence natural selection is expected to overcome more efficiently the randomizing effects of genetic drift among prokaryotes than among eukaryotes. In order to gain a new insight about this problem, we analysed the patterns of codon preferences of the nuclear genes of Entamoeba histolytica, a unicellular eukaryote characterised by an extremely AT-rich genome (GC = 25%). The overall codon usage is strongly biased towards A and T in the third codon positions, and among the presumed highly expressed sequences, there is an increased relative usage of a subset of codons, many of which are C-ending. Since an increase in C in third codon positions is 'against' the compositional bias, we conclude that codon usage in E. histolytica, as happens in D. discoideum and P. falciparum, is the result of an equilibrium between compositional pressure and selection. These findings raise the question of why strongly compositionally biased eukaryotic cells may be more sensitive to the (presumed) slight differences among synonymous codons than compositionally biased bacteria.

Individual variation in space use by female spotted hyenas

USGS Publications Warehouse

Boydston, Erin E.; Kapheim, Karen M.; Szykman, Micaela; Holekamp, Kay E.

2003-01-01

Large carnivores range more widely than many other terrestrial mammals, and this behavior tends to bring them into frequent conflict with humans. Within any carnivore population, individual variation in patterns of space use should be expected to make some animals more vulnerable than others to risks of mortality from humans and other sources. In this study, our goal was to document variation among individuals in space use by female spotted hyenas (Crocuta crocuta). We examined predictions of hypotheses suggesting that space use by female hyenas is affected by reproductive state, social rank, and local prey abundance. Home-range size, distance at which females were found from the current communal den, and distance at which they were found from the nearest territorial boundary all varied significantly with the 3 independent variables. Females with den-dwelling cubs had smaller home ranges, were found closer to the communal den, and were found farther from the territorial boundary than were females with no den-dwelling cubs. Neither social rank nor prey availability significantly influenced the space-use patterns of females with den-dwelling cubs. Among females with no den-dwelling cubs, high-ranking females had smaller home ranges, were closer to the communal den, and were farther from the territorial boundary than were low-ranking females. The females ranging most widely were low-ranking individuals with no den-dwelling cubs when they were observed during periods of prey scarcity.

A detailed analysis of codon usage patterns and influencing factors in Zika virus.

PubMed

Singh, Niraj K; Tyagi, Anuj

2017-07-01

Recent outbreaks of Zika virus (ZIKV) in Africa, Latin America, Europe, and Southeast Asia have resulted in serious health concerns. To understand more about evolution and transmission of ZIKV, detailed codon usage analysis was performed for all available strains. A high effective number of codons (ENC) value indicated the presence of low codon usage bias in ZIKV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations between nucleotide compositions at third codon positions and ENCs. Correlation analysis between Gravy values, Aroma values and nucleotide compositions at third codon positions also indicated some influence of natural selection. However, the low codon adaptation index (CAI) value of ZIKV with reference to human and mosquito indicated poor adaptation of ZIKV codon usage towards its hosts, signifying that natural selection has a weaker influence than mutational pressure. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern to some extent.

Take a Tip from the Cubs

ERIC Educational Resources Information Center

Fornaciari, James

2016-01-01

As legendary Cubs manager Joe Maddon did with his players, seeing students as people first works for teachers who hope to build cohesive classes that achieve. Maddon's strength was his emphasis on cultivating positive relationships among his players. Taking a tip from Maddon's strategy, Fornaciari, an Advanced Placement history teacher, shares…

Synonymous codon usage of genes in polymerase complex of Newcastle disease virus.

PubMed

Kumar, Chandra Shekhar; Kumar, Sachin

2017-06-01

Newcastle disease virus (NDV) is pathogenic to both avian and non-avian species but extensively finds poultry as its primary host and causes heavy economic losses in the poultry industry. In this study, a total of 186 polymerase complex comprising of nucleoprotein (N), phosphoprotein (P), and large polymerase (L) genes of NDV was analyzed for synonymous codon usage. The relative synonymous codon usage and effective number of codons (ENC) values were used to estimate codon usage variation in each gene. Correspondence analysis (COA) was used to study the major trend in codon usage variation. Analyzing the ENC plot values against GC3s (at synonymous third codon position) we concluded that mutational pressure was the main factor determining codon usage bias than translational selection in NDV N, P, and L genes. Moreover, correlation analysis indicated, that aromaticity of N, P, and L genes also influenced the codon usage variation. The varied distribution of pathotypes for N, P, and L gene clearly suggests that change in codon usage for NDV is pathotype specific. The codon usage preference similarity in N, P, and L gene might be detrimental for polymerase complex functioning. The study represents a comprehensive analysis to date of N, P, and L genes codon usage pattern of NDV and provides a basic understanding of the mechanisms for codon usage bias. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Poetry Workshop & Poster.

ERIC Educational Resources Information Center

Cullinan, Bee

2002-01-01

Suggests that Judith Nicholls'"Polar Cub" is a good wintery poem to share with students. In it, the poet invites the cub to come out of its cave and explore in the snow, just as teachers invite children to explore words and ideas in poetry. The article explains how to read the poem to students. A poster is included. (SM)

Views of Astronaut (Col.) Joe Engle and son Jon with L-5 Piper Cub

NASA Technical Reports Server (NTRS)

1981-01-01

Views of Astronaut (Col.) Joe Engle and son Jon with L-5 Piper Cub at Clover Airport. Photos include Engle turning propeller while his son sits in the cockpit (34323); both Engle and son examine propeller (34324); Engle works on engine while his son sits in cockpit (34325).

‘Neanderthal bone flutes’: simply products of Ice Age spotted hyena scavenging activities on cave bear cubs in European cave bear dens

PubMed Central

Diedrich, Cajus G.

2015-01-01

Punctured extinct cave bear femora were misidentified in southeastern Europe (Hungary/Slovenia) as ‘Palaeolithic bone flutes’ and the ‘oldest Neanderthal instruments’. These are not instruments, nor human made, but products of the most important cave bear scavengers of Europe, hyenas. Late Middle to Late Pleistocene (Mousterian to Gravettian) Ice Age spotted hyenas of Europe occupied mainly cave entrances as dens (communal/cub raising den types), but went deeper for scavenging into cave bear dens, or used in a few cases branches/diagonal shafts (i.e. prey storage den type). In most of those dens, about 20% of adult to 80% of bear cub remains have large carnivore damage. Hyenas left bones in repeating similar tooth mark and crush damage stages, demonstrating a butchering/bone cracking strategy. The femora of subadult cave bears are intermediate in damage patterns, compared to the adult ones, which were fully crushed to pieces. Hyenas produced round–oval puncture marks in cub femora only by the bone-crushing premolar teeth of both upper and lower jaw. The punctures/tooth impact marks are often present on both sides of the shaft of cave bear cub femora and are simply a result of non-breakage of the slightly calcified shaft compacta. All stages of femur puncturing to crushing are demonstrated herein, especially on a large cave bear population from a German cave bear den. PMID:26064624

Factors influencing breeding success, ovarian cyclicity, and cub survival in zoo-managed tigers (Panthera tigris).

PubMed

Saunders, Sarah P; Harris, Tara; Traylor-Holzer, Kathy; Beck, Karen Goodrowe

2014-01-10

Understanding factors that influence reproduction and offspring survival in zoo populations is critical for management of threatened and endangered species. Examination of long-term data (1989-2011) compiled from the Association of Zoos and Aquarium's zoo-managed tiger breeding program provides the basis for a more thorough understanding of reproduction and scientifically based decisions for effective population management in this endangered felid. Biological and management-related factors that could influence tiger breeding success and cub survival were evaluated using logistic mixed models. Breeding success improved with female age until approximately age five, then declined thereafter. Experienced female breeders had greater breeding success than inexperienced females. Litter size was most predictive of cub survival, with average-sized litters (3-4 cubs) experiencing the highest proportional survival. Management-related factors, such as whether the breeding institution had a recent tiger litter and whether both animals were already located at the same institution, also influenced breeding success and cub survival. These results highlight the importance of institutional husbandry experience and the need to retain knowledge through staff turnovers to achieve optimal reproductive success. Using fecal estrogen data, frequency of ovarian cyclicity and mean cycle length did not differ by female age or parity; thus, lack of cyclicity and/or increased cycle duration are not likely explanations for declining breeding success with age. These results provide valuable reproductive information that should improve scientific management of zoo-based tiger populations. Copyright © 2013 Elsevier B.V. All rights reserved.

Seroepidemiologic study on the prevalence of Toxoplasma gondii and Trichinella spp. infections in black bears (Ursus americanus) in Pennsylvania, USA.

PubMed

Dubey, Jitender P; Brown, Justin; Ternent, Mark; Verma, Shiv K; Hill, Dolores E; Cerqueira-Cézar, Camila K; Kwok, Oliver C H; Calero-Bernal, Rafael; Humphreys, Jan G

2016-10-15

The protozoan Toxoplasma gondii and the metazoan Trichinella spp. infect virtually all warm-blooded animals, including birds, humans, livestock, and marine mammals. Both parasitic infections can cause serious illness in human beings and can be acquired by ingesting under-cooked meat harboring infective stages. Approximately 3500 black bears (Ursus americanus) are legally-harvested each year in Pennsylvania, USA during the November hunting season. Among animals found infected with T. gondii, the prevalence of T. gondii is the highest among black bears in the USA; however, little is currently known of epidemiology of toxoplasmosis in this host species. Serum samples were collected during the winters of 2015 and 2016 from adult female bears and their nursing cubs or yearlings while they were still in their dens. Additionally, archived sera from bear samples collected throughout the year, including hunter-harvested bears in November and trapped bears in the summer, were serologically tested. Antibodies to T. gondii were assayed by the modified agglutination test (MAT, cut-off 1:25) and antibodies to Trichinella spp. were assayed using a commercial enzyme-linked immunosorbent assay (ELISA). Overall, T. gondii antibodies were found in 87.6% (206/235) of adults, and 44.1% (30/68) of yearlings. In March 2015/2016 sampling, antibodies to T. gondii were found in 94% (30/32) adult female bears while in their den. Antibodies were detected in 5% (3/66) of the nursing cubs in the dens of these sows. One positive cub had a MAT titer of 1:160 and two were positive at the 1:25 dilution but not at 1:50. The adult females of these cubs had MAT titers ranging from 1:400 to 1:3200. Antibodies to Trichinella spp. were found in 3% (6/181) of adults and 3.6% (1/28) of yearlings; these 7 bears were also seropositive for T. gondii. No antibodies to Trichinella spp. were detected in the sera of 44 nursing cubs tested. The finding of T. gondii antibodies in only 3 of 66 cubs, and higher antibody titers in their respective sows indicates that the colostrally-acquired antibodies wane to undetectable levels by 8-10 weeks, while the cubs are still in the den. The results indicate that there is no transplacental transmission of T. gondii, that antibodies acquired from colostrum are largely undetectable by the time cubs emerge from the den, and nearly that 50% of bears acquire infection postnatally by 10 months of age. This is the first report of disappearance of transcolostral antibodies of any infection in bears. Copyright © 2016. Published by Elsevier B.V.

Wave-Ice and Air-Ice-Ocean Interaction During the Chukchi Sea Ice Edge Advance

DTIC Science & Technology

2014-09-30

During cruise CU-B UAF UW Airborne expendable Ice Buoy (AXIB) Ahead, at and inside ice edge Surface meteorology T, SLP ~1 year CU-B UW...Balance (IMB) buoys Inside ice edge w/ >50cm thickness Ice mass balance T in snow-ice-ocean, T, SLP at surface ~1 year WHOI CRREL (SeaState DRI

Does taurine deficiency cause metabolic bone disease and rickets in polar bear cubs raised in captivity?

PubMed

Chesney, Russell W; Hedberg, Gail E; Rogers, Quinton R; Dierenfeld, Ellen S; Hollis, Bruce E; Derocher, Andrew; Andersen, Magnus

2009-01-01

Rickets and fractures have been reported in captive polar bears. Taurine (TAU) is key for the conjugation of ursodeoxycholic acid (UDCA), a bile acid unique to bears. Since TAU-conjugated UDCA optimizes fat and fat-soluble vitamin absorption, we asked if TAU deficiency could cause vitamin D malabsorption and lead to metabolic bone disease in captive polar bears. We measured TAU levels in plasma (P) and whole blood (WB) from captive and free-ranging cubs and adults, and vitamin D3 and TAU concentrations in milk samples from lactating sows. Plasma and WB TAU levels were significantly higher in cubs vs captive and free-ranging adult bears. Vitamin D in polar bear milk was 649.2 +/- 569.2 IU/L, similar to that found in formula. The amount of TAU in polar bear milk is 3166.4 +/- 771 nmol/ml, 26-fold higher than in formula. Levels of vitamin D in bear milk and formula as well as in plasma do not indicate classical nutritional vitamin D deficiency. Higher dietary intake of TAU by free-ranging cubs may influence bile acid conjugation and improve vitamin D absorption.

E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruneda, Jonathan N.; Smith, F. Donelson; Daurie, Angela

Pathogenic bacteria introduce effector proteins directly into the cytosol of eukaryotic cells to promote invasion and colonization. OspG, a Shigella spp. effector kinase, plays a role in this process by helping to suppress the host inflammatory response. OspG has been reported to bind host E2 ubiquitin-conjugating enzymes activated with ubiquitin (E2~Ub), a key enzyme complex in ubiquitin transfer pathways. A cocrystal structure of the OspG/UbcH5c~Ub complex reveals that complex formation has important ramifications for the activity of both OspG and the UbcH5c~Ub conjugate. OspG is a minimal kinase domain containing only essential elements required for catalysis. UbcH5c~Ub binding stabilizes anmore » active conformation of the kinase, greatly enhancing OspG kinase activity. In contrast, interaction with OspG stabilizes an extended, less reactive form of UbcH5c~Ub. Recognizing conserved E2 features, OspG can interact with at least ten distinct human E2s~Ub. Mouse oral infection studies indicate that E2~Ub conjugates act as novel regulators of OspG effector kinase function in eukaryotic host cells.« less

Predictors of postoperative outcomes of cubital tunnel syndrome treatments using multiple logistic regression analysis.

PubMed

Suzuki, Taku; Iwamoto, Takuji; Shizu, Kanae; Suzuki, Katsuji; Yamada, Harumoto; Sato, Kazuki

2017-05-01

This retrospective study was designed to investigate prognostic factors for postoperative outcomes for cubital tunnel syndrome (CubTS) using multiple logistic regression analysis with a large number of patients. Eighty-three patients with CubTS who underwent surgeries were enrolled. The following potential prognostic factors for disease severity were selected according to previous reports: sex, age, type of surgery, disease duration, body mass index, cervical lesion, presence of diabetes mellitus, Workers' Compensation status, preoperative severity, and preoperative electrodiagnostic testing. Postoperative severity of disease was assessed 2 years after surgery by Messina's criteria which is an outcome measure specifically for CubTS. Bivariate analysis was performed to select candidate prognostic factors for multiple linear regression analyses. Multiple logistic regression analysis was conducted to identify the association between postoperative severity and selected prognostic factors. Both bivariate and multiple linear regression analysis revealed only preoperative severity as an independent risk factor for poor prognosis, while other factors did not show any significant association. Although conflicting results exist regarding prognosis of CubTS, this study supports evidence from previous studies and concludes early surgical intervention portends the most favorable prognosis. Copyright © 2017 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.

Steppe lion remains imported by Ice Age spotted hyenas into the Late Pleistocene Perick Caves hyena den in northern Germany

NASA Astrophysics Data System (ADS)

Diedrich, Cajus G.

2009-05-01

Upper Pleistocene remains of the Ice Age steppe lion Panthera leo spelaea (Goldfuss, 1810) have been found in the Perick Caves, Sauerland Karst, NW Germany. Bones from many hyenas and their imported prey dating from the Lower to Middle Weichselian have also been recovered from the Perick Cave hyena den. These are commonly cracked or exhibit deep chew marks. The absence of lion cub bones, in contrast to hyena and cave bear cub remains in the Perick Caves, and other caves of northern Germany, excludes the possibility that P. leo spelaea used the cave for raising cubs. Only in the Wilhelms Cave was a single skeleton of a cub found in a hyena den. Evidence of the chewing, nibbling and cracking of lion bones and crania must have resulted from the importation and destruction of lion carcasses (4% of the prey fauna). Similar evidence was preserved at other hyena den caves and open air sites in Germany. The bone material from the Perick and other Central European caves points to antagonistic hyena and lion conflicts, similar to clashes of their modern African relatives.

HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it.

PubMed

Khrustalev, Vladislav Victorovich

2009-01-01

Guanine is the most mutable nucleotide in HIV genes because of frequently occurring G to A transitions, which are caused by cytosine deamination in viral DNA minus strands catalyzed by APOBEC enzymes. Distribution of guanine between three codon positions should influence the probability for G to A mutation to be nonsynonymous (to occur in first or second codon position). We discovered that nucleotide sequences of env genes coding for third variable regions (V3 loops) of gp120 from HIV1 and HIV2 have different kinds of guanine usage biases. In the HIV1 reference strain and 100 additionally analyzed HIV1 strains the guanine usage bias in V3 loop coding regions (2G>1G>3G) should lead to elevated nonsynonymous G to A transitions occurrence rates. In the HIV2 reference strain and 100 other HIV2 strains guanine usage bias in V3 loop coding regions (3G>2G>1G) should protect V3 loops from hypermutability. According to the HIV1 and HIV2 V3 alignment, insertion of the sequence enriched with 2G (21 codons in length) occurred during the evolution of HIV1 predecessor, while insertion of the different sequence enriched with 3G (19 codons in length) occurred during the evolution of HIV2 predecessor. The higher is the level of 3G in the V3 coding region, the lower should be the immune escaping mutation occurrence rates. This hypothesis was tested in this study by comparing the guanine usage in V3 loop coding regions from HIV1 fast and slow progressors. All calculations have been performed by our algorithms "VVK In length", "VVK Dinucleotides" and "VVK Consensus" (www.barkovsky.hotmail.ru).

Idiopathic acute onset myelopathy in cheetah (Acinonyx jubatus) cubs.

PubMed

Walzer, Christian; Url, Angelika; Robert, Nadia; Kübber-Heiss, Anna; Nowotny, Norbert; Schmidt, Peter

2003-03-01

Numerous cases of ataxia, hind limb paresis, and paralysis have occurred in cheetah (Acinonyx jubatus) cubs over the past 10 yr within the European Endangered Species Program population, including 12 in mainland Europe, two in the British Isles, one in Namibia, and one in Dubai. The condition is the most important medical factor limiting European cheetah population growth. Eight cubs at the Salzburg Zoo, Austria, were affected. They demonstrated upper motor neuron lesions when alive and bilateral, symmetrical myelin degeneration of the spinal cord on necropsy. Ballooning of myelin sheaths surrounded mostly preserved axons, and no spheroids, characteristic of acute axonal degeneration, were found. Myelin loss markedly exceeded axonal degeneration. The syndrome's etiology is unclear, although viral, bacterial, parasitic, genetic, nutritional-metabolic, toxic, and physical causes have been considered.

Reproductive success of farmed blue foxes.

PubMed

Ilukha, V A; Harri, M; Rekilä, T

1997-01-12

The aim of this study was to provide basic data for the different components of reproductive performance of blue foxes under farm conditions. The foxes were mated naturally and the perinatal mortality of cubs was carefully recorded. This data allowed the evaluation of the effect of females' age and differences between years, and the maternal and paternal components of reproductive success. Generally the results were similar for all four years of the study. Altogether 2047 females (84.8 % of the total) gave birth to 22 941 cubs, of which 5.9% were stillborn and 11.4% died before weaning. Only in a very few cases (1.3%) was it the whole litter that was lost, and more commonly, there were some cub losses in almost one-half of the litters (46.9%). Abnormal birth and abortion of a part of a litter contributed most to reproductive failure of the vixen. Infanticide played a minimal role as a cause of postnatal cub mortality (0.3%). Death of the vixen was extremely rare. One half of all parturitions were dated between May 14 and May 28 and May 8 and May 20, for primiparous and multiparous vixens, respectively. Thus the parturitions peaked 5 days earlier (p < 0.001, median test) for multiparous vixens. The litter size was smaller and cub losses were higher for primiparous vixens than for multiparous ones. With a few exceptions, the age of the father or date of birth did not affect litter size or cub mortality. Postnatal cub mortality (y, %) decreased with age of the cub (x, days) and can be described by a simple equation: y = 15.3 - 11.2 log x, r(2) = 0.933. Fractional cub mortality increased with increasing litter size. Despite being significant, this increase was modest in extent. Low h(2) -values were observed for litter size at birth. ZUSAMMENFASSUNG: Der Zweck dieser Untersuchung war es, Basisinformation über verschiedene Komponenten der Reproduktion bei farmgezüchteten Blaufüchsen zu gewinnen. Die Fähen wurden naturlich gepaart. Eine besondere Aufmerksamkeit wurde der perinatalen Jungsterblichkeit gewidmet. Im allgemeinen waren die Ergebnisse für alle vier Jahre der Untersuchung gleich. Insgesamt 2 047 Fähen (84.8% von) warfen 22 941 Jungen. Von diesen wurden 5.6% totgeboren, und 11.4% starben später. Nur sehr selten war der ganze Wurf verloren (1.3%), aber Verluste fanden fast in der Hälfte der Würfe (46.9%) statt. Abnormale Geburt und Abort waren die häufigsten Ursachen der Geburtsprobleme der Fähen. Nur sehr selten brachte die Fähe ihre Jungen um (0.3%). Ebenso selten war ein Tod der Fähe. Eine Hälfte der Geburten fanden zwischen 14 und 28 Mai, bei Jungfähen und zwischen 8 und 20 Mai bei älteren statt. Die Jungfähen hatten kleinere Würfe und höhere Jungverluste als die Altfähen, wobei die Rüden fast keinen Einfluß hatten. Die postnatale Jungsterblichkeit (y, %) nahm mit Alter der Jungen (x, Tage) rasch ab, und kann mit einer einfachen Gleichung dargestellt werden: y = 15.3 - 11.2 log x, r(2) = 0.933. Jungsterblichkeit nahm mit der Grösse des Wurfes zu. Diese Wirkung war statistisch significant, zwar klein in Quantität. Die Heritabilitätswerte (h(2) ) der Wurfgrösse waren klein. 1997 Blackwell Verlag GmbH.

Grizzly bear population vital rates and trend in the Northern Continental Divide Ecosystem, Montana

USGS Publications Warehouse

Mace, R.D.; Carney, D.W.; Chilton-Radandt, T.; Courville, S.A.; Haroldson, M.A.; Harris, R.B.; Jonkel, J.; McLellan, B.; Madel, M.; Manley, T.L.; Schwartz, C.C.; Servheen, C.; Stenhouse, G.; Waller, J.S.; Wenum, E.

2012-01-01

We estimated grizzly bear (Ursus arctos) population vital rates and trend for the Northern Continental Divide Ecosystem (NCDE), Montana, between 2004 and 2009 by following radio-collared females and observing their fate and reproductive performance. Our estimates of dependent cub and yearling survival were 0.612 (95% CI = 0.300–0.818) and 0.682 (95% CI = 0.258–0.898). Our estimates of subadult and adult female survival were 0.852 (95% CI = 0.628–0.951) and 0.952 (95% CI = 0.892–0.980). From visual observations, we estimated a mean litter size of 2.00 cubs/litter. Accounting for cub mortality prior to the first observations of litters in spring, our adjusted mean litter size was 2.27 cubs/litter. We estimated the probabilities of females transitioning from one reproductive state to another between years. Using the stable state probability of 0.322 (95% CI = 0.262–0.382) for females with cub litters, our adjusted fecundity estimate (mx) was 0.367 (95% CI = 0.273–0.461). Using our derived rates, we estimated that the population grew at a mean annual rate of approximately 3% (λ = 1.0306, 95% CI = 0.928–1.102), and 71.5% of 10,000 Monte Carlo simulations produced estimates of λ > 1.0. Our results indicate an increasing population trend of grizzly bears in the NCDE. Coupled with concurrent studies of population size, we estimate that over 1,000 grizzly bears reside in and adjacent to this recovery area. We suggest that monitoring of population trend and other vital rates using radioed females be continued.

Evaluation of two milk replacers fed to hand-reared cheetah cubs (Acinonyx jubatus): nutrient composition, apparent total tract digestibility, and comparison to maternal cheetah milk.

PubMed

Bell, Katherine M; Rutherfurd, Shane M; Cottam, Yvette H; Hendriks, Wouter H

2011-01-01

Commercially prepared milk replacers are frequently used to provide the sole source of nutrition for hand-reared cheetah cubs (Acinonyx jubatus). The nutrient composition of two commonly used milk replacers was determined. Using titanium dioxide as an indigestible marker, nutrient digestibility was calculated from the analyses of fecal samples collected from each cub (n = 4 on formula 1, and n = 2 on formula 2). Mean apparent total tract digestibility for both formulas was >90% for all nutrients analyzed (crude protein, amino acids, crude fat (CF), and dry matter). However, the total CF content and the concentration of the essential fatty acids, such as α-linolenic, linolenic, and arachidonic acid, of both formulas was lower than reported for maternal cheetah milk. Additionally, one formula contained a comparatively high amount of carbohydrate, at the expense of protein. Although data were lacking for cheetah maternal milk, comparison with domestic cat milk revealed high concentrations of a number of minerals (K, Fe, Zn, and Cu), while vitamin D(3) was not detected in one formula. Both formulas were low in the majority of essential amino acids compared with domestic cat maternal milk. Despite their apparently high digestibility, neither formula was complete or balanced in terms of nutrient concentrations and ratios when maternal cheetah milk and/or the requirements established for growth in domestic cats were used as estimates of ideal. On this basis, although all cubs in this study were healthy and maintained good body conditions for the duration of the trial, the results of dietary analyses indicate that these milk replacers may not provide optimal nutrition for growth in cheetah cubs when used for extended periods. © 2010 Wiley-Liss, Inc.

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

PubMed Central

Lara-Ramírez, Edgar E.; Salazar, Ma Isabel; López-López, María de Jesús; Salas-Benito, Juan Santiago; Sánchez-Varela, Alejandro

2014-01-01

The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution. PMID:25136631

The fate of mercury in coal utilization byproducts

DOE Office of Scientific and Technical Information (OSTI.GOV)

William Aljoe; Thomas Feeley; James Murphy

2005-05-01

The US Department of Energy National Energy Technology Laboratory's (DOE/NETL's) research has helped to further scientific understanding of the environmental characteristics of coal-utilization by-products (CUBs) in both disposal and beneficial utilization applications. The following general observations can be drawn from results of the research that has been carried out to date: There appears to be only minimal mercury release to the environment in typical disposal or utilization applications for CUBs generated using activated carbon injection (ACI) control technologies; There appears to be only minimal mercury release to the environment in typical disposal and utilization applications for CUBs generated using wetmore » FGD control technologies. The potential release of mercury from wet FGD gypsum during the manufacture of wallboard is still under evaluation; The amount of mercury leached from CUB samples tested by DOE/NETL is significantly lower than the federal drinking water standards and water quality criteria for the protection of aquatic life; in many cases, leachate concentrations were below the standard test method detection limits. DOE/NETL will continue to partner with industry and other key stakeholders in carrying out research to better understand the fate of mercury and other trace elements in the byproducts from coal combustion. 16 refs., 6 tabs.« less

Codon Usage Bias and Determining Forces in Taenia solium Genome.

PubMed

Yang, Xing; Ma, Xusheng; Luo, Xuenong; Ling, Houjun; Zhang, Xichen; Cai, Xuepeng

2015-12-01

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Integrating resource selection information with spatial capture--recapture

USGS Publications Warehouse

Royle, J. Andrew; Chandler, Richard B.; Sun, Catherine C.; Fuller, Angela K.

2013-01-01

4. Finally, we find that SCR models using standard symmetric and stationary encounter probability models may not fully explain variation in encounter probability due to space usage, and therefore produce biased estimates of density when animal space usage is related to resource selection. Consequently, it is important that space usage be taken into consideration, if possible, in studies focused on estimating density using capture–recapture methods.

Multiple human exposures to a rabid bear cub at a petting zoo and barnwarming--Iowa, August 1999.

PubMed

1999-09-03

On August 27, 1999, a black bear cub, approximately 5-6 months old, died after several hours of acute central nervous system symptoms; preliminary test results available on August 28 indicated the bear had rabies. The bear was part of the Swenson's Wild Midwest Exotic Petting Zoo in Clermont, Iowa (northeastern Iowa). At the petting zoo, visitors fed, wrestled, and may have been nipped by the bear. The bear also was taken to an August 14 barnwarming at the Tharp barn in Holy Cross, Iowa (eastern Iowa), where it reportedly nipped people. An estimated 400 people from 10 states (Arizona, California, Florida, Illinois, Iowa, Minnesota, New Mexico, New York, Ohio, and Wisconsin) and Australia had contact with the bear cub at either the petting zoo or the barnwarming during the 28 days before its death, during which the bear may have transmitted rabies virus.

Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.

PubMed

Matsumoto, Tomotaka; John, Anoop; Baeza-Centurion, Pablo; Li, Boyang; Akashi, Hiroshi

2016-06-01

A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estimated α) considerably larger than its true value. Nonstationary evolution (changes in population size, selection, or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, α-hat < α. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating α. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with α-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Male reproductive strategy explains spatiotemporal segregation in brown bears

PubMed Central

Steyaert, Sam MJG; Kindberg, Jonas; Swenson, Jon E; Zedrosser, Andreas

2013-01-01

1. Spatiotemporal segregation is often explained by the risk for offspring predation or by differences in physiology, predation risk vulnerability or competitive abilities related to size dimorphism. 2. Most large carnivores are size dimorphic and offspring predation is often intraspecific and related to nonparental infanticide (NPI). NPI can be a foraging strategy, a strategy to reduce competition, or a male reproductive strategy. Spatiotemporal segregation is widespread among large carnivores, but its nature remains poorly understood. 3. We evaluated three hypotheses to explain spatiotemporal segregation in the brown bear, a size-dimorphic large carnivore in which NPI is common; the ‘NPI – foraging/competition hypothesis', i.e. NPI as a foraging strategy or a strategy to reduce competition, the ‘NPI – sexual selection hypothesis’, i.e. infanticide as a male reproductive strategy and the ‘body size hypothesis’, i.e. body-size-related differences in physiology, predation risk vulnerability or competitive ability causes spatiotemporal segregation. To test these hypotheses, we quantified spatiotemporal segregation among adult males, lone adult females and females with cubs-of-the-year, based on GPS-relocation data (2006–2010) and resource selection functions in a Scandinavian population. 4. We found that spatiotemporal segregation was strongest between females with cubs-of-the-year and adult males during the mating season. During the mating season, females with cubs-of-the-year selected their resources, in contrast to adult males, in less rugged landscapes in relative close proximity to certain human-related variables, and in more open habitat types. After the mating season, females with cubs-of-the-year markedly shifted their resource selection towards a pattern more similar to that of their conspecifics. No strong spatiotemporal segregation was apparent between females with cubs-of-the-year and conspecifics during the mating and the postmating season. 5. The ‘NPI – sexual selection hypothesis’ best explained spatiotemporal segregation in our study system. We suggest that females with cubs-of-the-year alter their resource selection to avoid infanticidal males. In species exhibiting NPI as a male reproductive strategy, female avoidance of infanticidal males is probably more common than observed or reported, and may come with a fitness cost if females trade safety for optimal resources. PMID:23461483

Density dependence, whitebark pine, and vital rates of grizzly bears

USGS Publications Warehouse

van Manen, Frank T.; Haroldson, Mark A.; Bjornlie, Daniel D.; Ebinger, Michael R.; Thompson, Daniel J.; Costello, Cecily M.; White, Gary C.

2016-01-01

Understanding factors influencing changes in population trajectory is important for effective wildlife management, particularly for populations of conservation concern. Annual population growth of the grizzly bear (Ursus arctos) population in the Greater Yellowstone Ecosystem, USA has slowed from 4.2–7.6% during 1983–2001 to 0.3–2.2% during 2002–2011. Substantial changes in availability of a key food source and bear population density have occurred. Whitebark pine (Pinus albicaulis), the seeds of which are a valuable but variable fall food for grizzly bears, has experienced substantial mortality primarily due to a mountain pine beetle (Dendroctonus ponderosae) outbreak that started in the early 2000s. Positive growth rates of grizzly bears have resulted in populations reaching high densities in some areas and have contributed to continued range expansion. We tested research hypotheses to examine if changes in vital rates detected during the past decade were more associated with whitebark pine decline or, alternatively, increasing grizzly bear density. We focused our assessment on known-fate data to estimate survival of cubs-of-the-year (cubs), yearlings, and independent bears (≥2 yrs), and reproductive transition of females from having no offspring to having cubs. We used spatially and temporally explicit indices for grizzly bear density and whitebark pine mortality as individual covariates. Models indicated moderate support for an increase in survival of independent male bears over 1983–2012, whereas independent female survival did not change. Cub survival, yearling survival, and reproductive transition from no offspring to cubs all changed during the 30-year study period, with lower rates evident during the last 10–15 years. Cub survival and reproductive transition were negatively associated with an index of grizzly bear density, indicating greater declines where bear densities were higher. Our analyses did not support a similar relationship for the index of whitebark pine mortality. The results of our study support the interpretation that slowing of population growth during the last decade was associated more with increasing grizzly bear density than the decline in whitebark pine. Grizzly bear density and its potential effect on vital rates and population trajectory warrant consideration for management of the grizzly bear population in the Greater Yellowstone Ecosystem.

Views of Astronaut (Col.) Joe Engle and son Jon with L-5 Piper Cub

NASA Technical Reports Server (NTRS)

1981-01-01

Views of Astronaut (Col.) Joe Engle and son Jon with L-5 Piper Cub at Clover Airport. Photos includes Jon Engle sitting on side door frame working on portion of wing. Joe Engle is behind him working on a wing strut (34329); Joe Engle works on tightening bolt (34330); Jon Engle works on portion of wing which connects to the cockpit. Joe Engle works on connecting strut to wing (34331).

Transthyretin-binding activity of contaminants in blood from polar bear (Ursus maritimus) cubs.

PubMed

Bytingsvik, Jenny; Simon, Eszter; Leonards, Pim E G; Lamoree, Marja; Lie, Elisabeth; Aars, Jon; Derocher, Andrew E; Wiig, Oystein; Jenssen, Bjørn M; Hamers, Timo

2013-05-07

We determined the transthyretin (TTR)-binding activity of blood-accumulating contaminants in blood plasma samples of approximately 4-months-old polar bear (Ursus maritimus) cubs from Svalbard sampled in 1998 and 2008. The TTR-binding activity was measured as thyroxine (T4)-like equivalents (T4-EQMeas). Our findings show that the TTR-binding activity related to contaminant levels was significantly lower (45%) in 2008 than in 1998 (mean ± standard error of mean: 1998, 2265 ± 231 nM; 2008, 1258 ± 170 nM). Although we cannot exclude a potential influence of between-year differences in capture location and cub body mass, our findings most likely reflect reductions of TTR-binding contaminants or their precursors in the arctic environment (e.g., polychlorinated biphenyls [PCBs]). The measured TTR-binding activity correlated positively with the cubs' plasma levels of hydroxylated PCBs (OH-PCBs). No such association was found between TTR-binding activity and the plasma levels of perfluoroalkyl substances (PFASs). The OH-PCBs explained 60 ± 7% and 54 ± 4% of the TTR-binding activity in 1998 and 2008, respectively, and PFASs explained ≤1.2% both years. Still, almost half the TTR-binding activity could not be explained by the contaminants we examined. The considerable levels of TTR-binding contaminants warrant further effect directed analysis (EDA) to identify the contaminants responsible for the unexplained part of the observed TTR-binding activity.

Roles of CUB and LDL receptor class A domain repeats of a transmembrane serine protease matriptase in its zymogen activation

PubMed Central

Inouye, Kuniyo; Tomoishi, Marie; Yasumoto, Makoto; Miyake, Yuka; Kojima, Kenji; Tsuzuki, Satoshi; Fushiki, Tohru

2013-01-01

Matriptase is a type II transmembrane serine protease containing two complement proteases C1r/C1s–urchin embryonic growth factor–bone morphogenetic protein domains (CUB repeat) and four low-density lipoprotein receptor class A domains (LDLRA repeat). The single-chain zymogen of matriptase has been found to exhibit substantial protease activity, possibly causing its own activation (i.e. conversion to a disulfide-linked two-chain fully active form), although the activation seems to be mediated predominantly by two-chain molecules. Our aim was to assess the roles of CUB and LDLRA repeats in zymogen activation. Transient expression studies of soluble truncated constructs of recombinant matriptase in COS-1 cells showed that the CUB repeat had an inhibitory effect on zymogen activation, possibly because it facilitated the interaction of two-chain molecules with a matriptase inhibitor, hepatocyte growth factor activator inhibitor type-1. By contrast, the LDLRA repeat had a promoting effect on zymogen activation. The effect of the LDLRA repeat seems to reflect its ability to increase zymogen activity. The proteolytic activities were higher in pseudozymogen forms of recombinant matriptase containing the LDLRA repeat than in a pseudozymogen without the repeat. Our findings provide new insights into the roles of these non-catalytic domains in the generation of active matriptase. PMID:23038671

Thermal stability of ‘metastable’ cubic tin sulfide and its relevance to applications

NASA Astrophysics Data System (ADS)

González Flores, Victoria Elena; Nair, M. T. S.; Nair, P. K.

2018-07-01

Recently identified tin sulfide polymorph with a cubic crystalline structure (SnS-CUB) and a large direct bandgap (1.74 eV) is described in theoretical studies as ‘metastable’. This implies that it is less stable than the orthorhombic polymorph (SnS-ORT) with indirect bandgap (1.1 eV). We find that SnS-CUB thin film (400 nm in thickness) and powder prepared by a chemical deposition method remain structurally stable, with 64 atoms in a large cubic unit cell of lattice constant 11.6 Å, even after they have been heated at 500 °C. Upon such heating the optical bandgap (E g ) of thin films decreased from 1.76 eV—direct gap in as-prepared thin films to 1.6 eV, and the electrical conductivity (σ) reduced from 3 × 10‑7 to 1 × 10‑7 Ω‑1 cm‑1. During prolonged heating at 500 °C for 30 min, some structural changes do happen: there is a significant preferential orientation of (410) crystalline planes of SnS-CUB parallel to substrate surface, and/or of (400) planes of SnS-ORT with identical inter-planar distance of 2.816 Å. Consequently, E g was 1.24 eV and σ, 10‑3 Ω‑1 cm‑1 (p-type). We also found that at a reduced pressure of 30 Torr nitrogen, such changes in SnS-CUB set-in at a temperature of 435 °C. Grazing incidence x-ray diffraction suggested that this transformation initiated at the glass/film interface. The results on the stability and ‘meta-stability’ of SnS-CUB offer guidelines toward its applications in photovoltaics and in nonlinear optical devices which depends on its lack of center of symmetry persisting at higher operating temperatures.

Rickets in lion cubs at the London Zoo in 1889: some new insights.

PubMed

Chesney, Russell W; Hedberg, Gail

2009-05-01

In 1889, when Dr John Bland-Sutton, a prominent surgeon in London, England, was consulted concerning fatal rickets in more than 20 successive litters of lion cubs at the London Zoo, he evaluated the role of diet relative to the development of rickets. He prescribed goat meat and bones and cod-liver oil to be added to the lean horse-meat diet of the cubs and their mothers. Rickets reversed, the cubs survived, and litters were reared successfully. In classic controlled studies conducted in puppies and young rats 3 decades later, the crucial role of calcium, phosphate, and vitamin D in both prevention and therapy of rickets was elucidated. Later studies led to the identification of the structural features of vitamin D. Although the Bland-Sutton interventional diet obviously provides calcium and phosphate from bones and vitamin D from cod-liver oil, other benefits of this diet were not initially recognized. Chewing bones promotes tooth and gum health and removes bacteria-laden tartar. Cod-liver oil also contains vitamin A, which is essential for the prevention of infection and for epithelial cell health. Taurine-conjugated bile salts are also necessary for the intestinal absorption of fat-soluble vitamins, including A and D. Moreover, unlike dogs and rats, all feline species are unable to synthesize taurine yet can only conjugate bile acids with taurine. This sulfur-containing beta-amino acid must be provided in the carnivorous diet of a large cat. Taurine-conjugated bile salts were provided in the oil cold-pressed from cod liver. The now famous Bland-Sutton "experiment of nature," namely, fatal rickets in lion cubs, was cured by the addition of minerals and vitamin D. However, gum health and the presence of taurine-conjugated bile salts undoubtedly permitted absorption of vitamin A and D, the latter promoting the cure of rickets.

Relative codon adaptation: a generic codon bias index for prediction of gene expression.

PubMed

Fox, Jesse M; Erill, Ivan

2010-06-01

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias.

Parasitic helminths of black bear cubs (Ursus americanus) from Florida.

PubMed

Foster, Garry W; Cunningham, Mark W; Kinsella, John M; Forrester, Donald J

2004-02-01

Twenty-two Florida black bear (Ursus americanus floridanus) cubs (< or = 12 mo old) from Florida were examined for endoparasites between 1998 and 2003. Eleven species of helminths were found (8 nematodes, 2 trematodes, and 1 acanthocephalan). The most prevalent helminths were Ancylostoma caninum (64%), Macracanthorhynchus ingens (36%), Strongyloides sp. (27%), Baylisascaris transfuga (23%), and A. tubaeforme (14%). New host records include A. tubaeforme and Brachylaima virginianum. This is the first report of B. transfuga in black bears from Florida.

Multiple ocular colobomas in the snow leopard (Uncia uncia).

PubMed

Barnett, K C; Lewis, J C M

2002-09-01

Two singleton female snow leopard cubs are reported with bilateral central upper lid colobomas. In addition, one cub had a coloboma of the fundus in one eye extending from the lower optic disc region. Surgical treatment by wedge resection was successful in both cases. Details of ocular colobomas in other snow leopards reported in the literature are described and it is suggested that the exact etiology of the condition in this species may be discovered by further study of similar colobomas in the domestic cat.

Validation of objective records and misreporting of personal radio use in a cohort of British Police forces (the Airwave Health Monitoring Study).

PubMed

Vergnaud, Anne-Claire; Aresu, Maria; McRobie, Dennis; Singh, Deepa; Spear, Jeanette; Heard, Andy; Elliott, Paul

2016-07-01

Terrestrial Trunked Radio (TETRA) is a digital communication system progressively adopted by Police Forces in Great Britain since 2001. In 2000, the UK Independent Expert Group on Mobile Phones suggested that exposure to TETRA-like signal modulation might have adverse effects on health. The Airwave Health Monitoring Study was established to investigate possible long-term effects of TETRA use on health. This requires estimation of TETRA use among Police Force employees participating in the study. We investigated TETRA usage among 42,112 Police officers and staff. An algorithm was created to link each personal radio user to his/her objective radio usage records for the 26,035 participants with available data. We linked 16,577 personal radio users to their objective radio usage records and compared self-reported usage with data from the TETRA operator for those individuals. For weekly usage, the correlation between self-reported and operator-derived personal radio usage was r=0.69 for number and r=0.59 for the duration of calls. Compared with objective data, participants under-reported the number of calls and over-reported the duration of calls by a factor of around 4 and 1.6 respectively. Correlations were lower and bias higher when looking at daily usage. Where both objective and self-reported information were available, our study showed substantial misreporting in self-reported TETRA usage. Successful linkage of large numbers of TETRA users to objective data on their personal radios will allow objective assessment of TETRA radio usage for these participants and development of algorithms to correct bias in self-reported data for the remainder. Copyright © 2016 Elsevier Inc. All rights reserved.

Skill-Biased Technological Change. Evidence from a Firm-Level Survey.

ERIC Educational Resources Information Center

Siegel, Donald S.

A study addressed the effects of technological change using a new, rich source of firm-level data on technology usage and labor force composition. The empirical investigation is based on a survey of Long Island manufacturers' usage of computer-integrated manufacturing systems (CIMS) or advanced manufacturing technologies (AMTs). The study also…

Codon usage and amino acid usage influence genes expression level.

PubMed

Paul, Prosenjit; Malakar, Arup Kumar; Chakraborty, Supriyo

2018-02-01

Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

Large Omnivore Movements in Response to Surface Mining and Mine Reclamation.

PubMed

Cristescu, Bogdan; Stenhouse, Gordon B; Boyce, Mark S

2016-01-11

Increasing global demands have resulted in widespread proliferation of resource extraction. Scientists are challenged to develop environmental mitigation strategies that meet societal expectations of resource supply, while achieving minimal disruption to sensitive "wilderness" species. We used GPS collar data from a 9-year study on grizzly bears (Ursus arctos) (n = 18) in Alberta, Canada to assess movements and associated space use during versus after mining. Grizzly bear home range overlap with mined areas was lower during active mining except for females with cubs, that also had shortest movements on active mines. However, both females with cubs and males made shorter steps when on/close to mines following mine closure and reclamation. Our results show differences in bear movement and space-use strategies, with individuals from a key population segment (females with cubs) appearing most adaptable to mining disturbance. Preserving patches of original habitat, reclaiming the landscape and minimizing the risk of direct human-induced mortality during and after development can help conserve bears and other wildlife on industrially modified landscapes.

SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage

PubMed Central

Pouyet, Fanny; Bailly-Bechet, Marc; Mouchiroud, Dominique; Guéguen, Laurent

2016-01-01

Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences. PMID:27401173

Health disparities among common subcultural identities of young gay men: physical, mental, and sexual health.

PubMed

Lyons, Anthony; Hosking, Warwick

2014-11-01

Researchers, policymakers, and health agencies have tended to treat gay men as a relatively homogeneous population, with little attention given to its many subcultural identities. In this study, we focused on young gay men and investigated a range of health-related differences according to common subcultural identities, such as Bear, Cub, and Twink. In a nationwide cross-sectional online survey of 1,034 Australian gay men aged 18-39 years, 44% reported a subcultural identity, the two most common being Cub (9%) and Twink (20%). Logistic and linear regression analyses compared Cub- and Twink-identified men and those without a subcultural identity (Non-identified) on a range of health-related outcomes. After adjusting for differences in age and body mass index (BMI), Twink-identified men had the highest risk profile overall, including significantly higher rates of smoking tobacco and alcohol consumption. They were also significantly more likely to report engaging in receptive anal sex. In addition, Cub-identified men were significantly more likely to report being in an ongoing relationship while Non-identified men were significantly less likely to report experiences of discrimination in the past 12 months. Differences on measures of mental health between the three groups were no longer significant after adjusting for age and BMI. In summary, we found numerous health-related differences according to subcultural identity that warrant further investigation by researchers, health agencies, and others concerned with further understanding and addressing health-related challenges of gay men.

Sexual Maturity and Life Stage Influences Toxic Metal Accumulation in Croatian Brown Bears.

PubMed

Lazarus, Maja; Sekovanić, Ankica; Orct, Tatjana; Reljić, Slaven; Jurasović, Jasna; Huber, Đuro

2018-02-01

The influence of reproductive and (early) life stages on toxic metal levels was investigated in the brown bear (Ursus arctos), the largest mammalian predator species in Croatia. The purpose was to examine critical clusters in a population that might be at a higher risk of adverse health effects caused by metals as environmental contaminants. Levels of cadmium, mercury and lead in muscle, liver and kidney cortex of 325 male and 139 female bears, quantified by inductively coupled plasma mass spectrometry, were analysed according to distinct bear life stages (young: cub, yearling, subadult; mature: adult). Metal levels did not differ among sexes in young animals (< 4 years), except for mercury in muscles (higher in females), and adult females had higher cadmium and mercury. A trend of renal cadmium accumulation with age in immature male animals disappeared once they reached maturity, whereas for females this trend has only slowly declined in mature compared to immature bears. In early life stage (< 1 year), bear cubs had lower cadmium, comparable mercury, and higher lead in the kidneys than the bears of the following age category (yearlings). Due to a higher proportion of renal lead transfer from the mother to the cub compared with cadmium, it may be that the high burden of cadmium found in kidneys of older females has lower toxicological concern for their cubs than the lead content. Sex, reproductive, and life stages of bears were confirmed as important in assessing toxic metal burden.

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.

PubMed

Trotta, Edoardo

2016-05-17

The three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies. In this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences. In human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.

Examinations of Home Economics Textbooks for Sex Bias.

ERIC Educational Resources Information Center

Weis, Susan F.

1979-01-01

Four analyses were conducted on a sample of 100 randomly selected, secondary home economics textbooks published between 1964 and 1974. Results indicated that the contents presented sex bias in language usage, in pictures portraying male and female role environments, and in role behaviors and expectations emphasized. (Author/JH)

Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure?

PubMed Central

Lakshmanan, Lakshmi Narayanan; Gruber, Jan; Halliwell, Barry; Gunawan, Rudiyanto

2015-01-01

Non D-loop direct repeats (DRs) in mitochondrial DNA (mtDNA) have been commonly implicated in the mutagenesis of mtDNA deletions associated with neuromuscular disease and ageing. Further, these DRs have been hypothesized to put a constraint on the lifespan of mammals and are under a negative selection pressure. Using a compendium of 294 mammalian mtDNA, we re-examined the relationship between species lifespan and the mutagenicity of such DRs. Contradicting the prevailing hypotheses, we found no significant evidence that long-lived mammals possess fewer mutagenic DRs than short-lived mammals. By comparing DR counts in human mtDNA with those in selectively randomized sequences, we also showed that the number of DRs in human mtDNA is primarily determined by global mtDNA properties, such as the bias in synonymous codon usage (SCU) and nucleotide composition. We found that SCU bias in mtDNA positively correlates with DR counts, where repeated usage of a subset of codons leads to more frequent DR occurrences. While bias in SCU and nucleotide composition has been attributed to nucleotide mutational bias, mammalian mtDNA still exhibit higher SCU bias and DR counts than expected from such mutational bias, suggesting a lack of negative selection against non D-loop DRs. PMID:25855815

Growing cell-phone population and noncoverage bias in traditional random digit dial telephone health surveys.

PubMed

Lee, Sunghee; Brick, J Michael; Brown, E Richard; Grant, David

2010-08-01

Examine the effect of including cell-phone numbers in a traditional landline random digit dial (RDD) telephone survey. The 2007 California Health Interview Survey (CHIS). CHIS 2007 is an RDD telephone survey supplementing a landline sample in California with a sample of cell-only (CO) adults. We examined the degree of bias due to exclusion of CO populations and compared a series of demographic and health-related characteristics by telephone usage. When adjusted for noncoverage in the landline sample through weighting, the potential noncoverage bias due to excluding CO adults in landline telephone surveys is diminished. Both CO adults and adults who have both landline and cell phones but mostly use cell phones appear different from other telephone usage groups. Controlling for demographic differences did not attenuate the significant distinctiveness of cell-mostly adults. While careful weighting can mitigate noncoverage bias in landline telephone surveys, the rapid growth of cell-phone population and their distinctive characteristics suggest it is important to include a cell-phone sample. Moreover, the threat of noncoverage bias in telephone health survey estimates could mislead policy makers with possibly serious consequences for their ability to address important health policy issues.

Nonneutral GC3 and retroelement codon mimicry in Phytophthora.

PubMed

Jiang, Rays H Y; Govers, Francine

2006-10-01

Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.

Increasing Elementary School Teachers' Awareness of Gender Inequity in Student Computer Usage

ERIC Educational Resources Information Center

Luongo, Nicole

2012-01-01

This study was designed to increase gender equity awareness in elementary school teachers with respect to student computer and technology usage. Using professional development methods with a group of teachers, the writer attempted to help them become more aware of gender bias in technology instruction. An analysis of the data revealed that…

Designs that make a difference: the Cardiac Universal Bed model.

PubMed

Johnson, Jackie; Brown, Katherine Kay; Neal, Kelly

2003-01-01

Information contained in this article includes some of the findings from a joint research project conducted by Corazon Consulting and Ohio State University Medical Center on national trends in Cardiac Universal Bed (CUB) utilization. This article outlines current findings and "best practice" standards related to the benefits of developing care delivery models to differentiate an organization with a competitive advantage in the highly dynamic marketplace of cardiovascular care. (OSUMC, a Corazon client, is incorporating the CUB into their Ross Heart Hospital slated to open this spring.)

Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents.

PubMed

Chakraborty, Supriyo; Uddin, Arif; Mazumder, Tarikul Huda; Choudhury, Monisha Nath; Malakar, Arup Kumar; Paul, Prosenjit; Halder, Binata; Deka, Himangshu; Mazumder, Gulshana Akthar; Barbhuiya, Riazul Ahmed; Barbhuiya, Masuk Ahmed; Devi, Warepam Jesmi

2017-12-02

The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes. The codon usage bias was low as revealed from high ENC value. Correlation between codon usage and GC3 suggested that all the codons ending with G/C were positively correlated with GC3 but vice versa for A/T ending codons with the exception of ND4L and ND5 genes. Neutrality plot revealed that for the genes ATP6, COI, COIII, CYB, ND4 and ND4L, natural selection might have played a major role while mutation pressure might have played a dominant role in the codon usage bias of ATP8, COII, ND1, ND2, ND3, ND5 and ND6 genes. Phylogenetic analysis indicated that evolutionary relationships in each of 13 protein coding genes of human mitochondria were different across six continents and further suggested that geographical distance was an important factor for the origin and evolution of 13 protein coding genes of human mitochondria. Copyright © 2017 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

The CubeSat Imaging X-ray Solar Spectrometer (CubIXSS) Mission Concept

NASA Astrophysics Data System (ADS)

Caspi, Amir; Shih, Albert Y.; Warren, Harry; DeForest, Craig; Laurent, Glenn Thomas; Schwartz, Richard A.; Woods, Thomas N.; Mason, James; Palo, Scott; Steslicki, Marek; Sylwester, Janusz; Gburek, Szymon; Mrozek, Tomasz; Kowalinski, Miroslaw; Torre, Gabriele; Crowley, Geoffrey; Schattenburg, Mark

2017-08-01

Solar soft X-ray (SXR) observations provide important diagnostics of plasma heating, during solar flares and quiescent times. Spectrally- and temporally-resolved measurements are crucial for understanding the dynamics, origins, and evolution of these energetic processes, providing probes both into the temperature distributions and elemental compositions of hot plasmas; spatially-resolved measurements are critical for understanding energy transport and mass flow. A better understanding of the thermal plasma improves our understanding of the relationships between particle acceleration, plasma heating, and the underlying release of magnetic energy during reconnection. We introduce a new proposed small satellite mission, the CubeSat Imaging X-ray Solar Spectrometer (CubIXSS), to measure spectrally- and spatially-resolved SXRs from the quiescent and flaring Sun from a 6U CubeSat platform in low-Earth orbit during a nominal 1-year mission. CubIXSS includes the Amptek X123-FastSDD silicon drift detector, a low-noise, commercial off-the-shelf (COTS) instrument enabling solar SXR spectroscopy from ~0.5 to ~30 keV with ~0.15 keV FWHM spectral resolution with low power, mass, and volume requirements. Multiple detectors and tailored apertures provide sensitivity to a wide range of solar conditions, optimized for a launch during solar minimum. The precise spectra from these instruments will provide detailed measurements of the coronal temperature distribution and elemental abundances from the quiet Sun to active regions and flares. CubIXSS also includes a novel spectro-spatial imager -- the first ever solar imager on a CubeSat -- utilizing a custom pinhole camera and Chandra-heritage X-ray transmission diffraction grating to provide spatially- resolved, full-Sun imaging spectroscopy from ~0.1 to ~10 keV, with ~25 arcsec and ~0.1 Å FWHM spatial and spectral resolutions, respectively. MOXSI’s unique capabilities enable SXR spectroscopy and temperature diagnostics of individual active regions and flares. Through its groundbreaking new measurements, CubIXSS will improve our physical understanding of thermal plasma processes and impulsive energy release in the solar corona, from quiet Sun to solar flares.

Inoculation of female American black bears (Ursus americanus) with partially purified porcine zona pellucidae limits cub production.

PubMed

Lane, V M; Liu, I K M; Casey, K; vanLeeuwen, E M G; Flanagan, D R; Murata, K; Munro, C

2007-01-01

The present 2-year study investigated the feasibility of using porcine zona pellucidae (pZP) as antigen for immunocontraception in American black bears. Sows, 3-6 years of age, were administered either two doses of 250 microg pZP with Freund's adjuvant (n = 10) or adjuvant alone (n = 5), one in April and one in May, and were kept away from the boars until June. Serum samples were collected before injections and before denning (November). The presence of sows with cubs at side was observed during premature emergence from denning. First-year results indicated that anti-pZP antibody titres in vaccinated sows were 2.5-9.0-fold (range) higher compared with non-vaccinated sows and that the vaccinated sows were threefold less likely to become pregnant (P = 0.167). Control and vaccinated bears produced 1.6 and 0.2 cubs per sow, respectively (P = 0.06). The second-year study investigated the feasibility of using pZP sequestered in a controlled-release pellet and a water-soluble adjuvant (QS-21) to avoid regulatory problems associated with Freund's adjuvant. Sows in the treatment group (n = 22) were administered a single dose of an emulsion of 250 microg pZP and 150 microg QS-21 plus a pellet containing 70-90 microg pZP for delayed release as booster dose. Control sows (n = 5) received the QS-21 adjuvant in pellet alone. Serum samples were collected before inoculations (April) and before denning (November). Seven cubs were born to the five control sows, but none was born to the 22 vaccinated sows (P < 0.001). Anti-pZP antibody mean absorbance ratios in control sows remained at background levels, whereas vaccinated sows had ratios fourfold higher than controls. Two-dimensional polyacrylamide gel electrophoresis and immunohistochemical localisation confirmed immunoreactivity of sera from inoculated bears. We conclude that cub production in the American black bear can be effectively limited with either two injections of 250 microg pZP or a single inoculation of partially purified pZP sequestered in controlled-release pellets.

IQ Testing and Minority School Children: Imperatives for Change.

ERIC Educational Resources Information Center

Barnes, Edward

The inadequacy and misuse of intelligence testing for minority group children are examined. IQ test items, norms, examining procedures, and language usage are discussed in terms of their bias against minority children. The implications of this bias for the classroom teacher are explored with the view that teacher mental sets are powerful mediators…

Analysis of the breast milk of giant pandas (Ailuropoda melanoleuca) and the preparation of substitutes

PubMed Central

ZHANG, Zhihe; HOU, Rong; LAN, Jingchao; WANG, Hairui; KUROKAWA, Hiroyuki; TAKATSU, Zenta; KOBAYASHI, Toyokazu; KOIE, Hiroshi; KAMATA, Hiroshi; KANAYAMA, Kiichi; WATANABE, Toshi

2016-01-01

The first milk substitute for giant panda cubs was developed in 1988 based on limited data about giant panda breast milk and that of certain types of bear. Mixtures of other formulas have also been fed to cubs at some facilities. However, they are not of sufficient nutritional quality for promoting growth in panda cubs. Here, we report analysis of giant panda breast milk and propose new milk substitutes for cubs, which were developed based on the results of our analysis. The Chengdu Research Base of Giant Panda Breeding obtained breast milk samples from three giant pandas. Up to 30 ml of breast milk were collected from each mother by hand. Then, the milk samples were frozen and sent to Nihon University. The levels of protein, fat, carbohydrates, ash, moisture, vitamins, minerals, total amino acids, fatty acids, lactose and other carbohydrates in the milk were analyzed. The breast milk samples exhibited the following nutritional values: protein: 6.6–8.5%, fat: 6.9–16.4%, carbohydrates: 2.5–9.1%, ash: 0.9–1.0% and moisture: 67–83%. We designed two kinds of milk substitutes based on the data obtained and the nutritional requirements of dogs, cats and rodents. The nutritional composition of the milk substitutes for the first and second stages was as follows: protein: 38 and 26%, fat: 40 and 40%, carbohydrates: 13 and 25%, ash: 6 and 6% and moisture: 3 and 3%, respectively. In addition, the substitutes contained vitamins, minerals, taurine, docosahexaenoic acid, lactoferrin, nucleotides and other nutrients. PMID:26781707

Effects of Weather Conditions on Oxidative Stress, Oxidative Damage, and Antioxidant Capacity in a Wild-Living Mammal, the European Badger (Meles meles).

PubMed

Bilham, Kirstin; Newman, Chris; Buesching, Christina D; Noonan, Michael J; Boyd, Amy; Smith, Adrian L; Macdonald, David W

Wild-living animals are subject to weather variability that may cause the generation of reactive oxygen species, resulting in oxidative stress and tissue damage, potentially driving demographic responses. Our 3-yr field study investigated the effects of seasonal weather conditions on biomarkers for oxidative stress, oxidative damage, and antioxidant defense in the European badger (Meles meles). We found age class effects: cubs were more susceptible to oxidative stress and oxidative damage than adults, especially very young cubs in the spring, when they also exhibited lower antioxidant biomarkers than adults. Although previous studies have found that intermediate spring and summer rainfall and warmer temperatures favor cub survival, counterintuitively these conditions were associated with more severe oxidative damage. Oxidative damage was high in cubs even when antioxidant biomarkers were high. In contrast, adult responses accorded with previous survival analyses. Wetter spring and summer conditions were associated with higher oxidative damage, but they were also associated with higher antioxidant biomarkers. Autumnal weather did not vary substantially from normative values, and thus effects were muted. Winter carryover effects were partially evident, with drier and milder conditions associated with greater oxidative damage in the following spring but also with higher antioxidant capacity. Plausibly, warmer conditions promoted more badger activity, with associated metabolic costs at a time of year when food supply is limited. Modeling biomarkers against projected climate change scenarios predicted greater future risks of oxidative damage, although not necessarily exceeding antioxidant capacity. This interdisciplinary approach demonstrates that individual adaptive physiological responses are associated with variation in natural environmental conditions.

How Does Student Ability and Self-Efficacy Affect the Usage of Computer Technology?

ERIC Educational Resources Information Center

Isman, Aytekin; Celikli, Gulsun Ersoy

2009-01-01

The main aim of this research was to find out the self-efficacy level among participant students and analyze their beliefs. This study showed that male students are more confident comparing to female student, similar to research of Bimer (2000), the computer usage has been known as biased toward the interests and fashion of men, this research also…

Large Omnivore Movements in Response to Surface Mining and Mine Reclamation

PubMed Central

Cristescu, Bogdan; Stenhouse, Gordon B.; Boyce, Mark S.

2016-01-01

Increasing global demands have resulted in widespread proliferation of resource extraction. Scientists are challenged to develop environmental mitigation strategies that meet societal expectations of resource supply, while achieving minimal disruption to sensitive “wilderness” species. We used GPS collar data from a 9-year study on grizzly bears (Ursus arctos) (n = 18) in Alberta, Canada to assess movements and associated space use during versus after mining. Grizzly bear home range overlap with mined areas was lower during active mining except for females with cubs, that also had shortest movements on active mines. However, both females with cubs and males made shorter steps when on/close to mines following mine closure and reclamation. Our results show differences in bear movement and space-use strategies, with individuals from a key population segment (females with cubs) appearing most adaptable to mining disturbance. Preserving patches of original habitat, reclaiming the landscape and minimizing the risk of direct human-induced mortality during and after development can help conserve bears and other wildlife on industrially modified landscapes. PMID:26750094

Giant Panda Maternal Care: A Test of the Experience Constraint Hypothesis.

PubMed

Snyder, Rebecca J; Perdue, Bonnie M; Zhang, Zhihe; Maple, Terry L; Charlton, Benjamin D

2016-06-07

The body condition constraint and the experience condition constraint hypotheses have both been proposed to account for differences in reproductive success between multiparous (experienced) and primiparous (first-time) mothers. However, because primiparous mothers are typically characterized by both inferior body condition and lack of experience when compared to multiparous mothers, interpreting experience related differences in maternal care as support for either the body condition constraint hypothesis or the experience constraint hypothesis is extremely difficult. Here, we examined maternal behaviour in captive giant pandas, allowing us to simultaneously control for body condition and provide a rigorous test of the experience constraint hypothesis in this endangered animal. We found that multiparous mothers spent more time engaged in key maternal behaviours (nursing, grooming, and holding cubs) and had significantly less vocal cubs than primiparous mothers. This study provides the first evidence supporting the experience constraint hypothesis in the order Carnivora, and may have utility for captive breeding programs in which it is important to monitor the welfare of this species' highly altricial cubs, whose survival is almost entirely dependent on receiving adequate maternal care during the first few weeks of life.

Characterization of Rare Earth Element Minerals in Coal Utilization Byproducts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montross, Scott N.; Verba, Circe A.; Collins, Keith

The United States currently produces over 100 million tons of coal utilization byproducts (CUB) per year in the form of fly ash, bottom ash, slag, and flue gas (American Coal Ash Association (ACCA), 2015). But this “waste material” also contains potentially useful levels of rare earth elements (REE). Rare earth elements are crucial for many existing and emerging technologies, but the U.S. lacks a domestic, sustainable REE source. Our project explored the possibility of developing a supply of REEs for U.S. technologies by extracting REEs from CUBs. This work offers the potential to reduce our dependence on other countries formore » supply of these critical elements (NETL, REE 2016 Project Portfolio). Geologic and diagenetic history, industrial preparation methods, and the specific combustion process all play major roles in the composition of CUB. During combustion, inorganic mineral phases of coal particles are fluidized at temperatures higher than 1400oC, so inorganic mineral materials are oxidized, fused, disintegrated, or agglomerated into larger spherical and amorphous (non-crystalline) particles. The original mineralogy of the coal-containing rock and heating/cooling of the material significantly affects the composition and morphology of the particles in the combustion byproduct (Kutchko and Kim, 2006). Thus, different types of coal/refuse/ash must be characterized to better understand mineral evolution during the combustion process. Our research focused on developing a working model to address how REE minerals behave during the combustion process: this research should help determine the most effective engineering methods for extracting REEs from CUBs. We used multimodal imaging and image processing techniques to characterize six rock and ash samples from different coal power plants with respect to morphology, grain size, presence of mineral phases, and elemental composition. The results of these characterization activities provided thresholds for realizing the occurrence of REE mineral phases in CUB and allowed us to calculate structural and volumetric estimates of REE. Collectively, the rock and coal ash samples contained minerals such as quartz, kaolinite, muscovite/illite, iron oxide (as hematite or magnetite), mullite, and clinochlore. Trace minerals included pyrite, zircon, siderite, rutile, diopside, foresterite, gypsum, and barite. We identified REE phosphate minerals monazite (Ce,La,Nd,Th)(PO 4,SiO 4), xenotime (YPO 4,SiO 4), and apatite (Ca 5(PO 4) 3(F,Cl,OH) via SEM and electron microprobe analysis: these materials generally occurred as 1-10 μm-long crystals in the rock and ash samples. As has been shown in other studies, amorphous material-aluminosilicate glass or iron oxyhydroxide-are the major components of coal fly and bottom ash. Trace amounts of amorphous calcium oxide and mixed element (e.g., Al-Si-Ca-Fe) slag are also present. Quartz, mullite, hematite, and magnetite are the crystalline phases present. We found that REEs are present as monomineralic grains dispersed within the ash, as well as fused to or encapsulated by amorphous aluminosilicate glass particles. Monazite and xenotime have relatively high melting points (>1800 °C) compared to typical combustion temperatures; our observations indicate that the REE-phosphates, which presumably contribute a large percentage of REE to the bulk ash REE pool, as measured by mass spectroscopy, are largely unaltered by the combustion. Our study shows that conventional coal combustion processes sequester REE minerals into aluminosilicate glass phases, which presents a new engineering challenge for extracting REE from coal ash. The characterization work summarized in this report provides a semi-quantitative assessments of REE in coal-containing rock and CUB. The data we obtained from 2- and 3-D imaging, elemental mapping, volumetric estimates, and advanced high-resolution pixel classification successfully identified the different mineral phases present in CUB. Further, our characterization results can guide techniques for extracting REEs from CUB, or other geologic and engineered materials. Whilst, interpretations will inform future REE separation and extraction techniques and technologies practical for commercial utilization of combustion byproducts generated by power plants.« less

Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias.

PubMed

Esposito, Lauren A; Gupta, Swati; Streiter, Fraida; Prasad, Ashley; Dennehy, John J

2016-10-01

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis , a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it is possible that the primary host of many newly isolated mycobacteriophages is not M. smegmatis , but instead a range of closely related bacterial species. However, determining mycobacteriophage host range presents difficulties associated with mycobacterial cultivability, pathogenicity and growth. Another way to gain insight into mycobacteriophage host range and ecology is through bioinformatic analysis of their genomic sequences. To this end, we examined the correlations between the codon usage biases of 199 different mycobacteriophages and those of several fully sequenced mycobacterial species in order to gain insight into the natural host range of these mycobacteriophages. We find that UPGMA clustering tends to match, but not consistently, clustering by shared nucleotide sequence identify. In addition, analysis of GC content, tRNA usage and correlations between mycobacteriophage and mycobacterial codon usage bias suggests that the preferred host of many clustered mycobacteriophages is not M. smegmatis but other, as yet unknown, members of the mycobacteria complex or closely allied bacterial species.

Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias

PubMed Central

Esposito, Lauren A.; Gupta, Swati; Streiter, Fraida; Prasad, Ashley

2016-01-01

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it is possible that the primary host of many newly isolated mycobacteriophages is not M. smegmatis, but instead a range of closely related bacterial species. However, determining mycobacteriophage host range presents difficulties associated with mycobacterial cultivability, pathogenicity and growth. Another way to gain insight into mycobacteriophage host range and ecology is through bioinformatic analysis of their genomic sequences. To this end, we examined the correlations between the codon usage biases of 199 different mycobacteriophages and those of several fully sequenced mycobacterial species in order to gain insight into the natural host range of these mycobacteriophages. We find that UPGMA clustering tends to match, but not consistently, clustering by shared nucleotide sequence identify. In addition, analysis of GC content, tRNA usage and correlations between mycobacteriophage and mycobacterial codon usage bias suggests that the preferred host of many clustered mycobacteriophages is not M. smegmatis but other, as yet unknown, members of the mycobacteria complex or closely allied bacterial species. PMID:28348827

Toxocara canis in experimentally infected silver and arctic foxes.

PubMed

Saeed, Isam; Taira, Kensuke; Kapel, Christian M O

2005-09-01

In two experiments, thirty-six farm foxes of two species were inoculated with various doses of infective Toxocara canis eggs or tissue larvae isolated from mice. In experiment I, six adult arctic foxes (Alopex lagopus; 11-month old) were each inoculated with 20,000 eggs and sacrificed 100, 220, or 300 days post infection (dpi), while ten silver fox cubs (Vulpes vulpes; 6-9-week old) were infected with varying doses of eggs (30-3000) and necropsied 120 dpi. In experiment II, two groups of five cubs and two groups of five adult silver foxes received both a primary inoculation and either one or two challenge inoculations: primary inoculation (day 0) with 400 embryonated eggs were administered to five cubs and five adults and another five cubs and five adults received 400 larvae. At 50 dpi, the first challenge inoculation (400 eggs) was inoculated in all animals. At 100 dpi, three animals from each group were necropsied. The remaining two animals in each group were received a second challenge inoculation of 400 tissue larvae on 100 dpi and were subsequently necropsied at 150 dpi. In both experiments, the highest numbers of larvae per gram (lpg) of tissue was found in the kidneys (100-300 dpi). In adult foxes receiving a high dose (20,000 eggs), increasing larval burdens were found in the kidneys over the course of the experiment (up to 300 dpi). The larval migration from the lungs to other tissues appeared to be dose-dependent with the highest larval burdens found in adult foxes. The faecal egg excretion, larval burden and intestinal worm burdens decreased from the first to the second challenge infection.

Robot Faces that Follow Gaze Facilitate Attentional Engagement and Increase Their Likeability.

PubMed

Willemse, Cesco; Marchesi, Serena; Wykowska, Agnieszka

2018-01-01

Gaze behavior of humanoid robots is an efficient mechanism for cueing our spatial orienting, but less is known about the cognitive-affective consequences of robots responding to human directional cues. Here, we examined how the extent to which a humanoid robot (iCub) avatar directed its gaze to the same objects as our participants affected engagement with the robot, subsequent gaze-cueing, and subjective ratings of the robot's characteristic traits. In a gaze-contingent eyetracking task, participants were asked to indicate a preference for one of two objects with their gaze while an iCub avatar was presented between the object photographs. In one condition, the iCub then shifted its gaze toward the object chosen by a participant in 80% of the trials (joint condition) and in the other condition it looked at the opposite object 80% of the time (disjoint condition). Based on the literature in human-human social cognition, we took the speed with which the participants looked back at the robot as a measure of facilitated reorienting and robot-preference, and found these return saccade onset times to be quicker in the joint condition than in the disjoint condition. As indicated by results from a subsequent gaze-cueing tasks, the gaze-following behavior of the robot had little effect on how our participants responded to gaze cues. Nevertheless, subjective reports suggested that our participants preferred the iCub following participants' gaze to the one with a disjoint attention behavior, rated it as more human-like and as more likeable. Taken together, our findings show a preference for robots who follow our gaze. Importantly, such subtle differences in gaze behavior are sufficient to influence our perception of humanoid agents, which clearly provides hints about the design of behavioral characteristics of humanoid robots in more naturalistic settings.

Divergence and codon usage bias of Betanodavirus, a neurotropic pathogen in fish.

PubMed

He, Mei; Teng, Chun-Bo

2015-02-01

Betanodavirus is a small bipartite RNA virus of global economical significance that can cause severe neurological disorders to an increasing number of marine fish species. Herein, to further the understanding of the evolution of betanodavirus, Bayesian coalescent analyses were conducted to the time-stamped entire coding sequences of their RNA polymerase and coat protein genes. Similar moderate nucleotide substitution rates were then estimated for the two genes. According to age calculations, the divergence of the two genes into the four genotypes initiated nearly simultaneously at ∼700 years ago, despite the different scenarios, whereas the seven analyzed chimeric isolates might be the outcomes of a single genetic reassortment event taking place in the early 1980s in Southern Europe. Furthermore, codon usage bias analyses indicated that each gene had influences in addition to mutational bias and codon choice of betanodavirus was not completely complied with that of fish host. Copyright © 2014 Elsevier Inc. All rights reserved.

We Know the Yin—But Where Is the Yang? Toward a Balanced Approach on Common Source Bias in Public Administration Scholarship

PubMed Central

George, Bert; Pandey, Sanjay K.

2017-01-01

Surveys have long been a dominant instrument for data collection in public administration. However, it has become widely accepted in the last decade that the usage of a self-reported instrument to measure both the independent and dependent variables results in common source bias (CSB). In turn, CSB is argued to inflate correlations between variables, resulting in biased findings. Subsequently, a narrow blinkered approach on the usage of surveys as single data source has emerged. In this article, we argue that this approach has resulted in an unbalanced perspective on CSB. We argue that claims on CSB are exaggerated, draw upon selective evidence, and project what should be tentative inferences as certainty over large domains of inquiry. We also discuss the perceptual nature of some variables and measurement validity concerns in using archival data. In conclusion, we present a flowchart that public administration scholars can use to analyze CSB concerns. PMID:29046599

We Know the Yin-But Where Is the Yang? Toward a Balanced Approach on Common Source Bias in Public Administration Scholarship.

PubMed

George, Bert; Pandey, Sanjay K

2017-06-01

Surveys have long been a dominant instrument for data collection in public administration. However, it has become widely accepted in the last decade that the usage of a self-reported instrument to measure both the independent and dependent variables results in common source bias (CSB). In turn, CSB is argued to inflate correlations between variables, resulting in biased findings. Subsequently, a narrow blinkered approach on the usage of surveys as single data source has emerged. In this article, we argue that this approach has resulted in an unbalanced perspective on CSB. We argue that claims on CSB are exaggerated, draw upon selective evidence, and project what should be tentative inferences as certainty over large domains of inquiry. We also discuss the perceptual nature of some variables and measurement validity concerns in using archival data. In conclusion, we present a flowchart that public administration scholars can use to analyze CSB concerns.

Absence of classical heat shock response in the citrus pathogen Xylella fastidiosa.

PubMed

Martins-de-Souza, Daniel; Martins, Daniel; Astua-Monge, Gustavo; Coletta-Filho, Helvécio Della; Winck, Flavia Vischi; Baldasso, Paulo Aparecido; de Oliveira, Bruno Menezes; Marangoni, Sérgio; Machado, Marcos Antônio; Novello, José Camillo; Smolka, Marcus Bustamante

2007-02-01

The fastidious bacterium Xylella fastidiosa is associated with important crop diseases worldwide. We have recently shown that X. fastidiosa is a peculiar organism having unusually low values of gene codon bias throughout its genome and, unexpectedly, in the group of the most abundant proteins. Here, we hypothesized that the lack of codon usage optimization in X. fastidiosa would incapacitate this organism to undergo quick and massive changes in protein expression as occurs in a classical stress response. Proteomic analysis of the response to heat stress in X. fastidiosa revealed that no changes in protein expression can be detected. Moreover, stress-inducible proteins identified in the closely related citrus pathogen Xanthomonas axonopodis pv citri were found to be constitutively expressed in X. fastidiosa. These proteins have extremely high codon bias values in the X. citri and other well-studied organisms, but low values in X. fastidiosa. Because biased codon usage is well known to correlate to the rate of protein synthesis, we speculate that the peculiar codon bias distribution in X. fastidiosa is related to the absence of a classical stress response, and, probably, alternative strategies for survival of X. fastidiosa under stressfull conditions.

Exposure to violent video games and aggression in German adolescents: a longitudinal analysis.

PubMed

Möller, Ingrid; Krahé, Barbara

2009-01-01

The relationship between exposure to violent electronic games and aggressive cognitions and behavior was examined in a longitudinal study. A total of 295 German adolescents completed the measures of violent video game usage, endorsement of aggressive norms, hostile attribution bias, and physical as well as indirect/relational aggression cross-sectionally, and a subsample of N=143 was measured again 30 months later. Cross-sectional results at T1 showed a direct relationship between violent game usage and aggressive norms, and an indirect link to hostile attribution bias through aggressive norms. In combination, exposure to game violence, normative beliefs, and hostile attribution bias predicted physical and indirect/relational aggression. Longitudinal analyses using path analysis showed that violence exposure at T1 predicted physical (but not indirect/relational) aggression 30 months later, whereas aggression at T1 was unrelated to later video game use. Exposure to violent games at T1 influenced physical (but not indirect/relational) aggression at T2 via an increase of aggressive norms and hostile attribution bias. The findings are discussed in relation to social-cognitive explanations of long-term effects of media violence on aggression. Copyright 2008 Wiley-Liss, Inc.

Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the classical swine fever virus

PubMed Central

Chi, Xiaojuan; Wang, Song; Ma, Yanmei; Chen, Jilong

2017-01-01

The classical swine fever virus (CSFV), circulating worldwide, is a highly contagious virus. Since the emergence of CSFV, it has caused great economic loss in swine industry. The envelope glycoprotein E2 gene of the CSFV is an immunoprotective antigen that induces the immune system to produce neutralizing antibodies. Therefore, it is essential to study the codon usage of the E2 gene of the CSFV. In this study, 140 coding sequences of the E2 gene were analyzed. The value of effective number of codons (ENC) showed low codon usage bias in the E2 gene. Our study showed that codon usage could be described mainly by mutation pressure ENC plot analysis combined with principal component analysis (PCA) and translational selection-correlation analysis between the general average hydropathicity (Gravy) and aromaticity (Aroma), and nucleotides at the third position of codons (A3s, T3s, G3s, C3s and GC3s). Furthermore, the neutrality analysis, which explained the relationship between GC12s and GC3s, revealed that natural selection had a key role compared with mutational bias during the evolution of the E2 gene. These results lay a foundation for further research on the molecular evolution of CSFV. PMID:28880881

Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the classical swine fever virus.

PubMed

Chen, Ye; Li, Xinxin; Chi, Xiaojuan; Wang, Song; Ma, Yanmei; Chen, Jilong

2017-01-01

The classical swine fever virus (CSFV), circulating worldwide, is a highly contagious virus. Since the emergence of CSFV, it has caused great economic loss in swine industry. The envelope glycoprotein E2 gene of the CSFV is an immunoprotective antigen that induces the immune system to produce neutralizing antibodies. Therefore, it is essential to study the codon usage of the E2 gene of the CSFV. In this study, 140 coding sequences of the E2 gene were analyzed. The value of effective number of codons (ENC) showed low codon usage bias in the E2 gene. Our study showed that codon usage could be described mainly by mutation pressure ENC plot analysis combined with principal component analysis (PCA) and translational selection-correlation analysis between the general average hydropathicity (Gravy) and aromaticity (Aroma), and nucleotides at the third position of codons (A3s, T3s, G3s, C3s and GC3s). Furthermore, the neutrality analysis, which explained the relationship between GC12s and GC3s, revealed that natural selection had a key role compared with mutational bias during the evolution of the E2 gene. These results lay a foundation for further research on the molecular evolution of CSFV.

Sarcocystis sp. from white-fronted goose (Anser albifrons): cyst morphology and life cycle studies.

PubMed

Kutkiene, L; Sruoga, A; Butkauskas, D

2006-10-01

An experiment was carried out using three cubs of the arctic fox (Alopex lagopus). Twenty-five-day-old cubs were infected by feeding them with the leg muscles of the white-fronted goose (Anser albifrons) containing Sarcocystis sp. (cyst type III) cysts. Under the light microscope, the cysts were ribbon-shaped up to 4 mm long and up to 750 microm wide. On the surface of the wall (up to 2.4 microm), they had teat- or finger-like villar protrusions. Ultrastructurally, the cyst wall was a type-9 with villar protrusions (up to 2.3 microm long) different in size. The 11.4x1.7 (10.0-13.5x1.5-2.5)microm cystozoites were almost straight and shuttle-shaped. The fox cubs started shedding typical 12.0x8.0 (10.0-12.8x6.8-8.6)microm Sarcocystis sp. sporocysts on the 13th-14th days post-infection. The patent period lasted 19 days. The conclusion drawn was that the arctic fox (A. lagopus) can be one of the definitive hosts of Sarcocystis sp. (cyst type III) from the white-fronted goose.

Giant Panda Maternal Care: A Test of the Experience Constraint Hypothesis

PubMed Central

Snyder, Rebecca J.; Perdue, Bonnie M.; Zhang, Zhihe; Maple, Terry L.; Charlton, Benjamin D.

2016-01-01

The body condition constraint and the experience condition constraint hypotheses have both been proposed to account for differences in reproductive success between multiparous (experienced) and primiparous (first-time) mothers. However, because primiparous mothers are typically characterized by both inferior body condition and lack of experience when compared to multiparous mothers, interpreting experience related differences in maternal care as support for either the body condition constraint hypothesis or the experience constraint hypothesis is extremely difficult. Here, we examined maternal behaviour in captive giant pandas, allowing us to simultaneously control for body condition and provide a rigorous test of the experience constraint hypothesis in this endangered animal. We found that multiparous mothers spent more time engaged in key maternal behaviours (nursing, grooming, and holding cubs) and had significantly less vocal cubs than primiparous mothers. This study provides the first evidence supporting the experience constraint hypothesis in the order Carnivora, and may have utility for captive breeding programs in which it is important to monitor the welfare of this species’ highly altricial cubs, whose survival is almost entirely dependent on receiving adequate maternal care during the first few weeks of life. PMID:27272352

LAFD: TA-55 RLUOB/CUB Facility Familiarization Tour, OJT #55265

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rutherford, Victor Stephen

2017-09-14

Los Alamos National Laboratory (LANL) conducts familiarization tours for personnel of the Los Alamos County Fire Department (LAFD) at the RLUOB/CUB, technical area (TA)-55, 400/440, facility, Radiological Laboratory Utility Office Building (RLUOB)/Central Utility Building (CUB). These familiarization tours are official LANL business; the purpose of these tours is to orient LAFD firefighters to the facility so that they can respond efficiently and quickly to a variety of emergency situations. This orientation includes, among other topics, the ingress and egress of the area and buildings, layout and organization of the facility, evacuation procedures and assembly points, and areas of concern withinmore » the various buildings at the facility. LAFD firefighters have the skills and abilities to perform firefighting operations and other emergency response tasks that cannot be provided by other LANL personnel who have the required clearance level. This handout provides details of the information, along with maps and diagrams, to be presented during the familiarization tours. The handout is distributed to the trainees at the time of the tour; a corresponding checklist is also used as guidance during the familiarization tours to ensure that all required information is presented to LAFD personnel.« less

Patterns of den occupation by the spotted hyaena (Crocuta crocuta)

USGS Publications Warehouse

Boydston, E.E.; Kapheim, K.M.; Holekamp, K.E.

2006-01-01

Spotted hyaenas utilize isolated natal dens (NDs) and communal dens (CDs) for rearing their cubs. Here we describe patterns of natal and CD occupation by hyaenas belonging to one well-studied clan in the Maasai Mara National Reserve during a 10-year period. Locations of 98 den sites that were used as natal or CDs by hyaenas in the study clan were digitized in a Geographic Information System, and the duration of use of each den site, frequency of re-use, and distances involved in den moves were quantified. Hyaenas moved their CD monthly on average. Most CD sites were occupied only once during the study, but several sites were used repeatedly. On rare occasions, the movement of hyaenas to a new den site could be attributed to a disturbance event at the CD, but factors regularly prompting hyaenas to move to new CD sites were unclear. High-ranking female hyaenas were more likely to rear their cubs from birth in a CD than low-ranking females. Low-ranking females almost always utilized isolated NDs for the first few weeks of a litter's development, and low-ranking females transferred their cubs over longer distances than did high-ranking females. ?? 2006 East African Wild Life Society.

Photos provide information on age, but not kinship, of Andean bear

PubMed Central

Zug, Becky; Appleton, Robyn D.; Velez-Liendo, Ximena; Paisley, Susanna; LaCombe, Corrin

2015-01-01

Using photos of captive Andean bears of known age and pedigree, and photos of wild Andean bear cubs <6 months old, we evaluated the degree to which visual information may be used to estimate bears’ ages and assess their kinship. We demonstrate that the ages of Andean bear cubs ≤6 months old may be estimated from their size relative to their mothers with an average error of <0.01 ± 13.2 days (SD; n = 14), and that ages of adults ≥10 years old may be estimated from the proportion of their nose that is pink with an average error of <0.01 ± 3.5 years (n = 41). We also show that similarity among the bears’ natural markings, as perceived by humans, is not associated with pedigree kinship among the bears (R2 < 0.001, N = 1,043, p = 0.499). Thus, researchers may use photos of wild Andean bears to estimate the ages of young cubs and older adults, but not to infer their kinship. Given that camera trap photos are one of the most readily available sources of information on large cryptic mammals, we suggest that similar methods be tested for use in other poorly understood species. PMID:26213647

Performance of TB immunodiagnostic tests in Eurasian badgers (Meles meles) of different ages and the influence of duration of infection on serological sensitivity

PubMed Central

2009-01-01

Background In parts of Great Britain and Ireland, Eurasian badgers (Meles meles) constitute a reservoir of Mycobacterium bovis infection and a potential source of infection for cattle. In vitro diagnostic tests for live badgers are an important component of strategies to control TB in this species. Immunological tests have been developed for badgers, although little is known about the influence of the age of the animal on test performance. To address this, we evaluated the performance of three immunological tests for badgers with respect to the age of the animal: the Brock Test and BrockTB STAT-PAK® serological tests and the recently developed interferon-gamma enzyme immunoassay (IFNγ EIA). Data published elsewhere suggested that seropositivity was associated with more progressive forms of TB in the badger. To gain further evidence for this, we used longitudinal data from a well-studied population of badgers to test for an association between the sensitivity of the Brock Test and the duration of TB infection. Results Sensitivity of the two serological tests was approximately 54% for both cubs and adults. Sensitivity of the IFNγ EIA was lower in cubs (57%) compared with adults (85%) when a common cut-off value was used to define test positivity. Taking data from the cubs alone, the IFNγ EIA cut-off value could be adjusted to increase the sensitivity to 71% with no loss in specificity. As a general observation, specificity of all tests was higher in cubs, although only significantly so in the case of the Brock Test. Using logistic regression analysis to adjust for age, sensitivity of the Brock Test was significantly lower at first culture positive event (58%), but increased to >80% as infection progressed. Conclusion These data suggest that serodiagnosis could be a valuable tool for detecting a higher proportion of badgers with the greatest probability of transmitting infection. The age category of the badger appeared to exert little influence on the performance of the serological tests. Although data were only available for the IFNγ EIA in a small number of cubs, reduced sensitivity of the test in these individuals suggests a lower cut-off may be needed when testing younger animals. PMID:19919697

Validity of questionnaire self‐reports on computer, mouse and keyboard usage during a four‐week period

PubMed Central

Mikkelsen, Sigurd; Vilstrup, Imogen; Lassen, Christina Funch; Kryger, Ann Isabel; Thomsen, Jane Frølund; Andersen, Johan Hviid

2007-01-01

Objective To examine the validity and potential biases in self‐reports of computer, mouse and keyboard usage times, compared with objective recordings. Methods A study population of 1211 people was asked in a questionnaire to estimate the average time they had worked with computer, mouse and keyboard during the past four working weeks. During the same period, a software program recorded these activities objectively. The study was part of a one‐year follow‐up study from 2000–1 of musculoskeletal outcomes among Danish computer workers. Results Self‐reports on computer, mouse and keyboard usage times were positively associated with objectively measured activity, but the validity was low. Self‐reports explained only between a quarter and a third of the variance of objectively measured activity, and were even lower for one measure (keyboard time). Self‐reports overestimated usage times. Overestimation was large at low levels and declined with increasing levels of objectively measured activity. Mouse usage time proportion was an exception with a near 1:1 relation. Variability in objectively measured activity, arm pain, gender and age influenced self‐reports in a systematic way, but the effects were modest and sometimes in different directions. Conclusion Self‐reported durations of computer activities are positively associated with objective measures but they are quite inaccurate. Studies using self‐reports to establish relations between computer work times and musculoskeletal pain could be biased and lead to falsely increased or decreased risk estimates. PMID:17387136

Validity of questionnaire self-reports on computer, mouse and keyboard usage during a four-week period.

PubMed

Mikkelsen, Sigurd; Vilstrup, Imogen; Lassen, Christina Funch; Kryger, Ann Isabel; Thomsen, Jane Frølund; Andersen, Johan Hviid

2007-08-01

To examine the validity and potential biases in self-reports of computer, mouse and keyboard usage times, compared with objective recordings. A study population of 1211 people was asked in a questionnaire to estimate the average time they had worked with computer, mouse and keyboard during the past four working weeks. During the same period, a software program recorded these activities objectively. The study was part of a one-year follow-up study from 2000-1 of musculoskeletal outcomes among Danish computer workers. Self-reports on computer, mouse and keyboard usage times were positively associated with objectively measured activity, but the validity was low. Self-reports explained only between a quarter and a third of the variance of objectively measured activity, and were even lower for one measure (keyboard time). Self-reports overestimated usage times. Overestimation was large at low levels and declined with increasing levels of objectively measured activity. Mouse usage time proportion was an exception with a near 1:1 relation. Variability in objectively measured activity, arm pain, gender and age influenced self-reports in a systematic way, but the effects were modest and sometimes in different directions. Self-reported durations of computer activities are positively associated with objective measures but they are quite inaccurate. Studies using self-reports to establish relations between computer work times and musculoskeletal pain could be biased and lead to falsely increased or decreased risk estimates.

Effects of detector-source distance and detector bias voltage variations on time resolution of general purpose plastic scintillation detectors.

PubMed

Ermis, E E; Celiktas, C

2012-12-01

Effects of source-detector distance and the detector bias voltage variations on time resolution of a general purpose plastic scintillation detector such as BC400 were investigated. (133)Ba and (207)Bi calibration sources with and without collimator were used in the present work. Optimum source-detector distance and bias voltage values were determined for the best time resolution by using leading edge timing method. Effect of the collimator usage on time resolution was also investigated. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns.

PubMed

Zhou, Hao; Yan, Bing; Chen, Shun; Wang, Mingshu; Jia, Renyong; Cheng, Anchun

2015-10-01

Tembusu virus (TMUV) is a single-stranded, positive-sense RNA virus. As reported, TMUV infection has resulted in significant poultry losses, and the virus may also pose a threat to public health. To characterize TMUV evolutionarily and to understand the factors accounting for codon usage properties, we performed, for the first time, a comprehensive analysis of codon usage bias for the genomes of 60 TMUV strains. The most recently published TMUV strains were found to be widely distributed in coastal cities of southeastern China. Codon preference among TMUV genomes exhibits a low bias (effective number of codons (ENC)=53.287) and is maintained at a stable level. ENC-GC3 plots and the high correlation between composition constraints and principal component factor analysis of codon usage demonstrated that mutation pressure dominates over natural selection pressure in shaping the TMUV coding sequence composition. The high correlation between the major components of the codon usage pattern and hydrophobicity (Gravy) or aromaticity (Aromo) was obvious, indicating that properties of viral proteins also account for the observed variation in TMUV codon usage. Principal component analysis (PCA) showed that CQW1 isolated from Chongqing may have evolved from GX2013H or GX2013G isolated from Guangxi, thus indicating that TMUV likely disseminated from southeastern China to the mainland. Moreover, the preferred codons encoding eight amino acids were consistent with the optimal codons for human cells, indicating that TMUV may pose a threat to public health due to possible cross-species transmission (birds to birds or birds to humans). The results of this study not only have theoretical value for uncovering the characteristics of synonymous codon usage patterns in TMUV genomes but also have significant meaning with regard to the molecular evolutionary tendencies of TMUV. Copyright © 2015 Elsevier B.V. All rights reserved.

Event-driven visual attention for the humanoid robot iCub

PubMed Central

Rea, Francesco; Metta, Giorgio; Bartolozzi, Chiara

2013-01-01

Fast reaction to sudden and potentially interesting stimuli is a crucial feature for safe and reliable interaction with the environment. Here we present a biologically inspired attention system developed for the humanoid robot iCub. It is based on input from unconventional event-driven vision sensors and an efficient computational method. The resulting system shows low-latency and fast determination of the location of the focus of attention. The performance is benchmarked against an instance of the state of the art in robotics artificial attention system used in robotics. Results show that the proposed system is two orders of magnitude faster that the benchmark in selecting a new stimulus to attend. PMID:24379753

A Flight-Calibrated Methodology for Determination of Cassini Thruster On-Times for Reaction Wheel Biases

NASA Technical Reports Server (NTRS)

Sarani, Sam

2010-01-01

The Cassini spacecraft, the largest and most complex interplanetary spacecraft ever built, continues to undertake unique scientific observations of planet Saturn, Titan, Enceladus, and other moons of the ring world. In order to maintain a stable attitude during the course of its mission, this three-axis stabilized spacecraft uses two different control systems: the Reaction Control System (or RCS) and the Reaction Wheel Assembly (RWA) control system. In the course of its mission, Cassini performs numerous reaction wheel momentum biases (or unloads) using its reaction control thrusters. The use of the RCS thrusters often imparts undesired velocity changes (delta Vs) on the spacecraft and it is crucial for Cassini navigation and attitude control teams to be able to, quickly but accurately, predict the hydrazine usage and delta V vector in Earth Mean Equatorial (J2000) inertial coordinates for reaction wheel bias events, without actually having to spend time and resources simulating the event in a dynamic or hardware-in-the-loop simulation environments. The flight-calibrated methodology described in this paper, and the ground software developed thereof, are designed to provide the RCS thruster on-times, with acceptable accuracy and without any form of dynamic simulation, for reaction wheel biases, along with the hydrazine usage and the delta V in EME-2000 inertial frame.

Influence of codon usage bias on FGLamide-allatostatin mRNA secondary structure.

PubMed

Martínez-Pérez, Francisco; Bendena, William G; Chang, Belinda S W; Tobe, Stephen S

2011-03-01

The FGLamide allatostatins (ASTs) are invertebrate neuropeptides which inhibit juvenile hormone biosynthesis in Dictyoptera and related orders. They also show myomodulatory activity. FGLamide AST nucleotide frequencies and codon bias were investigated with respect to possible effects on mRNA secondary structure. 367 putative FGLamide ASTs and their potential endoproteolytic cleavage sites were identified from 40 species of crustaceans, chelicerates and insects. Among these, 55% comprised only 11 amino acids. An FGLamide AST consensus was identified to be (X)(1→16)Y(S/A/N/G)FGLGKR, with a strong bias for the codons UUU encoding for Phe and AAA for Lys, which can form strong Watson-Crick pairing in all peptides analyzed. The physical distance between these codons favor a loop structure from Ser/Ala-Phe to Lys-Arg. Other loop and hairpin loops were also inferred from the codon frequencies in the N-terminal motif, and the first amino acids from the C-terminal motif, or the dibasic potential endoproteolytic cleavage site. Our results indicate that nucleotide frequencies and codon usage bias in FGLamide ASTs tend to favor mRNA folds in the codon sequence in the C-terminal active peptide core and at the dibasic potential endoproteolytic cleavage site. Copyright © 2010 Elsevier Inc. All rights reserved.

Effect of self-deflection on a totally asymmetric simple exclusion process with functions of site assignments

NASA Astrophysics Data System (ADS)

Tsuzuki, Satori; Yanagisawa, Daichi; Nishinari, Katsuhiro

2018-04-01

This study proposes a model of a totally asymmetric simple exclusion process on a single-channel lane with functions of site assignments along the pit lane. The system model attempts to insert a new particle to the leftmost site at a certain probability by randomly selecting one of the empty sites in the pit lane, and reserving it for the particle. Thereafter, the particle is directed to stop at the site only once during its travel. Recently, the system was determined to show a self-deflection effect, in which the site usage distribution biases spontaneously toward the leftmost site, and the throughput becomes maximum when the site usage distribution is slightly biased to the rightmost site. Our exact analysis describes this deflection effect and show a good agreement with simulations.

Risk of POP mixtures on the Arctic food chain.

PubMed

Villa, Sara; Migliorati, Sonia; Monti, Gianna Serafina; Holoubek, Ivan; Vighi, Marco

2017-05-01

The exposure of the Arctic ecosystem to persistent organic pollutants (POPs) was assessed through a review of literature data. Concentrations of 19 chemicals or congeneric groups were estimated for the highest levels of the Arctic food chain (Arctic cod, ringed seals, and polar bears). The ecotoxicological risk for seals, bears, and bear cubs was estimated by applying the concentration addition (CA) concept. The risk of POP mixtures was very low in seals. By contrast, the risk was 2 orders of magnitude higher than the risk threshold for adult polar bears and even more (3 orders of magnitude above the threshold) for bear cubs fed with contaminated milk. Based on the temporal trends available for many of the chemicals, the temporal trend of the mixture risk for bear cubs was calculated. Relative to the 1980s, a decrease in risk from the POP mixture is evident, mainly because of international control measures. However, the composition of the mixture substantially changes, and the contribution of new POPs (particularly perfluorooctane sulfonate) increases. These results support the effectiveness of control measures, such as those promulgated in the Stockholm Convention, as well as the urgent need for their implementation for new and emerging POPs. Environ Toxicol Chem 2017;36:1181-1192. © 2017 SETAC. © 2017 SETAC.

Evaluation of rules to distinguish unique female grizzly bears with cubs in Yellowstone

USGS Publications Warehouse

Schwartz, C.C.; Haroldson, M.A.; Cherry, S.; Keating, K.A.

2008-01-01

The United States Fish and Wildlife Service uses counts of unduplicated female grizzly bears (Ursus arctos) with cubs-of-the-year to establish limits of sustainable mortality in the Greater Yellowstone Ecosystem, USA. Sightings are dustered into observations of unique bears based on an empirically derived rule set. The method has never been tested or verified. To evaluate the rule set, we used data from radiocollared females obtained during 1975-2004 to simulate populations under varying densities, distributions, and sighting frequencies. We tested individual rules and rule-set performance, using custom software to apply the rule-set and duster sightings. Results indicated most rules were violated to some degree, and rule-based dustering consistently underestimated the minimum number of females and total population size derived from a nonparametric estimator (Chao2). We conclude that the current rule set returns conservative estimates, but with minor improvements, counts of unduplicated females-with-cubs can serve as a reasonable index of population size useful for establishing annual mortality limits. For the Yellowstone population, the index is more practical and cost-effective than capture-mark-recapture using either DNA hair snagging or aerial surveys with radiomarked bears. The method has useful application in other ecosystems, but we recommend rules used to distinguish unique females be adapted to local conditions and tested.

Wildlife forensic entomology: determining time of death in two illegally killed black bear cubs.

PubMed

Anderson, G S

1999-07-01

Forensic entomology is now commonly used to determine time of death in human death investigations. However, it can be equally applicable to wildlife crimes. This paper describes the use of entomology to determine time of death in the illegal killing of two young bear cubs in Manitoba, Canada. Two cubs were found shot, disemboweled, with their gall bladders removed. Natural Resource officers (Conservation Officers) and a Royal Canadian Mounted Police (R.C.M.P.) officer examined the remains, and the R.C.M.P. officer collected insect evidence. The only insects on the remains were adult blow flies coming to lay eggs and the blow fly eggs themselves (Diptera: Calliphoridae). The time of hatch was recorded and the insects were reared to adulthood. Time of hatch, together with species identification, macro and micro climate and lab developmental data were used to determine the time of death. The time was consistent with the time that the defendants were seen at the scene and was used in their conviction. This case illustrates that insect evidence can be equally as valuable in poaching cases as in homicide cases. However, in most cases Conservation Officers are unaware of this science. It is therefore, extremely important for more Conservation Officers to be educated about this field.

A 14-gene region of rat chromosome 8 in SHR-derived polydactylous congenic substrain affects muscle-specific insulin resistance, dyslipidaemia and visceral adiposity.

PubMed

Seda, O; Liska, F; Sedová, L; Kazdová, L; Krenová, D; Kren, V

2005-01-01

The SHR and the PD/Cub are two established rodent models of human metabolic syndrome. Introgression of a ca 30 cM region of rat chromosome 8 from PD/Cub onto the genetic background of SHR was previously shown to influence several of the metabolic syndrome-related traits along with causing the PLS in the SHR-Lx congenic strain. In the process of identification of the causative alleles, we have produced several congenic sublines. The differential segment of SHR-Lx PD5 congenic substrain [SHR.PD(D8Rat42-D8Arb23)/Cub] spans approximately 1.4 Mb encompassing only 14 genes. When comparing the metabolic, morphometric and gene expression profiles of the SHR-Lx PD5 vs. SHR, the polydactyly and several distinct metabolic features observed in the original SHR-Lx congenic were still manifested, suggesting that the responsible genes were "trapped" within the relatively short differential segment of PD/Cub origin in SHR-Lx PD5. Particularly, the SHR-Lx PD5 displayed substantial reduction of insulin sensitivity confined to skeletal muscle. Among the candidate genes, the promyelocytic leukaemia zinc-finger Plzf (Zbtb16) transcription repressor is most likely responsible for the Lx mutation resulting in PLS and could also be involved in the alteration of metabolic pathways. The sequence analysis of the Plzf gene revealed a SNP leading to a threonine to serine substitution in SHR at aminoacid position 208 (T208S). In summary, we have isolated a 1.4 Mb genomic region syntenic to human chromosome 11q23, which, apart from causing polydactyly-luxate syndrome (PLS), affects total body weight, adiposity, lipid profile, insulin sensitivity of skeletal muscle and related gene expression as shown in the SHR-Lx PD5 congenic substrain.

Robot Faces that Follow Gaze Facilitate Attentional Engagement and Increase Their Likeability

PubMed Central

Willemse, Cesco; Marchesi, Serena; Wykowska, Agnieszka

2018-01-01

Gaze behavior of humanoid robots is an efficient mechanism for cueing our spatial orienting, but less is known about the cognitive–affective consequences of robots responding to human directional cues. Here, we examined how the extent to which a humanoid robot (iCub) avatar directed its gaze to the same objects as our participants affected engagement with the robot, subsequent gaze-cueing, and subjective ratings of the robot’s characteristic traits. In a gaze-contingent eyetracking task, participants were asked to indicate a preference for one of two objects with their gaze while an iCub avatar was presented between the object photographs. In one condition, the iCub then shifted its gaze toward the object chosen by a participant in 80% of the trials (joint condition) and in the other condition it looked at the opposite object 80% of the time (disjoint condition). Based on the literature in human–human social cognition, we took the speed with which the participants looked back at the robot as a measure of facilitated reorienting and robot-preference, and found these return saccade onset times to be quicker in the joint condition than in the disjoint condition. As indicated by results from a subsequent gaze-cueing tasks, the gaze-following behavior of the robot had little effect on how our participants responded to gaze cues. Nevertheless, subjective reports suggested that our participants preferred the iCub following participants’ gaze to the one with a disjoint attention behavior, rated it as more human-like and as more likeable. Taken together, our findings show a preference for robots who follow our gaze. Importantly, such subtle differences in gaze behavior are sufficient to influence our perception of humanoid agents, which clearly provides hints about the design of behavioral characteristics of humanoid robots in more naturalistic settings. PMID:29459842

Structural changes that occur upon photolysis of the Fe(II)a3 - CO complex in the cytochrome ba3-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to CuB

PubMed Central

Liu, Bin; Zhang, Yang; Sage, J. Timothy; Soltis, S. Michael; Doukov, Tzanko; Chen, Ying; Stout, C. David; Fee, James A.

2012-01-01

The purpose of the work was to provide a crystallographic demonstration of the venerable idea that CO photolyzed from ferrous heme-a3 moves to the nearby cuprous ion in the cytochrome c oxidases. Crystal structures of CO-bound cytochrome ba3-oxidase from Thermus thermophilus, determined at ~ 2.8 – 3.2 Å resolution, reveal a Fe-C distance of ~2.0 Å, a Cu-O distance of 2.4 Å and a Fe-C-O angle of ~126°. Upon photodissociation at 100 K, X-ray structures indicate loss of Fea3-CO and appearance of CuB-CO having a Cu-C distance of ~1.9 Å and an O-Fe distance of ~2.3 Å. Absolute FTIR spectra recorded from single crystals of reduced ba3–CO that had not been exposed to X-ray radiation, showed several peaks around 1975 cm−1; after photolysis at 100 K, the absolute FTIR spectra also showed a significant peak at 2050 cm−1. Analysis of the “light’ minus ‘dark’ difference spectra showed four very sharp CO stretching bands at 1970 cm−1, 1977 cm−1, 1981 cm−1, and 1985 cm−1, previously assigned to the Fea3-CO complex, and a significantly broader CO stretching band centered at ~2050 cm−1, previously assigned to the CO stretching frequency of CuB bound CO. As expected for light propagating along the tetragonal axis of the P43212 space group, the single crystal spectra exhibit negligible dichroism. Absolute FTIR spectrometry of a CO-laden ba3 crystal, exposed to an amount of X-ray radiation required to obtain structural data sets before FTIR characterization, showed a significant signal due to photogenerated CO2 at 2337 cm−1 and one from traces of CO at 2133 cm−1; while bands associated with CO bound to either Fea3 or to CuB in “light” minus “dark” FTIR difference spectra shifted and broadened in response to X-ray exposure. In spite of considerable radiation damage to the crystals, both X-ray analysis at 2.8 and 3.2 Å and FTIR spectra support the long-held position that photolysis of Fea3-CO in cytochrome c oxidases leads to significant trapping of the CO on the CuB atom; Fea3 and CuB ligation, at the resolutions reported here, are otherwise unaltered. PMID:22226917

Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD.

PubMed

Fu, Jingjing; Murphy, Katherine A; Zhou, Mian; Li, Ying H; Lam, Vu H; Tabuloc, Christine A; Chiu, Joanna C; Liu, Yi

2016-08-01

Codon usage bias is a universal feature of all genomes, but its in vivo biological functions in animal systems are not clear. To investigate the in vivo role of codon usage in animals, we took advantage of the sensitivity and robustness of the Drosophila circadian system. By codon-optimizing parts of Drosophila period (dper), a core clock gene that encodes a critical component of the circadian oscillator, we showed that dper codon usage is important for circadian clock function. Codon optimization of dper resulted in conformational changes of the dPER protein, altered dPER phosphorylation profile and stability, and impaired dPER function in the circadian negative feedback loop, which manifests into changes in molecular rhythmicity and abnormal circadian behavioral output. This study provides an in vivo example that demonstrates the role of codon usage in determining protein structure and function in an animal system. These results suggest a universal mechanism in eukaryotes that uses a codon usage "code" within genetic codons to regulate cotranslational protein folding. © 2016 Fu et al.; Published by Cold Spring Harbor Laboratory Press.

Comparing the Self-Report and Measured Smartphone Usage of College Students: A Pilot Study.

PubMed

Lee, Heyoung; Ahn, Heejune; Nguyen, Trung Giang; Choi, Sam-Wook; Kim, Dae Jin

2017-03-01

Nowadays smartphone overuse has become a social and medical concern. For the diagnosis and treatment, clinicians use the self-report information, but the report data often does not match actual usage pattern. The paper examines the similarity and variance in smartphone usage patterns between the measured data and self-reported data. Together with the self-reported data, the real usage log data is collected from 35 college students in a metropolitan region of Northeast Asia, using Android smartphone monitoring application developed by the authors. The unconscious users underestimate their usage time by 40%, in spite of 15% more use in the actual usage. Messengers are most-used application regardless of their self-report, and significant preference to SNS applications was observed in addict group. The actual hourly pattern is consistent with the reported one. College students use more in the afternoon, when they have more free time and cannot use PCs. No significant difference in hourly pattern is observed between the measured and self-report. The result shows there are significant cognitive bias in actual usage patterns exists in self report of smartphone addictions. Clinicians are recommended to utilize measurement tools in diagnosis and treatment of smartphone overusing subjects.

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells.

PubMed

Zhao, Fangzhou; Yu, Chien-Hung; Liu, Yi

2017-08-21

Codon usage biases are found in all eukaryotic and prokaryotic genomes and have been proposed to regulate different aspects of translation process. Codon optimality has been shown to regulate translation elongation speed in fungal systems, but its effect on translation elongation speed in animal systems is not clear. In this study, we used a Drosophila cell-free translation system to directly compare the velocity of mRNA translation elongation. Our results demonstrate that optimal synonymous codons speed up translation elongation while non-optimal codons slow down translation. In addition, codon usage regulates ribosome movement and stalling on mRNA during translation. Finally, we show that codon usage affects protein structure and function in vitro and in Drosophila cells. Together, these results suggest that the effect of codon usage on translation elongation speed is a conserved mechanism from fungi to animals that can affect protein folding in eukaryotic organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Energy efficiency trade-offs drive nucleotide usage in transcribed regions

PubMed Central

Chen, Wei-Hua; Lu, Guanting; Bork, Peer; Hu, Songnian; Lercher, Martin J.

2016-01-01

Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of ‘A' versus ‘T' and ‘G' versus ‘C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides ‘U' and ‘C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides ‘A' and ‘G' at non-synonymous coding sites. PMID:27098217

The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

PubMed Central

Cook, Charles E

2005-01-01

Background Animal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome evolution. Within the phylum Arthropoda the subphylum Crustacea includes over 50,000 named species with immense variation in body plans and habitats, yet only 23 complete mitochondrial genomes are available from this subphylum. Results I describe here the complete mitochondrial genome of the crustacean Squilla mantis (Crustacea: Malacostraca: Stomatopoda). This 15994-nucleotide genome, the first described from a hoplocarid, contains the standard complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region that is found in most other metazoans. The gene order is identical to that considered ancestral for hexapods and crustaceans. The 70% AT base composition is within the range described for other arthropods. A single unusual feature of the genome is a 230 nucleotide non-coding region between a serine transfer RNA and the nad1 gene, which has no apparent function. I also compare gene order, nucleotide composition, and codon usage of the S. mantis genome and eight other malacostracan crustaceans. A translocation of the histidine transfer RNA gene is shared by three taxa in the order Decapoda, infraorder Brachyura; Callinectes sapidus, Portunus trituberculatus and Pseudocarcinus gigas. This translocation may be diagnostic for the Brachyura. For all nine taxa nucleotide composition is biased towards AT-richness, as expected for arthropods, and is within the range reported for other arthropods. Codon usage is biased, and much of this bias is probably due to the skew in nucleotide composition towards AT-richness. Conclusion The mitochondrial genome of Squilla mantis contains one unusual feature, a 230 base pair non-coding region has so far not been described in any other malacostracan. Comparisons with other Malacostraca show that all nine genomes, like most other mitochondrial genomes, share a bias toward AT-richness and a related bias in codon usage. The nine malacostracans included in this analysis are not representative of the diversity of the class Malacostraca, and additional malacostracan sequences would surely reveal other unusual genomic features that could be useful in understanding mitochondrial evolution in this taxon. PMID:16091132

GC-Content of Synonymous Codons Profoundly Influences Amino Acid Usage

PubMed Central

Li, Jing; Zhou, Jun; Wu, Ying; Yang, Sihai; Tian, Dacheng

2015-01-01

Amino acids typically are encoded by multiple synonymous codons that are not used with the same frequency. Codon usage bias has drawn considerable attention, and several explanations have been offered, including variation in GC-content between species. Focusing on a simple parameter—combined GC proportion of all the synonymous codons for a particular amino acid, termed GCsyn—we try to deepen our understanding of the relationship between GC-content and amino acid/codon usage in more details. We analyzed 65 widely distributed representative species and found a close association between GCsyn, GC-content, and amino acids usage. The overall usages of the four amino acids with the greatest GCsyn and the five amino acids with the lowest GCsyn both vary with the regional GC-content, whereas the usage of the remaining 11 amino acids with intermediate GCsyn is less variable. More interesting, we discovered that codon usage frequencies are nearly constant in regions with similar GC-content. We further quantified the effects of regional GC-content variation (low to high) on amino acid usage and found that GC-content determines the usage variation of amino acids, especially those with extremely high GCsyn, which accounts for 76.7% of the changed GC-content for those regions. Our results suggest that GCsyn correlates with GC-content and has impact on codon/amino acid usage. These findings suggest a novel approach to understanding the role of codon and amino acid usage in shaping genomic architecture and evolutionary patterns of organisms. PMID:26248983

Bicluster Pattern of Codon Context Usages between Flavivirus and Vector Mosquito Aedes aegypti: Relevance to Infection and Transcriptional Response of Mosquito Genes

PubMed Central

Behura, Susanta K.; Severson, David W.

2014-01-01

The mosquito Aedes aegypti is the primary vector of dengue virus (DENV) infection in most of the subtropical and tropical countries. Besides DENV, yellow fever virus (YFV) is also transmitted by A. aegypti. Susceptibility of A. aegypti to West Nile virus (WNV) has also been confirmed. Although studies have indicated correlation of codon bias between flaviviridae and their animal/insect hosts, it is not clear if codon sequences have any relation to susceptibility of A. aegypti to DENV, YFV and WNV. In the current study, usages of codon context sequences (codon pairs for neighboring amino acids) of the vector (A. aegypti) genome as well as the flaviviral genomes are investigated. We used bioinformatics methods to quantify codon context bias in a genome-wide manner of A. aegypti as well as DENV, WNV and YFV sequences. Mutual information statistics was applied to perform bicluster analysis of codon context bias between vector and flaviviral sequences. Functional relevance of the bicluster pattern was inferred from published microarray data. Our study shows that codon context bias of DENV, WNV and YFV sequences varies in a bicluster manner with that of specific sets of genes of A. aegypti. Many of these mosquito genes are known to be differentially expressed in response to flaviviral infection suggesting that codon context sequences of A. aegypti and the flaviviruses may play a role in the susceptible interaction between flaviviruses and this mosquito. The bias inusages of codon context sequences likely has a functional association with susceptibility of A. aegypti to flaviviral infection. The results from this study will allow us to conduct hypothesis driven tests to examine the role of codon contexts bias in evolution of vector-virus interactions at the molecular level. PMID:24838953

Non-uniqueness of factors constraint on the codon usage in Bombyx mori.

PubMed

Jia, Xian; Liu, Shuyu; Zheng, Hao; Li, Bo; Qi, Qi; Wei, Lei; Zhao, Taiyi; He, Jian; Sun, Jingchen

2015-05-06

The analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori. A total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans). The codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the "optimal codons" of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization.

Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times

NASA Astrophysics Data System (ADS)

Sharma, Ajeet K.; Ahmed, Nabeel; O'Brien, Edward P.

2018-02-01

Ribosome profiling experiments have found greater than 100-fold variation in ribosome density along mRNA transcripts, indicating that individual codon elongation rates can vary to a similar degree. This wide range of elongation times, coupled with differences in codon usage between transcripts, suggests that the average codon translation-rate per gene can vary widely. Yet, ribosome run-off experiments have found that the average codon translation rate for different groups of transcripts in mouse stem cells is constant at 5.6 AA/s. How these seemingly contradictory results can be reconciled is the focus of this study. Here, we combine knowledge of the molecular factors shown to influence translation speed with genomic information from Escherichia coli, Saccharomyces cerevisiae and Homo sapiens to simulate the synthesis of cytosolic proteins in these organisms. The model recapitulates a near constant average translation rate, which we demonstrate arises because the molecular determinants of translation speed are distributed nearly randomly amongst most of the transcripts. Consequently, codon translation rates are also randomly distributed and fast-translating segments of a transcript are likely to be offset by equally probable slow-translating segments, resulting in similar average elongation rates for most transcripts. We also show that the codon usage bias does not significantly affect the near random distribution of codon translation rates because only about 10 % of the total transcripts in an organism have high codon usage bias while the rest have little to no bias. Analysis of Ribo-Seq data and an in vivo fluorescent assay supports these conclusions.

Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase.

PubMed

Alnazawi, Mohamed; Altaher, Abdallah; Kandeel, Mahmoud

2017-01-01

Middle East Respiratory Syndrome Coronavirus (MERS CoV) is a new emerging viral disease characterized by high fatality rate. Understanding MERS CoV genetic aspects and codon usage pattern is important to understand MERS CoV survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. In this work, we provide comprehensive analysis of 238 MERS CoV full genomes comprised of human (hMERS) and camel (cMERS) isolates of the virus. MERS CoV genome shaping seems to be under compositional and mutational bias, as revealed by preference of A/T over G/C nucleotides, preferred codons, nucleotides at the third position of codons (NT3s), relative synonymous codon usage, hydropathicity (Gravy), and aromaticity (Aromo) indices. Effective number of codons (ENc) analysis reveals a general slight codon usage bias. Codon adaptation index reveals incomplete adaptation to host environment. MERS CoV showed high ability to resist the innate immune response by showing lower CpG frequencies. Neutrality evolution analysis revealed a more significant role of mutation pressure in cMERS over hMERS. Correspondence analysis revealed that MERS CoV genomes have three genetic clusters, which were distinct in their codon usage, host, and geographic distribution. Additionally, virtual screening and binding experiments were able to identify three new virus-encoded helicase binding compounds. These compounds can be used for further optimization of inhibitors.

Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces

PubMed Central

Romero, Héctor; Zavala, Alejandro; Musto, Héctor

2000-01-01

The patterns of synonymous codon choices of the completely sequenced genome of the bacterium Chlamydia trachomatis were analysed. We found that the most important source of variation among the genes results from whether the sequence is located on the leading or lagging strand of replication, resulting in an over representation of G or C, respectively. This can be explained by different mutational biases associated to the different enzymes that replicate each strand. Next we found that most highly expressed sequences are located on the leading strand of replication. From this result, replicational-transcriptional selection can be invoked. Then, when the genes located on the leading strand are studied separately, the correspondence analysis detects a principal trend which discriminates between lowly and highly expressed sequences, the latter displaying a different codon usage pattern than the former, suggesting selection for translation, which is reinforced by the fact that Ks values between orthologous sequences from C.trachomatis and Chlamydia pneumoniae are much smaller in highly expressed genes. Finally, synonymous codon choices appear to be influenced by the hydropathy of each encoded protein and by the degree of amino acid conservation. Therefore, synonymous codon usage in C.trachomatis seems to be the result of a very complex balance among different factors, which rises the problem of whether the forces driving codon usage patterns among microorganisms are rather more complex than generally accepted. PMID:10773076

Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces.

PubMed

Romero, H; Zavala, A; Musto, H

2000-05-15

The patterns of synonymous codon choices of the completely sequenced genome of the bacterium Chlamydia trachomatis were analysed. We found that the most important source of variation among the genes results from whether the sequence is located on the leading or lagging strand of replication, resulting in an over representation of G or C, respectively. This can be explained by different mutational biases associated to the different enzymes that replicate each strand. Next we found that most highly expressed sequences are located on the leading strand of replication. From this result, replicational-transcriptional selection can be invoked. Then, when the genes located on the leading strand are studied separately, the correspondence analysis detects a principal trend which discriminates between lowly and highly expressed sequences, the latter displaying a different codon usage pattern than the former, suggesting selection for translation, which is reinforced by the fact that Ks values between orthologous sequences from C. trachomatis and Chlamydia pneumoniae are much smaller in highly expressed genes. Finally, synonymous codon choices appear to be influenced by the hydropathy of each encoded protein and by the degree of amino acid conservation. Therefore, synonymous codon usage in C.trachomatis seems to be the result of a very complex balance among different factors, which rises the problem of whether the forces driving codon usage patterns among microorganisms are rather more complex than generally accepted.

Ecological Change Drives a Decline in Mercury Concentrations in Southern Beaufort Sea Polar Bears.

PubMed

McKinney, Melissa A; Atwood, Todd C; Pedro, Sara; Peacock, Elizabeth

2017-07-18

We evaluated total mercury (THg) concentrations and trends in polar bears from the southern Beaufort Sea subpopulation from 2004 to 2011. Hair THg concentrations ranged widely among individuals from 0.6 to 13.3 μg g -1 dry weight (mean: 3.5 ± 0.2 μg g -1 ). Concentrations differed among sex and age classes: solitary adult females ≈ adult females with cubs ≈ subadults > adult males ≈ yearlings > cubs-of-the-year ≈ 2 year old dependent cubs. No variation was observed between spring and fall samples. For spring-sampled adults, THg concentrations declined by 13% per year, contrasting recent trends observed for other Western Hemispheric Arctic biota. Concentrations also declined by 15% per year considering adult males only, while a slower, nonsignificant decrease of 4.4% per year was found for adult females. Lower THg concentrations were associated with higher body mass index (BMI) and higher proportions of lower trophic position food resources consumed. Because BMI and diet were related, and the relationship to THg was strongest for BMI, trends were re-evaluated adjusting for BMI as the covariate. The adjusted annual decline was not significant. These findings indicate that changes in foraging ecology, not declining environmental concentrations of mercury, are driving short-term declines in THg concentrations in southern Beaufort Sea polar bears.

Ecological change drives a decline in mercury concentrations in southern Beaufort Sea polar bears

USGS Publications Warehouse

McKinney, Melissa A.; Atwood, Todd C.; Pedro, Sara; Peacock, Elizabeth

2017-01-01

We evaluated total mercury (THg) concentrations and trends in polar bears from the southern Beaufort Sea subpopulation from 2004 to 2011. Hair THg concentrations ranged widely among individuals from 0.6 to 13.3 μg g–1 dry weight (mean: 3.5 ± 0.2 μg g–1). Concentrations differed among sex and age classes: solitary adult females ≈ adult females with cubs ≈ subadults > adult males ≈ yearlings > cubs-of-the-year ≈ 2 year old dependent cubs. No variation was observed between spring and fall samples. For spring-sampled adults, THg concentrations declined by 13% per year, contrasting recent trends observed for other Western Hemispheric Arctic biota. Concentrations also declined by 15% per year considering adult males only, while a slower, nonsignificant decrease of 4.4% per year was found for adult females. Lower THg concentrations were associated with higher body mass index (BMI) and higher proportions of lower trophic position food resources consumed. Because BMI and diet were related, and the relationship to THg was strongest for BMI, trends were re-evaluated adjusting for BMI as the covariate. The adjusted annual decline was not significant. These findings indicate that changes in foraging ecology, not declining environmental concentrations of mercury, are driving short-term declines in THg concentrations in southern Beaufort Sea polar bears.

Fatal cytauxzoonosis in captive-reared lions in Brazil.

PubMed

Peixoto, P V; Soares, C O; Scofield, A; Santiago, C D; França, T N; Barros, S S

2007-04-30

Fatal cytauxzoonosis is described in a captive reared lioness (Panthera leo) and its 6-month-old cub. Clinical signs in the lioness included loss of weight, depression, anaemia, loss of hair, dark discolored urine, tachypnoea, nystagmus, deaphness and staggering gait. The cub died after a short period of depression. In the lioness, laboratory examination revealed normochromic normocytic anaemia, neutrophilia, lymphopenia, monocytosis, eosinopenia, thrombocytopenia, proteinuria, pyuria, haematuria and increased. At necropsy the lioness showed marked pulmonary edema and slight gelatinous translucent edema in the mediastinum, petechiae and echymosis disseminated in the serosae, and the intestinal content was red and semiliquid. The cub presented hemothorax, endocardial and pulmonary edema, petechiae in the cardiac serosae, hepatic and splenic congestion and segments of the small intestine with blood stained fluid contents and reddish mesenteric lymph nodes. Histopathological examination of liver, spleen, heart, lungs, intestines, pancreas, mesenteric lymph nodes, kidneys, skeletal muscle, brain and skin revealed large number of intravascular macrophages with their cytoplasm filled with various schizogonic stages of a Theileriidae. Electron microscopy confirmed the presence of schizonts in endothelial-associated macrophages. The diagnosis was established by the finding of the pathognomonic schizonts in macrophages within blood vessels in several organs and tissues from both lions. This is the first report of feline cytauxzoonosis in P. leo and of a confirmed infection by Cytauxzoon felis in felidae in South America.

Distribution of grizzly bears in the Greater Yellowstone Ecosystem, 2004

USGS Publications Warehouse

Schwartz, C.C.; Haroldson, M.A.; Gunther, K.; Moody, D.

2006-01-01

The US Fish and Wildlife Service (USFWS) proposed delisting the Yellowstone grizzly bear (Ursus arctos horribilis) in November 2005. Part of that process required knowledge of the most current distribution of the species. Here, we update an earlier estimate of occupied range (1990–2000) with data through 2004. We used kernel estimators to develop distribution maps of occupied habitats based on initial sightings of unduplicated females (n = 481) with cubs of the year, locations of radiomarked bears (n = 170), and spatially unique locations of conflicts, confrontations, and mortalities (n = 1,075). Although each data set was constrained by potential sampling bias, together they provided insight into areas in the Greater Yellowstone Ecosystem (GYE) currently occupied by grizzly bears. The current distribution of 37,258 km2 (1990–2004) extends beyond the distribution map generated with data from 1990–2000 (34,416 km2 ). Range expansion is particularly evident in parts of the Caribou–Targhee National Forest in Idaho and north of Spanish Peaks on the Gallatin National Forest in Montana.

Conflicts of interest in medical science: peer usage, peer review and 'CoI consultancy'.

PubMed

Charlton, Bruce G

2004-01-01

In recent years, the perception has grown that conflicts of interest are having a detrimental effect on medical science as it influences health policy and clinical practice, leading medical journals to enforce self-declaration of potential biases in the attempt to counteract or compensate for the problem. Conflict of interest (CoI) declarations have traditionally been considered inappropriate in pure science since its evaluation systems themselves constitute a mechanism for eliminating the effect of individual biases. Pure science is primarily evaluated by 'peer usage', in which scientific information is 'replicated' by being incorporated in the work of other scientists, and tested by further observation of the natural world. Over the long-term, the process works because significant biases impair the quality of science, and bad science tends to be neglected or refuted. However, scientific evaluation operates slowly over years and decades, and only a small proportion of published work is ever actually evaluated. But most of modern medical science no longer conforms to the model of pure science, and may instead be conceptualized as a system of 'applied' science having different aims and evaluation processes. The aim of applied medical science is to solve pre-specified problems, and to provide scientific information ready for implementation immediately following publication. The primary evaluation process of applied science is peer review, not peer usage. Peer review is much more rapid (with a timescale of weeks or months) and cheaper than peer usage and (consequently) has a much wider application: peer review is a prospective validation while peer usage is retrospective. Since applied science consists of incremental advances on existing knowledge achieved using established techniques, its results can usually be reliably evaluated by peer review. However, despite its considerable convenience, peer review has significant limitations related to its reliance on opinion. One major limitation of peer review has proved to be its inability to deal with conflicts of interest, especially in a 'big science' context when prestigious scientists may have similar biases, and conflicts of interest are widely shared among peer reviewers. When applied medical science has been later checked against the slower but more valid processes of peer usage, it seems that reliance on peer review may allow damaging distortions to become 'locked-in' to clinical practice and health policy for considerable periods. Scientific progress is generally underpinned by increasing specialization. Medical journals should specialize in the communication of scientific information, and they have neither the resources nor the motivation to investigate and measure conflicts of interest. Effectively dealing with the problem of conflicts of interest in applied medical science firstly requires a more explicit demarcation between the communications media of pure medical science and applied medical science. Greater specialization of these activities would then allow distinctive aims and evaluation systems to evolve with the expectation of improved performance in both pure and applied systems. In future, applied medical science should operate with an assumption of bias, with the onus of proof on applied medical scientists to facilitate the 'data transparency' necessary to validate their research. Journals of applied medical science will probably require more rigorous processes of peer review than at present, since their publications are intended to be ready for implementation. But since peer review does not adequately filter-out conflicts of interest in applied medical science, there is a need for the evolution of specialist post-publication institutional mechanisms. The suggested solution is to encourage the establishment of independent 'CoI consultancy' services, whose role would be to evaluate conflicts of interest and other biases in published applied medical science prior to their implementation. Such services would be paid-for by the groups who intend to implement applied medical research.

Self-association and domain rearrangements between complement C3 and C3u provide insight into the activation mechanism of C3.

PubMed

Li, Keying; Gor, Jayesh; Perkins, Stephen J

2010-10-01

Component C3 is the central protein of the complement system. During complement activation, the thioester group in C3 is slowly hydrolysed to form C3u, then the presence of C3u enables the rapid conversion of C3 into functionally active C3b. C3u shows functional similarities to C3b. To clarify this mechanism, the self-association properties and solution structures of C3 and C3u were determined using analytical ultracentrifugation and X-ray scattering. Sedimentation coefficients identified two different dimerization events in both proteins. A fast dimerization was observed in 50 mM NaCl but not in 137 mM NaCl. Low amounts of a slow dimerization was observed for C3u and C3 in both buffers. The X-ray radius of gyration RG values were unchanged for both C3 and C3u in 137 mM NaCl, but depend on concentration in 50 mM NaCl. The C3 crystal structure gave good X-ray fits for C3 in 137 mM NaCl. By randomization of the TED (thioester-containing domain)/CUB (for complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domains in the C3b crystal structure, X-ray fits showed that the TED/CUB domains in C3u are extended and differ from the more compact arrangement of C3b. This TED/CUB conformation is intermediate between those of C3 and C3b. The greater exposure of the TED domain in C3u (which possesses the hydrolysed reactive thioester) accounts for the greater self-association of C3u in low-salt conditions. This conformational variability of the TED/CUB domains would facilitate their interactions with a broad range of antigenic surfaces. The second dimerization of C3 and C3u may correspond to a dimer observed in one of the crystal structures of C3b.

Comparing the Self-Report and Measured Smartphone Usage of College Students: A Pilot Study

PubMed Central

Lee, Heyoung; Nguyen, Trung Giang; Choi, Sam-Wook; Kim, Dae Jin

2017-01-01

Objective Nowadays smartphone overuse has become a social and medical concern. For the diagnosis and treatment, clinicians use the self-report information, but the report data often does not match actual usage pattern. The paper examines the similarity and variance in smartphone usage patterns between the measured data and self-reported data. Methods Together with the self-reported data, the real usage log data is collected from 35 college students in a metropolitan region of Northeast Asia, using Android smartphone monitoring application developed by the authors. Results The unconscious users underestimate their usage time by 40%, in spite of 15% more use in the actual usage. Messengers are most-used application regardless of their self-report, and significant preference to SNS applications was observed in addict group. The actual hourly pattern is consistent with the reported one. College students use more in the afternoon, when they have more free time and cannot use PCs. No significant difference in hourly pattern is observed between the measured and self-report. Conclusion The result shows there are significant cognitive bias in actual usage patterns exists in self report of smartphone addictions. Clinicians are recommended to utilize measurement tools in diagnosis and treatment of smartphone overusing subjects. PMID:28326119

Complex codon usage pattern and compositional features of retroviruses.

PubMed

RoyChoudhury, Sourav; Mukherjee, Debaprasad

2013-01-01

Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition.

Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta

PubMed Central

Whittle, C. A.; Sun, Y.; Johannesson, H.

2011-01-01

Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems. PMID:21402862

Overcoming codon-usage bias in heterologous protein expression in Streptococcus gordonii.

PubMed

Lee, Song F; Li, Yi-Jing; Halperin, Scott A

2009-11-01

One of the limitations facing the development of Streptococcus gordonii into a successful vaccine vector is the inability of this bacterium to express high levels of heterologous proteins. In the present study, we have identified 12 codons deemed as rare codons in S. gordonii and seven other streptococcal species. tRNA genes encoding 10 of the 12 rare codons were cloned into a plasmid. The plasmid was transformed into strains of S. gordonii expressing the fusion protein SpaP/S1, the anti-complement receptor 1 (CR1) single-chain variable fragment (scFv) antibody, or the Toxoplasma gondii cyclophilin C18 protein. These three heterologous proteins contained high percentages of amino acids encoded by rare codons. The results showed that the production of SpaP/S1, anti-CR1 scFv and C18 increased by 2.7-, 120- and 10-fold, respectively, over the control strains. In contrast, the production of the streptococcal SpaP protein without the pertussis toxin S1 fragment was not affected by tRNA gene supplementation, indicating that the increased production of SpaP/S1 protein was due to the ability to overcome the limitation caused by rare codons required for the S1 fragment. The increase in anti-CR1 scFv production was also observed in Streptococcus mutans following tRNA gene supplementation. Collectively, the findings in the present study demonstrate for the first time, to the best of our knowledge, that codon-usage bias exists in Streptococcus spp. and the limitation of heterologous protein expression caused by codon-usage bias can be overcome by tRNA supplementation.

Di-codon Usage for Gene Classification

NASA Astrophysics Data System (ADS)

Nguyen, Minh N.; Ma, Jianmin; Fogel, Gary B.; Rajapakse, Jagath C.

Classification of genes into biologically related groups facilitates inference of their functions. Codon usage bias has been described previously as a potential feature for gene classification. In this paper, we demonstrate that di-codon usage can further improve classification of genes. By using both codon and di-codon features, we achieve near perfect accuracies for the classification of HLA molecules into major classes and sub-classes. The method is illustrated on 1,841 HLA sequences which are classified into two major classes, HLA-I and HLA-II. Major classes are further classified into sub-groups. A binary SVM using di-codon usage patterns achieved 99.95% accuracy in the classification of HLA genes into major HLA classes; and multi-class SVM achieved accuracy rates of 99.82% and 99.03% for sub-class classification of HLA-I and HLA-II genes, respectively. Furthermore, by combining codon and di-codon usages, the prediction accuracies reached 100%, 99.82%, and 99.84% for HLA major class classification, and for sub-class classification of HLA-I and HLA-II genes, respectively.

75 FR 56107 - Product Cancellation Order for Certain Pesticide Registrations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-15

..., human health, and agricultural advocates; the chemical industry; pesticide users; and members of the... Hide Away Circle, Cub Run, KY 42729. 70127 Novozymes Biologicals, Inc., 1150 Conn. Ave., NW., Suite...

Grounding Action Words in the Sensorimotor Interaction with the World: Experiments with a Simulated iCub Humanoid Robot

PubMed Central

Marocco, Davide; Cangelosi, Angelo; Fischer, Kerstin; Belpaeme, Tony

2010-01-01

This paper presents a cognitive robotics model for the study of the embodied representation of action words. The present research will present how an iCub humanoid robot can learn the meaning of action words (i.e. words that represent dynamical events that happen in time) by physically interacting with the environment and linking the effects of its own actions with the behavior observed on the objects before and after the action. The control system of the robot is an artificial neural network trained to manipulate an object through a Back-Propagation-Through-Time algorithm. We will show that in the presented model the grounding of action words relies directly to the way in which an agent interacts with the environment and manipulates it. PMID:20725503

Stabilizing Selection, Purifying Selection, and Mutational Bias in Finite Populations

PubMed Central

Charlesworth, Brian

2013-01-01

Genomic traits such as codon usage and the lengths of noncoding sequences may be subject to stabilizing selection rather than purifying selection. Mutations affecting these traits are often biased in one direction. To investigate the potential role of stabilizing selection on genomic traits, the effects of mutational bias on the equilibrium value of a trait under stabilizing selection in a finite population were investigated, using two different mutational models. Numerical results were generated using a matrix method for calculating the probability distribution of variant frequencies at sites affecting the trait, as well as by Monte Carlo simulations. Analytical approximations were also derived, which provided useful insights into the numerical results. A novel conclusion is that the scaled intensity of selection acting on individual variants is nearly independent of the effective population size over a wide range of parameter space and is strongly determined by the logarithm of the mutational bias parameter. This is true even when there is a very small departure of the mean from the optimum, as is usually the case. This implies that studies of the frequency spectra of DNA sequence variants may be unable to distinguish between stabilizing and purifying selection. A similar investigation of purifying selection against deleterious mutations was also carried out. Contrary to previous suggestions, the scaled intensity of purifying selection with synergistic fitness effects is sensitive to population size, which is inconsistent with the general lack of sensitivity of codon usage to effective population size. PMID:23709636

Distorted estimates of implicit and explicit learning in applications of the process-dissociation procedure to the SRT task.

PubMed

Stahl, Christoph; Barth, Marius; Haider, Hilde

2015-12-01

We investigated potential biases affecting the validity of the process-dissociation (PD) procedure when applied to sequence learning. Participants were or were not exposed to a serial reaction time task (SRTT) with two types of pseudo-random materials. Afterwards, participants worked on a free or cued generation task under inclusion and exclusion instructions. Results showed that pre-experimental response tendencies, non-associative learning of location frequencies, and the usage of cue locations introduced bias to PD estimates. These biases may lead to erroneous conclusions regarding the presence of implicit and explicit knowledge. Potential remedies for these problems are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura

PubMed Central

Boore, Jeffrey L

2004-01-01

Background Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although hundreds of these genome sequences have been reported, the taxonomic sampling is highly biased toward vertebrates and arthropods, with many whole phyla remaining unstudied. This is the first description of a complete mitochondrial genome sequence of a representative of the phylum Echiura, that of the fat innkeeper worm, Urechis caupo. Results This mtDNA is 15,113 nts in length and 62% A+T. It contains the 37 genes that are typical for animal mtDNAs in an arrangement somewhat similar to that of annelid worms. All genes are encoded by the same DNA strand which is rich in A and C relative to the opposite strand. Codons ending with the dinucleotide GG are more frequent than would be expected from apparent mutational biases. The largest non-coding region is only 282 nts long, is 71% A+T, and has potential for secondary structures. Conclusions Urechis caupo mtDNA shares many features with those of the few studied annelids, including the common usage of ATG start codons, unusual among animal mtDNAs, as well as gene arrangements, tRNA structures, and codon usage biases. PMID:15369601

Perceived driving safety and seatbelt usage.

PubMed

Svenson, O; Fischhoff, B; MacGregor, D

1985-04-01

Swedish and U.S. subjects judged their own driving skills and safety in relation to other drivers. As in earlier studies, most subjects showed an optimism bias: a tendency to judge oneself as safer and more skillful than the average driver, with a smaller risk of getting involved and injured in an accident. Different measures of the optimism effect were strongly correlated with one another, with driving experience and with the judged importance of human factors (as opposed to technical and chance factors) in causing accidents. Degree of optimism was positively, but weakly, correlated with reported seatbelt usage and worry about traffic accidents. Seatbelt usage was positively related to the extent to which belts are judged to be convenient and popular, and more modestly related to the belt's perceived contributions to safety. These results suggest that providing more information about the effectiveness of seatbelts may not be as efficient a way of increasing seatbelt usage as emphasizing other factors, such as comfort and social norms, which cannot be outweighed by optimism.

Facebook and romantic relationships: intimacy and couple satisfaction associated with online social network use.

PubMed

Hand, Matthew M; Thomas, Donna; Buboltz, Walter C; Deemer, Eric D; Buyanjargal, Munkhsanaa

2013-01-01

Online social networks, such as Facebook, have gained immense popularity and potentially affect the way people build and maintain interpersonal relationships. The present study sought to examine time spent on online social networks, as it relates to intimacy and relationship satisfaction experienced in romantic relationships. Results did not find relationships between an individual's usage of online social networks and his/her perception of relationship satisfaction and intimacy. However, the study found a negative relationship between intimacy and the perception of a romantic partner's use of online social networks. This finding may allude to an attributional bias in which individuals are more likely to perceive a partner's usage as negative compared to their own usage. Additionally, it was found that intimacy mediates the relationship between online social network usage and overall relationship satisfaction, which suggests that the level of intimacy experienced in a relationship may serve as a buffer that protects the overall level of satisfaction.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

PubMed

Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

2017-06-01

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose.

PubMed

Zhang, Wenping; Liu, Wenbin; Hou, Rong; Zhang, Liang; Schmitz-Esser, Stephan; Sun, Huaibo; Xie, Junjin; Zhang, Yunfei; Wang, Chengdong; Li, Lifeng; Yue, Bisong; Huang, He; Wang, Hairui; Shen, Fujun; Zhang, Zhihe

2018-05-01

The giant panda feeds almost exclusively on bamboo, a diet highly enriched in lignin and cellulose, but is characterized by a digestive tract similar to carnivores. It is still large unknown if and how the giant panda gut microbiota contributes to lignin and cellulose degradation. Here we show the giant pandas' gut microbiota does not significantly contribute to cellulose and lignin degradation. We found that no operational taxonomic unit had a nearest neighbor identified as a cellulolytic species or strain with a significant higher abundance in juvenile than cubs, a very low abundance of putative lignin and cellulose genes existed in part of analyzing samples but a significant higher abundance of genes involved in starch and hemicellulose degradation in juveniles than cubs. Moreover, a significant lower abundance of putative cellulolytic genes and a significant higher abundance of putative α-amylase and hemicellulase gene families were present in giant pandas than in omnivores or herbivores.

Direct detection of formate ligation in cytochrome c oxidase by ATR-FTIR spectroscopy.

PubMed

Iwaki, Masayo; Rich, Peter R

2004-03-03

The IR signature of binding of formate to the heme a(3-)Cu(B) binuclear site of bovine cytochrome c oxidase has been obtained by perfusion ATR-FTIR spectroscopy. The data show unequivocally that formate binds in its anionic form despite its binding being electroneutral overall. The bound formate can be distinguished from free ligand by the binding-induced sharpening and downshifting of vibrational bands. Formate ligation also causes shifts of vibrational modes of heme a(3) and its substituents and perturbation of histidine residues. The association of the accompanying protonation change with a carboxylate or tyrosine can be ruled out and may involve a histidine metal ligand or, more likely, a simple displacement into the bulk phase of a hydroxide ligand to heme a(3) or CU(B), a reaction which would account for stoichiometric proton uptake and maintenance of net charge within the binuclear center domain.

Serosurvey of selected zoonotic agents in polar bears (Ursus maritimus)

USGS Publications Warehouse

Rah, H.; Chomel, B.B.; Follmann, Erich H.; Kasten, R.W.; Hew, C.H.; Farver, T.B.; Garner, G.W.; Amstrup, Steven C.

2005-01-01

Between 1982 and 1999 blood samples were collected from 500 polar bears (Ursus maritimus) captured in the Beaufort and Chukchi seas, to determine the seroprevalence of Brucella species, Toxoplasma gondii, and Trichinella species infections. The bears were classified into four age groups, cubs, yearlings, subadults and adults. Brucella and Toxoplasma antibodies were detected by agglutination (a buffered acidified card antigen and rapid automated presumptive test for brucellosis and a commercial latex agglutination test for toxoplasmosis); an ELISA was used to detect Thichinella antibodies. The overall seroprevalence of Brucella species was 5 per cent, and subadults and yearlings were 2.62 times (95 per cent confidence interval 1-02 to 6-82) more likely to be seropositive for Brucella species than adults and their cubs. The antibody prevalence for Toxoplasma gondii was 6 per cent, and for Trichinella species 55.6 per cent. The prevalence of antibodies to Trichinella species increased with age (P<0.001).

Denning of grizzly bears in the Yellowstone National Park area

USGS Publications Warehouse

Judd, Steven L.; Knight, Richard R.; Blanchard, Bonnie M.

1986-01-01

Radiotelemetry was used to locate 101 grizzly bear (Ursus arctos) dens from 1975 to 1980; 35 dens were examined on the ground. Pregnant females denned in late October, and most other bears denned by mid-November. Duration of denning average 113, 132, and 170 days for males, females, and females with new cubs, respectively. Males emerged from mid-February to late March, followed by single females and females with yearlings and 2-year-olds. Females with new cubs emerged from early mid-April. Den sites were associated with moderate tree cover (26%-75% canopy cover) on 30°-60° slopes. Dens occurred on all aspects, although northerly exposures were most common. Grizzly bears usually dug new dens but occasionally used natural cavities or a den from a previous year. Males usually dug larger dens than females with young. Eight excavated and 2 natural dens of the 35 examined dens were used for more than 1 year.

Science learning through scouting: an understudied context for informal science education

NASA Astrophysics Data System (ADS)

Jarman, Ruth

2005-04-01

Worldwide, voluntary youth organizations such as the Scouts and Guides attract a large following. As part of their programme they provide science experiences for children and young people. From a research perspective, however, this context for informal science education has gone largely unexamined. This study explores the field, focusing on the Cub Scouts that cater, in the UK, for children aged between 8 and 10.5 years. The investigation involved an e-mail survey, in-depth interviews with 10 leaders, short interviews with 10 Cub Scouts and an unscripted role-play performed by the children. Documented is a distinctive and engaging out-of-school science provision for participants. The research revealed this learning experience to have features that, in terms of a continuum spanning formal to informal, lay more toward the informal than anticipated in respect of curriculum and assessment, although not pedagogy. The children's responses, affective and cognitive, suggest a fruitful area for further study.

Vigorous dynamics underlie a stable population of the endangered snow leopard Panthera uncia in Tost Mountains, South Gobi, Mongolia.

PubMed

Sharma, Koustubh; Bayrakcismith, Rana; Tumursukh, Lkhagvasumberel; Johansson, Orjan; Sevger, Purevsuren; McCarthy, Tom; Mishra, Charudutt

2014-01-01

Population monitoring programmes and estimation of vital rates are key to understanding the mechanisms of population growth, decline or stability, and are important for effective conservation action. We report, for the first time, the population trends and vital rates of the endangered snow leopard based on camera trapping over four years in the Tost Mountains, South Gobi, Mongolia. We used robust design multi-season mark-recapture analysis to estimate the trends in abundance, sex ratio, survival probability and the probability of temporary emigration and immigration for adult and young snow leopards. The snow leopard population remained constant over most of the study period, with no apparent growth (λ = 1.08+-0.25). Comparison of model results with the "known population" of radio-collared snow leopards suggested high accuracy in our estimates. Although seemingly stable, vigorous underlying dynamics were evident in this population, with the adult sex ratio shifting from being male-biased to female-biased (1.67 to 0.38 males per female) during the study. Adult survival probability was 0.82 (SE+-0.08) and that of young was 0.83 (SE+-0.15) and 0.77 (SE +-0.2) respectively, before and after the age of 2 years. Young snow leopards showed a high probability of temporary emigration and immigration (0.6, SE +-0.19 and 0.68, SE +-0.32 before and after the age of 2 years) though not the adults (0.02 SE+-0.07). While the current female-bias in the population and the number of cubs born each year seemingly render the study population safe, the vigorous dynamics suggests that the situation can change quickly. The reduction in the proportion of male snow leopards may be indicative of continuing anthropogenic pressures. Our work reiterates the importance of monitoring both the abundance and population dynamics of species for effective conservation.

Vigorous Dynamics Underlie a Stable Population of the Endangered Snow Leopard Panthera uncia in Tost Mountains, South Gobi, Mongolia

PubMed Central

Sharma, Koustubh; Bayrakcismith, Rana; Tumursukh, Lkhagvasumberel; Johansson, Orjan; Sevger, Purevsuren; McCarthy, Tom; Mishra, Charudutt

2014-01-01

Population monitoring programmes and estimation of vital rates are key to understanding the mechanisms of population growth, decline or stability, and are important for effective conservation action. We report, for the first time, the population trends and vital rates of the endangered snow leopard based on camera trapping over four years in the Tost Mountains, South Gobi, Mongolia. We used robust design multi-season mark-recapture analysis to estimate the trends in abundance, sex ratio, survival probability and the probability of temporary emigration and immigration for adult and young snow leopards. The snow leopard population remained constant over most of the study period, with no apparent growth (λ = 1.08+−0.25). Comparison of model results with the “known population” of radio-collared snow leopards suggested high accuracy in our estimates. Although seemingly stable, vigorous underlying dynamics were evident in this population, with the adult sex ratio shifting from being male-biased to female-biased (1.67 to 0.38 males per female) during the study. Adult survival probability was 0.82 (SE+−0.08) and that of young was 0.83 (SE+−0.15) and 0.77 (SE +−0.2) respectively, before and after the age of 2 years. Young snow leopards showed a high probability of temporary emigration and immigration (0.6, SE +−0.19 and 0.68, SE +−0.32 before and after the age of 2 years) though not the adults (0.02 SE+−0.07). While the current female-bias in the population and the number of cubs born each year seemingly render the study population safe, the vigorous dynamics suggests that the situation can change quickly. The reduction in the proportion of male snow leopards may be indicative of continuing anthropogenic pressures. Our work reiterates the importance of monitoring both the abundance and population dynamics of species for effective conservation. PMID:25006879

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius

USDA-ARS?s Scientific Manuscript database

We have previously identified the mycobacterial high G+C codon usage bias as a limiting factor in heterologous expression of MAP proteins from Lb.salivarius, and demonstrated that codon optimisation of a synthetic coding gene greatly enhances MAP protein production. Here, we effectively demonstrate ...

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

PubMed Central

2006-01-01

Background Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms. Results Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts. Conclusion Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes. PMID:26271136

Monitoring Antibiotic Use and Residue in Freshwater Aquaculture for Domestic Use in Vietnam.

PubMed

Pham, Dang Kim; Chu, Jacqueline; Do, Nga Thuy; Brose, François; Degand, Guy; Delahaut, Philippe; De Pauw, Edwin; Douny, Caroline; Nguyen, Kinh Van; Vu, Ton Dinh; Scippo, Marie-Louise; Wertheim, Heiman F L

2015-09-01

Vietnam is an important producer of aquaculture products, and aquatic products are essential to the Vietnamese diet. However, Vietnam also has very little enforced regulation pertaining to antibiotic usage in domestic aquaculture, which raises concerns for antibiotic resistance in pathogenic bacteria. In this study, analysis was conducted on the presence of antibiotic residues in domestically sold fish and shrimp raised in freshwater farms in Vietnam, and an assessment of farmers' knowledge of proper antibiotics usage was performed. The results indicated that a quarter of tested aquaculture products were antibiotic screening test positive, and there is a general lack of knowledge about the purpose and proper usage of antibiotics by aquaculture producers. Farmers' decision-making processes about antimicrobial use are influenced by biased sources of information, such as drug manufacturers and sellers, and by financial incentives.

Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.

PubMed

Mondal, Sunil Kanti; Kundu, Sudip; Das, Rabindranath; Roy, Sujit

2016-08-01

Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.

Analysis of codon usage in beta-tubulin sequences of helminths.

PubMed

von Samson-Himmelstjerna, G; Harder, A; Failing, K; Pape, M; Schnieder, T

2003-07-01

Codon usage bias has been shown to be correlated with gene expression levels in many organisms, including the nematode Caenorhabditis elegans. Here, the codon usage (cu) characteristics for a set of currently available beta-tubulin coding sequences of helminths were assessed by calculating several indices, including the effective codon number (Nc), the intrinsic codon deviation index (ICDI), the P2 value and the mutational response index (MRI). The P2 value gives a measure of translational pressure, which has been shown to be correlated to high gene expression levels in some organisms, but it has not yet been analysed in that respect in helminths. For all but two of the C. elegans beta-tubulin coding sequences investigated, the P2 value was the only index that indicated the presence of codon usage bias. Therefore, we propose that in general the helminth beta-tubulin sequences investigated here are not expressed at high levels. Furthermore, we calculated the correlation coefficients for the cu patterns of the helminth beta-tubulin sequences compared with those of highly expressed genes in organisms such as Escherichia coli and C. elegans. It was found that beta-tubulin cu patterns for all sequences of members of the Strongylida were significantly correlated to those for highly expressed C. elegans genes. This approach provides a new measure for comparing the adaptation of cu of a particular coding sequence with that of highly expressed genes in possible expression systems.Finally, using the cu patterns of the sequences studied, a phylogenetic tree was constructed. The topology of this tree was very much in concordance with that of a phylogeny based on small subunit ribosomal DNA sequence alignments.

Epidemiology of clinical feline herpesvirus infection in zoo-housed cheetahs (Acinonyx jubatus).

PubMed

Witte, Carmel L; Lamberski, Nadine; Rideout, Bruce A; Vaida, Florin; Citino, Scott B; Barrie, Michael T; Haefele, Holly J; Junge, Randall E; Murray, Suzan; Hungerford, Laura L

2017-10-15

OBJECTIVE To determine the incidence of and risk factors for clinical feline herpesvirus (FHV) infection in zoo-housed cheetahs and determine whether dam infection was associated with offspring infection. DESIGN Retrospective cohort study. ANIMALS 144 cheetah cubs born in 6 zoos from 1988 through 2007. PROCEDURES Data were extracted from the health records of cheetahs and their dams to identify incident cases of clinical FHV infection and estimate incidence from birth to 18 months of age. Univariate and multivariable Cox proportional hazards models, controlling for correlations among cheetahs with the same dam, were used to identify risk factors for incident FHV infection. RESULTS Cumulative incidence of FHV infection in cheetah cubs was 35% (50/144). No significant association between dam and offspring infection was identified in any model. Factors identified as significant through multivariable analysis varied by age group. For cheetahs up to 3 months of age, the most important predictor of FHV infection was having a dam that had received a preparturition FHV vaccine regimen that included a modified-live virus vaccine versus a dam that had received no preparturition vaccine. Other risk factors included being from a small litter, being born to a primiparous dam, and male sex. CONCLUSIONS AND CLINICAL RELEVANCE This study provided the first population-level characterization of the incidence of and risk factors for FHV infection in cheetahs, and findings confirmed the importance of this disease. Recognition that clinical FHV infection in the dam was not a significant predictor of disease in cubs and identification of other significant factors have implications for disease management.

The impact of roads on the demography of grizzly bears in Alberta.

PubMed

Boulanger, John; Stenhouse, Gordon B

2014-01-01

One of the principal factors that have reduced grizzly bear populations has been the creation of human access into grizzly bear habitat by roads built for resource extraction. Past studies have documented mortality and distributional changes of bears relative to roads but none have attempted to estimate the direct demographic impact of roads in terms of both survival rates, reproductive rates, and the interaction of reproductive state of female bears with survival rate. We applied a combination of survival and reproductive models to estimate demographic parameters for threatened grizzly bear populations in Alberta. Instead of attempting to estimate mean trend we explored factors which caused biological and spatial variation in population trend. We found that sex and age class survival was related to road density with subadult bears being most vulnerable to road-based mortality. A multi-state reproduction model found that females accompanied by cubs of the year and/or yearling cubs had lower survival rates compared to females with two year olds or no cubs. A demographic model found strong spatial gradients in population trend based upon road density. Threshold road densities needed to ensure population stability were estimated to further refine targets for population recovery of grizzly bears in Alberta. Models that considered lowered survival of females with dependant offspring resulted in lower road density thresholds to ensure stable bear populations. Our results demonstrate likely spatial variation in population trend and provide an example how demographic analysis can be used to refine and direct conservation measures for threatened species.

The Impact of Roads on the Demography of Grizzly Bears in Alberta

PubMed Central

2014-01-01

One of the principal factors that have reduced grizzly bear populations has been the creation of human access into grizzly bear habitat by roads built for resource extraction. Past studies have documented mortality and distributional changes of bears relative to roads but none have attempted to estimate the direct demographic impact of roads in terms of both survival rates, reproductive rates, and the interaction of reproductive state of female bears with survival rate. We applied a combination of survival and reproductive models to estimate demographic parameters for threatened grizzly bear populations in Alberta. Instead of attempting to estimate mean trend we explored factors which caused biological and spatial variation in population trend. We found that sex and age class survival was related to road density with subadult bears being most vulnerable to road-based mortality. A multi-state reproduction model found that females accompanied by cubs of the year and/or yearling cubs had lower survival rates compared to females with two year olds or no cubs. A demographic model found strong spatial gradients in population trend based upon road density. Threshold road densities needed to ensure population stability were estimated to further refine targets for population recovery of grizzly bears in Alberta. Models that considered lowered survival of females with dependant offspring resulted in lower road density thresholds to ensure stable bear populations. Our results demonstrate likely spatial variation in population trend and provide an example how demographic analysis can be used to refine and direct conservation measures for threatened species. PMID:25532035

Advanced Characterization of Rare Earth Elements in Coal Utilization Byproducts

NASA Astrophysics Data System (ADS)

Verba, C.; Scott, M.; Dieterich, M.; Poston, J.; Collins, K.

2016-12-01

Rare earth elements (REE) in various forms (e.g., crystalline mineral phases; adsorbed/absorbed state on and into organic macerals, neoformed glass from flyash or bottom ash) from domestic feedstocks such as coal deposits to coal utilization byproducts (CUB) have the potential to reduce foreign REE dependence and increase domestic resource security. Characterization is critical for understanding environmental risks related to their fate and transport as well as determining the most practical and economical techniques for concentrating the REE and converting them into chemical stocks for manufacturing. Several complementary electron microscopy (SEM-EDS, EPMA-WDS, FIB-SEM, cathodoluminescence, and XRD) and post image processing techniques were used to understand REE transition from coal to CUB. Sites of interest were identified and imaged and respective elemental x-ray maps acquired and montaged. Pixel classification of SEM imagers was completed using image analysis techniques to quantify the distribution of REE associated features. Quantitative elemental analysis of phases were completed using EMPA-WDS followed by FIB-SEM. The FIB-SEM results were reconstructed into 3D volumes and features of interest (e.g. monazite) were analyzed to determine the structure and volumetric estimation of REEs and thus predict detrital REE phases to ICP-MS results. Trace minerals were identified as pyrite, zircon, REE-phosphates' (monazite, xenotime), and barite within the coal tailings. In CUB, amorphous aluminosilicates, iron oxide cenospheres, and calcium oxides were present; monazite appear to be unaltered and unaffected by the combustion process in these samples. Thermal decomposition may have occurred due to presence of detrital zircon and xenotime and subsequent thin Ca-oxide coating enriched in trace REEs.

Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites

PubMed Central

Sun, Yu; Tamarit, Daniel

2017-01-01

Abstract The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bacterial genomes with extreme nucleotide composition biases provide informative model systems. Switches in the background substitution biases from GC to AT have occurred in Gardnerella vaginalis (GC = 32%), and from AT to GC in Lactobacillus delbrueckii (GC = 62%) and Lactobacillus fermentum (GC = 63%). We show that despite the large effects on codon usage patterns by these switches, all three species evolve under selection on synonymous sites. In G. vaginalis, the dramatic codon frequency changes coincide with shifts of optimal codons. In contrast, the optimal codons have not shifted in the two Lactobacillus genomes despite an increased fraction of GC-ending codons. We suggest that all three species are in different phases of an on-going shift of optimal codons, and attribute the difference to a stronger background substitution bias and/or longer time since the switch in G. vaginalis. We show that comparative and correlative methods for optimal codon identification yield conflicting results for genomes in flux and discuss possible reasons for the mispredictions. We conclude that switches in the direction of the background substitution biases can drive major shifts in codon preference patterns even under sustained selection on synonymous codon sites. PMID:27540085

Analyzing the impact of public transit usage on obesity.

PubMed

She, Zhaowei; King, Douglas M; Jacobson, Sheldon H

2017-06-01

The objective of this paper is to estimate the impact of county-level public transit usage on obesity prevalence in the United States and assess the potential for public transit usage as an intervention for obesity. This study adopts an instrumental regression approach to implicitly control for potential selection bias due to possible differences in commuting preferences among obese and non-obese populations. United States health data from the 2009 Behavioral Risk Factor Surveillance System and transportation data from the 2009 National Household Travel Survey are aggregated and matched at the county level. County-level public transit accessibility and vehicle ownership rates are chosen as instrumental variables to implicitly control for unobservable commuting preferences. The results of this instrumental regression analysis suggest that a one percent increase in county population usage of public transit is associated with a 0.221 percent decrease in county population obesity prevalence at the α=0.01 statistical significance level, when commuting preferences, amount of non-travel physical activity, education level, health resource, and distribution of income are fixed. Hence, this study provides empirical support for the effectiveness of encouraging public transit usage as an intervention strategy for obesity. Copyright © 2017 Elsevier Inc. All rights reserved.

Anabolic steroid usage in athletics: facts, fiction, and public relations.

PubMed

Berning, Joseph M; Adams, Kent J; Stamford, Bryant A

2004-11-01

Anecdotal evidence suggests the widespread usage of anabolic steroids among athletes (20-90%), particularly at the professional and elite amateur levels. In contrast, scientific studies indicate that usage is rare and no higher than 6%. Conclusions from scientific studies suggest that anabolic steroid usage declines progressively from high school to college and beyond; however, anecdotal evidence claims the opposite trend. In this clash between "hard" scientific data vs. "soft" anecdotal information, it is natural that professionals would gravitate toward scientifically based conclusions. However, in the case of anabolic steroids (a stigmatized and illegal substance), should word-of-mouth testimony from individuals closest to the issues--those who have participated in and coached sports, those who have served as drug-testing overseers, and journalists who relentlessly track leads and verify sources--be set aside as irrelevant? Not if a complete picture is to emerge. In this review, hard scientific evidence is placed on the table side-by-side with soft anecdotal evidence, without weighting or bias. The purpose is to allow the opportunity for each to illuminate the other and, in so doing, potentially bring us a step closer to determining the true extent of anabolic steroid usage in athletics.

Publications - GMC 348 | Alaska Division of Geological & Geophysical

Science.gov Websites

Territory, Canada: Some aspects of petrogenesis and mineralization at the Arctic Chief, Little Chief, and , Canada: Some aspects of petrogenesis and mineralization at the Arctic Chief, Little Chief, and Black Cub

Is alloparenting helpful for Mednyi Island arctic foxes, Alopex lagopus semenovi?

PubMed

Kruchenkova, Elena P; Goltsman, Michael; Sergeev, Sergei; Macdonald, David W

2009-04-01

The Arctic Fox Alopex lagopus semenovi population on Mednyi Island is completely isolated and subsists largely by scavenging on seabird colonies, which have remained abundant and spatio-temporally predictable for many years. We compared population data at the beginning of 1976/1978 and some time after 1994-2005, finding an 85% decline in fox numbers due to disease, to assess the effect of population size on social structure. A total of 81 groups of known size and composition was observed during this 29-year period. Overall, helpers (usually non-lactating yearling females) occurred in 25.7% of groups, and in 32.4% of groups there were two or three lactating females. Female engagement in alloparental behaviour decreased, but not statistically significantly, after the decline in population density. Total food availability was apparently constant throughout the study period, and therefore, the amount available per individual was much higher later in the study. Both communally nursing females and helpers brought food and helped to guard the litter. However, the benefits of communal rearing were unclear. While cubs were left without guards significantly more rarely in the groups with an additional adult, the number of cubs weaned per lactating female was greater in groups with one (3.93 +/- 1.60), as opposed to two or three (3.06 +/- 0.92), lactating females. Survival of cubs to 1 year of age in the groups with two lactating females and/or with helpers was lower than that in the families with one lactating female without helpers (22.2% vs 32.2%). Fewer second-generation litters were born to foxes produced by composite families than to those produced by pairs. Reproductive adults producing by pairs had, on average, 1.23 (+/-1.72) second-generation litters. In groups that initially included additional adults, the average number of second-generation litters per reproductive female was 0.21 (+/-0.49) and 0.46 (+/-0.81) litters per male. Thus, according to three measures, increased group size had no apparent positive impact on reproductive success. The increased parental investment and enhanced guarding of the cubs in the larger families could be beneficial under conditions of high population density and a saturated biotope to which the island fox population was presumably adapted before the population crash in the late 1970s.

Is alloparenting helpful for Mednyi Island arctic foxes, Alopex lagopus semenovi?

NASA Astrophysics Data System (ADS)

Kruchenkova, Elena P.; Goltsman, Michael; Sergeev, Sergei; MacDonald, David W.

2009-04-01

The Arctic Fox Alopex lagopus semenovi population on Mednyi Island is completely isolated and subsists largely by scavenging on seabird colonies, which have remained abundant and spatio-temporally predictable for many years. We compared population data at the beginning of 1976/1978 and some time after 1994-2005, finding an 85% decline in fox numbers due to disease, to assess the effect of population size on social structure. A total of 81 groups of known size and composition was observed during this 29-year period. Overall, helpers (usually non-lactating yearling females) occurred in 25.7% of groups, and in 32.4% of groups there were two or three lactating females. Female engagement in alloparental behaviour decreased, but not statistically significantly, after the decline in population density. Total food availability was apparently constant throughout the study period, and therefore, the amount available per individual was much higher later in the study. Both communally nursing females and helpers brought food and helped to guard the litter. However, the benefits of communal rearing were unclear. While cubs were left without guards significantly more rarely in the groups with an additional adult, the number of cubs weaned per lactating female was greater in groups with one (3.93 ± 1.60), as opposed to two or three (3.06 ± 0.92), lactating females. Survival of cubs to 1 year of age in the groups with two lactating females and/or with helpers was lower than that in the families with one lactating female without helpers (22.2% vs 32.2%). Fewer second-generation litters were born to foxes produced by composite families than to those produced by pairs. Reproductive adults producing by pairs had, on average, 1.23 (±1.72) second-generation litters. In groups that initially included additional adults, the average number of second-generation litters per reproductive female was 0.21 (±0.49) and 0.46 (±0.81) litters per male. Thus, according to three measures, increased group size had no apparent positive impact on reproductive success. The increased parental investment and enhanced guarding of the cubs in the larger families could be beneficial under conditions of high population density and a saturated biotope to which the island fox population was presumably adapted before the population crash in the late 1970s.

Vertebrate codon bias indicates a highly GC-rich ancestral genome.

PubMed

Nabiyouni, Maryam; Prakash, Ashwin; Fedorov, Alexei

2013-04-25

Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences. Copyright © 2013 Elsevier B.V. All rights reserved.

Essays on Experimental Economics and Education

ERIC Educational Resources Information Center

Ogawa, Scott Richard

2013-01-01

In Chapter 1 I consider three separate explanations for how price affects the usage rate of a purchased product: Screening, signaling, and sunk-cost bias. I propose an experimental design that disentangles the three effects. Furthermore, in order to quantify and compare these effects I introduce a simple structural model and show that the…

STUDY OF FEASIBILITY OF NEW EDUCATIONAL MEDIA FOR DEVELOPING COUNTRIES.

ERIC Educational Resources Information Center

VAIZEY, J.

COST DATA ON THE USE OF THE NEW INSTRUCTIONAL MEDIA ARE NECESSARY IN ORDER TO COMPARE DIFFERENT FORMS OF EDUCATION, TO DETERMINE THE ECONOMICALLY OPTIMUM RATE OF TECHNICAL USAGE, AND TO ASSIST ADMINISTRATORS. THE HISTORICAL INACCURACY OR STATISTICAL BIAS OF SOURCES AND THE INCOMPARABILITY OF DATA POSE DIFFICULTIES IN INTERPRETATION. THE COST OF…

Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities.

PubMed

Pal, Shilpee; Sarkar, Indrani; Roy, Ayan; Mohapatra, Pradeep K Das; Mondal, Keshab C; Sen, Arnab

2018-02-01

The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium. Most of the optimal codons as well as translationally optimal codons are C ending i.e. RNY (R-purine, N-any nucleotide base, and Y-pyrimidine) and reveal translational selection pressure on codon bias of Corynebacterium. Amino acid usage is affected by hydrophobicity, aromaticity, protein energy cost, etc. Highly expressed genes followed the cost minimization hypothesis and are less diverged at their synonymous positions of codons. Functional analysis of core genes shows significant difference in pathogenic and non-pathogenic Corynebacterium. The study reveals close relationship between non-pathogenic and opportunistic pathogenic Corynebaterium as well as between molecular evolution and survival niches of the organism.

A first-principles model of copper-boron interactions in Si: implications for the light-induced degradation of solar Si

NASA Astrophysics Data System (ADS)

Wright, E.; Coutinho, J.; Öberg, S.; Torres, V. J. B.

2017-02-01

The recent discovery that Cu contamination of Si combined with light exposure has a significant detrimental impact on carrier life-time has drawn much concern within the solar-Si community. The effect, known as the copper-related light-induced degradation (Cu-LID) of Si solar cells, has been connected to the release of Cu interstitials within the bulk (2016 Sol. Energy Mater. Sol. Cells 147 115-26). In this paper, we describe a comprehensive analysis of the formation/dissociation process of the CuB pair in Si by means of first-principles modelling, as well as the interaction of CuB defects with photo-excited minority carriers. We confirm that the long-range interaction between the \\text{Cu}\\text{i}+ cation and the \\text{B}\\text{s}- anion has a Coulomb-like behaviour, in line with the trapping-limited diffusivity of Cu observed by transient ion drift measurements. On the other hand, the short-range interaction between the d-electrons of Cu and the excess of negative charge on \\text{B}\\text{s}- produces a repulsive effect, thereby decreasing the binding energy of the pair when compared to the ideal point-charge Coulomb model. We also find that metastable CuB pairs produce acceptor states just below the conduction band minimum, which arise from the Cu level emptied by the B acceptor. Based on these results, we argue that photo-generated minority carriers trapped by the metastable pairs can switch off the Coulomb interaction that holds the pairs together, enhancing the release of Cu interstitials, and acting as a catalyst for Cu-LID.

Sexual Behavior and Condom Use among Gay Men, Female Sex Workers, and Their Customers: Evidence from South Korea

PubMed Central

Jung, Minsoo

2013-01-01

Background Despite the significance for sexually transmitted diseases (STD) control in East Asia, few studies have examined the relationship between high-risk sexual behavior and condom use. We investigated how three sexually vulnerable groups for STDs show differences in condom use behaviors (CUBs) depending on their STD infection. Methods The source of data came from the National Survey for STD Prevalence Rate and Sexual Behavior of the High-Risk Sexual Community. The effects of behavioral determinants on CUBs were estimated by using path analysis models. An 11-item questionnaire assessing subjects’ health risk behaviors, sexual beliefs, sexual risk behaviors, and condom use. Results Condom use was higher for men who have sex with men (MSM; n = 108) when they were bisexuals and had high self-efficacy, for Johns (Johns; n = 118) when they had experience of STD infection, and for female sex workers (FSWs; n = 1,083) when they had high self-efficacy, did not engage in drunken sex, and were anxious about infection. Regardless of whether they were infected with STDs, FSWs always used condom when they had high sexual beliefs. On the contrary, Johns exhibited a negative relationship between sexual risk behavior and condom use when they had experience of STD infection. The variable commonly significant to all three groups was the number of sex partners; but it exhibited a positive relationship with MSMs and Johns, and a negative one with FSWs. Conclusions CUBs were related to sexual beliefs as well as sexual risk behavior. At the same time, the experience of STD infection mediated the relationship between the two. Therefore, we need to draw social attention to promote safer sex among STD-vulnerable groups. PMID:23950786

Relationship of the estrogen surge and multiple mates to cub paternity in the giant panda (Ailuropoda melanoleuca): implications for optimal timing of copulation or artificial insemination.

PubMed

Huang, Yan; Zhang, Hemin; Li, Desheng; Zhang, Guiquan; Wei, Rongping; Huang, Zhi; Zhou, Yingmin; Zhou, Qiang; Liu, Yang; Wildt, David E; Hull, Vanessa

2012-11-01

The effectiveness of ex situ breeding programs for endangered species can be limited by challenges in mimicking mating competitions that naturally occur among multiple mates in the wild. The objective of this study was to evaluate the impact of timed natural matings and/or artificial inseminations in the context of the urinary estrogen surge on cub production in the giant panda (Ailuropoda melanoleuca). We used a large cohort of giant pandas, including 12 females and 17 males. DNA paternity exclusion was used to pinpoint accurately the interval during the estrogen surge that coincided with the ideal sperm deposition time to produce offspring. Of the 31 cubs (in 19 pregnancies), 22 (71.0%; 15 pregnancies) were produced from matings occurring on the day of or the day after the maximal urinary estrogen peak. Sixteen of the 19 pregnancies (84.2%) produced at least one offspring sired by the first male mating with the dam. There was a preponderance of twins (12 of 19; 63.2%), and dual paternities were discovered in 3 of 12 twin sets (25%). These findings indicate a strong relationship between the excreted estrogen surge and sperm deposition to achieve pregnancy in the giant panda. To ensure the production of the most genetically diverse young, it is imperative that the most appropriate male mate first and on the day of or the day after the highest detected estrogen value. There is no advantage to increasing the number of copulations or mating partners within 1 day of the estrogen peak on the incidence of twinning, although this practice may increase the prevalence of dual paternity in cases of multiple births.

Mutational analysis of Kaposica reveals that bridging of MG2 and CUB domains of target protein is crucial for the cofactor activity of RCA proteins

PubMed Central

Gautam, Avneesh Kumar; Panse, Yogesh; Ghosh, Payel; Reza, Malik Johid; Mullick, Jayati; Sahu, Arvind

2015-01-01

The complement system has evolved to annul pathogens, but its improper regulation is linked with diseases. Efficient regulation of the system is primarily provided by a family of proteins termed regulators of complement activation (RCA). The knowledge of precise structural determinants of RCA proteins critical for imparting the regulatory activities and the molecular events underlying the regulatory processes, nonetheless, is still limited. Here, we have dissected the structural requirements of RCA proteins that are crucial for one of their two regulatory activities, the cofactor activity (CFA), by using the Kaposi’s sarcoma-associated herpesvirus RCA homolog Kaposica as a model protein. We have scanned the entire Kaposica molecule by sequential mutagenesis using swapping and site-directed mutagenesis, which identified residues critical for its interaction with C3b and factor I. Mapping of these residues onto the modeled structure of C3b–Kaposica–factor I complex supported the mutagenesis data. Furthermore, the model suggested that the C3b-interacting residues bridge the CUB (complement C1r-C1s, Uegf, Bmp1) and MG2 (macroglobulin-2) domains of C3b. Thus, it seems that stabilization of the CUB domain with respect to the core of the C3b molecule is central for its CFA. Identification of CFA-critical regions in Kaposica guided experiments in which the equivalent regions of membrane cofactor protein were swapped into decay-accelerating factor. This strategy allowed CFA to be introduced into decay-accelerating factor, suggesting that viral and human regulators use a common mechanism for CFA. PMID:26420870

Model studies of the Cu(B) site of cytochrome c oxidase utilizing a Zn(II) complex containing an imidazole-phenol cross-linked ligand.

PubMed

Pesavento, Russell P; Pratt, Derek A; Jeffers, Jerry; van der Donk, Wilfred A

2006-07-21

Cytochrome c oxidase, the enzyme complex responsible for the four-electron reduction of O2 to H2O, contains an unusual histidine-tyrosine cross-link in its bimetallic heme a3-CuB active site. We have synthesised an unhindered, tripodal chelating ligand, BPAIP, containing the unusual ortho-imidazole-phenol linkage, which mimics the coordination environment of the CuB center. The ligand was used to investigate the physicochemical (pKa, oxidation potential) and coordination properties of the imidazole-phenol linkage when bound to a dication. Zn(II) coordination lowers the pKa of the phenol by 0.6 log units, and increases the potential of the phenolate/phenoxyl radical couple by approximately 50 mV. These results are consistent with inductive withdrawal of electron density from the phenolic ring. Spectroscopic data and theoretical calculations (DFT) were used to establish that the cationic complex [Zn(BPAIP)Br]+ has an axially distorted trigonal bipyramidal structure, with three coordinating nitrogen ligands (two pyridine and one imidazole) occupying the equatorial plane and the bromide and the tertiary amine nitrogen of the tripod in the axial positions. Interestingly, the Zn-Namine bonding interaction is weak or absent in [Zn(BPAIP)Br]+ and the complex gains stability in basic solutions, as indicated by 1H NMR spectroscopy. These observations are supported by theoretical calculations (DFT), which suggest that the electron-donating capacity of the equatorial imidazole ligand can be varied by modulation of the protonation and/or redox state of the cross-linked phenol. Deprotonation of the phenol makes the equatorial imidazole a stronger sigma-donor, resulting in an increased Zn-Nimd interaction and thereby leading to distortion of the axial ligand axis toward a more tetrahedral geometry.

A Flight-Calibrated Methodology for Determination of Cassini Thruster On-Times for Reaction Wheel Biases

NASA Technical Reports Server (NTRS)

Sarani, Siamak

2010-01-01

This paper describes a methodology for accurate and flight-calibrated determination of the on-times of the Cassini spacecraft Reaction Control System (RCS) thrusters, without any form of dynamic simulation, for the reaction wheel biases. The hydrazine usage and the delta V vector in body frame are also computed from the respective thruster on-times. The Cassini spacecraft, the largest and most complex interplanetary spacecraft ever built, continues to undertake ambitious and unique scientific observations of planet Saturn, Titan, Enceladus, and other moons of Saturn. In order to maintain a stable attitude during the course of its mission, this three-axis stabilized spacecraft uses two different control systems: the RCS and the reaction wheel assembly control system. The RCS is used to execute a commanded spacecraft slew, to maintain three-axis attitude control, control spacecraft's attitude while performing science observations with coarse pointing requirements, e.g. during targeted low-altitude Titan and Enceladus flybys, bias the momentum of reaction wheels, and to perform RCS-based orbit trim maneuvers. The use of RCS often imparts undesired delta V on the spacecraft. The Cassini navigation team requires accurate predictions of the delta V in spacecraft coordinates and inertial frame resulting from slews using RCS thrusters and more importantly from reaction wheel bias events. It is crucial for the Cassini spacecraft attitude control and navigation teams to be able to, quickly but accurately, predict the hydrazine usage and delta V for various reaction wheel bias events without actually having to spend time and resources simulating the event in flight software-based dynamic simulation or hardware-in-the-loop simulation environments. The methodology described in this paper, and the ground software developed thereof, are designed to provide just that. This methodology assumes a priori knowledge of thrust magnitudes and thruster pulse rise and tail-off time constants for eight individual attitude control thrusters, the spacecraft's wet mass and its center of mass location, and a few other key parameters.

Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness

NASA Astrophysics Data System (ADS)

Villanueva, Eneko; Martí-Solano, Maria; Fillat, Cristina

2016-06-01

Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development.

Grounding language in action and perception: From cognitive agents to humanoid robots

NASA Astrophysics Data System (ADS)

Cangelosi, Angelo

2010-06-01

In this review we concentrate on a grounded approach to the modeling of cognition through the methodologies of cognitive agents and developmental robotics. This work will focus on the modeling of the evolutionary and developmental acquisition of linguistic capabilities based on the principles of symbol grounding. We review cognitive agent and developmental robotics models of the grounding of language to demonstrate their consistency with the empirical and theoretical evidence on language grounding and embodiment, and to reveal the benefits of such an approach in the design of linguistic capabilities in cognitive robotic agents. In particular, three different models will be discussed, where the complexity of the agent's sensorimotor and cognitive system gradually increases: from a multi-agent simulation of language evolution, to a simulated robotic agent model for symbol grounding transfer, to a model of language comprehension in the humanoid robot iCub. The review also discusses the benefits of the use of humanoid robotic platform, and specifically of the open source iCub platform, for the study of embodied cognition.

Ovulation induction and artificial insemination of a captive polar bear (Ursus maritimus) using fresh semen.

PubMed

Curry, Erin; Wyatt, Jeff; Sorel, Lawrence J; MacKinnon, Katherine M; Roth, Terri L

2014-09-01

In 2008, polar bears were listed as a species threatened with extinction by the U.S. Endangered Species Act. Unfortunately, reproductive success has been poor despite breeding recommendations for almost every reproductively viable bear by the Species Survival Plan. Assisted reproductive technologies could complement breeding efforts by overcoming the challenges of behavioral incompatibilities and deficiencies, facilitating genetic management and increasing cub production. The goal of this study was to artificially inseminate a female polar bear after inducing ovarian activity and ovulation with exogenous hormones (equine chorionic gonadotropin and porcine luteinizing hormone). Fresh semen collected from an adult male via electroejaculation/urethral catheterization was used for the insemination. Fecal steroid monitoring indicated that the female ovulated following the exogenous hormone treatment. Progestin concentrations increased in late summer, at the time implantation was expected to occur; however, no cubs were produced. To the authors' knowledge, this is the first report of ovulation induction and artificial insemination in a polar bear.

Dietary change and stable isotopes: a model of growth and dormancy in cave bears.

PubMed Central

Lidén, K; Angerbjörn, A

1999-01-01

In order to discuss dietary change over time by the use of stable isotopes, it is necessary to sort out the underlying processes in isotopic variation. Together with the dietary signal other processes have been investigated, namely metabolic processes, collagen turnover and physical growth. However, growth and collagen turnover time have so far been neglected in dietary reconstruction based on stable isotopes. An earlier study suggested that cave bears (Ursus spelaeus) probably gave birth to cubs during dormancy. We provide an estimate of the effect on stable isotopes of growth and metabolism and discuss collagen turnover in a population of cave bears. Based on a quantitative model, we hypothesized that bear cubs lactated their mothers during their first and second winters, but were fed solid food together with lactation during their first summer. This demonstrates the need to include physical growth, metabolism and collagen turnover in dietary reconstruction. Whereas the effects of diet and metabolism are due to fractionation, growth and collagen turnover are dilution processes. PMID:10518325

The prevalence, distribution and severity of detectable pathological lesions in badgers naturally infected with Mycobacterium bovis

PubMed Central

JENKINS, H. E.; MORRISON, W. I.; COX, D. R.; DONNELLY, C. A.; JOHNSTON, W. T.; BOURNE, F. J.; CLIFTON-HADLEY, R. S.; GETTINBY, G.; McINERNEY, J. P.; WATKINS, G. H.; WOODROFFE, R.

2008-01-01

SUMMARY The Randomized Badger Culling Trial (RBCT) began in 1998 to determine the impact of badger culling in controlling bovine tuberculosis in cattle. A total of 1166 badgers (14% of total) proactively culled during the RBCT were found to be tuberculous, offering a unique opportunity to study the pathology caused by Mycobacterium bovis in a large sample of badgers. Of these, 39% of adults (~6% of all adults culled) had visible lesions (detectable at necropsy) of bovine tuberculosis; cubs had a lower prevalence of infection (9%) but a higher percentage of tuberculous cubs (55·5%) had visible lesions. Only ~1% of adult badgers had extensive, severe pathology. Tuberculous badgers with recorded bite wounds (~5%) had a higher prevalence of visible lesions and a different distribution of lesions, suggesting transmission via bite wounds. However, the predominance of lesions in the respiratory tract indicates that most transmission occurs by the respiratory route. PMID:18047751

Serengeti real estate: density vs. fitness-based indicators of lion habitat quality.

PubMed

Mosser, Anna; Fryxell, John M; Eberly, Lynn; Packer, Craig

2009-10-01

Habitat quality is typically inferred by assuming a direct relationship between consumer density and resource abundance, although it has been suggested that consumer fitness may be a more accurate measure of habitat quality. We examined density vs. fitness-based measures of habitat quality for lions in the Serengeti National Park, Tanzania. A 40-year average of female reproductive success (yearling cubs per female) was best explained by proximity to river confluences, whereas patterns of productivity (yearling cubs per km(2)) and adult female density (individuals per km(2)) were associated with more general measures of habitat quality and areas of shelter in poor habitat. This suggests that density may not accurately distinguish between high-quality 'source' areas and low-quality sites that merely provide refuges for effectively non-reproductive individuals. Our results indicate that density may be a misleading indicator of real estate value, particularly for populations that do not conform to an ideal free distribution.

New aspects of the structure of human hair on the basis of optical microscopic observations of disassembled hair parts.

PubMed

Yamauchi, Asao; Yamauchi, Kiyoshi

2015-01-01

Infant' and adult' scalp hair fibers were disassembled to various cellular components and blocks by chemical and enzymatic treatments, followed by random scission with rapidly rotating cutters. The hair fibers were also fractured by the use of a vise. The optical microscopic inspection of these specimens led to the discovery of many previously unknown structures in the hair shaft. In particular, a cuticular cell (Cu) was found to take a trowel-like shape consisting of a part with a blade-like shape (CuB) and a part with a handle-like shape (CuH), where CuB overlapped one another and fused partially to build the honeycomb-like structure on a large cuticular thin plate (CuP). Whereas CuH was closely similar to the cortical cell in dimensions and richness of macrofibrils (Mf). It was considered that human hair is stabilized structurally and physicochemically by the presence of the honeycomb-like structure, the CuP and the Mf.

Institutional Transformation 2.5 Building Module Help Manual.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villa, Daniel

The Institutional Transformation (IX) building module is a software tool developed at Sandia National Laboratories to evaluate energy conservation measures (ECMs) on hundreds of DOE-2 building energy models simultaneously. In IX, ECMs can be designed through parameterizing DOE-2 building models and doing further processing via visual basic for applications subroutines. IX provides the functionality to handle multiple building models for different years, which enables incrementally changing a site of hundreds of buildings over time. It also enables evaluation of the effects of changing climate, comparisons between data and modeling results, and energy use of centralized utility buildings (CUBs). IX consistsmore » of a Microsoft Excel(r) user interface, Microsoft Access(r) database, and Microsoft Excel(r) CUB build utility whose functionalities are described in detail in this report. In addition to descriptions of the user interfaces, descriptions of every ECM already designed in IX is included. SAND2016-8983 IX 2.5 Help Manual« less

Effect of laser irradiation for healing of the skin-muscle wounds of animals

NASA Astrophysics Data System (ADS)

Lapina, Victoria A.; Veremei, Eduard I.; Pancovets, Evgeniy A.

2000-05-01

The purpose of our investigation was to study the medical effect of low-intensity laser influence on healing of skin- muscle wounds of agricultural animals. We used the laser radiation of low intensity for cub's therapy: to sucking-pigs after herniotomy and castration, to cattle cubs after skin- muscle wounds. The animals were kept under clinical observation up to their recovery. The recuperation dynamic was observed by changing of blood quotients, leukograms, sizes of inflammatory edema, general behavior of animals. The positive dynamic of blood quotients of the experimental animal groups was really higher than that in control. The analysis of wound healing after laser influence shows that wound surface of experimental group was to a great extent smaller in comparison with control group of animals. So, these facts testify about anti-inflammatory action of laser radiation, which hastens regenerative and rehabilitative processes. Analysis of the obtained experimental data has revealed the positive influence of laser irradiation on the dynamics of wound adhesion of agricultural animals.

A Mobile Robot for Locomotion Through a 3D Periodic Lattice Environment

NASA Technical Reports Server (NTRS)

Jenett, Benjamin; Cellucci, Daniel; Cheung, Kenneth

2017-01-01

This paper describes a novel class of robots specifically adapted to climb periodic lattices, which we call 'Relative Robots'. These robots use the regularity of the structure to simplify the path planning, align with minimal feedback, and reduce the number of degrees of freedom (DOF) required to locomote. They can perform vital inspection and repair tasks within the structure that larger truss construction robots could not perform without modifying the structure. We detail a specific type of relative robot designed to traverse a cuboctahedral (CubOct) cellular solids lattice, show how the symmetries of the lattice simplify the design, and test these design methodologies with a CubOct relative robot that traverses a 76.2 mm (3 in.) pitch lattice, MOJO (Multi-Objective JOurneying robot). We perform three locomotion tasks with MOJO: vertical climbing, horizontal climbing, and turning, and find that, due to changes in the orientation of the robot relative to the gravity vector, the success rate of vertical and horizontal climbing is significantly different.

Rubber dam may increase the survival time of dental restorations.

PubMed

Keys, William; Carson, Susan J

2017-03-01

Data sourcesCochrane Oral Health's Trials Register, Cochrane Central Register of Controlled Trials (CENTRAL), Medline, Embase, LILACS, SciELO, Chinese BioMedical Literature Database, VIP, China National Knowledge Infrastructure, ClinicalTrials.gov, World Health Organization International Clinical Trials Registry Platform, OpenGrey and Sciencepaper Online databases. Handsearches in a number of journals.Study selectionRandomised controlled trials, including split-mouth studies assessing the effects of rubber dam isolation for restorative treatments in dental patients.Data extraction and synthesisTwo review authors independently screened the results of the electronic searches, extracted data and assessed the risk of bias of the included studies.ResultsFour studies involving a total of 1,270 patients were included. The studies were at high risk of bias. One trial was excluded from the analysis due to inconsistencies in the presented data. Restorations had a significantly higher survival rate in the rubber dam isolation group compared to the cotton roll isolation group at six months in participants receiving composite restorative treatment of non-carious cervical lesions (risk ratio (RR) 1.19, 95% confidence interval (CI) 1.04 to 1.37, very low-quality evidence). The rubber dam group had a lower risk of failure at two years in children undergoing proximal atraumatic restorative treatment in primary molars (hazard ratio (HR) 0.80, 95% CI 0.66 to 0.97, very low-quality evidence). One trial reported limited data showing that rubber dam usage during fissure sealing might shorten the treatment time. None of the included studies mentioned adverse effects or reported the direct cost of the treatment, or the level of patient acceptance/satisfaction. There was also no evidence evaluating the effects of rubber dam usage on the quality of the restorations.ConclusionsWe found some very low-quality evidence, from single studies, suggesting that rubber dam usage in dental direct restorative treatments may lead to a lower failure rate of the restorations, compared with the failure rate for cotton roll usage. Further high quality research evaluating the effects of rubber dam usage on different types of restorative treatments is required.

Bayesian Estimation of Circumplex Models Subject to Prior Theory Constraints and Scale-Usage Bias

ERIC Educational Resources Information Center

Lenk, Peter; Wedel, Michel; Bockenholt, Ulf

2006-01-01

This paper presents a hierarchical Bayes circumplex model for ordinal ratings data. The circumplex model was proposed to represent the circular ordering of items in psychological testing by imposing inequalities on the correlations of the items. We provide a specification of the circumplex, propose identifying constraints and conjugate priors for…

Oral contraceptives and benign breast disease.

PubMed

Hislop, T G; Threlfall, W J

1984-08-01

In 1980 a questionnaire was mailed to 726 nurses who had previously entered a study of breast disease in the late 1940s and 1950s; 665 responded. Between the ages of 30 to 49 years, 137 reported detecting their first signs of benign breast disease and 76 reported receiving their first biopsy for these signs. Long-term oral contraceptive usage reduced the risk of developing signs of benign breast disease and the risk of biopsy for these signs. The potential bias due to the effect of prior benign breast disease on the prescribing practices for oral contraceptives was minimized by considering oral contraceptive usage prior to detecting the first signs of benign breast disease.

Transcriptome Analysis of Core Dinoflagellates Reveals a Universal Bias towards "GC" Rich Codons.

PubMed

Williams, Ernest; Place, Allen; Bachvaroff, Tsvetan

2017-04-27

Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen "core" dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position. GC bias in the analyzed dataset and at the third codon position varied from 51% and 54% to 66% and 88%, respectively. Codons poor in GC were observed to be universally absent, but bias was most pronounced for codons ending in uracil followed by adenine (UA). GC bias at the third codon position was able to explain low abundance codons as well as the low effective number of codons. Thus, we propose that a bias towards codons rich in GC bases is a universal feature of core dinoflagellates, possibly relating to their unique chromosome structure, and not likely a major mechanism for controlling gene expression.

Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China

PubMed Central

Chen, Yanping; Wu, Jirong; Meng, Qingchang; Han, Xiaohua; Hao, Zhuanfang; Li, Mingshun; Yong, Hongjun; Zhang, Degui; Zhang, Shihuang; Li, Xinhai

2015-01-01

Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent. PMID:26121638

32 CFR 212.6 - Procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... (i) No person because of race, color, creed, sex, age, disability, or national origin shall be... that serve as the legal basis for the creation of Boy Scouts organizations (including Boy Scouts, Cub... Boy Scouts or their official affiliates; Boy Scouts activities on DoD installations; or sponsorship of...

32 CFR 212.6 - Procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... (i) No person because of race, color, creed, sex, age, disability, or national origin shall be... that serve as the legal basis for the creation of Boy Scouts organizations (including Boy Scouts, Cub... Boy Scouts or their official affiliates; Boy Scouts activities on DoD installations; or sponsorship of...

32 CFR 212.6 - Procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... (i) No person because of race, color, creed, sex, age, disability, or national origin shall be... that serve as the legal basis for the creation of Boy Scouts organizations (including Boy Scouts, Cub... Boy Scouts or their official affiliates; Boy Scouts activities on DoD installations; or sponsorship of...

32 CFR 212.6 - Procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (i) No person because of race, color, creed, sex, age, disability, or national origin shall be... that serve as the legal basis for the creation of Boy Scouts organizations (including Boy Scouts, Cub... Boy Scouts or their official affiliates; Boy Scouts activities on DoD installations; or sponsorship of...

32 CFR 212.6 - Procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (i) No person because of race, color, creed, sex, age, disability, or national origin shall be... that serve as the legal basis for the creation of Boy Scouts organizations (including Boy Scouts, Cub... Boy Scouts or their official affiliates; Boy Scouts activities on DoD installations; or sponsorship of...

U.S. National Cyberstrategy and Critical Infrastructure: The Protection Mandate and Its Execution

DTIC Science & Technology

2013-09-01

revising this thesis, and balancing the coordination needed for: (1) Piano; (2) Soccer /Baseball; (3) Cubmaster Cub Scout Pack-135; (4) Hospitality...disease and pest response; and provides nutritional assistance. Provides the financial infrastructure of the nation. This sector consists of commercial

Giant magnetic coercivity in YNi4B-type SmNi3TB (T=Mn-Cu) solid solutions

NASA Astrophysics Data System (ADS)

Yao, Jinlei; Yan, Chang; Yapaskurt, V. O.; Morozkin, A. V.

2016-12-01

The effects of transition metal substitution for Ni on the magnetic properties of the YNi4B-type SmNi4B via SmNi3TB (T=Mn, Fe, Co, Cu) solid solutions have been investigated. SmNi4B, SmNi3MnB, SmNi3FeB, SmNi3CoB and SmNi3CuB show ferromagnetic ordering at 40 K, 210 K, 322 K, 90 K and 57 K and field sensitive metamagnetic-like transitions at 15 K, 100 K, 185 K, 55 K and 15 K in a magnetic field of 10 kOe, respectively. The magnetocaloric effects of SmNi3TB (T=Mn-Cu) were calculated in terms of isothermal magnetic entropy change (ΔSm). The magnetic entropy ΔSm reaches value of -0.94 J/kg K at 40 K for SmNi4B, -1.5 J/kg K at 205 K for SmNi3MnB, -0.54 J/kg K at 320 K for SmNi3FeB, -0.49 J/kg K at 90 K for SmNi3CoB and -0.54 J/kg K at 60 K for SmNi3CuB in field change of 0-50 kOe around the Curie temperature. They show positive ΔSm of +0.71 J/kg K at ~10 K for SmNi4B, +1.69 J/kg K at 30 K for SmNi3MnB, +0.89 J/kg K at 110 K for SmNi3FeB, +1.08 J/kg K at 25 K for SmNi3CoB and +1.12 J/kg K at 10 K for SmNi3CuB in field change of 0-50 kOe around the low temperature metamagnetic-like transition. Below the field induced transition temperature (change of magnetic structure), SmNi3TB (T=Mn-Cu) exhibits giant magnetic coercivity of 74 kOe at 5 K for SmNi4B, 69 kOe at 20 K (90 kOe at 10 K) for SmNi3MnB, 77 kOe at 60 K for SmNi3FeB, 88 kOe at 20 K for SmNi3CoB and 52 kOe at 5 K for SmNi3CuB.

Roles of nonpolar and polar intermolecular interactions in the improvement of the drug loading capacity of PEO-b-PCL with increasing PCL content for two hydrophobic Cucurbitacin drugs.

PubMed

Patel, Sarthak K; Lavasanifar, Afsaneh; Choi, Phillip

2009-09-14

Molecular dynamics (MD) simulation was used to study the roles of nonpolar and polar intermolecular interactions in the improvement of the drug loading capacity of poly(ethylene oxide)-b-poly(epsilon-caprolactone) (PEO-b-PCL) with increasing PCL content for two water insoluble anticancer drugs: Cucurbitacin B (CuB) and Cucurbitacin I (CuI). In particular, random binary mixture models containing 10-12 wt % drug and remaining PEO-b-PCL with three different PCL/PEO (w/w) ratios (0.5, 1, and 2) were used to calculate their Flory-Huggins interaction parameters (chi). The MD simulation results show that, for both CuB and CuI, the computed chi decreases (i.e., affinity increases) with increasing PCL/PEO ratio. Such results are consistent with our experimental observation that increasing the PCL/PEO (w/w) ratio from 1 to 4.8 significantly increases the drug loading capacity of micelles formed by PEO-b-PCL for both drugs. Analysis of the energy data shows that increasing affinity (loading) at higher PCL/PEO ratio is attributed to the increase in favorable polar interactions and to the formation of additional hydrogen bonds (H-bonds) between the drugs and the PCL block rather than to the increase in the hydrophobic characteristics of the diblock copolymer as one would normally expect. In fact, the nonpolar intermolecular interactions became more unfavorable at higher PCL/PEO ratio. Analysis of the radial distribution functions of the model mixtures indicates that at high PCL/PEO ratio, multiple H-bond sites on the PCL block interacted with single H-bond sites on the drug molecules. However, at low PCL/PEO ratio, only single H-bonds formed between various H-bond sites on the drug molecules and those of the PCL and PEO blocks. It seems that formation of H-bonds between multiple H-bond sites on the PCL block and single H-bond sites on the drug molecules is responsible for inducing drug/PEO-b-PCL affinity. The finding also explains the experimental observation that release rates of both drugs decrease with increasing PCL/PEO ratio and that the decrease in the release rate of CuB is more pronounced than that of CuI. Our simulation results show that the number of H-bonds formed between CuB and the PCL block is much higher than that of CuI at high PCL/PEO ratio.

Adaptive servo ventilation for central sleep apnoea in heart failure: SERVE-HF on-treatment analysis.

PubMed

Woehrle, Holger; Cowie, Martin R; Eulenburg, Christine; Suling, Anna; Angermann, Christiane; d'Ortho, Marie-Pia; Erdmann, Erland; Levy, Patrick; Simonds, Anita K; Somers, Virend K; Zannad, Faiez; Teschler, Helmut; Wegscheider, Karl

2017-08-01

This on-treatment analysis was conducted to facilitate understanding of mechanisms underlying the increased risk of all-cause and cardiovascular mortality in heart failure patients with reduced ejection fraction and predominant central sleep apnoea randomised to adaptive servo ventilation versus the control group in the SERVE-HF trial.Time-dependent on-treatment analyses were conducted (unadjusted and adjusted for predictive covariates). A comprehensive, time-dependent model was developed to correct for asymmetric selection effects (to minimise bias).The comprehensive model showed increased cardiovascular death hazard ratios during adaptive servo ventilation usage periods, slightly lower than those in the SERVE-HF intention-to-treat analysis. Self-selection bias was evident. Patients randomised to adaptive servo ventilation who crossed over to the control group were at higher risk of cardiovascular death than controls, while control patients with crossover to adaptive servo ventilation showed a trend towards lower risk of cardiovascular death than patients randomised to adaptive servo ventilation. Cardiovascular risk did not increase as nightly adaptive servo ventilation usage increased.On-treatment analysis showed similar results to the SERVE-HF intention-to-treat analysis, with an increased risk of cardiovascular death in heart failure with reduced ejection fraction patients with predominant central sleep apnoea treated with adaptive servo ventilation. Bias is inevitable and needs to be taken into account in any kind of on-treatment analysis in positive airway pressure studies. Copyright ©ERS 2017.

Comprehensive characterization of immunoglobulin gene rearrangements in patients with chronic lymphocytic leukaemia

PubMed Central

René, Céline; Prat, Nathalie; Thuizat, Audrey; Broctawik, Mélanie; Avinens, Odile; Eliaou, Jean-François

2014-01-01

Previous studies have suggested a geographical pattern of immunoglobulin rearrangement in chronic lymphocytic leukaemia (CLL), which could be as a result of a genetic background or an environmental antigen. However, the characteristics of Ig rearrangements in the population from the South of France have not yet been established. Here, we studied CLL B-cell repertoire and mutational pattern in a Southern French cohort of patients using an in-house protocol for whole sequencing of the rearranged immunoglobulin heavy-chain genes. Described biased usage of variable, diversity and joining genes between the mutated and unmutated groups was found in our population. However, variable gene frequencies are more in accordance with those observed in the Mediterranean patients. We found that the third complementary-determining region (CDR) length was higher in unmutated sequences, because of bias in the diversity and joining genes usage and not due to the N diversity. Mutations found in CLL followed the features of canonical somatic hypermutation mechanism: preference of targeting for activation-induced cytidine deaminase and polymerase motifs, base change bias for transitions and more replacement mutations occurring in CDRs than in framework regions. Surprisingly, localization of activation-induced cytidine deaminase motifs onto the variable gene showed a preference for framework regions. The study of the characteristics at the age of diagnosis showed no difference in clinical outcome, but suggested a tendency of increased replacement and transition-over-transversion mutations and a longer third CDR length in older patients. PMID:24725733

75 FR 46926 - Notice of Receipt of Requests to Voluntarily Cancel Certain Pesticide Registrations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-04

... interest to a wide range of stakeholders including environmental, human health, and agricultural advocates... 07401 53883 Control Solutions, Inc. 427 Hide Away Circle Cub Run, KY 42729 70127 Novozymes Biologicals... or termination of any minor agricultural use before granting the request, unless: 1. The registrants...

Understanding Web Activity Patterns among Teachers, Students and Teacher Candidates

ERIC Educational Resources Information Center

Kimmons, Royce; Clark, B.; Lim, M.

2017-01-01

This study sought to understand generational and role differences in web usage of teachers, teacher candidates and K-12 students in a state in the USA (n = 2261). The researchers employed unique methods, which included using a custom-built persistent web browser to track user behaviours free of self-report, self-selection and perception bias.…

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome

PubMed Central

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest. PMID:19131380

Does adaptation to vertebrate codon usage relate to flavivirus emergence potential?

PubMed Central

Freire, Caio César de Melo

2018-01-01

Codon adaptation index (CAI) is a measure of synonymous codon usage biases given a usage reference. Through mutation, selection, and drift, viruses can optimize their replication efficiency and produce more offspring, which could increase the chance of secondary transmission. To evaluate how higher CAI towards the host has been associated with higher viral titers, we explored temporal trends of several historic and extensively sequenced zoonotic flaviviruses and relationships within the genus itself. To showcase evolutionary and epidemiological relationships associated with silent, adaptive synonymous changes of viruses, we used codon usage tables from human housekeeping and antiviral immune genes, as well as tables from arthropod vectors and vertebrate species involved in the flavivirus maintenance cycle. We argue that temporal trends of CAI changes could lead to a better understanding of zoonotic emergences, evolutionary dynamics, and host adaptation. CAI appears to help illustrate historically relevant trends of well-characterized viruses, in different viral species and genetic diversity within a single species. CAI can be a useful tool together with in vivo and in vitro kinetics, phylodynamics, and additional functional genomics studies to better understand species trafficking and viral emergence in a new host. PMID:29385205

Rapid Evolution of Ovarian-Biased Genes in the Yellow Fever Mosquito (Aedes aegypti).

PubMed

Whittle, Carrie A; Extavour, Cassandra G

2017-08-01

Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2927, 2013, and 4449 coding sequences (CDS) with ovary-biased, testis-biased, and unbiased expression, respectively, in the yellow fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes. Further, we observed higher dN/dS in ovary-biased genes than in testis-biased genes, even for genes coexpressed in nonsexual (embryo) tissues. Ovary-specific genes evolved exceptionally fast, as compared to testis- or embryo-specific genes, and exhibited higher frequency of positive selection. Genes with ovary expression were preferentially involved in olfactory binding and reception. We hypothesize that at least two potential mechanisms could explain rapid evolution of ovary-biased genes in this mosquito: (1) the evolutionary rate of ovary-biased genes may be accelerated by sexual selection (including female-female competition or male-mate choice) affecting olfactory genes during female swarming by males, and/or by adaptive evolution of olfactory signaling within the female reproductive system ( e.g. , sperm-ovary signaling); and/or (2) testis-biased genes may exhibit decelerated evolutionary rates due to the formation of mating plugs in the female after copulation, which limits male-male sperm competition. Copyright © 2017 by the Genetics Society of America.

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea

PubMed Central

2012-01-01

Background Archaea evoke interest among researchers for two enigmatic characteristics –a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Results Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Conclusions Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world. PMID:22691113

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea.

PubMed

Roy Chowdhury, Anindya; Dutta, Chitra

2012-06-12

Archaea evoke interest among researchers for two enigmatic characteristics -a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

A Novel Method to Predict Highly Expressed Genes Based on Radius Clustering and Relative Synonymous Codon Usage.

PubMed

Tran, Tuan-Anh; Vo, Nam Tri; Nguyen, Hoang Duc; Pham, Bao The

2015-12-01

Recombinant proteins play an important role in many aspects of life and have generated a huge income, notably in the industrial enzyme business. A gene is introduced into a vector and expressed in a host organism-for example, E. coli-to obtain a high productivity of target protein. However, transferred genes from particular organisms are not usually compatible with the host's expression system because of various reasons, for example, codon usage bias, GC content, repetitive sequences, and secondary structure. The solution is developing programs to optimize for designing a nucleotide sequence whose origin is from peptide sequences using properties of highly expressed genes (HEGs) of the host organism. Existing data of HEGs determined by practical and computer-based methods do not satisfy for qualifying and quantifying. Therefore, the demand for developing a new HEG prediction method is critical. We proposed a new method for predicting HEGs and criteria to evaluate gene optimization. Codon usage bias was weighted by amplifying the difference between HEGs and non-highly expressed genes (non-HEGs). The number of predicted HEGs is 5% of the genome. In comparison with Puigbò's method, the result is twice as good as Puigbò's one, in kernel ratio and kernel sensitivity. Concerning transcription/translation factor proteins (TF), the proposed method gives low TF sensitivity, while Puigbò's method gives moderate one. In summary, the results indicated that the proposed method can be a good optional applying method to predict optimized genes for particular organisms, and we generated an HEG database for further researches in gene design.

How the Sequence of a Gene Specifies Structural Symmetry in Proteins

PubMed Central

Shen, Xiaojuan; Huang, Tongcheng; Wang, Guanyu; Li, Guanglin

2015-01-01

Internal symmetry is commonly observed in the majority of fundamental protein folds. Meanwhile, sufficient evidence suggests that nascent polypeptide chains of proteins have the potential to start the co-translational folding process and this process allows mRNA to contain additional information on protein structure. In this paper, we study the relationship between gene sequences and protein structures from the viewpoint of symmetry to explore how gene sequences code for structural symmetry in proteins. We found that, for a set of two-fold symmetric proteins from left-handed beta-helix fold, intragenic symmetry always exists in their corresponding gene sequences. Meanwhile, codon usage bias and local mRNA structure might be involved in modulating translation speed for the formation of structural symmetry: a major decrease of local codon usage bias in the middle of the codon sequence can be identified as a common feature; and major or consecutive decreases in local mRNA folding energy near the boundaries of the symmetric substructures can also be observed. The results suggest that gene duplication and fusion may be an evolutionarily conserved process for this protein fold. In addition, the usage of rare codons and the formation of higher order of secondary structure near the boundaries of symmetric substructures might have coevolved as conserved mechanisms to slow down translation elongation and to facilitate effective folding of symmetric substructures. These findings provide valuable insights into our understanding of the mechanisms of translation and its evolution, as well as the design of proteins via symmetric modules. PMID:26641668

Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: compositional constraints and translational selection.

PubMed

Musto, H; Romero, H; Zavala, A; Jabbari, K; Bernardi, G

1999-07-01

We have analyzed the patterns of synonymous codon preferences of the nuclear genes of Plasmodium falciparum, a unicellular parasite characterized by an extremely GC-poor genome. When all genes are considered, codon usage is strongly biased toward A and T in third codon positions, as expected, but multivariate statistical analysis detects a major trend among genes. At one end genes display codon choices determined mainly by the extreme genome composition of this parasite, and very probably their expression level is low. At the other end a few genes exhibit an increased relative usage of a particular subset of codons, many of which are C-ending. Since the majority of these few genes is putatively highly expressed, we postulate that the increased C-ending codons are translationally optimal. In conclusion, while codon usage of the majority of P. falciparum genes is determined mainly by compositional constraints, a small number of genes exhibit translational selection.

Transcriptome Analysis of Core Dinoflagellates Reveals a Universal Bias towards “GC” Rich Codons

PubMed Central

Williams, Ernest; Place, Allen; Bachvaroff, Tsvetan

2017-01-01

Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen “core” dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position. GC bias in the analyzed dataset and at the third codon position varied from 51% and 54% to 66% and 88%, respectively. Codons poor in GC were observed to be universally absent, but bias was most pronounced for codons ending in uracil followed by adenine (UA). GC bias at the third codon position was able to explain low abundance codons as well as the low effective number of codons. Thus, we propose that a bias towards codons rich in GC bases is a universal feature of core dinoflagellates, possibly relating to their unique chromosome structure, and not likely a major mechanism for controlling gene expression. PMID:28448468

36 CFR 7.63 - Dinosaur National Monument.

Code of Federal Regulations, 2010 CFR

2010-07-01

... permittee after his stock are on the range. (vii) No building or other structure shall be erected nor shall... approved by the National Park Service. Any such facilities, structures, or buildings may be removed or... Cub Creek Road section extends from the Chew Ranch Road, 1 mile north of the Green River Bridge, to...

Grounding language in action and perception: from cognitive agents to humanoid robots.

PubMed

Cangelosi, Angelo

2010-06-01

In this review we concentrate on a grounded approach to the modeling of cognition through the methodologies of cognitive agents and developmental robotics. This work will focus on the modeling of the evolutionary and developmental acquisition of linguistic capabilities based on the principles of symbol grounding. We review cognitive agent and developmental robotics models of the grounding of language to demonstrate their consistency with the empirical and theoretical evidence on language grounding and embodiment, and to reveal the benefits of such an approach in the design of linguistic capabilities in cognitive robotic agents. In particular, three different models will be discussed, where the complexity of the agent's sensorimotor and cognitive system gradually increases: from a multi-agent simulation of language evolution, to a simulated robotic agent model for symbol grounding transfer, to a model of language comprehension in the humanoid robot iCub. The review also discusses the benefits of the use of humanoid robotic platform, and specifically of the open source iCub platform, for the study of embodied cognition. Copyright 2010 Elsevier B.V. All rights reserved.

The Crystal Structure of Cobra Venom Factor, a Cofactor for C3- and C5-Convertase CVFBb

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnan, Vengadesan; Ponnuraj, Karthe; Xu, Yuanyuan

2009-05-26

Cobra venom factor (CVF) is a functional analog of human complement component C3b, the active fragment of C3. Similar to C3b, in human and mammalian serum, CVF binds factor B, which is then cleaved by factor D, giving rise to the CVFBb complex that targets the same scissile bond in C3 as the authentic complement convertases C4bC2a and C3bBb. Unlike the latter, CVFBb is a stable complex and an efficient C5 convertase. We solved the crystal structure of CVF, isolated from Naja naja kouthia venom, at 2.6 {angstrom} resolution. The CVF crystal structure, an intermediate between C3b and C3c, lacksmore » the TED domain and has the CUB domain in an identical position to that seen in C3b. The similarly positioned CUB and slightly displaced C345c domains of CVF could play a vital role in the formation of C3 convertases by providing important primary binding sites for factor B.« less

Insights into the latent multinomial model through mark-resight data on female grizzly bears with cubs-of-the-year

USGS Publications Warehouse

Higgs, Megan D.; Link, William; White, Gary C.; Haroldson, Mark A.; Bjornlie, Daniel D.

2013-01-01

Mark-resight designs for estimation of population abundance are common and attractive to researchers. However, inference from such designs is very limited when faced with sparse data, either from a low number of marked animals, a low probability of detection, or both. In the Greater Yellowstone Ecosystem, yearly mark-resight data are collected for female grizzly bears with cubs-of-the-year (FCOY), and inference suffers from both limitations. To overcome difficulties due to sparseness, we assume homogeneity in sighting probabilities over 16 years of bi-annual aerial surveys. We model counts of marked and unmarked animals as multinomial random variables, using the capture frequencies of marked animals for inference about the latent multinomial frequencies for unmarked animals. We discuss undesirable behavior of the commonly used discrete uniform prior distribution on the population size parameter and provide OpenBUGS code for fitting such models. The application provides valuable insights into subtleties of implementing Bayesian inference for latent multinomial models. We tie the discussion to our application, though the insights are broadly useful for applications of the latent multinomial model.

The crystal structure of cobra venom factor, a cofactor for C3- and C5-convertase CVFBb.

PubMed

Krishnan, Vengadesan; Ponnuraj, Karthe; Xu, Yuanyuan; Macon, Kevin; Volanakis, John E; Narayana, Sthanam V L

2009-04-15

Cobra venom factor (CVF) is a functional analog of human complement component C3b, the active fragment of C3. Similar to C3b, in human and mammalian serum, CVF binds factor B, which is then cleaved by factor D, giving rise to the CVFBb complex that targets the same scissile bond in C3 as the authentic complement convertases C4bC2a and C3bBb. Unlike the latter, CVFBb is a stable complex and an efficient C5 convertase. We solved the crystal structure of CVF, isolated from Naja naja kouthia venom, at 2.6 A resolution. The CVF crystal structure, an intermediate between C3b and C3c, lacks the TED domain and has the CUB domain in an identical position to that seen in C3b. The similarly positioned CUB and slightly displaced C345c domains of CVF could play a vital role in the formation of C3 convertases by providing important primary binding sites for factor B.

Regulator-dependent mechanisms of C3b processing by factor I allow differentiation of immune responses.

PubMed

Xue, Xiaoguang; Wu, Jin; Ricklin, Daniel; Forneris, Federico; Di Crescenzio, Patrizia; Schmidt, Christoph Q; Granneman, Joke; Sharp, Thomas H; Lambris, John D; Gros, Piet

2017-08-01

The complement system labels microbes and host debris for clearance. Degradation of surface-bound C3b is pivotal to direct immune responses and protect host cells. How the serine protease factor I (FI), assisted by regulators, cleaves either two or three distant peptide bonds in the CUB domain of C3b remains unclear. We present a crystal structure of C3b in complex with FI and regulator factor H (FH; domains 1-4 with 19-20). FI binds C3b-FH between FH domains 2 and 3 and a reoriented C3b C-terminal domain and docks onto the first scissile bond, while stabilizing its catalytic domain for proteolytic activity. One cleavage in C3b does not affect its overall structure, whereas two cleavages unfold CUB and dislodge the thioester-containing domain (TED), affecting binding of regulators and thereby determining the number of cleavages. These data explain how FI generates late-stage opsonins iC3b or C3dg in a context-dependent manner, to react to foreign, danger or healthy self signals.

Multilocus patterns of polymorphism and selection across the X chromosome of Caenorhabditis remanei.

PubMed

Cutter, Asher D

2008-03-01

Natural selection and neutral processes such as demography, mutation, and gene conversion all contribute to patterns of polymorphism within genomes. Identifying the relative importance of these varied components in evolution provides the principal challenge for population genetics. To address this issue in the nematode Caenorhabditis remanei, I sampled nucleotide polymorphism at 40 loci across the X chromosome. The site-frequency spectrum for these loci provides no evidence for population size change, and one locus presents a candidate for linkage to a target of balancing selection. Selection for codon usage bias leads to the non-neutrality of synonymous sites, and despite its weak magnitude of effect (N(e)s approximately 0.1), is responsible for profound patterns of diversity and divergence in the C. remanei genome. Although gene conversion is evident for many loci, biased gene conversion is not identified as a significant evolutionary process in this sample. No consistent association is observed between synonymous-site diversity and linkage-disequilibrium-based estimators of the population recombination parameter, despite theoretical predictions about background selection or widespread genetic hitchhiking, but genetic map-based estimates of recombination are needed to rigorously test for a diversity-recombination relationship. Coalescent simulations also illustrate how a spurious correlation between diversity and linkage-disequilibrium-based estimators of recombination can occur, due in part to the presence of unbiased gene conversion. These results illustrate the influence that subtle natural selection can exert on polymorphism and divergence, in the form of codon usage bias, and demonstrate the potential of C. remanei for detecting natural selection from genomic scans of polymorphism.

An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses-Isotopic Composition Predictions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radulescu, Georgeta; Gauld, Ian C; Ilas, Germina

2011-01-01

The expanded use of burnup credit in the United States (U.S.) for storage and transport casks, particularly in the acceptance of credit for fission products, has been constrained by the availability of experimental fission product data to support code validation. The U.S. Nuclear Regulatory Commission (NRC) staff has noted that the rationale for restricting the Interim Staff Guidance on burnup credit for storage and transportation casks (ISG-8) to actinide-only is based largely on the lack of clear, definitive experiments that can be used to estimate the bias and uncertainty for computational analyses associated with using burnup credit. To address themore » issues of burnup credit criticality validation, the NRC initiated a project with the Oak Ridge National Laboratory to (1) develop and establish a technically sound validation approach for commercial spent nuclear fuel (SNF) criticality safety evaluations based on best-available data and methods and (2) apply the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The purpose of this paper is to describe the isotopic composition (depletion) validation approach and resulting observations and recommendations. Validation of the criticality calculations is addressed in a companion paper at this conference. For isotopic composition validation, the approach is to determine burnup-dependent bias and uncertainty in the effective neutron multiplication factor (keff) due to bias and uncertainty in isotopic predictions, via comparisons of isotopic composition predictions (calculated) and measured isotopic compositions from destructive radiochemical assay utilizing as much assay data as is available, and a best-estimate Monte Carlo based method. This paper (1) provides a detailed description of the burnup credit isotopic validation approach and its technical bases, (2) describes the application of the approach for representative pressurized water reactor and boiling water reactor safety analysis models to demonstrate its usage and applicability, (3) provides reference bias and uncertainty results based on a quality-assurance-controlled prerelease version of the Scale 6.1 code package and the ENDF/B-VII nuclear cross section data.« less

Factors affecting settling, survival, and viability of black bears reintroduced to Felsenthal National Wildlife Refuge, Arkansas

USGS Publications Warehouse

Wear, B.J.; Eastridge, R.; Clark, J.D.

2005-01-01

We used radiotelemetry and population modeling techniques to examine factors related to population establishment of black bears (Ursus americanus) reintroduced to Felsenthal National Wildlife Refuge (NWR), Arkansas. Our objectives were to determine whether settling (i.e., establishment of a home range at or near the release site), survival, recruitment, and population viability were related to age class of reintroduced bears, presence of cubs, time since release, or number of translocated animals. We removed 23 adult female black bears with 56 cubs from their winter dens at White River NWR and transported them 160 km to man-made den structures at Felsenthal NWR during spring 2000–2002. Total movement and average circuity of adult females decreased from 1 month, 6 months, and 1 year post-emergence (F2,14 =19.7, P < 0.001 and F2,14 =5.76, P=0.015, respectively). Mean first-year post-release survival of adult female bears was 0.624 (SE = 0.110, SEinterannual = 0.144), and the survival rate of their cubs was 0.750 (SE = 0.088, SEinterannual = 0.109). The homing rate (i.e., the proportion of bears that returned to White River NWR) was 13%. Annual survival for female bears that remained at the release site and survived >1-year post-release increased to 0.909 (SE = 0.097, SEinterannual=0.067; Z=3.5, P < 0.001). Based on stochastic population growth simulations, the average annual growth rate (λ) was 1.093 (SD = 0.053) and the probability of extinction with no additional stockings ranged from 0.56-1.30%. The bear population at Felsenthal NWR is at or above the number after which extinction risk declines dramatically, although additional releases of bears could significantly decrease time to population reestablishment. Poaching accounted for at least 3 of the 8 adult mortalities that we documented; illegal kills could be a significant impediment to population re-establishment at Felsenthal NWR should poaching rates escalate.

Cytologic atypia in the contralateral unaffected breast is related to parity and estrogen-related genes.

PubMed

Monahan, Denise A; Wang, Jun; Lee, Oukseub; Revesz, Elizabeth; Taft, Nancy; Ivancic, David; Hansen, Nora M; Bethke, Kevin P; Zalles, C; Khan, Seema A

2016-12-01

The contralateral unaffected breast (CUB) of women with unilateral breast cancer provides a model for the study of breast tissue-based risk factors. Using random fine needle aspiration (rFNA), we have investigated hormonal and gene expression patterns related to atypia in the CUBs of newly diagnosed breast cancer patients. 83 women underwent rFNA of the CUB. Cytologic analysis was performed using the Masood Score (MS), atypia was defined as MS > 14. RNA was extracted using 80% of the sample. The expression of 20 hormone related genes was quantified using Taqman Low Density Arrays. Statistical analysis was performed using 2-tailed t tests and linear regression. Cytological atypia was more frequent in multiparous women (P = 0.0392), and was not associated with any tumor-related features in the affected breast. Masood Score was higher with shorter interval since last pregnancy (R = 0.204, P = 0.0417), higher number of births (R = 0.369, P = 0.0006), and estrogen receptor (ER) negativity of the index cancer (R = -0.203, P = 0.065). Individual cytologic features were associated with aspects of parity. Specifically, anisonucleosis was correlated with shorter interval since last pregnancy (R = 0.318, P = 0.0201), higher number of births (R = 0.382, P = 0.0004), and ER status (R = -0.314, P = 0.0038). Eight estrogen-regulated genes were increased in atypical samples (P < 0.005), including TFF1, AGT, PDZK1, PGR, GREB1, PRLR, CAMK2B, and CCND1. Cytologic atypia, and particularly anisonucleosis, is associated with recent and multiple births and ER negative status of the index tumor. Atypical samples showed increased expression of estrogen-related genes, consistent with the role of estrogen exposure in breast cancer development. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of the effectiveness of two protocols of antirabies bait distribution for foxes (Vulpes vulpes).

PubMed

Vuillaume, P; Bruyere, V; Aubert, M

1998-01-01

In a plateau and hill region of France (the Doubs), two protocols of rabies vaccine bait distribution targeted at foxes were compared: helicopter distribution of vaccine baits alone (control zone) and a combined aerial distribution by helicopter with an additional deposit of vaccine baits at fox den entrances by foot (test zone). In the test zone covering an area of 436 km2, baits were distributed by helicopter at a rate of 13.4 baits/km2. Additionally, an average of 11.4 vaccine baits at the entrances of 871 fox dens were terrestrially distributed by 110 persons (9,964 baits). In this test zone, 90% of the young foxes were marked with tetracycline which permitted estimation of the bait consumption; however, only 38% had significant titre of rabies antibodies and less than one fox cub per 2.4 of those having consumed at least one bait were immunized. In the control zone, these percentages were significantly lower: respectively, 35 and 17% and one fox cub per 4.2. The relative lack of benefit between bait uptake and rate of immunological response may be due to maternal immunity which could have interfered with fox cub active immunization. A booster effect following a second distribution of baits by foot may be suggested in both adult foxes and their offspring. That these baits needed to be terrestrially distributed in order to obtain a booster effect is uncertain. Terrestrial distribution at fox den entrances is difficult to do and entails additional expenses not incurred in aerial distribution. The cost of terrestrial vaccination is 3.5 times higher than classical aerial vaccination and takes 63.5 times longer. A cost effective analysis of this type of supplementary terrestrial intervention determined that bait deposit at den entrances can be recommended for restricted areas, where residual focii exist, as a complement to the aerial distribution of baits.

Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China.

PubMed

Gao, San-Ji; Lin, Yi-Hua; Pan, Yong-Bao; Damaj, Mona B; Wang, Qin-Nan; Mirkov, T Erik; Chen, Ru-Kai

2012-10-01

Sugarcane yellow leaf virus (SCYLV) (genus Polerovirus, family Luteoviridae), the causal agent of sugarcane yellow leaf disease (YLD), was first detected in China in 2006. To assess the distribution of SCYLV in the major sugarcane-growing Chinese provinces, leaf samples from 22 sugarcane clones (Saccharum spp. hybrid) showing YLD symptoms were collected and analyzed for infection by the virus using reverse transcription PCR (RT-PCR), quantitative RT-PCR, and immunological assays. A complete genomic sequence (5,879 nt) of the Chinese SCYLV isolate CHN-FJ1 and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned, and sequenced. The genomic sequence of the CHN-FJ1 isolate was found to share a high identity (98.4-99.1 %) with those of the Brazilian (BRA) genotype isolates and a low identity (86.5-86.9 %) with those of the CHN1 and Cuban (CUB) genotype isolates. The genetic diversity of these 14 Chinese SCYLV isolates was assessed along with that of 29 SCYLV isolates of worldwide origin reported in the GenBank database, based on the full or partial genomic sequence. Phylogenetic analysis demonstrated that all the 14 Chinese SCYLV isolates clustered into one large group with the BRA genotype and 12 other reported SCYLV isolates. In addition, five reported Chinese SCYLV isolates were grouped with the Peruvian (PER), CHN1 and CUB genotypes. We therefore speculated that at least four SCYLV genotypes, BRA, PER, CHN1, and CUB, are associated with YLD in China. Interestingly, a 39-nt deletion was detected in the sequence of the CHN-GD3 isolate, in the middle of the ORF1 region adjacent to the overlap between ORF1 and ORF2. This location is known to be one of the recombination breakpoints in the Luteoviridae family.

Reciprocal modulation of internal and external factors determines individual movements.

PubMed

Martin, Jodie; van Moorter, Bram; Revilla, Eloy; Blanchard, Pierrick; Dray, Stéphane; Quenette, Pierre-Yves; Allainé, Dominique; Swenson, Jon E

2013-03-01

Movement is fundamental to individual and population dynamics, as it allows individuals to meet their basic requirements. Although movement patterns reflect interactions between internal and external factors, only few studies have examined the effects of these factors on movement simultaneously, and they generally focused on particular biological contexts (e.g. dispersal, foraging). However, the relative importance of these factors in driving individual routine movements might reflect a species' potential flexibility to cope with landscape changes and therefore buffer their potential impact on fitness. We used data from GPS collars on Scandinavian brown bears to investigate the relative role of these factors, as well as an additional factor (period of the year) on routine movements at two spatial scales (hourly and daily relocations). As expected, internal factors played a major role in driving movement, compared to external factors at both scales, but its relative importance was greater at a finer scale. In particular, the interaction between reproductive status and period of the year was one of the most influential variables, females being constrained by the movement capacity of their cubs in the first periods of the year. The effect of human disturbance on movement was also greater for females with cubs than for lone females. This study showed how reciprocal modulation of internal and external factors is shaping space use of brown bears. We stress that these factors should be studied simultaneously to avoid the risk of obtaining context-dependent inferences. Moreover, the study of their relative contribution is also highly relevant in the context of multiple-use landscapes, as human activities generally affect the landscape more than they affect the internal states of an individual. Species or individuals with important internal constraints should be less responsive to changes in their environment as they have less freedom from internal constraints and should thus be more sensitive to human alteration of the landscape, as shown for females with cubs in this study. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Human alpha2-macroglobulin is composed of multiple domains, as predicted by homology with complement component C3.

PubMed

Doan, Ninh; Gettins, Peter G W

2007-10-01

Human alpha2M (alpha2-macroglobulin) and the complement components C3 and C4 are thiol ester-containing proteins that evolved from the same ancestral gene. The recent structure determination of human C3 has allowed a detailed prediction of the location of domains within human alpha2M to be made. We describe here the expression and characterization of three alpha(2)M domains predicted to be involved in the stabilization of the thiol ester in native alpha2M and in its activation upon bait region proteolysis. The three newly expressed domains are MG2 (macroglobulin domain 2), TED (thiol ester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain. Together with the previously characterized RBD (receptor-binding domain), they represent approx. 42% of the alpha2M polypeptide. Their expression as folded domains strongly supports the predicted domain organization of alpha2M. An X-ray crystal structure of MG2 shows it to have a fibronectin type-3 fold analogous to MG1-MG8 of C3. TED is, as predicted, an alpha-helical domain. CUB is a spliced domain composed of two stretches of polypeptide that flank TED in the primary structure. In intact C3 TED interacts with RBD, where it is in direct contact with the thiol ester, and with MG2 and CUB on opposite, flanking sides. In contrast, these alpha2M domains, as isolated species, show negligible interaction with one another, suggesting that the native conformation of alpha2M, and the consequent thiol ester-stabilizing domain-domain interactions, result from additional restraints imposed by the physical linkage of these domains or by additional domains in the protein.

Human α2-macroglobulin is composed of multiple domains, as predicted by homology with complement component C3

PubMed Central

Doan, Ninh; Gettins, Peter G. W.

2007-01-01

Human α2M (α2-macroglobulin) and the complement components C3 and C4 are thiol ester-containing proteins that evolved from the same ancestral gene. The recent structure determination of human C3 has allowed a detailed prediction of the location of domains within human α2M to be made. We describe here the expression and characterization of three α2M domains predicted to be involved in the stabilization of the thiol ester in native α2M and in its activation upon bait region proteolysis. The three newly expressed domains are MG2 (macroglobulin domain 2), TED (thiol ester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain. Together with the previously characterized RBD (receptor-binding domain), they represent approx. 42% of the α2M polypeptide. Their expression as folded domains strongly supports the predicted domain organization of α2M. An X-ray crystal structure of MG2 shows it to have a fibronectin type-3 fold analogous to MG1–MG8 of C3. TED is, as predicted, an α-helical domain. CUB is a spliced domain composed of two stretches of polypeptide that flank TED in the primary structure. In intact C3 TED interacts with RBD, where it is in direct contact with the thiol ester, and with MG2 and CUB on opposite, flanking sides. In contrast, these α2M domains, as isolated species, show negligible interaction with one another, suggesting that the native conformation of α2M, and the consequent thiol ester-stabilizing domain–domain interactions, result from additional restraints imposed by the physical linkage of these domains or by additional domains in the protein. PMID:17608619

Polar Bear Population Status in the Southern Beaufort Sea

USGS Publications Warehouse

Regehr, Eric V.; Amstrup, Steven C.; Stirling, Ian

2006-01-01

Polar bears depend entirely on sea ice for survival. In recent years, a warming climate has caused major changes in the Arctic sea ice environment, leading to concerns regarding the status of polar bear populations. Here we present findings from long-term studies of polar bears in the southern Beaufort Sea (SBS) region of the U.S. and Canada, which are relevant to these concerns. We applied open population capture-recapture models to data collected from 2001 to 2006, and estimated there were 1,526 (95% CI = 1,211; 1,841) polar bears in the SBS region in 2006. The number of polar bears in this region was previously estimated to be approximately 1,800. Because precision of earlier estimates was low, our current estimate of population size and the earlier ones cannot be statistically differentiated. For the 2001-06 period, the best fitting capture-recapture model provided estimates of total apparent survival of 0.43 for cubs of the year (COYs), and 0.92 for all polar bears older than COYs. Because the survival rates for older polar bears included multiple sex and age strata, they could not be compared to previous estimates. Survival rates for COYs, however, were significantly lower than estimates derived in earlier studies (P = 0.03). The lower survival of COYs was corroborated by a comparison of the number of COYs per adult female for periods before (1967-89) and after (1990-2006) the winter of 1989-90, when warming temperatures and altered atmospheric circulation caused an abrupt change in sea ice conditions in the Arctic basin. In the latter period, there were significantly more COYs per adult female in the spring (P = 0.02), and significantly fewer COYs per adult female in the autumn (P < 0.001). Apparently, cub production was higher in the latter period, but fewer cubs survived beyond the first 6 months of life. Parallel with declining survival, skull measurements suggested that COYs captured from 1990 to 2006 were smaller than those captured before 1990. Similarly, both skull measurements and body weights suggested that adult males captured from 1990 to 2006 were smaller than those captured before 1990. The smaller stature of males was especially notable because it corresponded with a higher mean age of adult males. Male polar bears continue to grow into their teens, and if adequately nourished, the older males captured in the latter period should have been larger than those captured earlier. In western Hudson Bay, Canada, a significant decline in population size was preceded by observed declines in cub survival and physical stature. The evidence of declining recruitment and body size reported here, therefore, suggests vigilance regarding the future of polar bears in the SBS region.

Dynamic Nucleotide Mutation Gradients and Control Region Usage in Squamate Reptile Mitochondrial Genomes

PubMed Central

Castoe, T.A.; Gu, W.; de Koning, A.P.J.; Daza, J.M.; Jiang, Z.J.; Parkinson, C.L.; Pollock, D.D.

2010-01-01

Gradients of nucleotide bias and substitution rates occur in vertebrate mitochondrial genomes due to the asymmetric nature of the replication process. The evolution of these gradients has previously been studied in detail in primates, but not in other vertebrate groups. From the primate study, the strengths of these gradients are known to evolve in ways that can substantially alter the substitution process, but it is unclear how rapidly they evolve over evolutionary time or how different they may be in different lineages or groups of vertebrates. Given the importance of mitochondrial genomes in phylogenetics and molecular evolutionary research, a better understanding of how asymmetric mitochondrial substitution gradients evolve would contribute key insights into how this gradient evolution may mislead evolutionary inferences, and how it may also be incorporated into new evolutionary models. Most snake mitochondrial genomes have an additional interesting feature, 2 nearly identical control regions, which vary among different species in the extent that they are used as origins of replication. Given the expanded sampling of complete snake genomes currently available, together with 2 additional snakes sequenced in this study, we reexamined gradient strength and CR usage in alethinophidian snakes as well as several lizards that possess dual CRs. Our results suggest that nucleotide substitution gradients (and corresponding nucleotide bias) and CR usage is highly labile over the ∼200 m.y. of squamate evolution, and demonstrates greater overall variability than previously shown in primates. The evidence for the existence of such gradients, and their ability to evolve rapidly and converge among unrelated species suggests that gradient dynamics could easily mislead phylogenetic and molecular evolutionary inferences, and argues strongly that these dynamics should be incorporated into phylogenetic models. PMID:20215734

Proteome Adaptation to High Temperatures in the Ectothermic Hydrothermal Vent Pompeii Worm

PubMed Central

Jollivet, Didier; Mary, Jean; Gagnière, Nicolas; Tanguy, Arnaud; Fontanillas, Eric; Boutet, Isabelle; Hourdez, Stéphane; Segurens, Béatrice; Weissenbach, Jean; Poch, Olivier; Lecompte, Odile

2012-01-01

Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular ‘adaptive’ strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using codon-based Maximum likelihood analyses. We then provided a comparative analysis of codon usage and amino-acid replacements from a greater set of orthologous genes between the Pompeii worm and Paralvinella grasslei, one of its closest relatives living in a much cooler habitat. Analyses reveal that both species display the same high GC-biased codon usage and amino-acid patterns favoring both positively-charged residues and protein hydrophobicity. These patterns may be indicative of an ancestral adaptation to the deep sea and/or thermophily. In addition, the Pompeii worm displays a set of amino-acid change patterns that may explain its greater thermotolerance, with a significant increase in Tyr, Lys and Ala against Val, Met and Gly. Present results indicate that, together with a high content in charged residues, greater proportion of smaller aliphatic residues, and especially alanine, may be a different path for metazoans to face relatively ‘high’ temperatures and thus a novelty in thermophilic metazoans. PMID:22348046

Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm.

PubMed

Jollivet, Didier; Mary, Jean; Gagnière, Nicolas; Tanguy, Arnaud; Fontanillas, Eric; Boutet, Isabelle; Hourdez, Stéphane; Segurens, Béatrice; Weissenbach, Jean; Poch, Olivier; Lecompte, Odile

2012-01-01

Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular 'adaptive' strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using codon-based Maximum likelihood analyses. We then provided a comparative analysis of codon usage and amino-acid replacements from a greater set of orthologous genes between the Pompeii worm and Paralvinella grasslei, one of its closest relatives living in a much cooler habitat. Analyses reveal that both species display the same high GC-biased codon usage and amino-acid patterns favoring both positively-charged residues and protein hydrophobicity. These patterns may be indicative of an ancestral adaptation to the deep sea and/or thermophily. In addition, the Pompeii worm displays a set of amino-acid change patterns that may explain its greater thermotolerance, with a significant increase in Tyr, Lys and Ala against Val, Met and Gly. Present results indicate that, together with a high content in charged residues, greater proportion of smaller aliphatic residues, and especially alanine, may be a different path for metazoans to face relatively 'high' temperatures and thus a novelty in thermophilic metazoans.

On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli

PubMed Central

Supek, Fran; Šmuc, Tomislav

2010-01-01

A recent investigation concluded that codon bias did not affect expression of green fluorescent protein (GFP) variants in Escherichia coli, while stability of an mRNA secondary structure near the 5′ end played a dominant role. We demonstrate that combining the two variables using regression trees or support vector regression yields a biologically plausible model with better support in the GFP data set and in other experimental data: codon usage is relevant for protein levels if the 5′ mRNA structures are not strong. Natural E. coli genes had weaker 5′ mRNA structures than the examined set of GFP variants and did not exhibit a correlation between the folding free energy of 5′ mRNA structures and protein expression. PMID:20421604

TIGER CUBS Act

THOMAS, 113th Congress

Rep. Larsen, Rick [D-WA-2

2013-08-01

House - 08/01/2013 Referred to the Committee on Appropriations, and in addition to the Committee on the Budget, for a period to be subsequently determined by the Speaker, in each case for consideration of such provisions as fall within the jurisdiction of the committee concerned. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Galaxy of Images

Science.gov Websites

This site has moved! Please go to our new Image Gallery site! dot header Basic Image Search Options dot header Search Tips Enter a keyword term below: Submit Use this search to find ANY words you Irish Lion Cubs Taxonomic (Scientific) Keyword Search: Submit Many of the images in the Galaxy of Images

Determination of Coreceptor Usage of Human Immunodeficiency Virus Type 1 from Patient Plasma Samples by Using a Recombinant Phenotypic Assay

PubMed Central

Trouplin, Virginie; Salvatori, Francesca; Cappello, Fanny; Obry, Veronique; Brelot, Anne; Heveker, Nikolaus; Alizon, Marc; Scarlatti, Gabriella; Clavel, François; Mammano, Fabrizio

2001-01-01

We developed a recombinant virus technique to determine the coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from plasma samples, the source expected to represent the most actively replicating virus population in infected subjects. This method is not subject to selective bias associated with virus isolation in culture, a step required for conventional tropism determination procedures. The addition of a simple subcloning step allowed semiquantitative evaluation of virus populations with a different coreceptor (CCR5 or CXCR4) usage specificity present in each plasma sample. This procedure detected mixtures of CCR5- and CXCR4-exclusive virus populations as well as dualtropic viral variants, in variable proportions. Sequence analysis of dualtropic clones indicated that changes in the V3 loop are necessary for the use of CXCR4 as a coreceptor, but the overall context of the V1-V3 region is important to preserve the capacity to use CCR5. This convenient technique can greatly assist the study of virus evolution and compartmentalization in infected individuals. PMID:11119595

Canine parvovirus type 2 (CPV-2) and Feline panleukopenia virus (FPV) codon bias analysis reveals a progressive adaptation to the new niche after the host jump.

PubMed

Franzo, Giovanni; Tucciarone, Claudia Maria; Cecchinato, Mattia; Drigo, Michele

2017-09-01

Based on virus dependence from host cell machinery, their codon usage is expected to show a strong relation with the host one. Even if this association has been stated, especially for bacteria viruses, the linkage is considered to be less consistent for more complex organisms and a codon bias adaptation after host jump has never been proven. Canine parvovirus type 2 (CPV-2) was selected as a model because it represents a well characterized case of host jump, originating from Feline panleukopenia virus (FPV). The current study demonstrates that the adaptation to specific tissue and host codon bias affected CPV-2 evolution. Remarkably, FPV and CPV-2 showed a higher closeness toward the codon bias of the tissues they display the higher tropism for. Moreover, after the host jump, a clear and significant trend was evidenced toward a reduction in the distance between CPV-2 and the dog codon bias over time. This evidence was not confirmed for FPV, suggesting that an equilibrium has been reached during the prolonged virus-host co-evolution. Additionally, the presence of an intermediate pattern displayed by some strains infecting wild species suggests that these could have facilitated the host switch also by acting on codon bias. Copyright © 2017 Elsevier Inc. All rights reserved.

Training Cubs for the Celtic Tiger: The Volume Production of Technical Graduates in the Irish Educational System

ERIC Educational Resources Information Center

Wickham, James; Boucher, Gerard W.

2004-01-01

This article examines the claim that the Irish educational system was one cause of Ireland's rapid economic growth in the 1990s. For decades Irish economic policy has assumed that economic growth depended on foreign direct investment (FDI). During the 1990s, Irish exports largely comprised high-technology manufacturing products; foreign-owned…

The Impact of Assistive Technology on Curriculum Accommodation for a Braille-Reading Student

ERIC Educational Resources Information Center

Farnsworth, Charles R.; Luckner, John L.

2008-01-01

Over 5 months, the authors evaluated the efficacy of electronic assistive technology (the BrailleNote mPower BT-32 notetaker and Tiger Cub Jr. embosser) and associated software components in creating curriculum materials for a middle school Braille-reading student. The authors collected data at the beginning and end of the study from parents,…

The Inside Story [Learning Packages for Exploratory Career Education--7th and 8th Grades: Teacher and Student Editions.

ERIC Educational Resources Information Center

Kemp, Louie E., Comp.

The four learning packages for exploratory career education are designed for use at the seventh and eighth grade levels. Each unit includes coordinated teacher and student editions. The units are: Culinary Cubs, focusing on occupations in the areas of food management, production, and services, with special reference to dietitians; Mini Nursery,…

Characterization of Uterine Derived Growth Inhibitor (UDGI): A Novel Growth Inhibitor of Estrogen Receptor Negative Breast Cancer Cells

DTIC Science & Technology

2000-06-01

1988. 23. Rawlings, N. D. and Barrett, A. J. Families of serine peptidases . Methods Enzymol., 244: 19-61, 1994. 24. Bork, P. and Beckmann, G. The CUB...suppression of IGF-1 gene expression and serum level by a somatostatin analogue. Biochem. Biophys. Res. Commun. 203:254-259 38. Huynh, H., Tetenes, E

Writing toward Community Engagement in Honors

ERIC Educational Resources Information Center

Camp, Heather C.

2015-01-01

On a late Sunday afternoon in 1934, a park superintendent entered the cage of two black bears that he tended at the park's zoo. His intent was to retrieve a purse dropped by a zoo visitor. The superintendent knew the bears well, having acquired them as cubs and raised them, and he didn't expect any trouble. But trouble was imminent. "ENTERED…

Reduced body size and cub recruitment in polar bears associated with sea ice decline.

PubMed

Rode, Karyn D; Amstrup, Steven C; Regehr, Eric V

2010-04-01

Rates of reproduction and survival are dependent upon adequate body size and condition of individuals. Declines in size and condition have provided early indicators of population decline in polar bears (Ursus maritimus) near the southern extreme of their range. We tested whether patterns in body size, condition, and cub recruitment of polar bears in the southern Beaufort Sea of Alaska were related to the availability of preferred sea ice habitats and whether these measures and habitat availability exhibited trends over time, between 1982 and 2006. The mean skull size and body length of all polar bears over three years of age declined over time, corresponding with long-term declines in the spatial and temporal availability of sea ice habitat. Body size of young, growing bears declined over time and was smaller after years when sea ice availability was reduced. Reduced litter mass and numbers of yearlings per female following years with lower availability of optimal sea ice habitat, suggest reduced reproductive output and juvenile survival. These results, based on analysis of a long-term data set, suggest that declining sea ice is associated with nutritional limitations that reduced body size and reproduction in this population.

Robot initiative in a team learning task increases the rhythm of interaction but not the perceived engagement.

PubMed

Ivaldi, Serena; Anzalone, Salvatore M; Rousseau, Woody; Sigaud, Olivier; Chetouani, Mohamed

2014-01-01

We hypothesize that the initiative of a robot during a collaborative task with a human can influence the pace of interaction, the human response to attention cues, and the perceived engagement. We propose an object learning experiment where the human interacts in a natural way with the humanoid iCub. Through a two-phases scenario, the human teaches the robot about the properties of some objects. We compare the effect of the initiator of the task in the teaching phase (human or robot) on the rhythm of the interaction in the verification phase. We measure the reaction time of the human gaze when responding to attention utterances of the robot. Our experiments show that when the robot is the initiator of the learning task, the pace of interaction is higher and the reaction to attention cues faster. Subjective evaluations suggest that the initiating role of the robot, however, does not affect the perceived engagement. Moreover, subjective and third-person evaluations of the interaction task suggest that the attentive mechanism we implemented in the humanoid robot iCub is able to arouse engagement and make the robot's behavior readable.

Influence of facial feedback during a cooperative human-robot task in schizophrenia.

PubMed

Cohen, Laura; Khoramshahi, Mahdi; Salesse, Robin N; Bortolon, Catherine; Słowiński, Piotr; Zhai, Chao; Tsaneva-Atanasova, Krasimira; Di Bernardo, Mario; Capdevielle, Delphine; Marin, Ludovic; Schmidt, Richard C; Bardy, Benoit G; Billard, Aude; Raffard, Stéphane

2017-11-03

Rapid progress in the area of humanoid robots offers tremendous possibilities for investigating and improving social competences in people with social deficits, but remains yet unexplored in schizophrenia. In this study, we examined the influence of social feedbacks elicited by a humanoid robot on motor coordination during a human-robot interaction. Twenty-two schizophrenia patients and twenty-two matched healthy controls underwent a collaborative motor synchrony task with the iCub humanoid robot. Results revealed that positive social feedback had a facilitatory effect on motor coordination in the control participants compared to non-social positive feedback. This facilitatory effect was not present in schizophrenia patients, whose social-motor coordination was similarly impaired in social and non-social feedback conditions. Furthermore, patients' cognitive flexibility impairment and antipsychotic dosing were negatively correlated with patients' ability to synchronize hand movements with iCub. Overall, our findings reveal that patients have marked difficulties to exploit facial social cues elicited by a humanoid robot to modulate their motor coordination during human-robot interaction, partly accounted for by cognitive deficits and medication. This study opens new perspectives for comprehension of social deficits in this mental disorder.

Reduced body size and cub recruitment in polar bears associated with sea ice decline

USGS Publications Warehouse

Rode, Karyn D.; Amstrup, Steven C.; Regehr, Eric V.

2010-01-01

Rates of reproduction and survival are dependent upon adequate body size and condition of individuals. Declines in size and condition have provided early indicators of population decline in polar bears (Ursus maritimus) near the southern extreme of their range. We tested whether patterns in body size, condition, and cub recruitment of polar bears in the southern Beaufort Sea of Alaska were related to the availability of preferred sea ice habitats and whether these measures and habitat availability exhibited trends over time, between 1982 and 2006. The mean skull size and body length of all polar bears over three years of age declined over time, corresponding with long‐term declines in the spatial and temporal availability of sea ice habitat. Body size of young, growing bears declined over time and was smaller after years when sea ice availability was reduced. Reduced litter mass and numbers of yearlings per female following years with lower availability of optimal sea ice habitat, suggest reduced reproductive output and juvenile survival. These results, based on analysis of a long‐term data set, suggest that declining sea ice is associated with nutritional limitations that reduced body size and reproduction in this population.

Robot initiative in a team learning task increases the rhythm of interaction but not the perceived engagement

PubMed Central

Ivaldi, Serena; Anzalone, Salvatore M.; Rousseau, Woody; Sigaud, Olivier; Chetouani, Mohamed

2014-01-01

We hypothesize that the initiative of a robot during a collaborative task with a human can influence the pace of interaction, the human response to attention cues, and the perceived engagement. We propose an object learning experiment where the human interacts in a natural way with the humanoid iCub. Through a two-phases scenario, the human teaches the robot about the properties of some objects. We compare the effect of the initiator of the task in the teaching phase (human or robot) on the rhythm of the interaction in the verification phase. We measure the reaction time of the human gaze when responding to attention utterances of the robot. Our experiments show that when the robot is the initiator of the learning task, the pace of interaction is higher and the reaction to attention cues faster. Subjective evaluations suggest that the initiating role of the robot, however, does not affect the perceived engagement. Moreover, subjective and third-person evaluations of the interaction task suggest that the attentive mechanism we implemented in the humanoid robot iCub is able to arouse engagement and make the robot's behavior readable. PMID:24596554

Computational Identification Of CDR3 Sequence Archetypes Among Immunoglobulin Sequences in Chronic Lymphocytic Leukemia

PubMed Central

Messmer, Bradley T; Raphael, Benjamin J; Aerni, Sarah J; Widhopf, George F; Rassenti, Laura Z; Gribben, John G; Kay, Neil E; Kipps, Thomas J

2009-01-01

The leukemia cells of unrelated patients with chronic lymphocytic leukemia (CLL) display a restricted repertoire of immunoglobulin (Ig) gene rearrangements with preferential usage of certain Ig gene segments. We developed a computational method to rigorously quantify biases in Ig sequence similarity in large patient databases and to identify groups of patients with unusual levels of sequence similarity. We applied our method to sequences from 1577 CLL patients through the CLL Research Consortium (CRC), and identified 67 similarity groups into which roughly 20% of all patients could be assigned. Immunoglobulin light chain class was highly correlated within all groups and light chain gene usage was similar within sets. Surprisingly, over 40% of the identified groups were composed of somatically mutated genes. This study significantly expands the evidence that antigen selection shapes the Ig repertoire in CLL. PMID:18640719

Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia.

PubMed

Messmer, Bradley T; Raphael, Benjamin J; Aerni, Sarah J; Widhopf, George F; Rassenti, Laura Z; Gribben, John G; Kay, Neil E; Kipps, Thomas J

2009-03-01

The leukemia cells of unrelated patients with chronic lymphocytic leukemia (CLL) display a restricted repertoire of immunoglobulin (Ig) gene rearrangements with preferential usage of certain Ig gene segments. We developed a computational method to rigorously quantify biases in Ig sequence similarity in large patient databases and to identify groups of patients with unusual levels of sequence similarity. We applied our method to sequences from 1577 CLL patients through the CLL Research Consortium (CRC), and identified 67 similarity groups into which roughly 20% of all patients could be assigned. Immunoglobulin light chain class was highly correlated within all groups and light chain gene usage was similar within sets. Surprisingly, over 40% of the identified groups were composed of somatically mutated genes. This study significantly expands the evidence that antigen selection shapes the Ig repertoire in CLL.

[Transformation of Chlamydomonas reinhardtii CW-15 with the hygromycin phosphotransferase gene as a selective marker].

PubMed

Ladygin, V G; Butanaev, A M

2002-09-01

To transform Chlamydomonas reinhardtii Dang. Cells, plasmid pCTVHyg was constructed with the use of the Escherichia coli hygromycin phosphotransferase gene (hpt) controlled by the SV40 early promoter. Cells of the CW-15 mutant strain were transformed by electroporation, with the yield reaching 10(3) hygromycin-resistant (HygR) clones per 10(6) recipient cells. The exogenous DNA integrated in the Ch. reinhardtii nuclear genome showed stable transmission for approximately 350 cell generations, while hygromycin resistance was expressed as an unstable character. Codon usage was compared for the hpt gene and Ch. reinhardtii nuclear genes. The results testified that codon usage bias, which is characteristic of Ch. reinhardtii, is not the major factor affecting foreign gene expression. The advantages of the selective system for studying Ch. reinhardtii transformation with heterologous genes are discussed.

Real-time image annotation by manifold-based biased Fisher discriminant analysis

NASA Astrophysics Data System (ADS)

Ji, Rongrong; Yao, Hongxun; Wang, Jicheng; Sun, Xiaoshuai; Liu, Xianming

2008-01-01

Automatic Linguistic Annotation is a promising solution to bridge the semantic gap in content-based image retrieval. However, two crucial issues are not well addressed in state-of-art annotation algorithms: 1. The Small Sample Size (3S) problem in keyword classifier/model learning; 2. Most of annotation algorithms can not extend to real-time online usage due to their low computational efficiencies. This paper presents a novel Manifold-based Biased Fisher Discriminant Analysis (MBFDA) algorithm to address these two issues by transductive semantic learning and keyword filtering. To address the 3S problem, Co-Training based Manifold learning is adopted for keyword model construction. To achieve real-time annotation, a Bias Fisher Discriminant Analysis (BFDA) based semantic feature reduction algorithm is presented for keyword confidence discrimination and semantic feature reduction. Different from all existing annotation methods, MBFDA views image annotation from a novel Eigen semantic feature (which corresponds to keywords) selection aspect. As demonstrated in experiments, our manifold-based biased Fisher discriminant analysis annotation algorithm outperforms classical and state-of-art annotation methods (1.K-NN Expansion; 2.One-to-All SVM; 3.PWC-SVM) in both computational time and annotation accuracy with a large margin.

Do Reports of Age and Circumstances of First Intercourse Differ in a Birth Cohort When Asked Seventeen Years Apart?

PubMed

Dickson, Nigel P; Righarts, Antoinette; van Roode, Thea; Cameron, Claire; Connor, Jennie

2016-01-01

Conclusions about temporal changes in age and circumstances of first intercourse are generally derived from retrospective reports by people of various ages in cross-sectional studies, with an inherent assumption of no bias stemming from time since the event. We examined this assumption through repeated questions on age and circumstances of first heterosexual intercourse (FHI) at ages 21 and 38 in a birth cohort. Despite considerable movement in individual reports, there was no bias in reported age of FHI. However, a greater proportion of both men and women stated at the later assessment both partners had been equally willing (versus persuading or persuaded). The distribution of current views of the appropriateness of the timing did not differ markedly between assessments, although there were many individual changes. Reports of contraceptive usage were similar at the two assessments for men but differed among women, mainly through more reporting that they could not remember. These findings imply that among cohorts born in the 1970s, there is no bias in reports of age of FHI many years after the event, and views on the appropriateness of timing persist. However, time biases reports in favor of a more mutual willingness.

Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies.

PubMed

Pfeifer, Nico; Walter, Hauke; Lengauer, Thomas

2014-10-01

Recently discovered broadly neutralizing antibodies have revitalized hopes of developing a universal vaccine against HIV-1. Mainly responsible for new infections are variants only using CCR5 for cell entry, whereas CXCR4-using variants can become dominant in later infection stages. We performed a statistical analysis on two different previously published data sets. The first data set was a panel of 199 diverse HIV-1 isolates for which IC50 neutralization titers were determined for the broadly neutralizing antibodies VRC01, VRC-PG04, PG9, and PG16. The second data set contained env sequences of viral variants extracted from HIV-1-infected humanized mice treated with the antibody PGT128 and from untreated control mice. For the panel of 199 diverse HIV-1 isolates, we found a statistically significant association between viral resistance to PG9 and PG16 and CXCR4 coreceptor usage (P = 0.0011 and P = 0.0010, respectively). Our analysis of viral variants from HIV-1-infected humanized mice under treatment with the broadly neutralizing antibody PGT128 indicated that certain antibodies might drive a viral population toward developing CXCR4 coreceptor usage capability (P = 0.0011 for the comparison between PGT128 and control measurement). These analyses highlight the importance of accounting for a possible coreceptor usage bias pertaining to the effectiveness of an HIV vaccine and to passive antibody transfer as therapeutic approach.

Effects of Hand-Rearing on Reproductive Success in Captive Large Cats Panthera tigris altaica, Uncia uncia, Acinonyx jubatus and Neofelis nebulosa.

PubMed

Hampson, Maja Coulthard; Schwitzer, Christoph

2016-01-01

Species Survival Plans and European Endangered Species Programmes have been developed for several species of endangered felids in order to build up captive reserve populations and support their conservation in the wild. The Siberian tiger (Panthera tigris altaica), snow leopard (Uncia uncia), cheetah (Acinonyx jubatus) and clouded leopard (Neofelis nebulosa) are managed in such ex situ conservation programmes. Many zoological institutions hand-rear offspring if rearing by the mother fails. Hand-rearing can cause behavioural problems, resulting in decreased copulation and lower breeding success in some species. In this study, studbook data subsets were examined: from 1901 to 2011; and 2000 to 2011. We analysed records from 4273 Siberian tigers, 2045 snow leopards, 3435 cheetahs, and 804 clouded leopards. We assessed the number of offspring produced, litter size, age at first reproduction, longevity, infant mortality and generational rearing of hand-reared versus parent-reared individuals. Hand-reared Siberian tigers (p<0.01; p = 0.0113), snow leopards (p<0.01), male cheetahs (p<0.01) and female clouded leopards (p<0.01) produced fewer offspring than parent-reared individuals. Hand-reared snow leopard breeding pairs had larger litters than parent-reared pairs (p = 0.0404). Hand-reared snow leopard females reproduced later in life (p<0.01). Hand-reared female Siberian tigers lived shorter lives, while hand-reared cheetahs lived longer (p<0.01; p = 0.0107). Infant mortality was higher in hand-reared snow leopards (p<0.01) and male cheetahs (p = 0.0395) in the 1901-2011 dataset and lower in hand-reared female Siberian tiger and male snow leopard cubs (p = 0.0404; p = 0.0349) in the 2000-2011 dataset. The rearing of the mother and subsequent rearing of offspring showed a significant relationship for all species (p<0.01 for Siberian tiger and snow leopard cubs; p<0.001 for cheetah and snow leopard cubs). Taking into account the limited carrying capacity of zoos, the results of this study highlight that careful consideration should be taken when deciding whether or not to hand-rear individuals that are part of Species Survival Plans and European Endangered Species Programmes.

Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus.

PubMed

Du, Wen-Ge Han; Noodleman, Louis

2013-12-16

Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.

First flight of SMASH, the SwRI Miniature Assembly for Solar Hard X-rays

NASA Astrophysics Data System (ADS)

Caspi, Amir; Laurent, Glenn Thomas; Shoffner, Michael; Higuera Caubilla, David; Meurisse, Jeremie; Smith, Kelly; Shih, Albert Y.; Saint-Hilaire, Pascal; DeForest, Craig; Mansour, Nagi N.; Hathaway, David H.

2016-05-01

The SwRI Miniature Assembly for Solar Hard X-rays (SMASH) was successfully flown from Antarctica in January (19-30) 2016, as a piggy-back instrument on the Gamma-Ray Imager/Polarimeter for Solar flares (GRIPS) high altitude balloon payload. SMASH is a technological demonstration of a new miniaturized hard X-ray (HXR) detector for use on CubeSats and other small spacecraft, including the proposed CubeSat Imaging X-ray Solar Spectrometer (CubIXSS).HXRs are the observational signatures of energetic processes on the Sun, including plasma heating and particle acceleration. One of the goals of CubIXSS will be to address the question of how plasma is heated during solar flares, including the relationship between thermal plasma and non-thermal particles. SMASH demonstrated the space-borne application of the commercial off-the-shelf Amptek X123-CdTe, a miniature cadmium telluride photon-counting HXR spectrometer. The CdTe detector has a physical area of 25 mm^2 and 1 mm fully-depleted thickness, with a ~100 micron Be window; with on-board thermoelectric cooling and pulse pile-up rejection, it is sensitive to solar photons from ~5 to ~100 keV with ~0.5-1.0 keV FWHM resolution. Photons are accumulated into histogram spectra with customizable energy binning and integration time. With modest resource requirements (~1/8 U, ~200 g, ~2.5 W) and low cost (~$10K), the X123-CdTe is an attractive solution for HXR measurements from budget- and resource-limited platforms such as CubeSats. SMASH flew two identical X123-CdTe detectors for redundancy and increased collecting area; the supporting electronics (power, CPU) were largely build-to-print using the Miniature X-ray Solar Spectrometer (MinXSS) CubeSat design.We review the SMASH mission, design, and detector performance during the 12-day Antarctic flight. We present current progress on our data analysis of observed solar flares, and discuss future applications of the space-qualified X123-CdTe detector, including the CubIXSS mission concept that incorporates two such detectors.

Analysis of the structural organization and thermal stability of two spermadhesins. Calorimetric, circular dichroic and Fourier-transform infrared spectroscopic studies.

PubMed

Menéndez, M; Gasset, M; Laynez, J; López-Zumel, C; Usobiaga, P; Töpfer-Petersen, E; Calvete, J J

1995-12-15

The CUB domain is a widespread 110-amino-acid module found in functionally diverse, often developmentally regulated proteins, for which an antiparallel beta-barrel topology similar to that in immunoglobulin V domains has been predicted. Spermadhesins have been proposed as a subgroup of this protein family built up by a single CUB domain architecture. To test the proposed structural model, we have analyzed the structural organization of two members of the spermadhesin protein family, porcine seminal plasma proteins I/II (PSP-I/PSP-II) heterodimer and bovine acidic seminal fluid protein (aSFP) homodimer, using differential scanning calorimetry, far-ultraviolet circular dichroism and Fourier-transform infrared spectroscopy. Thermal unfolding of PSP-I/PSP-II and aSFP were irreversible and followed a one-step process with transition temperatures (Tm) of 60.5 degrees C and 78.6 degrees C, respectively. The calorimetric enthalpy changes (delta Hcat) of thermal denaturation were 439 kJ/mol for PSP-I/PSP-II and 660 kJ/mol for aSFP dimer. Analysis of the calorimetric curves of PSP-I/PSP-II showed that the entire dimer constituted the cooperative unfolding unit. Fourier-transform infrared spectroscopy and deconvolution of circular dichroic spectra using a convex constraint analysis indicated that beta-structure and turns are the major structural element of both PSP-I/PSP-II (53% of beta-sheet, 21% of turns) and aSFP (44% of beta-sheet, 36% of turns), and that the porcine and the bovine proteins contain little, if any, alpha-helical structure. Taken together, our results indicate that the porcine and the bovine spermadhesin molecules are probably all-beta-structure proteins, and would support a beta-barrel topology like that predicted for the CUB domain. Other beta-structure folds, such as the Greek-key pattern characteristic of many carbohydrate-binding protein domains cannot be eliminated. Finally, the same combination of biophysical techniques was used to characterize the residual secondary structure of thermally denatured forms of PSP-I/PSP-II and aSFP, and to emphasize the aggregation tendency of these forms.

Flexibility in the duration of parental care: Female leopards prioritise cub survival over reproductive output.

PubMed

Balme, Guy A; Robinson, Hugh S; Pitman, Ross T; Hunter, Luke T B

2017-09-01

Deciding when to terminate care of offspring is a key consideration for parents. Prolonging care may increase fitness of current offspring, but it can also reduce opportunities for future reproduction. Despite its evolutionary importance, few studies have explored the optimal duration of parental care, particularly among large carnivores. We used a 40-year dataset to assess the trade-offs associated with the length of maternal care in leopards in the Sabi Sand Game Reserve, South Africa. We compared the costs imposed by care on the survival and residual reproductive value of leopard mothers against the benefits derived from maternal care in terms of increased offspring survival, recruitment and reproduction. We also examined the demographic and ecological factors affecting the duration of care in the light of five explanatory hypotheses: litter size, sex allocation, resource limitation, timing of independence and terminal investment. Duration of care exhibited by female leopards varied markedly, from 9 to 35 months. Mothers did not appear to suffer any short- or long-term survival costs from caring for cubs, but extending care reduced the number of litters that mothers could produce during their lifetimes. Interestingly, the duration of care did not appear to affect the post-independence survival or reproductive success of offspring (although it may have indirectly affected offspring survival by influencing dispersal distance). However, results from generalised linear mixed models showed that mothers prolonged care during periods of prey scarcity, supporting the resource limitation hypothesis. Female leopards also cared for sons longer than daughters, in line with the sex-allocation hypothesis. Cub survival is an important determinant of the lifetime reproductive success in leopards. By buffering offspring against environmental perturbation without jeopardising their own survivorship, female leopards apparently "hedge their bets" with current offspring rather than gamble on future offspring which have a small probability of surviving. In many species, parents put their own needs before that of their offspring. Leopard mothers appear sensitive to their offspring's demands, and adjust levels of care accordingly. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Opposite GC skews at the 5' and 3' ends of genes in unicellular fungi

PubMed Central

2011-01-01

Background GC-skews have previously been linked to transcription in some eukaryotes. They have been associated with transcription start sites, with the coding strand G-biased in mammals and C-biased in fungi and invertebrates. Results We show a consistent and highly significant pattern of GC-skew within genes of almost all unicellular fungi. The pattern of GC-skew is asymmetrical: the coding strand of genes is typically C-biased at the 5' ends but G-biased at the 3' ends, with intermediate skews at the middle of genes. Thus, the initiation, elongation, and termination phases of transcription are associated with different skews. This pattern influences the encoded proteins by generating differential usage of amino acids at the 5' and 3' ends of genes. These biases also affect fourfold-degenerate positions and extend into promoters and 3' UTRs, indicating that skews cannot be accounted by selection for protein function or translation. Conclusions We propose two explanations, the mutational pressure hypothesis, and the adaptive hypothesis. The mutational pressure hypothesis is that different co-factors bind to RNA pol II at different phases of transcription, producing different mutational regimes. The adaptive hypothesis is that cytidine triphosphate deficiency may lead to C-avoidance at the 3' ends of transcripts to control the flow of RNA pol II molecules and reduce their frequency of collisions. PMID:22208287

Body Bias usage in UTBB FDSOI designs: A parametric exploration approach

NASA Astrophysics Data System (ADS)

Puschini, Diego; Rodas, Jorge; Beigne, Edith; Altieri, Mauricio; Lesecq, Suzanne

2016-03-01

Some years ago, UTBB FDSOI has appeared in the horizon of low-power circuit designers. With the 14 nm and 10 nm nodes in the road-map, the industrialized 28 nm platform promises highly efficient designs with Ultra-Wide Voltage Range (UWVR) thanks to extended Body Bias properties. From the power management perspective, this new opportunity is considered as a new degree of freedom in addition to the classic Dynamic Voltage Scaling (DVS), increasing the complexity of the power optimization problem at design time. However, so far no formal or empiric tool allows to early evaluate the real need for a Dynamic Body Bias (DBB) mechanism on future designs. This paper presents a parametric exploration approach that analyzes the benefits of using Body Bias in 28 nm UTBB FDSOI circuits. The exploration is based on electrical simulations of a ring-oscillator structure. These experiences show that a Body Bias strategy is not always required but, they underline the large power reduction that can be achieved when mandatory. Results are summarized in order to help designers to analyze how to choose the best dynamic power management strategy for a given set of operating conditions in terms of temperature, circuit activity and process choice. This exploration contributes to the identification of conditions that make DBB more efficient than DVS, and vice versa, and when both methods are mandatory to optimize power consumption.

[Use of the hygromycin phosphotransferase gene as the dominant selective marker for Chlamydomonas reinhardtii transformation].

PubMed

Butanaev, A M

1994-01-01

The hygromycin phosphotransferase gene (hpt) from E. coli under the control of the SV40 early promoter was used as a dominant selectable marker for transformation of Chlamydomonas reinhardtii. Cells were transformed by electroporation (pulse length, 2 ms, field strength, 1 kV/cm). The culture growth phase was a crucial parameter for transformation (optimal density approximately 10(6) cells/ml). It was possible to obtain approximately 10(3) Hyg-resistant colonies under these conditions. Foreign DNA integrated into the Chlamydomonas genome was maintained for at least 8 months but the Hyg-resistant phenotype of the transformed clones was unstable. The frequency of codon usage in the hpt gene was compared with the one in Chlamydomonas nuclear genes. It is supposed that highly biased codon usage in Chlamydomonas does not preclude expression. Advantages of this selection system for studying Chlamydomonas transformation by heterologous genes are discussed.

An Empirical Development of Parallelization Guidelines for Time-Driven Simulation

DTIC Science & Technology

1989-12-01

wives, who though not Cub fans, put on a good show during our trip, to waich some games . I would also like to recognize the help of my professors at...program parallelization. in this research effort a Ballistic Missile Defense (BMD) time driven simulation program, developed by DESE Research and...continuously, or continuously with discrete changes superimposed. The distinguishing feature of these simulations is the interaction between discretely

Six Years in the Life of a Mother Bear - The Longest Continuous Heart Rate Recordings from a Free-Ranging Mammal

NASA Astrophysics Data System (ADS)

Laske, Timothy G.; Iaizzo, Paul A.; Garshelis, David L.

2017-01-01

Physiological monitoring of free-ranging wild animals is providing new insights into their adaptations to a changing environment. American black bears (Ursus americanus) are highly adaptable mammals, spending up to half the year hibernating, and the remainder of the year attempting to gain weight on a landscape with foods that vary seasonally and year to year. We recorded heart rate (HR) and corresponding activity of an adult female black bear over the course of six years, using an implanted monitor. Despite yearly differences in food, and an every-other year reproductive cycle, this bear exhibited remarkable consistency in HR and activity. HR increased for 12 weeks in spring, from minimal hibernation levels (mean 20-25 beats/minute [bpm]; min 10 bpm) to summer active levels (July daytime: mean 95 bpm). Timing was delayed following one cold winter. In August the bear switched from primarily diurnal to nocturnal, coincident with the availability of baits set by legal hunters. Activity in autumn was higher when the bear was with cubs. Birthing of cubs in January was identified by a transient increase in HR and activity. Long-term physiological and behavioral monitoring is valuable for understanding adaptations of free-ranging animals to climate change, food availability, and human-related stressors.

Cloning and sequence analysis of Bufo arenarum oviductin cDNA and detection of its orthologous gene expression in the mouse female reproductive tract.

PubMed

Barrera, Daniel; Valdecantos, Pablo A; García, E Vanesa; Miceli, Dora C

2012-02-01

The glycoprotein envelope surrounding the Bufo arenarum egg exists in different functional forms. Conversion between types involves proteolysis of specific envelope glycoproteins. When the egg is released from the ovary, the envelope cannot be penetrated by sperm. Conversion to a penetrable state occurs during passage through the pars recta portion of the oviduct, where oviductin, a serine protease with trypsin-like substrate specificity, hydrolyzes two kinds of envelope glycoproteins: gp84 and gp55. The nucleotide sequence of a 3203 bp B. arenarum oviductin cDNA was obtained. Deduced amino acid sequence showed a complete open reading frame encoding 980 amino acids. B. arenarum oviductin is a multi-domain protein with a protease domain at the N-terminal region followed by two CUB domains and toward the C-terminal region another protease domain, which lacked an active histidine site, and one CUB domain. Expression of ovochymase 2, the mammalian orthologous of amphibian oviductin, was assayed in mouse female reproductive tract. Ovochymase 2 mRNA was unnoticeable in the mouse oviduct but expression was remarkable in the uterus. Phylogenetic relationship between oviductin and ovochymase 2 opens the possibility to understand the role of this enzyme in mammalian reproduction.

Six Years in the Life of a Mother Bear - The Longest Continuous Heart Rate Recordings from a Free-Ranging Mammal.

PubMed

Laske, Timothy G; Iaizzo, Paul A; Garshelis, David L

2017-01-17

Physiological monitoring of free-ranging wild animals is providing new insights into their adaptations to a changing environment. American black bears (Ursus americanus) are highly adaptable mammals, spending up to half the year hibernating, and the remainder of the year attempting to gain weight on a landscape with foods that vary seasonally and year to year. We recorded heart rate (HR) and corresponding activity of an adult female black bear over the course of six years, using an implanted monitor. Despite yearly differences in food, and an every-other year reproductive cycle, this bear exhibited remarkable consistency in HR and activity. HR increased for 12 weeks in spring, from minimal hibernation levels (mean 20-25 beats/minute [bpm]; min 10 bpm) to summer active levels (July daytime: mean 95 bpm). Timing was delayed following one cold winter. In August the bear switched from primarily diurnal to nocturnal, coincident with the availability of baits set by legal hunters. Activity in autumn was higher when the bear was with cubs. Birthing of cubs in January was identified by a transient increase in HR and activity. Long-term physiological and behavioral monitoring is valuable for understanding adaptations of free-ranging animals to climate change, food availability, and human-related stressors.

Selection of den sites by black bears in the southern Appalachians

USGS Publications Warehouse

Reynolds-Hogland, M. J.; Mitchell, M.S.; Powell, R.A.; Brown, D.C.

2007-01-01

We evaluated selection of den sites by American black bears (Ursus americanus) in the Pisgah Bear Sanctuary, western North Carolina, by comparing characteristics of dens at 53 den sites with availability of habitat characteristics in annual home ranges of bears and in the study area. We also tested whether den-site selection differed by sex, age, and reproductive status of bears. In addition, we evaluated whether the den component of an existing habitat model for black bears predicted where bears would select den sites. We found bears selected den sites far from gravel roads, on steep slopes, and at high elevations relative to what was available in both annual home ranges and in the study area. Den-site selection did not differ by sex or age, but it differed by reproductive status. Adult females with cubs preferred to den in areas that were relatively far from gravel roads, but adult females without cubs did not. The habitat model overestimated the value of areas near gravel roads, underestimated the value of moderately steep areas, and did not include elevation as a predictor variable. Our results highlight the importance of evaluating den selection in terms of both use and availability of den characteristics. ?? 2007 American Society of Mammalogists.

Performance comparison of independent component analysis algorithms for fetal cardiac signal reconstruction: a study on synthetic fMCG data

NASA Astrophysics Data System (ADS)

Mantini, D.; Hild, K. E., II; Alleva, G.; Comani, S.

2006-02-01

Independent component analysis (ICA) algorithms have been successfully used for signal extraction tasks in the field of biomedical signal processing. We studied the performances of six algorithms (FastICA, CubICA, JADE, Infomax, TDSEP and MRMI-SIG) for fetal magnetocardiography (fMCG). Synthetic datasets were used to check the quality of the separated components against the original traces. Real fMCG recordings were simulated with linear combinations of typical fMCG source signals: maternal and fetal cardiac activity, ambient noise, maternal respiration, sensor spikes and thermal noise. Clusters of different dimensions (19, 36 and 55 sensors) were prepared to represent different MCG systems. Two types of signal-to-interference ratios (SIR) were measured. The first involves averaging over all estimated components and the second is based solely on the fetal trace. The computation time to reach a minimum of 20 dB SIR was measured for all six algorithms. No significant dependency on gestational age or cluster dimension was observed. Infomax performed poorly when a sub-Gaussian source was included; TDSEP and MRMI-SIG were sensitive to additive noise, whereas FastICA, CubICA and JADE showed the best performances. Of all six methods considered, FastICA had the best overall performance in terms of both separation quality and computation times.

The impact of biases in mobile phone ownership on estimates of human mobility

PubMed Central

Wesolowski, Amy; Eagle, Nathan; Noor, Abdisalan M.; Snow, Robert W.; Buckee, Caroline O.

2013-01-01

Mobile phone data are increasingly being used to quantify the movements of human populations for a wide range of social, scientific and public health research. However, making population-level inferences using these data is complicated by differential ownership of phones among different demographic groups that may exhibit variable mobility. Here, we quantify the effects of ownership bias on mobility estimates by coupling two data sources from the same country during the same time frame. We analyse mobility patterns from one of the largest mobile phone datasets studied, representing the daily movements of nearly 15 million individuals in Kenya over the course of a year. We couple this analysis with the results from a survey of socioeconomic status, mobile phone ownership and usage patterns across the country, providing regional estimates of population distributions of income, reported airtime expenditure and actual airtime expenditure across the country. We match the two data sources and show that mobility estimates are surprisingly robust to the substantial biases in phone ownership across different geographical and socioeconomic groups. PMID:23389897

The impact of biases in mobile phone ownership on estimates of human mobility.

PubMed

Wesolowski, Amy; Eagle, Nathan; Noor, Abdisalan M; Snow, Robert W; Buckee, Caroline O

2013-04-06

Mobile phone data are increasingly being used to quantify the movements of human populations for a wide range of social, scientific and public health research. However, making population-level inferences using these data is complicated by differential ownership of phones among different demographic groups that may exhibit variable mobility. Here, we quantify the effects of ownership bias on mobility estimates by coupling two data sources from the same country during the same time frame. We analyse mobility patterns from one of the largest mobile phone datasets studied, representing the daily movements of nearly 15 million individuals in Kenya over the course of a year. We couple this analysis with the results from a survey of socioeconomic status, mobile phone ownership and usage patterns across the country, providing regional estimates of population distributions of income, reported airtime expenditure and actual airtime expenditure across the country. We match the two data sources and show that mobility estimates are surprisingly robust to the substantial biases in phone ownership across different geographical and socioeconomic groups.

Attrition bias in a U.S. Internet survey of alcohol use among college freshmen.

PubMed

McCoy, Thomas P; Ip, Edward H; Blocker, Jill N; Champion, Heather; Rhodes, Scott D; Wagoner, Kimberly G; Mitra, Ananda; Wolfson, Mark

2009-07-01

Attrition bias is an important issue in survey research on alcohol, tobacco, and other drug use. The issue is even more salient for Internet studies, because these studies often have higher rates of attrition than face-to-face or telephone surveys, and there is limited research examining the issue in the field of drug usage, specifically for college underclassmen. This study assessed whether measures of high-risk drinking and alcohol-related consequences were related to attrition groups ("stayers" or "leavers") in a cohort of college freshmen. Data were collected in 2003 and 2004 from 2,144 first-year college students at 10 universities in the southeastern United States. Demographics, indicators of high-risk drinking, and alcohol-related consequences were compared between cohort stayers and leavers in statistical analyses using two methods. Analyses indicated that cohort leavers reported significantly higher levels of high-risk drinking (past-30-day heavy episodic drinking, weekly drunkenness) and past-30-day smoking but not significantly increased alcohol-related consequences. The directionality of bias was modestly consistent across outcomes and comparison methods. The current study's findings suggest that intervention efforts to reduce smoking or high-risk drinking need to consider attrition bias during study follow-up or account for it in analyses.

Attrition Bias in a U.S. Internet Survey of Alcohol Use Among College Freshmen*

PubMed Central

McCoy, Thomas P.; Ip, Edward H.; Blocker, Jill N.; Champion, Heather; Rhodes, Scott D.; Wagoner, Kimberly G.; Mitra, Ananda; Wolfson, Mark

2009-01-01

Objective: Attrition bias is an important issue in survey research on alcohol, tobacco, and other drug use. The issue is even more salient for Internet studies, because these studies often have higher rates of attrition than face-to-face or telephone surveys, and there is limited research examining the issue in the field of drug usage, specifically for college underclassmen. This study assessed whether measures of high-risk drinking and alcohol-related consequences were related to attrition groups (“stayers” or “leavers”) in a cohort of college freshmen. Method: Data were collected in 2003 and 2004 from 2,144 first-year college students at 10 universities in the southeastern United States. Demographics, indicators of high-risk drinking, and alcohol-related consequences were compared between cohort stayers and leavers in statistical analyses using two methods. Results: Analyses indicated that cohort leavers reported significantly higher levels of high-risk drinking (past-30-day heavy episodic drinking, weekly drunkenness) and past-30-day smoking but not significantly increased alcohol-related consequences. The directionality of bias was modestly consistent across outcomes and comparison methods. Conclusions: The current study's findings suggest that intervention efforts to reduce smoking or high-risk drinking need to consider attrition bias during study follow-up or account for it in analyses. PMID:19515302

Role of Ocean Initial Conditions to Diminish Dry Bias in the Seasonal Prediction of Indian Summer Monsoon Rainfall: A Case Study Using Climate Forecast System

NASA Astrophysics Data System (ADS)

Koul, Vimal; Parekh, Anant; Srinivas, G.; Kakatkar, Rashmi; Chowdary, Jasti S.; Gnanaseelan, C.

2018-03-01

Coupled models tend to underestimate Indian summer monsoon (ISM) rainfall over most of the Indian subcontinent. Present study demonstrates that a part of dry bias is arising from the discrepancies in Oceanic Initial Conditions (OICs). Two hindcast experiments are carried out using Climate Forecast System (CFSv2) for summer monsoons of 2012-2014 in which two different OICs are utilized. With respect to first experiment (CTRL), second experiment (AcSAL) differs by two aspects: usage of high-resolution atmospheric forcing and assimilation of only ARGO observed temperature and salinity profiles for OICs. Assessment of OICs indicates that the quality of OICs is enhanced due to assimilation of actual salinity profiles. Analysis reveals that AcSAL experiment showed 10% reduction in the dry bias over the Indian land region during the ISM compared to CTRL. This improvement is consistently apparent in each month and is highest for June. The better representation of upper ocean thermal structure of tropical oceans at initial stage supports realistic upper ocean stability and mixing. Which in fact reduced the dominant cold bias over the ocean, feedback to air-sea interactions and land sea thermal contrast resulting better representation of monsoon circulation and moisture transport. This reduced bias of tropospheric moisture and temperature over the Indian land mass and also produced better tropospheric temperature gradient over land as well as ocean. These feedback processes reduced the dry bias in the ISM rainfall. Study concludes that initializing the coupled models with realistic OICs can reduce the underestimation of ISM rainfall prediction.

Modeling the CO2-effects of forest management and wood usage on a regional basis.

PubMed

Knauf, Marcus; Köhl, Michael; Mues, Volker; Olschofsky, Konstantin; Frühwald, Arno

2015-12-01

At the 15 th Conference of Parties of the UN Framework Convention on Climate Change, Copenhagen, 2009, harvested wood products were identified as an additional carbon pool. This modification eliminates inconsistencies in greenhouse gas reporting by recognizing the role of the forest and timber sector in the global carbon cycle. Any additional CO 2 -effects related to wood usage are not considered by this modification. This results in a downward bias when the contribution of the forest and timber sector to climate change mitigation is assessed. The following article analyses the overall contribution to climate protection made by the forest management and wood utilization through CO 2 -emissions reduction using an example from the German state of North Rhine-Westphalia. Based on long term study periods (2011 to 2050 and 2100, respectively). Various alternative scenarios for forest management and wood usage are presented. In the mid- to long-term (2050 and 2100, respectively) the net climate protection function of scenarios with varying levels of wood usage is higher than in scenarios without any wood usage. This is not observed for all scenarios on short and mid term evaluations. The advantages of wood usage are evident although the simulations resulted in high values for forest storage in the C pools. Even the carbon sink effect due to temporal accumulation of deadwood during the period from 2011 to 2100 is outbalanced by the potential of wood usage effects. A full assessment of the CO 2 -effects of the forest management requires an assessment of the forest supplemented with an assessment of the effects of wood usage. CO 2 -emission reductions through both fuel and material substitution as well as CO 2 sink in wood products need to be considered. An integrated assessment of the climate protection function based on the analysis of the study's scenarios provides decision parameters for a strategic approach to climate protection with regard to forest management and wood use at regional and national levels. The short-term evaluation of subsystems can be misleading, rendering long-term evaluations (until 2100, or even longer) more effective. This is also consistent with the inherently long-term perspective of forest management decisions and measures.

Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation.

PubMed

Mandlik, Vineetha; Shinde, Sonali; Singh, Shailza

2014-06-21

Selection pressure governs the relative mutability and the conservedness of a protein across the protein family. Biomolecules (DNA, RNA and proteins) continuously evolve under the effect of evolutionary pressure that arises as a consequence of the host parasite interaction. IPCS (Inositol phosphorylceramide synthase), SPL (Sphingosine-1-P lyase) and SPT (Serine palmitoyl transferase) represent three important enzymes involved in the sphingolipid metabolism of Leishmania. These enzymes are responsible for maintaining the viability and infectivity of the parasite and have been classified as druggable targets in the parasite metabolome. The present work relates to the role of selection pressure deciding functional conservedness and divergence of the drug targets. IPCS and SPL protein families appear to diverge from the SPT family. The three protein families were largely under the influence of purifying selection and were moderately conserved baring two residues in the IPCS protein which were under the influence of positive selection. To further explore the selection pressure at the codon level, codon usage bias indices were calculated to analyze genes for their synonymous codon usage pattern. IPCS gene exhibited slightly lower codon bias as compared to SPL and SPT protein families. Evolutionary tracing of the proposed drug targets has been done with a viewpoint that the amino-acids lining the drug binding pocket should have a lower evolvability. Sites under positive selection (HIS20 and CYS30 of IPCS) should be avoided during devising strategies for inhibitor design.

Validation of Methods to Assess the Immunoglobulin Gene Repertoire in Tissues Obtained from Mice on the International Space Station.

PubMed

Rettig, Trisha A; Ward, Claire; Pecaut, Michael J; Chapes, Stephen K

2017-07-01

Spaceflight is known to affect immune cell populations. In particular, splenic B cell numbers decrease during spaceflight and in ground-based physiological models. Although antibody isotype changes have been assessed during and after space flight, an extensive characterization of the impact of spaceflight on antibody composition has not been conducted in mice. Next Generation Sequencing and bioinformatic tools are now available to assess antibody repertoires. We can now identify immunoglobulin gene- segment usage, junctional regions, and modifications that contribute to specificity and diversity. Due to limitations on the International Space Station, alternate sample collection and storage methods must be employed. Our group compared Illumina MiSeq sequencing data from multiple sample preparation methods in normal C57Bl/6J mice to validate that sample preparation and storage would not bias the outcome of antibody repertoire characterization. In this report, we also compared sequencing techniques and a bioinformatic workflow on the data output when we assessed the IgH and Igκ variable gene usage. This included assessments of our bioinformatic workflow on Illumina HiSeq and MiSeq datasets and is specifically designed to reduce bias, capture the most information from Ig sequences, and produce a data set that provides other data mining options. We validated our workflow by comparing our normal mouse MiSeq data to existing murine antibody repertoire studies validating it for future antibody repertoire studies.

Evolutionary and genetic analysis of the VP2 gene of canine parvovirus.

PubMed

Li, Gairu; Ji, Senlin; Zhai, Xiaofeng; Zhang, Yuxiang; Liu, Jie; Zhu, Mengyan; Zhou, Jiyong; Su, Shuo

2017-07-17

Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar to some RNA viruses. Therefore, it is important to trace the evolution of CPV to monitor the appearance of mutations that might affect vaccine effectiveness. Our analysis shows that the VP2 genes of CPV isolated from 1979 to 2016 are divided into six groups: GI, GII, GIII, GIV, GV, and GVI. Amino acid mutation analysis revealed several undiscovered important mutation sites: F267Y, Y324I, and T440A. Of note, the evolutionary rate of the CPV VP2 gene from Asia and Europe decreased. Codon usage analysis showed that the VP2 gene of CPV exhibits high bias with an ENC ranging from 34.93 to 36.7. Furthermore, we demonstrate that natural selection plays a major role compared to mutation pressure driving CPV evolution. There are few studies on the codon usage of CPV. Here, we comprehensively studied the genetic evolution, codon usage pattern, and evolutionary characterization of the VP2 gene of CPV. The novel findings revealing the evolutionary process of CPV will greatly serve future CPV research.

Effects of Hand-Rearing on Reproductive Success in Captive Large Cats Panthera tigris altaica, Uncia uncia, Acinonyx jubatus and Neofelis nebulosa

PubMed Central

Hampson, Maja Coulthard; Schwitzer, Christoph

2016-01-01

Species Survival Plans and European Endangered Species Programmes have been developed for several species of endangered felids in order to build up captive reserve populations and support their conservation in the wild. The Siberian tiger (Panthera tigris altaica), snow leopard (Uncia uncia), cheetah (Acinonyx jubatus) and clouded leopard (Neofelis nebulosa) are managed in such ex situ conservation programmes. Many zoological institutions hand-rear offspring if rearing by the mother fails. Hand-rearing can cause behavioural problems, resulting in decreased copulation and lower breeding success in some species. In this study, studbook data subsets were examined: from 1901 to 2011; and 2000 to 2011. We analysed records from 4273 Siberian tigers, 2045 snow leopards, 3435 cheetahs, and 804 clouded leopards. We assessed the number of offspring produced, litter size, age at first reproduction, longevity, infant mortality and generational rearing of hand-reared versus parent-reared individuals. Hand-reared Siberian tigers (p<0.01; p = 0.0113), snow leopards (p<0.01), male cheetahs (p<0.01) and female clouded leopards (p<0.01) produced fewer offspring than parent-reared individuals. Hand-reared snow leopard breeding pairs had larger litters than parent-reared pairs (p = 0.0404). Hand-reared snow leopard females reproduced later in life (p<0.01). Hand-reared female Siberian tigers lived shorter lives, while hand-reared cheetahs lived longer (p<0.01; p = 0.0107). Infant mortality was higher in hand-reared snow leopards (p<0.01) and male cheetahs (p = 0.0395) in the 1901–2011 dataset and lower in hand-reared female Siberian tiger and male snow leopard cubs (p = 0.0404; p = 0.0349) in the 2000–2011 dataset. The rearing of the mother and subsequent rearing of offspring showed a significant relationship for all species (p<0.01 for Siberian tiger and snow leopard cubs; p<0.001 for cheetah and snow leopard cubs). Taking into account the limited carrying capacity of zoos, the results of this study highlight that careful consideration should be taken when deciding whether or not to hand-rear individuals that are part of Species Survival Plans and European Endangered Species Programmes. PMID:27214261

Effects of capturing and collaring on polar bears: findings from long-term research on the southern Beaufort Sea population

USGS Publications Warehouse

Rode, Karyn D.; Pagano, Anthony M.; Bromaghin, Jeffrey F.; Atwood, Todd C.; Durner, George M.; Simac, Kristin S.; Amstrup, Steven C.

2014-01-01

Context: The potential for research methods to affect wildlife is an increasing concern among both scientists and the public. This topic has a particular urgency for polar bears because additional research is needed to monitor and understand population responses to rapid loss of sea ice habitat.Aims: This study used data collected from polar bears sampled in the Alaska portion of the southern Beaufort Sea to investigate the potential for capture to adversely affect behaviour and vital rates. We evaluated the extent to which capture, collaring and handling may influence activity and movement days to weeks post-capture, and body mass, body condition, reproduction and survival over 6 months or more.Methods: We compared post-capture activity and movement rates, and relationships between prior capture history and body mass, body condition and reproductive success. We also summarised data on capture-related mortality.Key results: Individual-based estimates of activity and movement rates reached near-normal levels within 2–3 days and fully normal levels within 5 days post-capture. Models of activity and movement rates among all bears had poor fit, but suggested potential for prolonged, lower-level rate reductions. Repeated captures was not related to negative effects on body condition, reproduction or cub growth or survival. Capture-related mortality was substantially reduced after 1986, when immobilisation drugs were changed, with only 3 mortalities in 2517 captures from 1987–2013.Conclusions: Polar bears in the southern Beaufort Sea exhibited the greatest reductions in activity and movement rates 3.5 days post-capture. These shorter-term, post-capture effects do not appear to have translated into any long-term effects on body condition, reproduction, or cub survival. Additionally, collaring had no effect on polar bear recovery rates, body condition, reproduction or cub survival.Implications: This study provides empirical evidence that current capture-based research methods do not have long-term implications, and are not contributing to observed changes in body condition, reproduction or survival in the southern Beaufort Sea. Continued refinement of capture protocols, such as the use of low-impact dart rifles and reversible drug combinations, might improve polar bear response to capture and abate short-term reductions in activity and movement post-capture.

TIGA-CUB - manualised psychoanalytic child psychotherapy versus treatment as usual for children aged 5-11 years with treatment-resistant conduct disorders and their primary carers: study protocol for a randomised controlled feasibility trial.

PubMed

Edginton, Elizabeth; Walwyn, Rebecca; Burton, Kayleigh; Cicero, Robert; Graham, Liz; Reed, Sadie; Tubeuf, Sandy; Twiddy, Maureen; Wright-Hughes, Alex; Ellis, Lynda; Evans, Dot; Hughes, Tom; Midgley, Nick; Wallis, Paul; Cottrell, David

2017-09-15

The National Institute for Health and Care Excellence (NICE) recommends evidence-based parenting programmes as a first-line intervention for conduct disorders (CD) in children aged 5-11 years. As these are not effective in 25-33% of cases, NICE has requested research into second-line interventions. Child and Adolescent Psychotherapists (CAPTs) address highly complex problems where first-line treatments have failed and there have been small-scale studies of Psychoanalytic Child Psychotherapy (PCP) for CD. A feasibility trial is needed to determine whether a confirmatory trial of manualised PCP (mPCP) versus Treatment as Usual (TaU) for CD is practicable or needs refinement. The aim of this paper is to publish the abridged protocol of this feasibility trial. TIGA-CUB (Trial on improving Inter-Generational Attachment for Children Undergoing Behaviour problems) is a two-arm, pragmatic, parallel-group, multicentre, individually randomised (1:1) controlled feasibility trial (target n = 60) with blinded outcome assessment (at 4 and 8 months), which aims to develop an optimum practicable protocol for a confirmatory, pragmatic, randomised controlled trial (RCT) (primary outcome: child's behaviour; secondary outcomes: parental reflective functioning and mental health, child and parent quality of life), comparing mPCP and TaU as second-line treatments for children aged 5-11 years with treatment-resistant CD and inter-generational attachment difficulties, and for their primary carers. Child-primary carer dyads will be recruited following a referral to, or re-referral within, National Health Service (NHS) Child and Adolescent Mental Health Services (CAMHS) after an unsuccessful first-line parenting intervention. PCP will be delivered by qualified CAPTs working in routine NHS clinical practice, using a trial-specific PCP manual (a brief version of established PCP clinical practice). Outcomes are: (1) feasibility of recruitment methods, (2) uptake and follow-up rates, (3) therapeutic delivery, treatment retention and attendance, intervention adherence rates, (4) follow-up data collection, and (5) statistical, health economics, process evaluation, and qualitative outcomes. TIGA-CUB will provide important information on the feasibility and potential challenges of undertaking a confirmatory RCT to evaluate the effectiveness and cost-effectiveness of mPCP. Current Controlled Trials, ID: ISRCTN86725795 . Registered on 31 May 2016.

Electronic and structural properties of B i2S e3:Cu

NASA Astrophysics Data System (ADS)

Sobczak, Kamil; Strak, Pawel; Kempisty, Pawel; Wolos, Agnieszka; Hruban, Andrzej; Materna, Andrzej; Borysiuk, Jolanta

2018-04-01

Electronic and structural properties of B i2S e3 and its extension to copper doped B i2S e3:Cu were studied using combined ab initio simulations and transmission electron microscopy based techniques, including electron energy loss spectroscopy, energy filtered transmission electron microscopy, and energy dispersive x-ray spectroscopy. The stability of the mixed phases was investigated for substitutional and intercalation changes of basic B i2S e3 structure. Four systems were compared: B i2S e3 , structures obtaining by Cu intercalation of the van der Waals gap, by substitution of Bi by Cu in quintuple layers, and C u2Se . The structures were identified and their electronic properties were obtained. Transmission electron microscopy measurements of B i2S e3 and the B i2S e3:Cu system identified the first structure as uniform and the second as composite, consisting of a nonuniform lower-Cu-content matrix and randomly distributed high-Cu-concentration precipitates. Critical comparison of the ab initio and experimental data identified the matrix as having a B i2S e3 dominant part with randomly distributed Cu-intercalated regions having 1Cu-B i2S e3 structure. The precipitates were determined to have 3Cu-B i2S e3 structure.

Environmental variation at the onset of independent foraging affects full-grown body mass in the red fox

PubMed Central

Soulsbury, Carl D; Iossa, Graziella; Baker, Philip J; Harris, Stephen

2008-01-01

The period following the withdrawal of parental care has been highlighted as a key developmental period for juveniles. One reason for this is that juveniles cannot forage as competently as adults, potentially placing them at greater risk from environmentally-induced changes in food availability. However, no study has examined this topic. Using a long-term dataset on red foxes (Vulpes vulpes), we examined (i) dietary changes that occurred in the one-month period following the attainment of nutritional independence, (ii) diet composition in relation to climatic variation, and (iii) the effect of climatic variation on subsequent full-grown mass. Diet at nutritional independence contained increased quantities of easy-to-catch food items (earthworms and insects) when compared with pre-independence. Interannual variation in the volume of rainfall at nutritional independence was positively correlated to the proportion of earthworms in cub diet. Pre-independence cub mass and rainfall immediately following nutritional independence explained a significant proportion of variance in full-grown mass, with environmental variation affecting full-grown mass of the entire cohorts. Thus, weather-mediated availability of easy-to-catch food items at a key developmental stage has lifelong implications for the development of juvenile foxes by affecting full-grown mass, which in turn appears to be an important component of individual reproductive potential. PMID:18628118

Exosomal microRNAs in giant panda (Ailuropoda melanoleuca) breast milk: potential maternal regulators for the development of newborn cubs.

PubMed

Ma, Jideng; Wang, Chengdong; Long, Keren; Zhang, Hemin; Zhang, Jinwei; Jin, Long; Tang, Qianzi; Jiang, Anan; Wang, Xun; Tian, Shilin; Chen, Li; He, Dafang; Li, Desheng; Huang, Shan; Jiang, Zhi; Li, Mingzhou

2017-06-14

The physiological role of miRNAs is widely understood to include fine-tuning the post-transcriptional regulation of a wide array of biological processes. Extensive studies have indicated that exosomal miRNAs in the bodily fluids of various organisms can be transferred between living cells for the delivery of gene silencing signals. Here, we illustrated the expression characteristics of exosomal miRNAs in giant panda breast milk during distinct lactation periods and highlighted the enrichment of immune- and development-related endogenous miRNAs in colostral and mature giant panda milk. These miRNAs are stable, even under certain harsh conditions, via the protection of extracellular vesicles. These findings indicate that breast milk may facilitate the dietary intake of maternal miRNAs by infants for the regulation of postnatal development. We also detected exogenous plant miRNAs from the primary food source of the giant panda (bamboo) in the exosomes of giant panda breast milk that were associated with regulatory roles in basic metabolism and neuron development. This result suggested that dietary plant miRNAs are absorbed by host cells and subsequently secreted into bodily fluids as potential cross-kingdom regulators. In conclusion, exosomal miRNAs in giant panda breast milk may be crucial maternal regulators for the development of intrinsic 'slink' newborn cubs.

Grounding the Meanings in Sensorimotor Behavior using Reinforcement Learning

PubMed Central

Farkaš, Igor; Malík, Tomáš; Rebrová, Kristína

2012-01-01

The recent outburst of interest in cognitive developmental robotics is fueled by the ambition to propose ecologically plausible mechanisms of how, among other things, a learning agent/robot could ground linguistic meanings in its sensorimotor behavior. Along this stream, we propose a model that allows the simulated iCub robot to learn the meanings of actions (point, touch, and push) oriented toward objects in robot’s peripersonal space. In our experiments, the iCub learns to execute motor actions and comment on them. Architecturally, the model is composed of three neural-network-based modules that are trained in different ways. The first module, a two-layer perceptron, is trained by back-propagation to attend to the target position in the visual scene, given the low-level visual information and the feature-based target information. The second module, having the form of an actor-critic architecture, is the most distinguishing part of our model, and is trained by a continuous version of reinforcement learning to execute actions as sequences, based on a linguistic command. The third module, an echo-state network, is trained to provide the linguistic description of the executed actions. The trained model generalizes well in case of novel action-target combinations with randomized initial arm positions. It can also promptly adapt its behavior if the action/target suddenly changes during motor execution. PMID:22393319

IF YOU BUILD IT WILL THEY COME? TEACHERS’ ONLINE USE OF STUDENT PERFORMANCE DATA

PubMed Central

Tyler, John H.

2014-01-01

Testing of students and computer systems to store, manage, analyze, and report the resulting test data have grown hand-in-hand. Extant research on teacher use of electronically stored data are largely qualitative and focused on the conditions necessary (but not sufficient) for effective teacher data use. Absent from the research is objective information on how much and in what ways teachers use computer-based student test data, even when supposed precursors of usage are in place. This paper addresses this knowledge gap by analyzing the online activities of teachers in one mid-size urban district. Utilizing Web logs collected between 2008 and 2010, I find low teacher interaction with Web-based pages that contain student test information that could potentially inform practice. I also find no evidence that teacher usage of Web-based student data are related to student achievement gains, but there is reason to believe these estimates are downwardly biased. PMID:25593564

An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses--Criticality (keff) Predictions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scaglione, John M; Mueller, Don; Wagner, John C

2011-01-01

One of the most significant remaining challenges associated with expanded implementation of burnup credit in the United States is the validation of depletion and criticality calculations used in the safety evaluation - in particular, the availability and use of applicable measured data to support validation, especially for fission products. Applicants and regulatory reviewers have been constrained by both a scarcity of data and a lack of clear technical basis or approach for use of the data. U.S. Nuclear Regulatory Commission (NRC) staff have noted that the rationale for restricting their Interim Staff Guidance on burnup credit (ISG-8) to actinide-only ismore » based largely on the lack of clear, definitive experiments that can be used to estimate the bias and uncertainty for computational analyses associated with using burnup credit. To address the issue of validation, the NRC initiated a project with the Oak Ridge National Laboratory to (1) develop and establish a technically sound validation approach (both depletion and criticality) for commercial spent nuclear fuel (SNF) criticality safety evaluations based on best-available data and methods and (2) apply the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The purpose of this paper is to describe the criticality (k{sub eff}) validation approach, and resulting observations and recommendations. Validation of the isotopic composition (depletion) calculations is addressed in a companion paper at this conference. For criticality validation, the approach is to utilize (1) available laboratory critical experiment (LCE) data from the International Handbook of Evaluated Criticality Safety Benchmark Experiments and the French Haut Taux de Combustion (HTC) program to support validation of the principal actinides and (2) calculated sensitivities, nuclear data uncertainties, and the limited available fission product LCE data to predict and verify individual biases for relevant minor actinides and fission products. This paper (1) provides a detailed description of the approach and its technical bases, (2) describes the application of the approach for representative pressurized water reactor and boiling water reactor safety analysis models to demonstrate its usage and applicability, (3) provides reference bias results based on the prerelease SCALE 6.1 code package and ENDF/B-VII nuclear cross-section data, and (4) provides recommendations for application of the results and methods to other code and data packages.« less

An Amperometric Glucose Sensor Integrated into an Insulin Delivery Cannula: In Vitro and In Vivo Evaluation

PubMed Central

Heinrich, Gabriel; Breen, Matthew; Benware, Sheila; Vollum, Nicole; Morris, Kristin; Knutsen, Chad; Kowalski, Joseph D.; Campbell, Scott; Biehler, Jerry; Vreeke, Mark S.; Vanderwerf, Scott M.; Castle, Jessica R.; Cargill, Robert S.

2017-01-01

Abstract Background: Labeling prohibits delivery of insulin at the site of subcutaneous continuous glucose monitoring (CGM). Integration of the sensing and insulin delivery functions into a single device would likely increase the usage of CGM in persons with type 1 diabetes. Methods: To understand the nature of such interference, we measured glucose at the site of bolus insulin delivery in swine using a flexible electrode strip that was laminated to the outer wall of an insulin delivery cannula. In terms of sensing design, we compared H2O2-measuring sensors biased at 600 mV with redox mediator-type sensors biased at 175 mV. Results: In H2O2-measuring sensors, but not in sensors with redox-mediated chemistry, a spurious rise in current was seen after insulin lis-pro boluses. This prolonged artifact was accompanied by electrode poisoning. In redox-mediated sensors, the patterns of sensor signals acquired during delivery of saline and without any liquid delivery were similar to those acquired during insulin delivery. Conclusion: Considering in vitro and in vivo findings together, it became clear that the mechanism of interference is the oxidation, at high bias potentials, of phenolic preservatives present in insulin formulations. This effect can be avoided by the use of redox mediator chemistry using a low bias potential. PMID:28221814

Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias.

PubMed

Barik, Sailen

2017-12-01

A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes.

Safety and Efficacy of Catheter Direct Thrombolysis in Management of Acute Iliofemoral Deep Vein Thrombosis: A Systematic Review.

PubMed

Elbasty, Ahmed; Metcalf, James

2017-12-01

Catheter direct thrombolysis (CDT) has been shown to be an effective treatment for deep venous thrombosis. The objective of the review is to improve safety and efficacy of the CDT by using ward based protocol, better able to predict complications and treatment outcome through monitoring of haemostatic parameters and clinical observation during thrombolysis procedure. MEDLINE, EMBASE, CENTRAL and Web of Science were searched for all articles on deep venous thrombosis, thrombolysis and correlations of clinical events (bleeding, successful thrombolysis) during thrombolysis with hemostatic parameters to March 2016. The risk of bias in included studies was assessed by Cochrane Collaboration's tool and Cochrane Risk of Bias Assessment Tool: for Non-Randomized Studies of Interventions. Twenty-four studies were included in the review and we found that improving safety and efficacy of CDT by using ward based protocol depending on eight factors; strict patient selection criteria, types of fibrinolytic drugs, mode of fibrinolytic drug injection, biochemical markers monitoring (fibrinogen, D-dimer, activated partial thromboplastin time, plasminogen activator inhibitor-1), timing of intervention, usage of intermittent pneumatic calf, ward monitoring and thrombolysis imaging assessment (intravascular ultrasound). These factors may help to improve safety and efficacy by reducing total thrombolytic drug dosage and at the same time ensure successful lysis. There is a marked lack of randomized controlled trials discussing the safety and efficacy of catheter direct thrombolysis. CDT can be performed safely and efficiently in clinical ward, providing that careful nursing, biochemical monitoring, proper selection and mode of infusion of fibrinolytic drugs, usage of Intermittent pneumatic calf and adequate thrombolysis imaging assessment are ensured.

Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia

PubMed Central

Wu, Jing Qin; Wang, Xi; Beveridge, Natalie J.; Tooney, Paul A.; Scott, Rodney J.; Carr, Vaughan J.; Cairns, Murray J.

2012-01-01

Background While hybridization based analysis of the cortical transcriptome has provided important insight into the neuropathology of schizophrenia, it represents a restricted view of disease-associated gene activity based on predetermined probes. By contrast, sequencing technology can provide un-biased analysis of transcription at nucleotide resolution. Here we use this approach to investigate schizophrenia-associated cortical gene expression. Methodology/Principal Findings The data was generated from 76 bp reads of RNA-Seq, aligned to the reference genome and assembled into transcripts for quantification of exons, splice variants and alternative promoters in postmortem superior temporal gyrus (STG/BA22) from 9 male subjects with schizophrenia and 9 matched non-psychiatric controls. Differentially expressed genes were then subjected to further sequence and functional group analysis. The output, amounting to more than 38 Gb of sequence, revealed significant alteration of gene expression including many previously shown to be associated with schizophrenia. Gene ontology enrichment analysis followed by functional map construction identified three functional clusters highly relevant to schizophrenia including neurotransmission related functions, synaptic vesicle trafficking, and neural development. Significantly, more than 2000 genes displayed schizophrenia-associated alternative promoter usage and more than 1000 genes showed differential splicing (FDR<0.05). Both types of transcriptional isoforms were exemplified by reads aligned to the neurodevelopmentally significant doublecortin-like kinase 1 (DCLK1) gene. Conclusions This study provided the first deep and un-biased analysis of schizophrenia-associated transcriptional diversity within the STG, and revealed variants with important implications for the complex pathophysiology of schizophrenia. PMID:22558445

Equilibria of a Two-Person Non-Zerosum Noisy Game of Timing,

DTIC Science & Technology

1981-01-01

AD-A097 158 YALE UNIV NEW HAVEN CT COWLES FOUNDATION FOR RESEARC -ETC F/B 12/1 EQUILIBRIA OF A TWO-PERSON ON-ZEROSUN OISY GAME OF TIMING, CUb .JAN al...pubUo zeleale Distribution Unlimited. 1. Introduction Two toothpaste manufacturers are competing for a larger share of the dentifrice market . Each is...successfully capturing a share of the market , if its product hits the stores first. (This is assuming that the toothpaste is being technologically

The Measurement of International Military Commitments for Crisis Early Warning

DTIC Science & Technology

1976-09-01

34generalized cultural expectations", to use Becker’s phraseology. Foreign policy and strategic analysts are familiar with such expectations (Harkabi, 1966:20...commitment. A third characteristic is the public nature of a commitment. In order to accurately identify a commitment, there must be explicit evidence...PAR YUG TAI CON JAM PER ZAM TUR COP JAP POL USA Cos JOR RHO CUB KEN RUM CYP KON RWA CZE KOS SAU DAH KUd SEN DOM LAO SIE PAGE 11 and American

Reproductive maturation and senescence in the female brown bear

USGS Publications Warehouse

Schwartz, Charles C.; Keating, Kim A.; Reynolds III, Harry V.; Barnes, Victor G.; Sellers, Richard A.; Swenson, J.E.; Miller, Sterling D.; McLellan, B.N.; Keay, Jeffrey A.; McCann, Robert; Gibeau, Michael; Wakkinen, Wayne F.; Mace, Richard D.; Kasworm, Wayne; Smith, Rodger; Herrero, Steven

2003-01-01

Changes in age-specific reproductive rates can have important implications for managing populations, but the number of female brown (grizzly) bears (Ursus arctos) observed in any one study is usually inadequate to quantify such patterns, especially for older females and in hunted areas. We examined patterns of reproductive maturation and senescence in female brown bears by combining data from 20 study areas from Sweden, Alaska, Canada, and the continental United States. We assessed reproductive performance based on 4,726 radiocollared years for free-ranging female brown bears (age 3); 482 of these were for bears 20 years of age. We modeled age-specific probability of litter production using extreme value distributions to describe probabilities for young- and old-age classes, and a power distribution function to describe probabilities for prime-aged animals. We then fit 4 models to pooled observations from our 20 study areas. We used Akaike’s Information Criterion (AIC) to select the best model. Inflection points suggest that major shifts in litter production occur at 4–5 and 28–29 years of age. The estimated model asymptote (0.332, 95% CI ¼ 0.319–0.344) was consistent with the expected reproductive cycle of a cub litter every 3 years (0.333). We discuss assumptions and biases in data collection relative to the shape of the model curve. Our results conform to senescence theory and suggest that female age structure in contemporary brown bear populations is considerably younger than would be expected in the absence of modern man. This implies that selective pressures today differ from those that influenced brown bear evolution.

Transferring control demands across incidental learning tasks – stronger sequence usage in serial reaction task after shortcut option in letter string checking

PubMed Central

Gaschler, Robert; Marewski, Julian N.; Wenke, Dorit; Frensch, Peter A.

2014-01-01

After incidentally learning about a hidden regularity, participants can either continue to solve the task as instructed or, alternatively, apply a shortcut. Past research suggests that the amount of conflict implied by adopting a shortcut seems to bias the decision for vs. against continuing instruction-coherent task processing. We explored whether this decision might transfer from one incidental learning task to the next. Theories that conceptualize strategy change in incidental learning as a learning-plus-decision phenomenon suggest that high demands to adhere to instruction-coherent task processing in Task 1 will impede shortcut usage in Task 2, whereas low control demands will foster it. We sequentially applied two established incidental learning tasks differing in stimuli, responses and hidden regularity (the alphabet verification task followed by the serial reaction task, SRT). While some participants experienced a complete redundancy in the task material of the alphabet verification task (low demands to adhere to instructions), for others the redundancy was only partial. Thus, shortcut application would have led to errors (high demands to follow instructions). The low control demand condition showed the strongest usage of the fixed and repeating sequence of responses in the SRT. The transfer results are in line with the learning-plus-decision view of strategy change in incidental learning, rather than with resource theories of self-control. PMID:25506336

Discovery of a novel hepatovirus (Phopivirus of seals) related to human Hepatitis A Virus

USGS Publications Warehouse

Anthony. S.J.,; St. Leger, J.A; Liang, E.; Hicks, A.L.; Sanchez-Leon, M.D; Ip, Hon S.; Jain, K.; Lefkowitch, J. H.; Navarrete-Macias, I.; Knowles, N.; Goldstein, T.; Pugliares, K.; Rowles, T.; Lipkin, W.I.

2015-01-01

Describing the viral diversity of wildlife can provide interesting and useful insights into the natural history of established human pathogens. In this study, we describe a previously unknown picornavirus in harbor seals (tentatively named phopivirus) that is related to human hepatitis A virus (HAV). We show that phopivirus shares several genetic and phenotypic characteristics with HAV, including phylogenetic relatedness across the genome, a specific and seemingly quiescent tropism for hepatocytes, structural conservation in a key functional region of the type III internal ribosomal entry site (IRES), and a codon usage bias consistent with that of HAV.

Rubber dam isolation for restorative treatment in dental patients.

PubMed

Wang, Yan; Li, Chunjie; Yuan, He; Wong, May Cm; Zou, Jing; Shi, Zongdao; Zhou, Xuedong

2016-09-20

Successful restorations in dental patients depend largely on the effective control of moisture and microbes during the procedure. The rubber dam technique has been one of the most widely used isolation methods in dental restorative treatments. The evidence on the effects of rubber dam usage on the longevity of dental restorations is conflicting. Therefore, it is important to summarise the available evidence to determine the effects of this method. To assess the effects of rubber dam isolation compared with other types of isolation used for direct and indirect restorative treatments in dental patients. We searched the following electronic databases: Cochrane Oral Health's Trials Register (searched 17 August 2016), Cochrane Central Register of Controlled Trials (CENTRAL; 2016, Issue 7) in the Cochrane Library (searched 17 August 2016), MEDLINE Ovid (1946 to 17 August 2016), Embase Ovid (1980 to 17 August 2016), LILACS BIREME Virtual Health Library (Latin American and Caribbean Health Science Information database; 1982 to 17 August 2016), SciELO BIREME Virtual Health Library (1998 to 17 August 2016), Chinese BioMedical Literature Database (CBM, in Chinese) (1978 to 30 August 2016), VIP (in Chinese) (1989 to 30 August 2016), and China National Knowledge Infrastructure (CNKI, in Chinese) (1994 to 30 August 2016). We searched ClinicalTrials.gov and the World Health Organization International Clinical Trials Registry Platform, OpenGrey and Sciencepaper Online (in Chinese) for ongoing trials. There were no restrictions on the language or date of publication when searching the electronic databases. We included randomised controlled trials (including split-mouth trials) assessing the effects of rubber dam isolation for restorative treatments in dental patients. Two review authors independently screened the results of the electronic searches, extracted data and assessed the risk of bias of the included studies. We resolved disagreement by discussion. We included four studies that analysed 1270 participants (among which 233 participants were lost to follow-up). All the included studies were at high risk of bias. We excluded one trial from the analysis due to inconsistencies in the presented data.The results indicated that dental restorations had a significantly higher survival rate in the rubber dam isolation group compared to the cotton roll isolation group at six months in participants receiving composite restorative treatment of non-carious cervical lesions (risk ratio (RR) 1.19, 95% confidence interval (CI) 1.04 to 1.37, very low-quality evidence). It also showed that the rubber dam group had a lower risk of failure at two years in children undergoing proximal atraumatic restorative treatment in primary molars (hazard ratio (HR) 0.80, 95% CI 0.66 to 0.97, very low-quality evidence). One trial reported limited data showing that rubber dam usage during fissure sealing might shorten the treatment time. None of the included studies mentioned adverse effects or reported the direct cost of the treatment, or the level of patient acceptance/satisfaction. There was also no evidence evaluating the effects of rubber dam usage on the quality of the restorations. We found some very low-quality evidence, from single studies, suggesting that rubber dam usage in dental direct restorative treatments may lead to a lower failure rate of the restorations, compared with the failure rate for cotton roll usage. Further high quality research evaluating the effects of rubber dam usage on different types of restorative treatments is required.

Interpretation of the Electron Paramagnetic Resonance Spectra of Copper(II)-Tyrosine Complex

NASA Astrophysics Data System (ADS)

Xu, Xiao-Hui; Kuang, Min-Quan

2017-12-01

The electron paramagnetic resonance (EPR) spectra of [Cu(l-tyrosine)2]n (CuA) were interpreted based on the fourth-order perturbation treatments where the contributions due to the local distortion, ligand orbit and spin-orbit coupling were included. The calculated band transitions d_{x^2} - y^2 to dxy (≈16412 cm-1) and d_{z^2} (≈14845 cm-1) agree well with the band analysis results (d_{x^2} - y^2 \\to d_{xy} ≈16410 and d_{x^2} - y^2 \\to d_{z^2} ≈14850 cm-1). The unresolved separations d_{x^2} - y^2 \\to d_{xz} and d_{x^2} - y^2 \\to d_{yz} in the absorption spectra were evaluated as 26283 and 26262 cm-1, respectively. For CuA, copper chromophores in 1,3-diaminorpropane isophtalate copper(II) complex (CuB) and N-methyl-1,2-diaminoetaane-bis copper(II) polymer (CuC), the transition d_{x^2} - y^2 \\to d_{xy} (=E1≈10Dq) suffered an increase with a decrease in R̅L which was evaluated as the mean value of the copper-ligand bond lengths. The correlations between the tetragonal elongation ratio ρ (=(Rz-R̅L)/R̅L) (or the ratio G=(gz-ge)/((gx+gy)/2-ge)) and the g isotropy gav (=(gx+gy+gz)/3) (or the covalency factor N) for CuA, CuB and CuC were acquired and all the results were discussed.

Congenital vestibular disease in captive Sumatran tigers (Panthera tigris ssp. sumatrae) in Australasia.

PubMed

Wheelhouse, Jaimee L; Hulst, Frances; Beatty, Julia A; Hogg, Carolyn J; Child, Georgina; Wade, Claire M; Barrs, Vanessa R

2015-11-01

The Sumatran tiger (Panthera tigris ssp. sumatrae) is a critically endangered species in the wild. To ensure that demographic and genetic integrity are maintained in the longer term, those Sumatran tigers held in captivity are managed as a global population under a World Association of Zoos and Aquariums Global Species Management Plan (GSMP). A retrospective study, including segregation and pedigree analysis, was conducted to investigate potential cases of congenital vestibular disease (CVD) in captive Sumatran tigers in Australasian zoos using medical and husbandry records, as well as video footage obtained from 50 tigers between 1975 and 2013. Data from the GSMP Sumatran tiger studbook were made available for pedigree and segregation analysis. Fourteen cases of CVD in 13 Sumatran tiger cubs and one hybrid cub (Panthera tigris ssp. sumatrae × Panthera tigris) were identified. Vestibular signs including head tilt, circling, ataxia, strabismus and nystagmus were observed between birth and 2 months of age. These clinical signs persisted for a median of 237 days and had resolved by 2 years of age in all cases. Pedigree analysis revealed that all affected tigers were closely related and shared a single common ancestor in the last four generations. A genetic cause for the disease is suspected and, based on pedigree and segregation analysis, an autosomal dominant mode of inheritance is likely. Further investigations to determine the world-wide prevalence and underlying pathology of this disorder are warranted. Copyright © 2015 Elsevier Ltd. All rights reserved.

Germ cell survival and differentiation after xenotransplantation of testis tissue from three endangered species: Iberian lynx (Lynx pardinus), Cuvier's gazelle (Gazella cuvieri) and Mohor gazelle (G. dama mhorr).

PubMed

Arregui, Lucía; Dobrinski, Ina; Roldan, Eduardo R S

2014-01-01

The use of assisted reproductive techniques for endangered species is a major goal for conservation. One of these techniques, testis tissue xenografting, allows for the development of spermatozoa from animals that die before reaching sexual maturity. To assess the potential use of this technique with endangered species, testis tissue from six Iberian lynxes (one fetus, two perinatal cubs, two 6-month-old and one 2-year-old lynx), two Cuvier's gazelle fetuses and one 8-month-old Mohor gazelle were transplanted ectopically into nude mice. Tissue from the lynx fetus, perinatal cubs and 2-year-old donors degenerated, whereas spermatogonia were present in 15% of seminiferous tubules more than 70 weeks after grafting in transplanted testis tissue from 6-month-old donors. Seminal vesicle weights (indicative of testosterone production) increased over time in mice transplanted with tissue from 6-month-old lynxes. Progression of spermatogenesis was observed in xenografts from gazelles and was donor age dependent. Tissue from Cuvier's gazelle fetuses contained spermatocytes 40 weeks after grafting. Finally, round spermatids were found 28 weeks after transplantation in grafts from the 8-month-old Mohor gazelle. This is the first time that xenotransplantation of testicular tissue has been performed with an endangered felid and the first successful xenotransplantation in an endangered species. Our results open important options for the preservation of biological diversity.

Splitting of the O–O bond at the heme-copper catalytic site of respiratory oxidases

PubMed Central

Poiana, Federica; von Ballmoos, Christoph; Gonska, Nathalie; Blomberg, Margareta R. A.; Ädelroth, Pia; Brzezinski, Peter

2017-01-01

Heme-copper oxidases catalyze the four-electron reduction of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier experimental studies have shown that the O–O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR; Fe4+=O2−, CuB2+–OH−). We show that with the Thermus thermophilus ba3 oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the PR ferryl (τ ≅110 μs), which indicates that O2 is reduced before the splitting of the O–O bond. Application of density functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe3+–O−–O−(H+)], which is formed before the PR ferryl. The rates of heme b oxidation and PR ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined experimental and theoretical data suggest a general mechanism for O2 reduction by heme-copper oxidases. PMID:28630929

Post-den emergence behavior of polar bears (Ursus maritimus) in Northern Alaska

USGS Publications Warehouse

Smith, T.S.; Partridge, Steven T.; Amstrup, Steven C.; Schliebe, S.

2007-01-01

We observed polar bear (Ursus maritimus) maternity den sites on Alaska’s North Slope in March 2002 and 2003 in an effort to describe bears’ post-den emergence behavior. During 40 sessions spanning 459 h, we observed 8 adults and 14 dependent cubs outside dens for 37.5 h (8.2% of total observation time). There was no significant difference between den emergence dates in 2002 (mean = 15 Mar ± 4.1 d) and 2003 (mean = 21 Mar ± 2.1 d). Following initial den breakout, polar bears remained at their den sites for 1.5 to 14 days (mean = 8.1 ± 5.1 d). The average length of stay in dens between emergent periods was significantly shorter in 2002 (1.79 h) than in 2003 (4.82 h). While outside, adult bears were inactive 49.5% of the time, whereas cubs were inactive 13.4% of the time. We found no significant relationships between den emergence activity and weather. Adult polar bears at den sites subjected to industrial activity exhibited significantly fewer bouts of vigilance than denned bears in undisturbed areas (t = -5.5164, df = 4, p= 0.00). However, the duration of vigilance behaviors at sites near industrial activity was not significantly shorter than at the other sites studied (t = -1.8902, df = 4, p = 0.07). Results for these bears were within the range of findings in other studies of denned polar bears.

The role of membrane microdomains in transmembrane signaling through the epithelial glycoprotein Gp140/CDCP1

PubMed Central

Alvares, Stacy M.; Dunn, Clarence A.; Brown, Tod A.; Wayner, Elizabeth E.; Carter, William G.

2008-01-01

Cell adhesion to the extracellular matrix (ECM) via integrin adhesion receptors initiates signaling cascades leading to changes in cell behavior. While integrin clustering is necessary to initiate cell attachment to the matrix, additional membrane components are necessary to mediate the transmembrane signals and the cell adhesion response that alter downstream cell behavior. Many of these signaling components reside in glycosphingolipid-rich and cholesterol-rich membrane domains such as Tetraspanin Enriched Microdomains (TEMs)/Glycosynapse 3 and Detergent-Resistant Microdomains (DRMs), also known as lipid rafts. In the following article, we will review examples of how components in these membrane microdomains modulate integrin adhesion after initial attachment to the ECM. Additionally, we will present data on a novel adhesion-responsive transmembrane glycoprotein Gp140/CUB Domain Containing Protein 1, which clusters in epithelial cell-cell contacts. Gp140 can then be phosphorylated by Src Family Kinases at tyrosine 734 in response to outside-in signals- possibly through interactions involving the extracellular CUB domains. Data presented here suggests that outside-in signals through Gp140 in cell-cell contacts assemble membrane clusters that associate with membrane microdomains to recruit and activate SFKs. Active SFKs then mediate phosphorylation of Gp140, SFK and PKCδ with Gp140 acting as a transmembrane scaffold for these kinases. We propose that the clustering of Gp140 and signaling components in membrane microdomains in cell-cell contacts contributes to changes in cell behavior. PMID:18269919

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth--Three Phases in Early Lactation and Progressive Individual Differences.

PubMed

Zhang, Tong; Zhang, Rong; Zhang, Liang; Zhang, Zhihe; Hou, Rong; Wang, Hairui; Loeffler, I Kati; Watson, David G; Kennedy, Malcolm W

2015-01-01

Ursids (bears) in general, and giant pandas in particular, are highly altricial at birth. The components of bear milks and their changes with time may be uniquely adapted to nourish relatively immature neonates, protect them from pathogens, and support the maturation of neonatal digestive physiology. Serial milk samples collected from three giant pandas in early lactation were subjected to untargeted metabolite profiling and multivariate analysis. Changes in milk metabolites with time after birth were analysed by Principal Component Analysis, Hierarchical Cluster Analysis and further supported by Orthogonal Partial Least Square-Discriminant Analysis, revealing three phases of milk maturation: days 1-6 (Phase 1), days 7-20 (Phase 2), and beyond day 20 (Phase 3). While the compositions of Phase 1 milks were essentially indistinguishable among individuals, divergences emerged during the second week of lactation. OPLS regression analysis positioned against the growth rate of one cub tentatively inferred a correlation with changes in the abundance of a trisaccharide, isoglobotriose, previously observed to be a major oligosaccharide in ursid milks. Three artificial milk formulae used to feed giant panda cubs were also analysed, and were found to differ markedly in component content from natural panda milk. These findings have implications for the dependence of the ontogeny of all species of bears, and potentially other members of the Carnivora and beyond, on the complexity and sequential changes in maternal provision of micrometabolites in the immediate period after birth.

Diagnostic value of signal peptide-CUB-EGF domain-containing protein 1 as an early and late biochemical marker in the ovarian torsion rat model.

PubMed

Uzun, Özgür; Kaban, Işık; Midi, Ahmet; Uysal, Hande; Boran, Ahmet B; Bacanakgil, Besim H; Tarbaghia, Marwa

2018-04-02

Signal peptide-CUB-EGF (epidermal growth factor-like protein) domain-containing protein 1 (SCUBE1) is an experimental marker of ischemia that has been previously studied both in rat models and humans. In this study, we aim to investigate the importance of SCUBE1 levels in ovarian torsion using an ovarian torsion model in rats. A total of 18 Sprague-Dawley rats were equally divided into three groups. Group 1 (n = 6) was the Sham group and was only given a laparotomy procedure. Group 2 (n = 6) underwent bilateral ovarian torsion and ovarian ischemia lasting 8 h. Group 3 (n = 6) was subjected to bilateral ovarian torsion and ischemia lasting 24 h. Blood samples were collected from all three groups after the operations, and SCUBE1 levels were studied. Ovarian samples were collected, and microscopic evaluation was performed. The correlation of SCUBE1 levels and histopathological findings were investigated. The mean SCUBE1 level of group 3 was statistically higher than other groups (P < 0.01). Follicular degeneration and infiltration of inflammatory cells were, respectively, statistically significant in groups 2 and 3 (P = 0.002 and P = 0.045, respectively). SCUBE1 can be useful in diagnosing ovarian torsion during the first 24 h, but more randomized controlled studies are necessary in order to implement it in clinical settings. © 2018 Japan Society of Obstetrics and Gynecology.

Ubiquitin in Motion: Structural Studies of the Ubiquitin-Conjugating Enzyme~Ubiquitin Conjugate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pruneda, Jonathan N.; Stoll, Kate E.; Bolton, Laura J.

2011-03-15

Ubiquitination of proteins provides a powerful and versatile post-translational signal in the eukaryotic cell. The formation of a thioester bond between ubiquitin (Ub) and the active site of a ubiquitin-conjugating enzyme (E2) is critical for the transfer of Ub to substrates. Assembly of a functional ubiquitin ligase (E3) complex poised for Ub transfer involves recognition and binding of an E2~Ub conjugate. Therefore, full characterization of the structure and dynamics of E2~Ub conjugates is required for further mechanistic understanding of Ub transfer reactions. Here we present characterization of the dynamic behavior of E2~Ub conjugates of two human enzymes, UbcH5c~Ub and Ubc13~Ub,more » in solution as determined by nuclear magnetic resonance and small-angle X-ray scattering. Within each conjugate, Ub retains great flexibility with respect to the E2, indicative of highly dynamic species that adopt manifold orientations. The population distribution of Ub conformations is dictated by the identity of the E2: the UbcH5c~Ub conjugate populates an array of extended conformations, and the population of Ubc13~Ub conjugates favors a closed conformation in which the hydrophobic surface of Ub faces helix 2 of Ubc13. Finally, we propose that the varied conformations adopted by Ub represent available binding modes of the E2~Ub species and thus provide insight into the diverse E2~Ub protein interactome, particularly with regard to interaction with Ub ligases.« less

An Improved BeiDou-2 Satellite-Induced Code Bias Estimation Method.

PubMed

Fu, Jingyang; Li, Guangyun; Wang, Li

2018-04-27

Different from GPS, GLONASS, GALILEO and BeiDou-3, it is confirmed that the code multipath bias (CMB), which originate from the satellite end and can be over 1 m, are commonly found in the code observations of BeiDou-2 (BDS) IGSO and MEO satellites. In order to mitigate their adverse effects on absolute precise applications which use the code measurements, we propose in this paper an improved correction model to estimate the CMB. Different from the traditional model which considering the correction values are orbit-type dependent (estimating two sets of values for IGSO and MEO, respectively) and modeling the CMB as a piecewise linear function with a elevation node separation of 10°, we estimate the corrections for each BDS IGSO + MEO satellite on one hand, and a denser elevation node separation of 5° is used to model the CMB variations on the other hand. Currently, the institutions such as IGS-MGEX operate over 120 stations which providing the daily BDS observations. These large amounts of data provide adequate support to refine the CMB estimation satellite by satellite in our improved model. One month BDS observations from MGEX are used for assessing the performance of the improved CMB model by means of precise point positioning (PPP). Experimental results show that for the satellites on the same orbit type, obvious differences can be found in the CMB at the same node and frequency. Results show that the new correction model can improve the wide-lane (WL) ambiguity usage rate for WL fractional cycle bias estimation, shorten the WL and narrow-lane (NL) time to first fix (TTFF) in PPP ambiguity resolution (AR) as well as improve the PPP positioning accuracy. With our improved correction model, the usage of WL ambiguity is increased from 94.1% to 96.0%, the WL and NL TTFF of PPP AR is shorten from 10.6 to 9.3 min, 67.9 to 63.3 min, respectively, compared with the traditional correction model. In addition, both the traditional and improved CMB model have a better performance in these aspects compared with the model which does not account for the CMB correction.

An Improved BeiDou-2 Satellite-Induced Code Bias Estimation Method

PubMed Central

Fu, Jingyang; Li, Guangyun; Wang, Li

2018-01-01

Different from GPS, GLONASS, GALILEO and BeiDou-3, it is confirmed that the code multipath bias (CMB), which originate from the satellite end and can be over 1 m, are commonly found in the code observations of BeiDou-2 (BDS) IGSO and MEO satellites. In order to mitigate their adverse effects on absolute precise applications which use the code measurements, we propose in this paper an improved correction model to estimate the CMB. Different from the traditional model which considering the correction values are orbit-type dependent (estimating two sets of values for IGSO and MEO, respectively) and modeling the CMB as a piecewise linear function with a elevation node separation of 10°, we estimate the corrections for each BDS IGSO + MEO satellite on one hand, and a denser elevation node separation of 5° is used to model the CMB variations on the other hand. Currently, the institutions such as IGS-MGEX operate over 120 stations which providing the daily BDS observations. These large amounts of data provide adequate support to refine the CMB estimation satellite by satellite in our improved model. One month BDS observations from MGEX are used for assessing the performance of the improved CMB model by means of precise point positioning (PPP). Experimental results show that for the satellites on the same orbit type, obvious differences can be found in the CMB at the same node and frequency. Results show that the new correction model can improve the wide-lane (WL) ambiguity usage rate for WL fractional cycle bias estimation, shorten the WL and narrow-lane (NL) time to first fix (TTFF) in PPP ambiguity resolution (AR) as well as improve the PPP positioning accuracy. With our improved correction model, the usage of WL ambiguity is increased from 94.1% to 96.0%, the WL and NL TTFF of PPP AR is shorten from 10.6 to 9.3 min, 67.9 to 63.3 min, respectively, compared with the traditional correction model. In addition, both the traditional and improved CMB model have a better performance in these aspects compared with the model which does not account for the CMB correction. PMID:29702559

Evidence of Biased Advertising in the Case of Social Egg Freezing.

PubMed

Barbey, Christopher

2017-11-01

Oocyte cryopreservation, or 'egg freezing,' is the practice of preserving unfertilised oocytes for later fertilisation. This practice allows women to extend their reproductive years. In 2014, Facebook and Apple announced that they would subsidise their female employees' elective - or 'social' - use of egg freezing so that these women can more easily reconcile the demands of career and family life. This announcement engendered controversy and moral debate. Given that social egg freezing (SEF) is becoming more popular, ethical and empirical analyses are warranted. Here, I utilise content analysis to examine media messages in advertising for SEF. I conclude that many fertility clinics engage in biased advertising - i.e. they advertise the service persuasively, not informatively, emphasising indirect benefits while minimising risks and the low chance of successfully bringing a child to term. As advertising for medical services has been shown to influence the use of those services, advertising for SEF should emphasise clear and easily interpretable statistics about success rate, usage rate, cost, and risk.

Host influence in the genomic composition of flaviviruses: A multivariate approach.

PubMed

Simón, Diego; Fajardo, Alvaro; Sóñora, Martín; Delfraro, Adriana; Musto, Héctor

2017-10-28

Flaviviruses present substantial differences in their host range and transmissibility. We studied the evolution of base composition, dinucleotide biases, codon usage and amino acid frequencies in the genus Flavivirus within a phylogenetic framework by principal components analysis. There is a mutual interplay between the evolutionary history of flaviviruses and their respective vectors and/or hosts. Hosts associated to distinct phylogenetic groups may be driving flaviviruses at different pace and through various sequence landscapes, as can be seen for viruses associated with Aedes or Culex spp., although phylogenetic inertia cannot be ruled out. In some cases, viruses face even opposite forces. For instance, in tick-borne flaviviruses, while vertebrate hosts exert pressure to deplete their CpG, tick vectors drive them to exhibit GC-rich codons. Within a vertebrate environment, natural selection appears to be acting on the viral genome to overcome the immune system. On the other side, within an arthropod environment, mutational biases seem to be the dominant forces. Copyright © 2017 Elsevier Inc. All rights reserved.

Biological causal links on physiological and evolutionary time scales.

PubMed

Karmon, Amit; Pilpel, Yitzhak

2016-04-26

Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

PubMed Central

Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

2015-01-01

Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins. PMID:25527834

Effect of portal access system and surgery type on surgery times during laparoscopic ovariectomy and salpingectomy in captive African lions and cheetahs.

PubMed

Hartman, Marthinus Jacobus; Monnet, Eric; Kirberger, Robert Murco; Schoeman, Johan Petrus

2016-03-02

A prospective randomized study was used to compare surgery times for laparoscopic ovariectomy and salpingectomy in female African lion (Panthera leo) (n = 14) and cheetah (Acinonyx jubatus) (n = 20) and to compare the use of a multiple portal access system (MPAS) and single portal access system (SPAS) between groups. Two different portal techniques were used, namely MPAS (three separate ports) in lions and SPAS (SILS™ port) in cheetahs, using standard straight laparoscopic instruments. Portal access system and first ovary was not randomized. Five different surgery times were compared for the two different procedures as well as evaluating the use and application of MPAS and SPAS. Carbon dioxide volumes for lions were recorded. In adult lionesses operative time (OPT) (P = 0.016) and total surgical time (TST) (P = 0.032) were significantly shorter for salpingectomy compared to ovariectomy. Similarly in cheetahs OPT (P = 0.001) and TST (P = 0.005) were also shorter for salpingectomy compared to ovariectomy. In contrast, in lion cubs no difference was found in surgery times for ovariectomy and salpingectomy. Total unilateral procedure time was shorter than the respective bilateral time for both procedures (P = 0.019 and P = 0.001) respectively and unilateral salpingectomy was also faster than unilateral ovariectomy (P = 0.035) in cheetahs. Port placement time, suturing time and TST were significantly shorter for SPAS compared to MPAS (P = 0.008). There was, however, no difference in OPT between SPAS and MPAS. Instrument cluttering with SPAS was found to be negligible. There was no difference in mean volume CO2 required to complete ovariectomy in lions but the correlation between bodyweight and total volume of CO2 in lions was significant (rs = 0.867; P = 0.002). Laparoscopic salpingectomy was faster than ovariectomy in both adult lions and cheetahs. Using SPAS, both unilateral procedures were faster than bilateral procedures in cheetahs. Placement and suturing of SPAS in cheetahs was easier and faster compared to three separate ports in lions and lion cubs. The use of standard straight instruments during SPAS did not prolong surgery. Surgery was faster in cubs and CO2 required for laparoscopic sterilization in lions could be determined. Predictable surgery times and CO2 volumes will facilitate the accurate planning and execution of surgery in lions and cheetahs.

Safety and Efficacy of Catheter Direct Thrombolysis in Management of Acute Iliofemoral Deep Vein Thrombosis: A Systematic Review

PubMed Central

Elbasty, Ahmed; Metcalf, James

2017-01-01

Purpose Catheter direct thrombolysis (CDT) has been shown to be an effective treatment for deep venous thrombosis. The objective of the review is to improve safety and efficacy of the CDT by using ward based protocol, better able to predict complications and treatment outcome through monitoring of haemostatic parameters and clinical observation during thrombolysis procedure. Materials and Methods MEDLINE, EMBASE, CENTRAL and Web of Science were searched for all articles on deep venous thrombosis, thrombolysis and correlations of clinical events (bleeding, successful thrombolysis) during thrombolysis with hemostatic parameters to March 2016. The risk of bias in included studies was assessed by Cochrane Collaboration’s tool and Cochrane Risk of Bias Assessment Tool: for Non-Randomized Studies of Interventions. Results Twenty-four studies were included in the review and we found that improving safety and efficacy of CDT by using ward based protocol depending on eight factors; strict patient selection criteria, types of fibrinolytic drugs, mode of fibrinolytic drug injection, biochemical markers monitoring (fibrinogen, D-dimer, activated partial thromboplastin time, plasminogen activator inhibitor-1), timing of intervention, usage of intermittent pneumatic calf, ward monitoring and thrombolysis imaging assessment (intravascular ultrasound). These factors may help to improve safety and efficacy by reducing total thrombolytic drug dosage and at the same time ensure successful lysis. There is a marked lack of randomized controlled trials discussing the safety and efficacy of catheter direct thrombolysis. Conclusion CDT can be performed safely and efficiently in clinical ward, providing that careful nursing, biochemical monitoring, proper selection and mode of infusion of fibrinolytic drugs, usage of Intermittent pneumatic calf and adequate thrombolysis imaging assessment are ensured. PMID:29354622

Effects of the Advanced Combat Helmet (ACH) and Selected Communication and Hearing Protection Systems (C&HPSs) on Speech Communication: Talk-Through Systems

DTIC Science & Technology

2007-04-01

collection are commonly encountered and in wide use. Under no circumstance, will you experience hazardous listening levels that exceed the limits...voluntary participation, duration, and purpose of the study, the methods and means by which it is to be conducted, and the inconveniences and hazards ...cub cuff cup cud cuss 6 dig dip did dim dill din 7 duck dud dung dub dug dun 8 fill fig fin fizz fib fit 9 hear heath heal heave heat heap 10 kick

Discovery of a Novel Hepatovirus (Phopivirus of Seals) Related to Human Hepatitis A Virus

PubMed Central

St. Leger, J. A.; Liang, E.; Hicks, A. L.; Sanchez-Leon, M. D.; Jain, K.; Lefkowitch, J. H.; Navarrete-Macias, I.; Knowles, N.; Goldstein, T.; Pugliares, K.; Rowles, T.; Lipkin, W. I.

2015-01-01

ABSTRACT Describing the viral diversity of wildlife can provide interesting and useful insights into the natural history of established human pathogens. In this study, we describe a previously unknown picornavirus in harbor seals (tentatively named phopivirus) that is related to human hepatitis A virus (HAV). We show that phopivirus shares several genetic and phenotypic characteristics with HAV, including phylogenetic relatedness across the genome, a specific and seemingly quiescent tropism for hepatocytes, structural conservation in a key functional region of the type III internal ribosomal entry site (IRES), and a codon usage bias consistent with that of HAV. PMID:26307166

Modeling Population-Level Consequences of Polychlorinated Biphenyl Exposure in East Greenland Polar Bears.

PubMed

Pavlova, Viola; Grimm, Volker; Dietz, Rune; Sonne, Christian; Vorkamp, Katrin; Rigét, Frank F; Letcher, Robert J; Gustavson, Kim; Desforges, Jean-Pierre; Nabe-Nielsen, Jacob

2016-01-01

Polychlorinated biphenyls (PCBs) can cause endocrine disruption, cancer, immunosuppression, or reproductive failure in animals. We used an individual-based model to explore whether and how PCB-associated reproductive failure could affect the dynamics of a hypothetical polar bear (Ursus maritimus) population exposed to PCBs to the same degree as the East Greenland subpopulation. Dose-response data from experimental studies on a surrogate species, the mink (Mustela vision), were used in the absence of similar data for polar bears. Two alternative types of reproductive failure in relation to maternal sum-PCB concentrations were considered: increased abortion rate and increased cub mortality. We found that the quantitative impact of PCB-induced reproductive failure on population growth rate depended largely on the actual type of reproductive failure involved. Critical potencies of the dose-response relationship for decreasing the population growth rate were established for both modeled types of reproductive failure. Comparing the model predictions of the age-dependent trend of sum-PCBs concentrations in females with actual field measurements from East Greenland indicated that it was unlikely that PCB exposure caused a high incidence of abortions in the subpopulation. However, on the basis of this analysis, it could not be excluded that PCB exposure contributes to higher cub mortality. Our results highlight the necessity for further research on the possible influence of PCBs on polar bear reproduction regarding their physiological pathway. This includes determining the exact cause of reproductive failure, i.e., in utero exposure versus lactational exposure of offspring; the timing of offspring death; and establishing the most relevant reference metrics for the dose-response relationship.

Movements and distribution of polar bears in the Beaufort sea

USGS Publications Warehouse

Amstrup, Steven C.; Durner, George M.; Stirling, I.; Lunn, N.J.; Messier, F.

2000-01-01

We fitted 173 satellite radio collars (platform transmitter terminals) to 121 adult female polar bears in the Beaufort Sea and relocated the bears 44 736 times between 1985 and 1995. We regularly resighted many instrumented bears so that we could ascertain whether changes in movements or distribution were related to reproductive status. Mean short-term movement rates were less than 2 km/h for all classes of bears. Maximum movement rates occurred in winter and early summer. In the southern Beaufort Sea (SBS), net geographic movements from the beginning to the end of each month were smaller for females with cubs of the year than for solitary females, and larger in November than in April, May, or July. In May, June, July, and August, radio-collared bears in the SBS moved north. They moved south in October. In the northern Beaufort Sea (NBS), bears moved north in June and south in March and September. Total annual movements ranged from 1406 to 6203 km. Mean total distances moved each month ranged from 79 to 420 km. Total monthly movements by SBS bears were largest in early winter and smallest in early spring. In the NBS, movements were largest in summer and smallest in winter. In the SBS, females with cubs moved less each month than other females. Annual activity areas ranged from 7264 to 596 800 km2. Monthly activity areas ranged from 88 to 9760 km2. Seasonal fidelity to activity areas of bears captured in all parts of the Beaufort Sea was strongest in summer and weakest in spring.

Mating-related behaviour of grizzly bears inhabiting marginal habitat at the periphery of their North American range.

PubMed

Edwards, Mark A; Derocher, Andrew E

2015-02-01

In comparison to core populations, peripheral populations have low density and recruitment, and are subject to different selective pressures, such as environmental conditions, food type and availability, predation, disease, etc., which may result in behavioural modifications to mating. We test the roam-to-mate hypothesis for a peripheral population of grizzly bears (Ursus arctos) at the northern extent of their North American range, in Canada's Arctic. If bears are roaming-to-mate, we predicted greater range size and daily displacement, and more linear movements for receptive animals during the mating period compared to post-mating. In contrast to our predictions, we found that in general range size and displacement increased from mating to post-mating regardless of reproductive status. When considered across both periods, females with cubs-of-the-year had smaller range use metrics than other reproductive groups, which we attribute to a counter-strategy against sexually selected infanticide and the reduced mobility of cubs. Linearity of movements remained near zero during both periods across all groups, suggesting tortuous movements more characteristic of foraging than of mate-searching. We suggest that for this population, finding quality habitat takes precedence over mate-searching in this marginal Arctic landscape. Alternatively, a more monogamous mating system and sequestering behaviour may have obscured movement differences between the two periods. The behavioural differences in mating that we observed from what is typical of core populations may reflect local adaptation to marginal conditions and could benefit the species in the face of ongoing environmental change. Copyright © 2014 Elsevier B.V. All rights reserved.

Signal peptide-CUB-EGF domain-containing protein 1 (SCUBE1) levels in patients with overt and subclinical hyperthyroidism: effects of treatment.

PubMed

Erem, Cihangir; Civan, Nadim; Coskun, Hulya; Mentese, Ahmet; Suleyman, Akile Karacin; Altay, Diler Us; Akgul, Zeynep; Deger, Orhan

2016-06-01

Signal peptide-CUB-EGF domain-containing protein 1 (SCUBE1) has been shown to increase in parallel with platelet activation in acute ischaemic and thrombotic diseases. There has been no study evaluating SCUBE1 levels in patients with overt hyperthyroidism (OHyper) and subclinical hyperthyroidism (SHyper), conditions which are known to show impairment of both endothelial and platelet function. This study sought to evaluate SCUBE1 concentrations in patients with SHyper and OHyper, and assessed the effects of antithyroid drug (ATD) therapy on circulating SCUBE1 levels. Forty-five untreated patients with OHyper, 20 untreated patients with SHyper and 30 age- and sex-matched healthy controls were prospectively included in the study. Biochemical and hormonal parameters were evaluated in all patients before and after treatment. Compared with the control subjects, SCUBE1 levels were significantly increased in patients with SHyper and OHyper (P < 0·0001 and P = 0·002, respectively). SCUBE1 levels were not significantly different in patients with OHyper compared with patients with SHyper. There was no significant correlation between serum thyroid hormones and SCUBE1 levels. Plasma SCUBE1 levels decreased significantly in both OHyper and SHyper after ATD treatment (P < 0·05). Increased SCUBE1 levels in both SHyper and OHyper patients may reflect increased platelet activation and possible endothelial dysfunction, which might augment the risk for atherosclerotic and atherothrombotic complications. SCUBE1 may be used as a reliable marker of endothelial damage in hyperthyroidism, especially in the subclinical period. © 2015 John Wiley & Sons Ltd.

Discoidin, CUB and LCCL domain-containing protein 2 (DCBLD2) is a novel biomarker of myxofibrosarcoma invasion identified by global protein expression profiling.

PubMed

Kikuta, Kazutaka; Kubota, Daisuke; Yoshida, Akihiko; Qiao, Zhiwei; Morioka, Hideo; Nakamura, Masaya; Matsumoto, Morio; Chuman, Hirokazu; Kawai, Akira; Kondo, Tadashi

2017-09-01

Myxofibrosarcoma (MFS) is a mesenchymal malignancy characterized by frequent recurrence even after radical wide resection. To optimize therapy for MFS patients, we aimed to identify candidate tissue biomarkers of MFS invasion potential. Invasion characteristics of MFS were evaluated by magnetic resonance imaging and protein expression profiling of primary tumor tissues performed using two-dimensional difference gel electrophoresis (2D-DIGE). Protein expression profiles were compared between invasive and non-invasive tumors surgically resected from 11 patients. Among the 3453 protein spots observed, 59 demonstrated statistically significant difference in intensity (≥2-fold) between invasive and non-invasive tumors (p<0.01 by Wilkoxon test), and were identified by mass spectrometry as 47 individual proteins. Among them, we further focused on discoidin, CUB and LCCL domain-containing protein 2 (DCBLD2), a receptor tyrosine kinase with aberrant expression in malignant tumors. Immunohistochemistry analysis of 21 additional MFS cases revealed that higher DCBLD2 expression was significantly associated with invasive properties of tumor cells. DCBLD2 sensitivity and specificity, and positive and negative predictive values for MFS invasion were 69.2%, 87.5%, 90%, and 63.6%, respectively. The expression level of DCBLD2 was consistent in different portions of tumor tissues. Thus, DCBLD2 expression can be a useful biomarker to evaluate invasive properties of MFS. Further validation studies based on multi-institutional collaboration and comprehensive analysis of DCBLD2 biological functions in MFS are required to confirm its prognostic utility for clinical application. Copyright © 2017 Elsevier B.V. All rights reserved.

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences

PubMed Central

Zhang, Tong; Zhang, Rong; Zhang, Liang; Zhang, Zhihe; Hou, Rong; Wang, Hairui; Loeffler, I. Kati; Watson, David G.; Kennedy, Malcolm W.

2015-01-01

Ursids (bears) in general, and giant pandas in particular, are highly altricial at birth. The components of bear milks and their changes with time may be uniquely adapted to nourish relatively immature neonates, protect them from pathogens, and support the maturation of neonatal digestive physiology. Serial milk samples collected from three giant pandas in early lactation were subjected to untargeted metabolite profiling and multivariate analysis. Changes in milk metabolites with time after birth were analysed by Principal Component Analysis, Hierarchical Cluster Analysis and further supported by Orthogonal Partial Least Square-Discriminant Analysis, revealing three phases of milk maturation: days 1–6 (Phase 1), days 7–20 (Phase 2), and beyond day 20 (Phase 3). While the compositions of Phase 1 milks were essentially indistinguishable among individuals, divergences emerged during the second week of lactation. OPLS regression analysis positioned against the growth rate of one cub tentatively inferred a correlation with changes in the abundance of a trisaccharide, isoglobotriose, previously observed to be a major oligosaccharide in ursid milks. Three artificial milk formulae used to feed giant panda cubs were also analysed, and were found to differ markedly in component content from natural panda milk. These findings have implications for the dependence of the ontogeny of all species of bears, and potentially other members of the Carnivora and beyond, on the complexity and sequential changes in maternal provision of micrometabolites in the immediate period after birth. PMID:26630345

Evaluation of 2-soft-release techniques to reintroduce black bears

USGS Publications Warehouse

Eastridge, Rick; Clark, Joseph D.

2002-01-01

Black bear (Ursus americanus) were extirpated from most of their range by the early 1900s by habitat destruction and unregulated hunting. Since then, bear habitat has recovered in many areas, but isolation may prevent natural recolonization. Black bear translocations often have limited success because of high mortality rates and low site fidelity. We tested 2 reintroduction techniques designed to overcome those problems. The first technique used a winter release whereby pre- or post-parturient female bears were removed from their dens and placed in new dens at the release area. The second technique involved translocating female bears to the reintroduction area during summer and holding them in pens for a 2-week acclimation period before release. We translocated 8 female bears with cubs with the winter-release technique and 6 female with the summer-release technique. After release, total distance moved, net distance moved, mean daily distance moved, and circuity for winter-released bears (x̄=18.3 km, 7.1 km, 1.4 km, and 0.36, respectively) were less than summer-released bears (x̄=97.6, 63.4 km 5.1 km, and 0.74; P=0.010, 0.040, 0.019, and 0.038, respectively). Also, survival of winter-released bears (0.88) was greater than that for summer-released bears (0.2, P=0.001). Population modeling indicated that the least one additional stocking of 6 adult females with 12 cubs would greatly increase chances of population reestablishment. the winter-release technique has distinct advantages over the summer-release technique, limiting post-release movements and increasing survival of translocated bears.

The effect of auditory verbal imagery on signal detection in hallucination-prone individuals

PubMed Central

Moseley, Peter; Smailes, David; Ellison, Amanda; Fernyhough, Charles

2016-01-01

Cognitive models have suggested that auditory hallucinations occur when internal mental events, such as inner speech or auditory verbal imagery (AVI), are misattributed to an external source. This has been supported by numerous studies indicating that individuals who experience hallucinations tend to perform in a biased manner on tasks that require them to distinguish self-generated from non-self-generated perceptions. However, these tasks have typically been of limited relevance to inner speech models of hallucinations, because they have not manipulated the AVI that participants used during the task. Here, a new paradigm was employed to investigate the interaction between imagery and perception, in which a healthy, non-clinical sample of participants were instructed to use AVI whilst completing an auditory signal detection task. It was hypothesized that AVI-usage would cause participants to perform in a biased manner, therefore falsely detecting more voices in bursts of noise. In Experiment 1, when cued to generate AVI, highly hallucination-prone participants showed a lower response bias than when performing a standard signal detection task, being more willing to report the presence of a voice in the noise. Participants not prone to hallucinations performed no differently between the two conditions. In Experiment 2, participants were not specifically instructed to use AVI, but retrospectively reported how often they engaged in AVI during the task. Highly hallucination-prone participants who retrospectively reported using imagery showed a lower response bias than did participants with lower proneness who also reported using AVI. Results are discussed in relation to prominent inner speech models of hallucinations. PMID:26435050

Neural mechanisms underlying ecstasy-related attentional bias.

PubMed

Roberts, Gloria M P; Garavan, Hugh

2013-08-30

Conditioned responses to cues associated with drug taking play a pivotal role in a number of theories of drug addiction. This study examined whether attentional biases towards drug-related cues exist in recreational drug users who predominantly used ecstasy (3,4-methylenedioxymethamphetamine). Experiment 1 compared 30 ecstasy users, 25 cannabis users, and 30 controls in an attentional distraction task in which neutral, evocative, and ecstasy-related pictures were presented within a coloured border, requiring participants to respond as quickly as possible to the border colour. Experiment 2 employed functional magnetic resonance imaging (fMRI) and the attentional distraction task and tested 20 ecstasy users and 20 controls. Experiment 1 revealed significant response speed interference by the ecstasy-related pictures in the ecstasy users only. Experiment 2 revealed increased prefrontal and occipital activity in ecstasy users in all conditions. Activations in response to the ecstasy stimuli in these regions showed an apparent antagonism whereby ecstasy users, relative to controls, showed increased occipital but decreased right prefrontal activation. These results are interpreted to reflect increased visual processing of, and decreased prefrontal control over, the irrelevant but salient ecstasy-related stimuli. These results suggest that right inferior frontal cortex may play an important role in controlling drug-related attentional biases and may thus play an important role in mediating control over drug usage. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Printed Circuit Board Surface Finish and Effects of Chloride Contamination, Electric Field, and Humidity on Corrosion Reliability

NASA Astrophysics Data System (ADS)

Conseil-Gudla, Hélène; Jellesen, Morten S.; Ambat, Rajan

2017-02-01

Corrosion reliability is a serious issue today for electronic devices, components, and printed circuit boards (PCBs) due to factors such as miniaturization, globalized manufacturing practices which can lead to process-related residues, and global usage effects such as bias voltage and unpredictable user environments. The investigation reported in this paper focuses on understanding the synergistic effect of such parameters, namely contamination, humidity, PCB surface finish, pitch distance, and potential bias on leakage current under different humidity levels, and electrochemical migration probability under condensing conditions. Leakage currents were measured on interdigitated comb test patterns with three different types of surface finish typically used in the electronics industry, namely gold, copper, and tin. Susceptibility to electrochemical migration was studied under droplet conditions. The level of base leakage current (BLC) was similar for the different surface finishes and NaCl contamination levels up to relative humidity (RH) of 65%. A significant increase in leakage current was found for comb patterns contaminated with NaCl above 70% to 75% RH, close to the deliquescent RH of NaCl. Droplet tests on Cu comb patterns with varying pitch size showed that the initial BLC before dendrite formation increased with increasing NaCl contamination level, whereas electrochemical migration and the frequency of dendrite formation increased with bias voltage. The effect of different surface finishes on leakage current under humid conditions was not very prominent.

Electrochemical Migration of Fine-Pitch Nanopaste Ag Interconnects

NASA Astrophysics Data System (ADS)

Tsou, Chia-Hung; Liu, Kai-Ning; Lin, Heng-Tien; Ouyang, Fan-Yi

2016-12-01

With the development of intelligent electronic products, usage of fine-pitch interconnects has become mainstream in high performance electronic devices. Electrochemical migration (ECM) of interconnects would be a serious reliability problem under temperature, humidity and biased voltage environments. In this study, ECM behavior of nanopaste Ag interconnects with pitch size from 20 μm to 50 μm was evaluated by thermal humidity bias (THB) and water drop (WD) tests with deionized water through in situ leakage current-versus-time (CVT) curve. The results indicate that the failure time of ECM in fine-pitch samples occurs within few seconds under WD testing and it increases with increasing pitch size. The microstructure examination indicated that intensive dendrite formation of Ag through the whole interface was found to bridge the two electrodes. In the THB test, the CVT curve exhibited two stages, incubation and ramp-up; failure time of ECM was about 173.7 min. In addition, intensive dendrite formation was observed only at the protrusion of the Ag interconnects due to the concentration of the electric field at the protrusion of the Ag interconnects.

Uncertainty Analysis of Inertial Model Attitude Sensor Calibration and Application with a Recommended New Calibration Method

NASA Technical Reports Server (NTRS)

Tripp, John S.; Tcheng, Ping

1999-01-01

Statistical tools, previously developed for nonlinear least-squares estimation of multivariate sensor calibration parameters and the associated calibration uncertainty analysis, have been applied to single- and multiple-axis inertial model attitude sensors used in wind tunnel testing to measure angle of attack and roll angle. The analysis provides confidence and prediction intervals of calibrated sensor measurement uncertainty as functions of applied input pitch and roll angles. A comparative performance study of various experimental designs for inertial sensor calibration is presented along with corroborating experimental data. The importance of replicated calibrations over extended time periods has been emphasized; replication provides independent estimates of calibration precision and bias uncertainties, statistical tests for calibration or modeling bias uncertainty, and statistical tests for sensor parameter drift over time. A set of recommendations for a new standardized model attitude sensor calibration method and usage procedures is included. The statistical information provided by these procedures is necessary for the uncertainty analysis of aerospace test results now required by users of industrial wind tunnel test facilities.

Validating a two-high-threshold measurement model for confidence rating data in recognition.

PubMed

Bröder, Arndt; Kellen, David; Schütz, Julia; Rohrmeier, Constanze

2013-01-01

Signal Detection models as well as the Two-High-Threshold model (2HTM) have been used successfully as measurement models in recognition tasks to disentangle memory performance and response biases. A popular method in recognition memory is to elicit confidence judgements about the presumed old/new status of an item, allowing for the easy construction of ROCs. Since the 2HTM assumes fewer latent memory states than response options are available in confidence ratings, the 2HTM has to be extended by a mapping function which models individual rating scale usage. Unpublished data from 2 experiments in Bröder and Schütz (2009) validate the core memory parameters of the model, and 3 new experiments show that the response mapping parameters are selectively affected by manipulations intended to affect rating scale use, and this is independent of overall old/new bias. Comparisons with SDT show that both models behave similarly, a case that highlights the notion that both modelling approaches can be valuable (and complementary) elements in a researcher's toolbox.

Bayesian modeling of consumer behavior in the presence of anonymous visits

NASA Astrophysics Data System (ADS)

Novak, Julie Esther

Tailoring content to consumers has become a hallmark of marketing and digital media, particularly as it has become easier to identify customers across usage or purchase occasions. However, across a wide variety of contexts, companies find that customers do not consistently identify themselves, leaving a substantial fraction of anonymous visits. We develop a Bayesian hierarchical model that allows us to probabilistically assign anonymous sessions to users. These probabilistic assignments take into account a customer's demographic information, frequency of visitation, activities taken when visiting, and times of arrival. We present two studies, one with synthetic and one with real data, where we demonstrate improved performance over two popular practices (nearest-neighbor matching and deleting the anonymous visits) due to increased efficiency and reduced bias driven by the non-ignorability of which types of events are more likely to be anonymous. Using our proposed model, we avoid potential bias in understanding the effect of a firm's marketing on its customers, improve inference about the total number of customers in the dataset, and provide more precise targeted marketing to both previously observed and unobserved customers.

Cannibalism and predation on black bears by grizzly bears in the Yellowstone ecosystem, 1975-1990

USGS Publications Warehouse

Mattson, D.J.; Knight, R.R.; Blanchard, B.M.

1992-01-01

We documented one instance of an adult male grizzly bear preying upon a black bear and four instances where circumstantial evidence suggested that grizzly bears (two cubs-of-the-year, one yearling female that was injured, and one adult male) had been preyed upon by conspecifics. We also examined feces of grizzly bears for bear remains. Remains of bears tended to be more common in spring feces and did not differ in frequency between early and late years of the study. Our observations generally support existing hypotheses concerning cannibalism among bears.

Pt-B System Revisited: Pt2B, a New Structure Type of Binary Borides. Ternary WAl12-Type Derivative Borides.

PubMed

Sologub, Oksana; Salamakha, Leonid; Rogl, Peter; Stöger, Berthold; Bauer, Ernst; Bernardi, Johannes; Giester, Gerald; Waas, Monika; Svagera, Robert

2015-11-16

On the basis of a detailed study applying X-ray single-crystal and powder diffraction, differential scanning calorimetry, and scanning electron microscopy analysis, it was possible to resolve existing uncertainties in the Pt-rich section (≥65 atom % Pt) of the binary Pt-B phase diagram above 600 °C. The formation of a unique structure has been observed for Pt2B [X-ray single-crystal data: space group C2/m, a = 1.62717(11) nm, b = 0.32788(2) nm, c = 0.44200(3) nm, β = 104.401(4)°, RF2 = 0.030]. Within the homogeneity range of "Pt3B", X-ray powder diffraction phase analysis prompted two structural modifications as a function of temperature. The crystal structure of "hT-Pt3B" complies with the hitherto reported structure of anti-MoS2 [space group P63/mmc, a = 0.279377(2) nm, c = 1.04895(1) nm, RF = 0.075, RI = 0.090]. The structure of the new "[Formula: see text]T-Pt3B" is still unknown. The formation of previously reported Pt∼4B has not been confirmed from binary samples. Exploration of the Pt-rich section of the Pt-Cu-B system at 600 °C revealed a new ternary compound, Pt12CuB6-y [X-ray single-crystal data: space group Im3̅, a = 0.75790(2) nm, y = 3, RF2 = 0.0129], which exhibits the filled WAl12-type structure accommodating boron in the interstitial trigonal-prismatic site 12e. The isotypic platinum-aluminum-boride was synthesized and studied. The solubility of copper in binary platinum borides has been found to attain ∼7 atom % Cu for Pt2B but to be insignificant for "[Formula: see text]T-Pt3B". The architecture of the new Pt2B structure combines puckered layers of boron-filled and empty [Pt6] octahedra (anti-CaCl2-type fragment) alternating along the x axis with a double layer of boron-semifilled [Pt6] trigonal prisms interbedded with a layer of empty tetrahedra and tetragonal pyramids (B-deficient α-T[Formula: see text]I fragment). Assuming boron vacancies ordering (space group R3), the Pt12CuB6-y structure exhibits serpentine-like columns of edge-connected boron-filled [Pt6] trigonal prisms running infinitely along the z axis and embedding the icosahedrally coordinated Cu atom. Pt2B, (Pt1-yCuy)2B (y = 0.045), and Pt12CuB6-y (y = 3) behave metallically, as revealed by temperature-dependent electrical resistivity measurements.

Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11

PubMed Central

Li, Manqing; Kao, Elaine; Gao, Xia; Sandig, Hilary; Limmer, Kirsten; Pavon-Eternod, Mariana; Jones, Thomas E.; Landry, Sebastien; Pan, Tao; Weitzman, Matthew D.; David, Michael

2013-01-01

In mammals, one of the most pronounced consequences of viral infection is the induction of type I interferons, cytokines with potent antiviral activity. Schlafen (Slfn) genes are a subset of interferon-stimulated early response genes (ISGs) that are also induced directly by pathogens via the interferon regulatory factor 3 (IRF3) pathway1. However, many ISGs are of unknown or incompletely understood function. Here we show that human SLFN11 potently and specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1). Our study revealed that SLFN11 has no effect on the early steps of the retroviral infection cycle, including reverse transcription, integration and transcription. Rather, SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner. We further find that SLFN11 binds transfer RNA, and counteracts changes in the tRNA pool elicited by the presence of HIV. Our studies identified a novel antiviral mechanism within the innate immune response, in which SLFN11 selectively inhibits viral protein synthesis in HIV-infected cells by means of codon-bias discrimination. PMID:23000900

Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11.

PubMed

Li, Manqing; Kao, Elaine; Gao, Xia; Sandig, Hilary; Limmer, Kirsten; Pavon-Eternod, Mariana; Jones, Thomas E; Landry, Sebastien; Pan, Tao; Weitzman, Matthew D; David, Michael

2012-11-01

In mammals, one of the most pronounced consequences of viral infection is the induction of type I interferons, cytokines with potent antiviral activity. Schlafen (Slfn) genes are a subset of interferon-stimulated early response genes (ISGs) that are also induced directly by pathogens via the interferon regulatory factor 3 (IRF3) pathway. However, many ISGs are of unknown or incompletely understood function. Here we show that human SLFN11 potently and specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1). Our study revealed that SLFN11 has no effect on the early steps of the retroviral infection cycle, including reverse transcription, integration and transcription. Rather, SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner. We further find that SLFN11 binds transfer RNA, and counteracts changes in the tRNA pool elicited by the presence of HIV. Our studies identified a novel antiviral mechanism within the innate immune response, in which SLFN11 selectively inhibits viral protein synthesis in HIV-infected cells by means of codon-bias discrimination.

Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses

PubMed Central

Félez-Sánchez, Marta; Trösemeier, Jan-Hendrik; Bedhomme, Stéphanie; González-Bravo, Maria Isabel; Kamp, Christel; Bravo, Ignacio G.

2015-01-01

Viruses rely completely on the hosts’ machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response. PMID:26139833

Energy use of televisions and video cassette recorders in the U.S.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meier, Alan; Rosen, Karen

1999-03-01

In an effort to more accurately determine nationwide energy consumption, the U.S. Department of Energy has recently commissioned studies with the goal of improving its understanding of the energy use of appliances in the miscellaneous end-use category. This study presents an estimate of the residential energy consumption of two of the most common domestic appliances in the miscellaneous end-use category: color televisions (TVs) and video cassette recorders (VCRs). The authors used a bottom-up approach in estimating national TV and VCR energy consumption. First, they obtained estimates of stock and usage from national surveys, while TV and VCR power measurements andmore » other data were recorded at repair and retail shops. Industry-supplied shipment and sales distributions were then used to minimize bias in the power measurement samples. To estimate national TV and VCR energy consumption values, ranges of power draw and mode usage were created to represent situations in homes with more than one unit. Average energy use values for homes with one unit, two units, etc. were calculated and summed to provide estimates of total national TV and VCR energy consumption.« less

Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats.

PubMed

Rajneesh; Pathak, Jainendra; Kannaujiya, Vinod K; Singh, Shailendra P; Sinha, Rajeshwar P

2017-07-01

Nucleotide and amino acid compositions were studied to determine the genomic and structural relationship of photolyase gene in freshwater, marine and hot spring cyanobacteria. Among three habitats, photolyase encoding genes from hot spring cyanobacteria were found to have highest GC content. The genomic GC content was found to influence the codon usage and amino acid variability in photolyases. The third position of codon was found to have more effect on amino acid variability in photolyases than the first and second positions of codon. The variation of amino acids Ala, Asp, Glu, Gly, His, Leu, Pro, Gln, Arg and Val in photolyases of three different habitats was found to be controlled by first position of codon (G1C1). However, second position (G2C2) of codon regulates variation of Ala, Cys, Gly, Pro, Arg, Ser, Thr and Tyr contents in photolyases. Third position (G3C3) of codon controls incorporation of amino acids such as Ala, Phe, Gly, Leu, Gln, Pro, Arg, Ser, Thr and Tyr in photolyases from three habitats. Photolyase encoding genes of hot spring cyanobacteria have 85% codons with G or C at third position, whereas marine and freshwater cyanobacteria showed 82 and 60% codons, respectively, with G or C at third position. Principal component analysis (PCA) showed that GC content has a profound effect in separating the genes along the first major axis according to their RSCU (relative synonymous codon usage) values, and neutrality analysis indicated that mutational pressure has resulted in codon bias in photolyase genes of cyanobacteria.

The layout of a bacterial genome.

PubMed

Képès, François; Jester, Brian C; Lepage, Thibaut; Rafiei, Nafiseh; Rosu, Bianca; Junier, Ivan

2012-07-16

Recently the mismatch between our newly acquired capacity to synthetize DNA at genome scale, and our low capacity to design ab initio a functional genome has become conspicuous. This essay gathers a variety of constraints that globally shape natural genomes, with a focus on eubacteria. These constraints originate from chromosome replication (leading/lagging strand asymmetry; gene dosage gradient from origin to terminus; collisions with the transcription complexes), from biased codon usage, from noise control in gene expression, and from genome layout for co-functional genes. On the basis of this analysis, lessons are drawn for full genome design. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

PrionHome: a database of prions and other sequences relevant to prion phenomena.

PubMed

Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M A; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M

2012-01-01

Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion.

PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena

PubMed Central

Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M. A.; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M.

2012-01-01

Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion. PMID:22363733

Analyzing time-ordered event data with missed observations.

PubMed

Dokter, Adriaan M; van Loon, E Emiel; Fokkema, Wimke; Lameris, Thomas K; Nolet, Bart A; van der Jeugd, Henk P

2017-09-01

A common problem with observational datasets is that not all events of interest may be detected. For example, observing animals in the wild can difficult when animals move, hide, or cannot be closely approached. We consider time series of events recorded in conditions where events are occasionally missed by observers or observational devices. These time series are not restricted to behavioral protocols, but can be any cyclic or recurring process where discrete outcomes are observed. Undetected events cause biased inferences on the process of interest, and statistical analyses are needed that can identify and correct the compromised detection processes. Missed observations in time series lead to observed time intervals between events at multiples of the true inter-event time, which conveys information on their detection probability. We derive the theoretical probability density function for observed intervals between events that includes a probability of missed detection. Methodology and software tools are provided for analysis of event data with potential observation bias and its removal. The methodology was applied to simulation data and a case study of defecation rate estimation in geese, which is commonly used to estimate their digestive throughput and energetic uptake, or to calculate goose usage of a feeding site from dropping density. Simulations indicate that at a moderate chance to miss arrival events ( p  = 0.3), uncorrected arrival intervals were biased upward by up to a factor 3, while parameter values corrected for missed observations were within 1% of their true simulated value. A field case study shows that not accounting for missed observations leads to substantial underestimates of the true defecation rate in geese, and spurious rate differences between sites, which are introduced by differences in observational conditions. These results show that the derived methodology can be used to effectively remove observational biases in time-ordered event data.

An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses: Criticality (k eff) Predictions

DOE PAGES

Scaglione, John M.; Mueller, Don E.; Wagner, John C.

2014-12-01

One of the most important remaining challenges associated with expanded implementation of burnup credit in the United States is the validation of depletion and criticality calculations used in the safety evaluation—in particular, the availability and use of applicable measured data to support validation, especially for fission products (FPs). Applicants and regulatory reviewers have been constrained by both a scarcity of data and a lack of clear technical basis or approach for use of the data. In this study, this paper describes a validation approach for commercial spent nuclear fuel (SNF) criticality safety (k eff) evaluations based on best-available data andmore » methods and applies the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The criticality validation approach utilizes not only available laboratory critical experiment (LCE) data from the International Handbook of Evaluated Criticality Safety Benchmark Experiments and the French Haut Taux de Combustion program to support validation of the principal actinides but also calculated sensitivities, nuclear data uncertainties, and limited available FP LCE data to predict and verify individual biases for relevant minor actinides and FPs. The results demonstrate that (a) sufficient critical experiment data exist to adequately validate k eff calculations via conventional validation approaches for the primary actinides, (b) sensitivity-based critical experiment selection is more appropriate for generating accurate application model bias and uncertainty, and (c) calculated sensitivities and nuclear data uncertainties can be used for generating conservative estimates of bias for minor actinides and FPs. Results based on the SCALE 6.1 and the ENDF/B-VII.0 cross-section libraries indicate that a conservative estimate of the bias for the minor actinides and FPs is 1.5% of their worth within the application model. Finally, this paper provides a detailed description of the approach and its technical bases, describes the application of the approach for representative pressurized water reactor and boiling water reactor safety analysis models, and provides reference bias results based on the prerelease SCALE 6.1 code package and ENDF/B-VII nuclear cross-section data.« less

Mitochondrial Copper Metabolism and Delivery to Cytochrome c Oxidase

PubMed Central

Horn, Darryl; Barrientos, Antoni

2010-01-01

Summary Metals are essential elements of all living organisms. Among them, copper is required for a multiplicity of functions including mitochondrial oxidative phosphorylation and protection against oxidative stress. Here we will focus on describing the pathways involved in the delivery of copper to cytochrome c oxidase (COX), a mitochondrial metalloenzyme acting as the terminal enzyme of the mitochondrial respiratory chain. The catalytic core of COX is formed by three mitochondrially-encoded subunits and contains three copper atoms. Two copper atoms bound to subunit 2 constitute the CuA site, the primary acceptor of electrons from ferrocytochrome c. The third copper, CuB, is associated with the high-spin heme a3 group of subunit 1. Recent studies, mostly performed in the yeast Saccharomyces cerevisiae, have provided new clues about 1- the source of the copper used for COX metallation; 2- the roles of Sco1p and Cox11p, the proteins involved in the direct delivery of copper to the CuA and CuB sites, respectively; 3- the action mechanism of Cox17p, a copper chaperone that provides copper to Sco1p and Cox11p; 4- the existence of at least four Cox17p homologues carrying a similar twin CX9C domain suggestive of metal binding, Cox19p, Cox23p, Pet191p and Cmc1p, that could be part of the same pathway; and 5- the presence of a disulfide relay system in the intermembrane space of mitochondria that mediates import of proteins with conserved cysteines motifs such as the CX9C characteristic of Cox17p and its homologues. The different pathways are reviewed and discussed in the context of both mitochondrial COX assembly and copper homeostasis. PMID:18459161

A potential oncogenic activity of platelet-derived growth factor d in prostate cancer progression.

PubMed

Ustach, Carolyn V; Taube, Marcus E; Hurst, Newton J; Bhagat, Sunita; Bonfil, R Daniel; Cher, Michael L; Schuger, Lucia; Kim, Hyeong-Reh Choi

2004-03-01

The platelet-derived growth factor (PDGF) proteins are potent stimulators of cell proliferation/transformation and play a major role in cell-cell communication. For over two decades, PDGFs were thought to exist as three dimeric polypeptides (the homodimers AA and BB and the heterodimer AB). Recently, however, the PDGF C and D chains were discovered in a BLAST search of the expressed sequence tag databases. The PDGF CC and DD dimers have a unique two-domain structure with an NH(2)-terminal CUB (compliment subcomponents C1r/C1s, Uegf, and Bmp1) domain and a COOH-terminal PDGF/vascular endothelial growth factor domain. Whereas secreted PDGF AA, BB, and AB readily activate their cell surface receptors, it was suggested that extracellular proteolytic removal of the CUB domain is required for the PDGF/vascular endothelial growth factor domain of PDGF CC and DD to activate PDGF receptors. In the present study, we examined the processing of latent PDGF D into its active form and the effects of PDGF D expression on prostate cancer progression. We show that LNCaP cells auto-activate latent PDGF DD into the active PDGF domain, which can induce phosphorylation of the beta-PDGF receptor and stimulates LNCaP cell proliferation in an autocrine manner. Additionally, LNCaP-PDGF D-conditioned medium induces migration of the prostate fibroblast cell line 1532-FTX, indicating LNCaP-processed PDGF DD is active in a paracrine manner as well. In a severe combined immunodeficient mouse model, PDGF DD expression accelerates early onset of prostate tumor growth and drastically enhances prostate carcinoma cell interaction with surrounding stromal cells. These demonstrate a potential oncogenic activity of PDGF DD in the development and/or progression of prostate cancer.

A Potential Oncogenic Activity of Platelet-Derived Growth Factor D in Prostate Cancer Progression

PubMed Central

Ustach, Carolyn V.; Taube, Marcus E.; Hurst, Newton J.; Bhagat, Sunita; Bonfil, R. Daniel; Cher, Michael L.; Schuger, Lucia; Kim, Hyeong-Reh Choi

2014-01-01

The platelet-derived growth factor (PDGF) proteins are potent stimulators of cell proliferation/transformation and play a major role in cell-cell communication. For over two decades, PDGFs were thought to exist as three dimeric polypeptides (the homodimers AA and BB and the heterodimer AB). Recently, however, the PDGF C and D chains were discovered in a BLAST search of the expressed sequence tag databases. The PDGF CC and DD dimers have a unique two-domain structure with an NH2-terminal CUB (compliment subcomponents C1r/C1s, Uegf, and Bmp1) domain and a COOH-terminal PDGF/vascular endothelial growth factor domain. Whereas secreted PDGF AA, BB, and AB readily activate their cell surface receptors, it was suggested that extracellular proteolytic removal of the CUB domain is required for the PDGF/vascular endothelial growth factor domain of PDGF CC and DD to activate PDGF receptors. In the present study, we examined the processing of latent PDGF D into its active form and the effects of PDGF D expression on prostate cancer progression. We show that LNCaP cells auto-activate latent PDGF DD into the active PDGF domain, which can induce phosphorylation of the β-PDGF receptor and stimulates LNCaP cell proliferation in an autocrine manner. Additionally, LNCaP-PDGF D-conditioned medium induces migration of the prostate fibroblast cell line 1532-FTX, indicating LNCaP-processed PDGF DD is active in a paracrine manner as well. In a severe combined immunodeficient mouse model, PDGF DD expression accelerates early onset of prostate tumor growth and drastically enhances prostate carcinoma cell interaction with surrounding stromal cells. These demonstrate a potential oncogenic activity of PDGF DD in the development and/or progression of prostate cancer. PMID:14996732

Functionalized biochar derived from heavy metal rich feedstock: Phosphate recovery and reusing the exhausted biochar as an enriched soil amendment.

PubMed

Mosa, Ahmed; El-Ghamry, Ayman; Tolba, Mona

2018-05-01

This paper provides a circular win-win approach for recycling rhizofiltration biomass into multifunctional engineered biochar for various environmental applications (e.g. phosphate recovery) with a potential reuse of the exhausted biochar as an enriched soil amendment. Functionalized biochars were derived from the disposals of water hyacinth (Eichhornia crassipes) plants grown in synthetic contaminated water spiked with either Fe 2+ (Fe-B), Mn 2+ (Mn-B), Zn 2+ (Zn-B) or Cu 2+ (Cu-B) comparing with the original drainage water as a control treatment (O-B). The in-situ functionalization of biochar via the inherently heavy metal-rich feedstock produced homogenous organo-mineral complexes on biochar matrix without environmental hazards (e.g. volatilization or chemical sludge formation) associated with other post-synthetic functionalization methods. Physicochemical analyses (SEM-EDS, XRD, FTIR, BET and zeta potential (ζ)) confirmed the functionalization of Fe-B, Zn-B and Cu-B due to organo-mineral complexes formation, maximizing specific surface area, lowering the electronegativity, originating positively charged functional groups, and thus improving the anion exchange capacity (AEC) comparing with O-B. In contrary, physicochemical characteristics of Mn-B was in similarity with those of O-B. Phosphate recovery by the functionalized biochar was much greater than that of the unfunctionalized forms (O-B and Mn-B). Precipitation was the dominant chemisorption mechanisms for phosphate sorption onto biochar compared to other mechanisms (ion exchange, electrostatic attraction and complexation with active functional groups). The exhausted biochar showed an ameliorating effect on the low water and nutrient supply potentials of sandy soil, and thus improved fresh biomass yield and nutritional status of maize seedlings with some restrictions on its high micronutrient content. Copyright © 2018 Elsevier Ltd. All rights reserved.

Spatial patterns of breeding success of grizzly bears derived from hierarchical multistate models.

PubMed

Fisher, Jason T; Wheatley, Matthew; Mackenzie, Darryl

2014-10-01

Conservation programs often manage populations indirectly through the landscapes in which they live. Empirically, linking reproductive success with landscape structure and anthropogenic change is a first step in understanding and managing the spatial mechanisms that affect reproduction, but this link is not sufficiently informed by data. Hierarchical multistate occupancy models can forge these links by estimating spatial patterns of reproductive success across landscapes. To illustrate, we surveyed the occurrence of grizzly bears (Ursus arctos) in the Canadian Rocky Mountains Alberta, Canada. We deployed camera traps for 6 weeks at 54 surveys sites in different types of land cover. We used hierarchical multistate occupancy models to estimate probability of detection, grizzly bear occupancy, and probability of reproductive success at each site. Grizzly bear occupancy varied among cover types and was greater in herbaceous alpine ecotones than in low-elevation wetlands or mid-elevation conifer forests. The conditional probability of reproductive success given grizzly bear occupancy was 30% (SE = 0.14). Grizzly bears with cubs had a higher probability of detection than grizzly bears without cubs, but sites were correctly classified as being occupied by breeding females 49% of the time based on raw data and thus would have been underestimated by half. Repeated surveys and multistate modeling reduced the probability of misclassifying sites occupied by breeders as unoccupied to <2%. The probability of breeding grizzly bear occupancy varied across the landscape. Those patches with highest probabilities of breeding occupancy-herbaceous alpine ecotones-were small and highly dispersed and are projected to shrink as treelines advance due to climate warming. Understanding spatial correlates in breeding distribution is a key requirement for species conservation in the face of climate change and can help identify priorities for landscape management and protection. © 2014 Society for Conservation Biology.

Late Pleistocene steppe lion Panthera leo spelaea (Goldfuss, 1810) footprints and bone records from open air sites in northern Germany - Evidence of hyena-lion antagonism and scavenging in Europe

NASA Astrophysics Data System (ADS)

Diedrich, Cajus G.

2011-07-01

Bone remains and a trackway of Pantheraichnus bottropensis nov. ichg. ichnsp. of the Late Pleistocene lion Panthera leo spelaea ( Goldfuss, 1810) have been recovered from Bottrop and other open air sites in northern Germany. Some of these bones are from open air hyena den sites. A relative high proportion of lion bones (20%) exhibit bite, chew or nibble marks, or bone crushing and nibbling caused by a large carnivore. Repeated patterns of similar bone damage have been compared to bone remains found at hyena dens in gypsum karst areas and cave sites in northern Germany. Ice Age spotted hyenas have been the main antagonists and the main scavengers on lion carcasses. The remains appear to have been imported often by hyenas into their communal dens, supporting the theory of strong hyena-lion antagonism, similar to the well documented antagonism between modern African lions and spotted hyenas. Most of the lion bones from the open air hyena den at Bottrop are probably a result of such antagonism, as are the rare remains of these carnivores found within large hyena prey bone accumulations along the Pleistocene rivers. The Emscher River terrace also has the largest quantity of hyena remains from open air river terrace sites in northern Germany. Their cub remains, and incomplete chewed prey bones from mammoths and woolly rhinoceroses, typical of hyena activity, underline the character of these sites as cub-raising and communal dens, where their prey was accumulated along the riverbanks in a similar manner to modern African hyenas.

Cytochrome bo(3) from Escherichia coli: the binding and turnover of nitric oxide.

PubMed

Butler, Clive; Forte, Elena; Maria Scandurra, Francesca; Arese, Marzia; Giuffré, Alessandro; Greenwood, Colin; Sarti, Paolo

2002-09-06

The reaction of nitric oxide (NO) with fast and reduced cytochrome bo(3)(cyt bo(3)) from Escherichia coli has been investigated. The stoichiometry of NO binding to cyt bo(3) was determined using an NO electrode in the [NO] range 1-14 microM. Under reducing conditions, the initial decrease in [NO] following the addition of cyt bo(3) corresponded to binding of 1 NO molecule per cyt bo(3) functional unit. After this "rapid" NO binding phase, there was a slow, but significant rate of NO consumption ( approximately 0.3molNOmol bo(3)(-1)min(-1)), indicating that cyt bo(3) possesses a low level of NO reductase activity. The binding of NO to fast pulsed enzyme was also investigated. The results show that in the [NO] range used (1-14 microM) both fast and pulsed oxidised cyt bo(3) bind NO with a stoichiometry of 1:1 with an observed dissociation constant of K(d)=5.6+/-0.6 microM and that NO binding was inhibited by the presence of Cl(-). The binding of nitrite to the binuclear centre causes spectral changes similar to those observed upon NO binding to fast cyt bo(3). These results are discussed in relation to the model proposed by Wilson and co-workers [FEBS Lett. 414 (1997) 281] where the binding of NO to Cu(B)(II) results in the formation of the nitrosonium (Cu(B)(I)-NO(+)) complex. NO(+) then reacts with OH(-), a Cu(B) ligand, to form nitrite, which can bind at the binuclear centre. This work suggests for the first time that the binding of NO to oxidised cyt bo(3) does result in the reduction of Cu(B).

CUB domain-containing protein 1 and the epidermal growth factor receptor cooperate to induce cell detachment.

PubMed

Law, Mary E; Ferreira, Renan B; Davis, Bradley J; Higgins, Paul J; Kim, Jae-Sung; Castellano, Ronald K; Chen, Sixue; Luesch, Hendrik; Law, Brian K

2016-08-05

While localized malignancies often respond to available therapies, most disseminated cancers are refractory. Novel approaches, therefore, are needed for the treatment of metastatic disease. CUB domain-containing protein1 (CDCP1) plays an important role in metastasis and drug resistance; the mechanism however, is poorly understood. Breast cancer cell lines were engineered to stably express EGFR, CDCP1 or phosphorylation site mutants of CDCP1. These cell lines were used for immunoblot analysis or affinity purification followed by immunoblot analysis to assess protein phosphorylation and/or protein complex formation with CDCP1. Kinase activity was evaluated using phosphorylation site-specific antibodies and immunoblot analysis in in vitro kinase assays. Protein band excision and mass spectrometry was utilized to further identify proteins complexed with CDCP1 or ΔCDCP1, which is a mimetic of the cleaved form of CDCP1. Cell detachment was assessed using cell counting. This paper reports that CDCP1 forms ternary protein complexes with Src and EGFR, facilitating Src activation and Src-dependent EGFR transactivation. Importantly, we have discovered that a class of compounds termed Disulfide bond Disrupting Agents (DDAs) blocks CDCP1/EGFR/Src ternary complex formation and downstream signaling. CDCP1 and EGFR cooperate to induce detachment of breast cancer cells from the substratum and to disrupt adherens junctions. Analysis of CDCP1-containing complexes using proteomics techniques reveals that CDCP1 associates with several proteins involved in cell adhesion, including adherens junction and desmosomal cadherins, and cytoskeletal elements. Together, these results suggest that CDCP1 may facilitate loss of adhesion by promoting activation of EGFR and Src at sites of cell-cell and cell-substratum contact.

A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations.

PubMed

Schweikardt, Thorsten; Olivares, Concepción; Solano, Francisco; Jaenicke, Elmar; García-Borrón, José Carlos; Decker, Heinz

2007-10-01

Tyrosinases are the first and rate-limiting enzymes in the synthesis of melanin pigments responsible for colouring hair, skin and eyes. Mutation of tyrosinases often decreases melanin production resulting in albinism, but the effects are not always understood at the molecular level. Homology modelling of mouse tyrosinase based on recently published crystal structures of non-mammalian tyrosinases provides an active site model accounting for loss-of-function mutations. According to the model, the copper-binding histidines are located in a helix bundle comprising four densely packed helices. A loop containing residues M374, S375 and V377 connects the CuA and CuB centres, with the peptide oxygens of M374 and V377 serving as hydrogen acceptors for the NH-groups of the imidazole rings of the copper-binding His367 and His180. Therefore, this loop is essential for the stability of the active site architecture. A double substitution (374)MS(375) --> (374)GG(375) or a single M374G mutation lead to a local perturbation of the protein matrix at the active site affecting the orientation of the H367 side chain, that may be unable to bind CuB reliably, resulting in loss of activity. The model also accounts for loss of function in two naturally occurring albino mutations, S380P and V393F. The hydroxyl group in S380 contributes to the correct orientation of M374, and the substitution of V393 for a bulkier phenylalanine sterically impedes correct side chain packing at the active site. Therefore, our model explains the mechanistic necessity for conservation of not only active site histidines but also adjacent amino acids in tyrosinase.

Dietary changes during weaning shape the gut microbiota of red pandas (Ailurus fulgens)

PubMed Central

Williams, Candace L; Dill-McFarland, Kimberly A; Sparks, Darrell L; Kouba, Andrew J; Willard, Scott T; Suen, Garret

2018-01-01

Abstract Mammalian herbivores have developed numerous adaptations to utilize their plant-based diets including a modified gastrointestinal tract (GIT) and symbiosis with a GIT microbiota that plays a major role in digestion and the maintenance of host health. The red panda (Ailurus fulgens) is a herbivorous carnivore that lacks the specialized GIT common to other herbivores but still relies on microorganisms for survival on its almost entirely bamboo diet. The GIT microbiota is of further importance in young red pandas, as high cub mortality is problematic and has been attributed to failure to meet nutritional requirements. To gain insight into the establishment of the GIT microbiota of red pandas, we examined microbial communities in two individuals following dietary changes associated with weaning using next-generation 16S rRNA Illumina MiSeq paired-end sequencing of faecal samples. Across all four stages (pre-weaning, during weaning, post-weaning and adult), the GIT microbial community displayed low diversity and was dominated by bacteria in the phylum Firmicutes with lesser contributions from the Proteobacteria. A core community was found consistently across all weaning stages and included species within the taxa Escherichia-Shigella, Streptococcus, Clostridium and an unclassified Clostridiaceae. Analysis of the overall community composition and structure showed that although the GIT microbiota is established early in red pandas, dietary changes during weaning further shape the community and are correlated with the presence of new bacterial species. This work is the first analysis of the GIT microbiota for red panda cubs during weaning and provides a framework for understanding how diet and host microbiota impact the development of these threatened animals. PMID:29399361

Dietary changes during weaning shape the gut microbiota of red pandas (Ailurus fulgens).

PubMed

Williams, Candace L; Dill-McFarland, Kimberly A; Sparks, Darrell L; Kouba, Andrew J; Willard, Scott T; Suen, Garret; Brown, Ashli E

2018-01-01

Mammalian herbivores have developed numerous adaptations to utilize their plant-based diets including a modified gastrointestinal tract (GIT) and symbiosis with a GIT microbiota that plays a major role in digestion and the maintenance of host health. The red panda ( Ailurus fulgens ) is a herbivorous carnivore that lacks the specialized GIT common to other herbivores but still relies on microorganisms for survival on its almost entirely bamboo diet. The GIT microbiota is of further importance in young red pandas, as high cub mortality is problematic and has been attributed to failure to meet nutritional requirements. To gain insight into the establishment of the GIT microbiota of red pandas, we examined microbial communities in two individuals following dietary changes associated with weaning using next-generation 16S rRNA Illumina MiSeq paired-end sequencing of faecal samples. Across all four stages (pre-weaning, during weaning, post-weaning and adult), the GIT microbial community displayed low diversity and was dominated by bacteria in the phylum Firmicutes with lesser contributions from the Proteobacteria. A core community was found consistently across all weaning stages and included species within the taxa Escherichia-Shigella, Streptococcus , Clostridium and an unclassified Clostridiaceae. Analysis of the overall community composition and structure showed that although the GIT microbiota is established early in red pandas, dietary changes during weaning further shape the community and are correlated with the presence of new bacterial species. This work is the first analysis of the GIT microbiota for red panda cubs during weaning and provides a framework for understanding how diet and host microbiota impact the development of these threatened animals.

How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient.

PubMed

Blomberg, Margareta R A; Siegbahn, Per E M

2015-03-01

Experiments have shown that the A-family cytochrome c oxidases pump four protons per oxygen molecule, also at a high electrochemical gradient. This has been considered a puzzle, since two of the reduction potentials involved, Cu(II) and Fe(III), were estimated from experiments to be too low to afford proton pumping at a high gradient. The present quantum mechanical study (using hybrid density functional theory) suggests a solution to this puzzle. First, the calculations show that the charge compensated Cu(II) potential for CuB is actually much higher than estimated from experiment, of the same order as the reduction potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and experiment is the very large uncertainty in the experimental observations used to estimate the equilibrium potentials, mainly caused by the lack of methods for direct determination of reduced CuB. Second, the calculations show that a high energy metastable state, labeled EH, is involved during catalytic turnover. The EH state mixes the low reduction potential of Fe(III) in heme a3 with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient. In contrast, the corresponding metastable oxidized state, OH, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy EH state it is suggested that only one proton is taken up via the K-channel during catalytic turnover. Copyright © 2014 Elsevier B.V. All rights reserved.

Transient binding of CO to Cu(B) in cytochrome c oxidase is dynamically linked to structural changes around a carboxyl group: a time-resolved step-scan Fourier transform infrared investigation.

PubMed Central

Heitbrink, Dirk; Sigurdson, Håkan; Bolwien, Carsten; Brzezinski, Peter; Heberle, Joachim

2002-01-01

The redox-driven proton pump cytochrome c oxidase is that enzymatic machinery of the respiratory chain that transfers electrons from cytochrome c to molecular oxygen and thereby splits molecular oxygen to form water. To investigate the reaction mechanism of cytochrome c oxidase on the single vibrational level, we used time-resolved step-scan Fourier transform infrared spectroscopy and studied the dynamics of the reduced enzyme after photodissociation of bound carbon monoxide across the mid-infrared range (2300-950 cm(-1)). Difference spectra of the bovine complex were obtained at -20 degrees C with 5 micros time resolution. The data demonstrate a dynamic link between the transient binding of CO to Cu(B) and changes in hydrogen bonding at the functionally important residue E(I-286). Variation of the pH revealed that the pK(a) of E(I-286) is >9.3 in the fully reduced CO-bound oxidase. Difference spectra of cytochrome c oxidase from beef heart are compared with those of the oxidase isolated from Rhodobacter sphaeroides. The bacterial enzyme does not show the environmental change in the vicinity of E(I-286) upon CO dissociation. The characteristic band shape appears, however, in redox-induced difference spectra of the bacterial enzyme but is absent in redox-induced difference spectra of mammalian enzyme. In conclusion, it is demonstrated that the dynamics of a large protein complex such as cytochrome c oxidase can be resolved on the single vibrational level with microsecond Fourier transform infrared spectroscopy. The applied methodology provides the basis for future investigations of the physiological reaction steps of this important enzyme. PMID:11751290

Novel Methods to Explore Building Energy Sensitivity to Climate and Heat Waves Using PNNL's BEND Model

NASA Astrophysics Data System (ADS)

Burleyson, C. D.; Voisin, N.; Taylor, T.; Xie, Y.; Kraucunas, I.

2017-12-01

The DOE's Pacific Northwest National Laboratory (PNNL) has been developing the Building ENergy Demand (BEND) model to simulate energy usage in residential and commercial buildings responding to changes in weather, climate, population, and building technologies. At its core, BEND is a mechanism to aggregate EnergyPlus simulations of a large number of individual buildings with a diversity of characteristics over large spatial scales. We have completed a series of experiments to explore methods to calibrate the BEND model, measure its ability to capture interannual variability in energy demand due to weather using simulations of two distinct weather years, and understand the sensitivity to the number and location of weather stations used to force the model. The use of weather from "representative cities" reduces computational costs, but often fails to capture spatial heterogeneity that may be important for simulations aimed at understanding how building stocks respond to a changing climate (Fig. 1). We quantify the potential reduction in temperature and load biases from using an increasing number of weather stations across the western U.S., ranging from 8 to roughly 150. Using 8 stations results in an average absolute summertime temperature bias of 4.0°C. The mean absolute bias drops to 1.5°C using all available stations. Temperature biases of this magnitude translate to absolute summertime mean simulated load biases as high as 13.8%. Additionally, using only 8 representative weather stations can lead to a 20-40% bias of peak building loads under heat wave or cold snap conditions, a significant error for capacity expansion planners who may rely on these types of simulations. This analysis suggests that using 4 stations per climate zone may be sufficient for most purposes. Our novel approach, which requires no new EnergyPlus simulations, could be useful to other researchers designing or calibrating aggregate building model simulations - particularly those looking at the impact of future climate scenarios. Fig. 1. An example of temperature bias that results from using 8 representative weather stations: (a) surface temperature from NLDAS on 5-July 2008 at 2000 UTC; (b) temperature from 8 representative stations at the same time mapped to all counties within a given IECC climate zone; (c) the difference between (a) and (b).

Examining the associations between HIV-related stigma and health outcomes in people living with HIV/AIDS: a series of meta-analyses

PubMed Central

Mitra, Sanjana; Chen, Shiyi; Gogolishvili, David; Globerman, Jason; Chambers, Lori; Wilson, Mike; Logie, Carmen H; Shi, Qiyun; Morassaei, Sara; Rourke, Sean B

2016-01-01

Objective To conduct a systematic review and series of meta-analyses on the association between HIV-related stigma and health among people living with HIV. Data sources A structured search was conducted on 6 electronic databases for journal articles reporting associations between HIV-related stigma and health-related outcomes published between 1996 and 2013. Study eligibility criteria Controlled studies, cohort studies, case-control studies and cross-sectional studies in people living with HIV were considered for inclusion. Outcome measures Mental health (depressive symptoms, emotional and mental distress, anxiety), quality of life, physical health, social support, adherence to antiretroviral therapy, access to and usage of health/social services and risk behaviours. Results 64 studies were included in our meta-analyses. We found significant associations between HIV-related stigma and higher rates of depression, lower social support and lower levels of adherence to antiretroviral medications and access to and usage of health and social services. Weaker relationships were observed between HIV-related stigma and anxiety, quality of life, physical health, emotional and mental distress and sexual risk practices. While risk of bias assessments revealed overall good quality related to how HIV stigma and health outcomes were measured on the included studies, high risk of bias among individual studies was observed in terms of appropriate control for potential confounders. Additional research should focus on elucidating the mechanisms behind the negative relationship between stigma and health to better inform interventions to reduce the impact of stigma on the health and well-being of people with HIV. Conclusions This systematic review and series of meta-analyses support the notion that HIV-related stigma has a detrimental impact on a variety of health-related outcomes in people with HIV. This review can inform the development of multifaceted, intersectoral interventions to reduce the impact of HIV-related stigma on the health and well-being of people living with HIV. PMID:27412106

A General Purpose Mini-Computer Based Digital Signal Processing Laboratory.

DTIC Science & Technology

1982-06-01

DOUBLE PPEC IC I DM C0CT2 C3 0) - C0CET4 . 3 0> DOUBLE PPEC ISI Oh CUB 1 CS 0) < CUEE ɠ 0 > , SUB3 ɠ 0> DOUELE PPECICION CUE6O30> » SUB7 ɠQ> »SUB3CB0...97 J — MUM = 1.30 DEM = I.DO DO JO J=l«f HUM = NUM*< SUEI <J;>+SUB2<J>*C0ST2<:D «•suB3O>*C0S2T4<.i1 DEN • DEN*<SUB6’CJ>+ SUB7 <J

ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.

PubMed

Meiler, Arno; Klinger, Claudia; Kaufmann, Michael

2012-09-08

The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

PubMed Central

2012-01-01

Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills. PMID:22958836

Enablers and barriers to using two-way information technology in the management of adults with diabetes: A descriptive systematic review.

PubMed

Macdonald, Emma M; Perrin, Byron M; Kingsley, Michael Ic

2017-01-01

Background This systematic review aimed to explore the enablers and barriers faced by adults with diabetes using two-way information communication technologies to support diabetes self-management. Methods Relevant literature was obtained from five databases using search strategies combining four major constructs: adults with diabetes, biomedical technology, communication technology and patient utilisation. Results Of 8430 unique articles identified, 48 were included for review. Risk of bias was assessed using either the Newcastle-Ottowa or Cochrane risk of bias assessment tools. Seventy-one percent of studies were of cohort design with the majority of studies assessed at high or unclear risk of bias. Consistently identified barriers included poorly designed interfaces requiring manual data entry and systems that lacked functionalities valued by patients. Commonly cited enablers included access to reliable technology, highly automated data entry and transmission, graphical display of data with immediate feedback, and supportive health care professionals and family members. Conclusions People with diabetes face a number of potentially modifiable barriers in using technology to support their diabetes management. In order to address these barriers, end users should be consulted in the design process and consideration given to theories of technology adoption to inform design and implementation. Systems should be designed to solve clinical or behavioural problems that are identified by patients as priorities. Technology should be as automated, streamlined, mobile, low cost and integrated as possible in order to limit the burden of usage for the patient and maximise clinical usefulness.

Mixtures of Berkson and classical covariate measurement error in the linear mixed model: Bias analysis and application to a study on ultrafine particles.

PubMed

Deffner, Veronika; Küchenhoff, Helmut; Breitner, Susanne; Schneider, Alexandra; Cyrys, Josef; Peters, Annette

2018-05-01

The ultrafine particle measurements in the Augsburger Umweltstudie, a panel study conducted in Augsburg, Germany, exhibit measurement error from various sources. Measurements of mobile devices show classical possibly individual-specific measurement error; Berkson-type error, which may also vary individually, occurs, if measurements of fixed monitoring stations are used. The combination of fixed site and individual exposure measurements results in a mixture of the two error types. We extended existing bias analysis approaches to linear mixed models with a complex error structure including individual-specific error components, autocorrelated errors, and a mixture of classical and Berkson error. Theoretical considerations and simulation results show, that autocorrelation may severely change the attenuation of the effect estimations. Furthermore, unbalanced designs and the inclusion of confounding variables influence the degree of attenuation. Bias correction with the method of moments using data with mixture measurement error partially yielded better results compared to the usage of incomplete data with classical error. Confidence intervals (CIs) based on the delta method achieved better coverage probabilities than those based on Bootstrap samples. Moreover, we present the application of these new methods to heart rate measurements within the Augsburger Umweltstudie: the corrected effect estimates were slightly higher than their naive equivalents. The substantial measurement error of ultrafine particle measurements has little impact on the results. The developed methodology is generally applicable to longitudinal data with measurement error. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

PubMed Central

Andersson, Jan O; Sjögren, Åsa M; Horner, David S; Murphy, Colleen A; Dyal, Patricia L; Svärd, Staffan G; Logsdon, John M; Ragan, Mark A; Hirt, Robert P; Roger, Andrew J

2007-01-01

Background Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). Results The analyses revealed a compact genome with few, if any, introns and very short 3' untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes – mostly encoding metabolic proteins – that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. Conclusion Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution. PMID:17298675

Complete mitochondrial genome of the giant African snail, Achatina fulica (Mollusca: Achatinidae): a novel location of putative control regions (CR) in the mitogenome within Pulmonate species.

PubMed

He, Zhang-Ping; Dai, Xia-Bin; Zhang, Shuai; Zhi, Ting-Ting; Lun, Zhao-Rong; Wu, Zhong-Dao; Yang, Ting-Bao

2016-01-01

The whole sequence (15,057 bp) of the mitochondrial DNA (mtDNA) of the terrestrial snail Achatina fulica (order Stylommatophora) was determined. The mitogenome, as the typical metazoan mtDNA, contains 13 protein-coding genes (PCG), 2 ribosomal RNA genes (rRNA) and 22 transfer RNA genes (tRNA). The tRNA genes include two trnS without standard secondary structure. Interestingly, among the known mitogenomes of Pulmonata species, we firstly characterized an unassigned lengthy sequence (551 bp) between the cox1 and the trnV which may be the CR for the sake of its AT bases usage bias (65.70%) and potential hairpin structure.

Insulated electrocardiographic electrodes. [without paste electrolyte

NASA Technical Reports Server (NTRS)

David, R. M.; Portnoy, W. A. (Inventor)

1975-01-01

An integrated system is disclosed including an insulated electrode and an impedance transformer which can be assembled in a small plastic housing and used for the acquisition of electrocardiographic data. The electrode may be employed without a paste electrolyte and may be attached to the body for extended usage without producing skin reaction. The electrode comprises a thin layer of suitable nontoxic dielectric material preferably deposited by radio frequency sputtering onto a conductive substrate. The impedance transformer preferably comprises an operational amplifier having an FET input stage connected in the unity gain configuration which provides a very low lower cut-off frequency, a high input impedance with a very small input bias current, a low output impedance, and a high signal-to-noise ratio.

Evidence-based recommendations for antibiotic usage to treat endodontic infections and pain: A systematic review of randomized controlled trials.

PubMed

Aminoshariae, Anita; Kulild, James C

2016-03-01

The purpose of this investigation was to identify evidence-based scientific methodologies to aid dental clinicians in establishing the indications for prescribing antibiotics for endodontic infection or pain. The authors prepared and registered a protocol on PROSPERO. They conducted electronic searches in MEDLINE, Scopus, Cochrane Library, and ClinicalTrials.gov. In addition, the authors hand searched the bibliographies of all relevant articles, the gray literature, and textbooks for randomized controlled clinical studies. The authors independently selected the relevant articles. The overall quality of the studies was fair with a low risk of bias, but 2 studies had a moderate risk of bias. The best available clinical evidence signals no indications for prescribing antibiotics preoperatively or postoperatively to prevent endodontic infection or pain unless the spread of infection is systemic, the patient is febrile, or both. Generally, an accurate diagnosis coupled with effective endodontic treatment will decrease microbial flora enough for healing to occur. To help decrease the number of drug-resistant microbes, oral health care providers should not prescribe antibiotics when they are not indicated. Copyright © 2016 American Dental Association. Published by Elsevier Inc. All rights reserved.

A Bayesian phylogenetic approach to estimating the stability of linguistic features and the genetic biasing of tone.

PubMed

Dediu, Dan

2011-02-07

Language is a hallmark of our species and understanding linguistic diversity is an area of major interest. Genetic factors influencing the cultural transmission of language provide a powerful and elegant explanation for aspects of the present day linguistic diversity and a window into the emergence and evolution of language. In particular, it has recently been proposed that linguistic tone-the usage of voice pitch to convey lexical and grammatical meaning-is biased by two genes involved in brain growth and development, ASPM and Microcephalin. This hypothesis predicts that tone is a stable characteristic of language because of its 'genetic anchoring'. The present paper tests this prediction using a Bayesian phylogenetic framework applied to a large set of linguistic features and language families, using multiple software implementations, data codings, stability estimations, linguistic classifications and outgroup choices. The results of these different methods and datasets show a large agreement, suggesting that this approach produces reliable estimates of the stability of linguistic data. Moreover, linguistic tone is found to be stable across methods and datasets, providing suggestive support for the hypothesis of genetic influences on its distribution.

Characterization of Hard Piezoelectric Lead-Free Ceramics

PubMed Central

Zhang, Shujun; Lim, Jong Bong; Lee, Hyeong Jae; Shrout, Thomas R.

2010-01-01

K4CuNb8O23 doped K0.45Na0.55NbO3 (KNN-KCN) ferroelectric ceramics were found to exhibit asymmetrical polarization hysteresis loops, related to the development of an internal bias field. The internal bias field is believed to be the result of defect dipoles of acceptor ions and oxygen vacancies, which lead to piezoelectric “hardening” effect, by stabilizing and pinning of the domain wall motion. The dielectric loss for the hard lead-free piezoelectric ceramic was found to be 0.6%, with mechanical quality factors Q on the order of >1500. Furthermore, the piezoelectric properties were found to decrease and the coercive field increased, when compared with the undoped material, exhibiting a typical characteristic of “hard” behavior. The temperature usage range was limited by the polymorphic phase transition temperature, being 188°C. The full set of material constants was determined for the KNN-KCN materials. Compared with conventional hard PZT ceramics, the lead-free possessed lower dielectric and piezoelectric properties; however, comparable values of mechanical Q, dielectric loss, and coercive fields were obtained, making acceptor modified KNN based lead-free piezoelectric material promising for high-power applications, where lead-free materials are desirable. PMID:19686966

Dynamics and functional model of the 2012-13 flank fissure eruption of Tolbachik volcano in Kamchatka, Russia

NASA Astrophysics Data System (ADS)

Belousov, Alexander; Belousova, Marina; Edwards, Benjamin

2017-04-01

The 2012-13 flank fissure eruption of Tolbachik in Kamchatka Peninsula lasted more than nine months and discharged 0.55 cub.km DRE of basaltic trachyandesite magma. It is one of the most voluminous historical eruptions of mafic magma at subduction-related volcano globally, and is the second largest in Kamchatka. We present a broad overview of the eruption as well as a model for the magma storage and transport system of Plosky Tolbachik Volcano. The 2012-13 eruption was preceded by five months of elevated seismicity and ground inflation, both of which peaked a day before the eruption commenced on 27 November 2012. The batch of high-Al magma ascended from depths of 5-10 km; its apical part contained 54-55 wt.% SiO2, and the main body 52-53 wt.% SiO2. The eruption started by the opening of a 6 km-long radial fissure on the southwestern slope of the volcano that fed multi-vent phreatomagmatic and magmatic explosive activity, as well as intensive effusion of lava with an initial discharge of 440 cub.m/s. After 10 days the eruption continued only at the lower part of the fissure, where explosive and effusive activity of Hawaiian-Strombolian type occurred from a lava pond in the crater of the main growing scoria cone. The discharge rate for the nine month long, effusion-dominated eruption gradually declined from 140 to 18 cub.m/s and formed a compound lava field with a total area of 36 sq.km; the effusive activity evolved from high-discharge channel-fed 'a'a lavas to dominantly low-discharge tube-fed pahoehoe lavas. On 23 August, the effusion of lava ceased and the intra-crater lava pond drained. Weak Strombolian-type explosions continued for several more days on the crater bottom until the end of the eruption around 5 September 2013. The volcanic system, comprising the stratovolcano Plosky Tolbachik and its two radial volcanic rifts, produces alternating eruptions of two genetically related magma types: high-Al basalt (eruptions at the summit and along both rift zones) and high-Mg basalt (eruptions only along the southwest rift). The high-Al magma ascends to the surface from a magma storage zone at a depth of about 5 km below the summit of Plosky Tolbachik. During the 2012-13 eruption the high-Al magma first ascended along the central conduit of the volcano. Then the feeding dyke deviated from the conduit and propagated sub-horizontally along the southwest rift at a depth about 1 km below sea level. The 1975-76 Southern Breakthrough of the volcano was fed in a similar way. In contrast, the 1975-76 Northern Breakthrough of the volcano was fed by vertical dyke of high-Mg magma that ascended to the ground surface from the magma storage zone located directly below the area of the Breakthrough at a depth of approximately 20 km.

Media education in pediatric residencies: a national survey.

PubMed

Christakis, Dimitri A; Frintner, Mary Pat; Mulligan, Deborah A; Fuld, Gilbert L; Olson, Lynn M

2013-01-01

Little is known about the current state of residency education with respect to counseling parents about media usage and whether trainees consider it to be adequate. A national survey of graduating pediatric residents was conducted in the United States to determine the amount of training they receive on traditional and new media, their perceptions of its quality, and their self-reported practices regarding talking to families about media usage. A 58% response rate was achieved with no evidence of response bias based on age or gender. Only 38% rated their residency program as "very good" or "excellent" in preparing them to provide anticipatory guidance on the effects of media on children and adolescents. In logistic regression analyses, controlling for demographic characteristics, more training on media issues was a significant predictor for usually/always advising families on traditional, passive media (adjusted odds ratio = 3.29; 95% confidence interval 2.26-4.81) and usually/always advising families on new, interactive media use (adjusted odds ratio = 3.96; 95% confidence interval 2.61-6.00) during well-child visits. The majority of residents believe their training on children in media is inadequate. Enhanced training on media is needed in US pediatric residencies. Copyright © 2013 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Large-scale, multi-genome analysis of alternate open reading frames in bacteria and archaea.

PubMed

Veloso, Felipe; Riadi, Gonzalo; Aliaga, Daniela; Lieph, Ryan; Holmes, David S

2005-01-01

Analysis of over 300,000 annotated genes in 105 bacterial and archaeal genomes reveals an unexpectedly high frequency of large (>300 nucleotides) alternate open reading frames (ORFs). Especially notable is the very high frequency of alternate ORFs in frames +3 and -1 (where the annotated gene is defined as frame +1). The occurrence of alternate ORFs is correlated with genomic G+C content and is strongly influenced by synonymous codon usage bias. The frequency of alternate ORFs in frame -1 is also influenced by the occurrence of codons encoding leucine and serine in frame +1. Although some alternate ORFs have been shown to encode proteins, many others are probably not expressed because they lack appropriate signals for transcription and translation. These latter can be mis-annotated by automatic gene finding programs leading to errors in public databases. Especially prone to mis-annotation is frame -1, because it exhibits a potential codon usage and theoretical capacity to encode proteins with an amino acid composition most similar to real genes. Some alternate ORFs are conserved across bacterial or archaeal species, and can give rise to misannotated "conserved hypothetical" genes, while others are unique to a genome and are misidentified as "hypothetical orphan" genes, contributing significantly to the orphan gene paradox.

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius.

PubMed

Johnston, Christopher D; Bannantine, John P; Govender, Rodney; Endersen, Lorraine; Pletzer, Daniel; Weingart, Helge; Coffey, Aidan; O'Mahony, Jim; Sleator, Roy D

2014-01-01

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease.

Essentiality, conservation, evolutionary pressure and codon bias in bacterial genomes.

PubMed

Dilucca, Maddalena; Cimini, Giulio; Giansanti, Andrea

2018-07-15

Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias. Confirming previous results on E. coli, we show the existence of a universal exponential relation between gene essentiality and conservation in bacteria. Moreover, we show that, within each bacterial genome, there are at least two groups of functionally distinct genes, characterised by different levels of conservation and codon bias: i) a core of essential genes, mainly related to cellular information processing; ii) a set of less conserved nonessential genes with prevalent functions related to metabolism. In particular, the genes in the first group are more retained among species, are subject to a stronger purifying conservative selection and display a more limited repertoire of synonymous codons. The core of essential genes is close to the minimal bacterial genome, which is in the focus of recent studies in synthetic biology, though we confirm that orthologs of genes that are essential in one species are not necessarily essential in other species. We also list a set of highly shared genes which, reasonably, could constitute a reservoir of targets for new anti-microbial drugs. Copyright © 2018 Elsevier B.V. All rights reserved.

Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli.

PubMed

Pek, Han Bin; Klement, Maximilian; Ang, Kok Siong; Chung, Bevan Kai-Sheng; Ow, Dave Siak-Wei; Lee, Dong-Yup

2015-01-01

Various isoforms of invertases from prokaryotes, fungi, and higher plants has been expressed in Escherichia coli, and codon optimisation is a widely-adopted strategy for improvement of heterologous enzyme expression. Successful synthetic gene design for recombinant protein expression can be done by matching its translational elongation rate against heterologous host organisms via codon optimization. Amongst the various design parameters considered for the gene synthesis, codon context bias has been relatively overlooked compared to individual codon usage which is commonly adopted in most of codon optimization tools. In addition, matching the rates of transcription and translation based on secondary structure may lead to enhanced protein folding. In this study, we evaluated codon context fitness as design criterion for improving the expression of thermostable invertase from Thermotoga maritima in Escherichia coli and explored the relevance of secondary structure regions for folding and expression. We designed three coding sequences by using (1) a commercial vendor optimized gene algorithm, (2) codon context for the whole gene, and (3) codon context based on the secondary structure regions. Then, the codon optimized sequences were transformed and expressed in E. coli. From the resultant enzyme activities and protein yield data, codon context fitness proved to have the highest activity as compared to the wild-type control and other criteria while secondary structure-based strategy is comparable to the control. Codon context bias was shown to be a relevant parameter for enhancing enzyme production in Escherichia coli by codon optimization. Thus, we can effectively design synthetic genes within heterologous host organisms using this criterion. Copyright © 2015 Elsevier Inc. All rights reserved.

Using multiple data types and integrated population models to improve our knowledge of apex predator population dynamics.

PubMed

Bled, Florent; Belant, Jerrold L; Van Daele, Lawrence J; Svoboda, Nathan; Gustine, David; Hilderbrand, Grant; Barnes, Victor G

2017-11-01

Current management of large carnivores is informed using a variety of parameters, methods, and metrics; however, these data are typically considered independently. Sharing information among data types based on the underlying ecological, and recognizing observation biases, can improve estimation of individual and global parameters. We present a general integrated population model (IPM), specifically designed for brown bears ( Ursus arctos ), using three common data types for bear ( U . spp.) populations: repeated counts, capture-mark-recapture, and litter size. We considered factors affecting ecological and observation processes for these data. We assessed the practicality of this approach on a simulated population and compared estimates from our model to values used for simulation and results from count data only. We then present a practical application of this general approach adapted to the constraints of a case study using historical data available for brown bears on Kodiak Island, Alaska, USA. The IPM provided more accurate and precise estimates than models accounting for repeated count data only, with credible intervals including the true population 94% and 5% of the time, respectively. For the Kodiak population, we estimated annual average litter size (within one year after birth) to vary between 0.45 [95% credible interval: 0.43; 0.55] and 1.59 [1.55; 1.82]. We detected a positive relationship between salmon availability and adult survival, with survival probabilities greater for females than males. Survival probabilities increased from cubs to yearlings to dependent young ≥2 years old and decreased with litter size. Linking multiple information sources based on ecological and observation mechanisms can provide more accurate and precise estimates, to better inform management. IPMs can also reduce data collection efforts by sharing information among agencies and management units. Our approach responds to an increasing need in bear populations' management and can be readily adapted to other large carnivores.

Using multiple data types and integrated population models to improve our knowledge of apex predator population dynamics

USGS Publications Warehouse

Bled, Florent; Belant, Jerrold L.; Van Daele, Lawrence J.; Svoboda, Nathan; Gustine, David D.; Hilderbrand, Grant V.; Barnes, Victor G.

2017-01-01

Current management of large carnivores is informed using a variety of parameters, methods, and metrics; however, these data are typically considered independently. Sharing information among data types based on the underlying ecological, and recognizing observation biases, can improve estimation of individual and global parameters. We present a general integrated population model (IPM), specifically designed for brown bears (Ursus arctos), using three common data types for bear (U. spp.) populations: repeated counts, capture–mark–recapture, and litter size. We considered factors affecting ecological and observation processes for these data. We assessed the practicality of this approach on a simulated population and compared estimates from our model to values used for simulation and results from count data only. We then present a practical application of this general approach adapted to the constraints of a case study using historical data available for brown bears on Kodiak Island, Alaska, USA. The IPM provided more accurate and precise estimates than models accounting for repeated count data only, with credible intervals including the true population 94% and 5% of the time, respectively. For the Kodiak population, we estimated annual average litter size (within one year after birth) to vary between 0.45 [95% credible interval: 0.43; 0.55] and 1.59 [1.55; 1.82]. We detected a positive relationship between salmon availability and adult survival, with survival probabilities greater for females than males. Survival probabilities increased from cubs to yearlings to dependent young ≥2 years old and decreased with litter size. Linking multiple information sources based on ecological and observation mechanisms can provide more accurate and precise estimates, to better inform management. IPMs can also reduce data collection efforts by sharing information among agencies and management units. Our approach responds to an increasing need in bear populations’ management and can be readily adapted to other large carnivores.

Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila

PubMed Central

Jackson, Benjamin C.; Campos, José L.; Haddrill, Penelope R.; Charlesworth, Brian

2017-01-01

Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism data set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution. PMID:28082609

TRMM-3B43 Bias Correction over the High Elevations of the Contiguous United States

NASA Astrophysics Data System (ADS)

Hashemi, H.; Nordin, K. M.; Lakshmi, V.; Knight, R. J.

2016-12-01

Precipitation can be quantified using a rain gauge network, or a remotely sensed precipitation product. Ultimately, the choice of dataset depends on the particular application, the catchment size, climate and the time period of study. In a region with a long record and a dense rain gauge network, the elevation-modified ground-based precipitation product, PRISM, has been found to work well. However, in poorly gauged regions the use of remotely sensed precipitation products is an absolute necessity. The Tropical Rainfall Measuring Mission (TRMM) has provided valuable precipitation datasets for hydrometeorological studies over the past two decades (1998-2015). One concern regarding the usage of TRMM data is the accuracy of the precipitation estimates, when compared to those obtained using PRISM. The reason for this concern is that TRMM and PRISM do not always agree and, typically, TRMM underestimates PRISM over the mountainous regions of the United States. In this study, we develop a correction function to improve the accuracy of the TRMM monthly product (TRMM-3B43) by estimating and removing the bias in the satellite data using the ground-based precipitation product, PRISM. We observe a strong relationship between the bias and land surface elevation; TRMM-3B43 tends to underestimate the PRISM product at altitudes greater than 1500 m above mean sea level (m.amsl) in the contiguous United States. A relationship is developed between TRMM-PRISM bias and elevation. The correction function is used to adjust the TRMM monthly precipitation using PRISM and elevation data. The model is calibrated using 25% of the available time period and the remaining 75% of the time period is used for validation. The corrected TRMM-3B43 product is verified for the high elevations over the contiguous United States and two local regions in the mountainous areas of the western United States. The results show a significant improvement in the accuracy of the TRMM product in the high elevations of the contiguous United States.

Population growth of Yellowstone grizzly bears: Uncertainty and future monitoring

USGS Publications Warehouse

Harris, R.B.; White, Gary C.; Schwartz, C.C.; Haroldson, M.A.

2007-01-01

Grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem of the US Rocky Mountains have recently increased in numbers, but remain vulnerable due to isolation from other populations and predicted reductions in favored food resources. Harris et al. (2006) projected how this population might fare in the future under alternative survival rates, and in doing so estimated the rate of population growth, 1983–2002. We address issues that remain from that earlier work: (1) the degree of uncertainty surrounding our estimates of the rate of population change (λ); (2) the effect of correlation among demographic parameters on these estimates; and (3) how a future monitoring system using counts of females accompanied by cubs might usefully differentiate between short-term, expected, and inconsequential fluctuations versus a true change in system state. We used Monte Carlo re-sampling of beta distributions derived from the demographic parameters used by Harris et al. (2006) to derive distributions of λ during 1983–2002 given our sampling uncertainty. Approximate 95% confidence intervals were 0.972–1.096 (assuming females with unresolved fates died) and 1.008–1.115 (with unresolved females censored at last contact). We used well-supported models of Haroldson et al. (2006) and Schwartz et al. (2006a,b,c) to assess the strength of correlations among demographic processes and the effect of omitting them in projection models. Incorporating correlations among demographic parameters yielded point estimates of λ that were nearly identical to those from the earlier model that omitted correlations, but yielded wider confidence intervals surrounding λ. Finally, we suggest that fitting linear and quadratic curves to the trend suggested by the estimated number of females with cubs in the ecosystem, and using AICc model weights to infer population sizes and λ provides an objective means to monitoring approximate population trajectories in addition to demographic analysis.

Demography of the Giant Otter (Pteronura brasiliensis) in Manu National Park, South-Eastern Peru: Implications for Conservation

PubMed Central

Groenendijk, Jessica; Hajek, Frank; Johnson, Paul J.; Macdonald, David W.; Calvimontes, Jorge; Staib, Elke; Schenck, Christof

2014-01-01

The giant otter (Pteronura brasiliensis) is an endangered semi-aquatic carnivore of South America. We present findings on the demography of a population inhabiting the floodplain of Manu National Park, south-eastern Peru, arising from 14 annual dry season censuses over a 16 year period. The breeding system of territorial groups, including only a single breeding female with non-reproductive adult ‘helpers’, resulted in a low intrinsic rate of increase (0.03) and a slow recovery from decades of hunting for the pelt trade. This is explained by a combination of factors: (1) physiological traits such as late age at first reproduction and long generation time, (2) a high degree of reproductive skew, (3) small litters produced only once a year, and (4) a 50% mortality between den emergence and age of dispersal, as well as high mortality amongst dispersers (especially males). Female and male giant otters show similar traits with respect to average reproductive life-spans (female 5.4 yrs., male 5.2 yrs.) and average cub productivity (female 6.9, male 6.7 cubs per lifetime); the longest reproductive life spans were 11 and 13 years respectively. Individual reproductive success varied substantially and depended mainly on the duration of dominance tenure in the territory. When breeding females died, the reproductive position in the group was usually occupied by sisters or daughters (n = 11), with immigrant male partners. Male philopatry was not observed. The vulnerability of the Manu giant otter population to anthropogenic disturbance emphasises the importance of effective protection of core lake habitats in particular. Riverine forests are the most endangered ecosystem in the Department of Madre de Dios due to the concentration of gold mining, logging and agricultural activities in floodplains, highlighting the need for a giant otter habitat conservation corridor along the Madre de Dios River. PMID:25162684

Effect of the tyrosine kinase inhibitor lapatinib on CUB-domain containing protein (CDCP1)-mediated breast cancer cell survival and migration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seidel, Jeanette; Kunc, Klaudia; Possinger, Kurt

2011-10-14

Highlights: {yields} CDCP1 downregulation reduces anchorage free survival of breast cancer cells. {yields} Anoikis of CDCP1-positive breast cancer cells is increased after CDCP1 downregulation. {yields} CDCP1 knockdown decreases migration and extensively reduces invasiveness in vitro. {yields} Proliferation rate does not correlate with CDCP1 expression. {yields} Lapatinib does not influence tyrosine kinases of CDCP1 signal transduction. -- Abstract: The surface receptor CUB domain-containing protein 1 (CDCP1) is highly expressed in several adenocarcinomas and speculated to participate in anchorage-independent cell survival and cell motility. Tyrosine kinase phosphorylation seems to be crucial for intracellular signaling of CDCP1. Lapatinib, a tyrosine kinase inhibitor (TKI),more » is approved for treatment of HER-2/neu overexpressing metastatic breast cancer and functions by preventing autophosphorylation following HER-2/neu receptor activation. This study aimed to investigate the effect of CDCP1 expression on anchorage-independent growth and cell motility of breast cancer cells. Moreover, studies were performed to examine if lapatinib provided any beneficial effect on HER-2/neu{sup (+)/-}/CDCP1{sup +} breast cancer cell lines. In our studies, we affirmed that CDCP1 prevents cells from undergoing apoptosis when cultured in the absence of cell-substratum anchorage and that migratory and invasive properties of these cells were decreased when CDCP1 was down-regulated. However, only HER-2/neu{sup +}, but not HER-2/neu{sup (+)/-} cells showed decreased proliferation and invasion and an enhanced level of apoptosis towards loss of anchorage when treated with lapatinib. Therefore, we conclude that CDCP1 might be involved in regulating adhesion and motility of breast cancer cells but that lapatinib has no effect on tyrosine kinases regulating CDCP1. Nonetheless, other TKIs might offer therapeutic approaches for CDCP1-targeted breast cancer therapy and should be studied considering this aspect.« less

Contaminants in Svalbard polar bear samples archived since 1967 and possible population level effects.

PubMed

Derocher, Andrew E; Wolkers, Hans; Colborn, Theo; Schlabach, Martin; Larsen, Thor S; Wiig, Øystein

2003-01-01

Blood plasma samples were collected in 1967 from 32 polar bears (Ursus maritimus) in eastern Svalbard. These samples were stored frozen until 2001 and then analyzed for 33 polychlorinated biphenyls (PCB), two toxaphene congeners, DDTs, chlordanes (CHL), hexachlorobenzene, hexachlorocyclohexanes (HCHs), and polybrominated flame retardants (biphenyls and diphenyl ethers). The 1967 pollutant levels were compared with values from 1993 to 1994 for adult females and adult males to obtain insights into the historical development of pollution in the Norwegian Arctic. Differences in the OC levels measured between 1967 and 1993-1994 ranged from a decrease (PCB 187 and p,p-DDE) to unchanged in both sexes (PCBs 105, 118, 209, and HCH) to an increase in females (PCBs 99, 128, and CHL), to increases in both sexes (PCBs 138, 153, 156, 157, 170, 180, 194, and 206). The maximum change was a nine-fold increase in PCB 157 in adult females. Changes from 1967 to 1993-1994 in contaminant pattern expressed relative to PCB 153 could be explained by a combination of selective metabolism and accumulation of organochlorines in polar bears and temporal changes in the contaminant mixture being transported to the Arctic. Harvest of polar bears in Svalbard ended in 1973 and it appears that most pollutant levels were increasing at the same time that the population was expected to recover from over-harvest. The mean age of adult females in the Svalbard population was similar to other populations where pollution levels are lower but harvest is intense. Females with cubs-of-the-year > or =16 years old are uncommon in the population for unknown reasons. The impacts of contaminants on the Svalbard polar bear population are inconclusive but there are suggestions of contaminant-related population level effects that could have resulted from reproductive impairment of females, lower survival rates of cubs, or increased mortality of reproductive females. Copyright 2002 Elsevier Science B.V.

Demography of the giant otter (Pteronura brasiliensis) in Manu National Park, south-eastern Peru: implications for conservation.

PubMed

Groenendijk, Jessica; Hajek, Frank; Johnson, Paul J; Macdonald, David W; Calvimontes, Jorge; Staib, Elke; Schenck, Christof

2014-01-01

The giant otter (Pteronura brasiliensis) is an endangered semi-aquatic carnivore of South America. We present findings on the demography of a population inhabiting the floodplain of Manu National Park, south-eastern Peru, arising from 14 annual dry season censuses over a 16 year period. The breeding system of territorial groups, including only a single breeding female with non-reproductive adult 'helpers', resulted in a low intrinsic rate of increase (0.03) and a slow recovery from decades of hunting for the pelt trade. This is explained by a combination of factors: (1) physiological traits such as late age at first reproduction and long generation time, (2) a high degree of reproductive skew, (3) small litters produced only once a year, and (4) a 50% mortality between den emergence and age of dispersal, as well as high mortality amongst dispersers (especially males). Female and male giant otters show similar traits with respect to average reproductive life-spans (female 5.4 yrs., male 5.2 yrs.) and average cub productivity (female 6.9, male 6.7 cubs per lifetime); the longest reproductive life spans were 11 and 13 years respectively. Individual reproductive success varied substantially and depended mainly on the duration of dominance tenure in the territory. When breeding females died, the reproductive position in the group was usually occupied by sisters or daughters (n = 11), with immigrant male partners. Male philopatry was not observed. The vulnerability of the Manu giant otter population to anthropogenic disturbance emphasises the importance of effective protection of core lake habitats in particular. Riverine forests are the most endangered ecosystem in the Department of Madre de Dios due to the concentration of gold mining, logging and agricultural activities in floodplains, highlighting the need for a giant otter habitat conservation corridor along the Madre de Dios River.

Effects of climate warming on polar bears: a review of the evidence.

PubMed

Stirling, Ian; Derocher, Andrew E

2012-09-01

Climate warming is causing unidirectional changes to annual patterns of sea ice distribution, structure, and freeze-up. We summarize evidence that documents how loss of sea ice, the primary habitat of polar bears (Ursus maritimus), negatively affects their long-term survival. To maintain viable subpopulations, polar bears depend on sea ice as a platform from which to hunt seals for long enough each year to accumulate sufficient energy (fat) to survive periods when seals are unavailable. Less time to access to prey, because of progressively earlier breakup in spring, when newly weaned ringed seal (Pusa hispida) young are available, results in longer periods of fasting, lower body condition, decreased access to denning areas, fewer and smaller cubs, lower survival of cubs as well as bears of other age classes and, finally, subpopulation decline toward eventual extirpation. The chronology of climate-driven changes will vary between subpopulations, with quantifiable negative effects being documented first in the more southerly subpopulations, such as those in Hudson Bay or the southern Beaufort Sea. As the bears' body condition declines, more seek alternate food resources so the frequency of conflicts between bears and humans increases. In the most northerly areas, thick multiyear ice, through which little light penetrates to stimulate biological growth on the underside, will be replaced by annual ice, which facilitates greater productivity and may create habitat more favorable to polar bears over continental shelf areas in the short term. If the climate continues to warm and eliminate sea ice as predicted, polar bears will largely disappear from the southern portions of their range by mid-century. They may persist in the northern Canadian Arctic Islands and northern Greenland for the foreseeable future, but their long-term viability, with a much reduced global population size in a remnant of their former range, is uncertain. © 2012 Blackwell Publishing Ltd.

Courtship and mating in free-living spotted hyenas

USGS Publications Warehouse

Szykman, M.; Van Horn, R. C.; Engh, A.L.; Boydston, E.E.; Holekamp, K.E.

2007-01-01

Female spotted hyenas (Crocuta crocuta) are larger and more aggressive than males, and their genitalia are heavily 'masculinized'. These odd traits in females pose unusual challenges for males during courtship and copulation. Here our goals were to describe and quantify the behavior patterns involved in courtship and copulation in Crocuta, and determine whether rates of affiliative behavior directed toward females by males vary with female age, social rank, or time to conception. We also inquired whether consort formation with a particular female was necessary for a male to sire that female's cubs. Behavioral observations and paternity data based on 12 microsatellite loci were collected over 11 years from free-ranging hyenas in Kenya. Several of the courtship displays exhibited by male hyenas differed from those found in other carnivores, and appeared to reflect intense motivational conflict between tendencies to approach and flee from females. Most male advances were either ignored by females or elicited aggression from females toward males. Rates of male affiliative behavior toward females peaked around the time of conception. Although males behaved similarly toward young and old females in the highest social rank category, males directed more affiliative behavior toward older than younger females that were mid- and low-ranking. Multiple short mounts usually preceded a long mount, but intromission and ejaculation appeared to occur only during long mounts. Female receptivity was indicated by inhibited aggression toward the male and assumption of a distinctive receptive stance. The only behavior indicative of female proceptivity was following of the male by the female in mating contexts. Some males who sired cubs formed consortships with females whereas others did not, suggesting that individual male hyenas may adopt alternative reproductive tactics to attract and acquire mates. Our results also suggest that low fertility may be an important cost of female virilization in this species. ?? 2007 Brill Academic Publishers.

Genome characterization of sugarcane yellow leaf virus from China reveals a novel recombinant genotype.

PubMed

Lin, Yi-Hua; Gao, San-Ji; Damaj, Mona B; Fu, Hua-Ying; Chen, Ru-Kai; Mirkov, T Erik

2014-06-01

Sugarcane yellow leaf virus (SCYLV; genus Polerovirus, family Luteoviridae) is a recombinant virus associated with yellow leaf disease, a serious threat to sugarcane in China and worldwide. Among the nine known SCYLV genotypes existing worldwide, COL, HAW, REU, IND, CHN1, CHN2, BRA, CUB and PER, the last five have been reported in China. In this study, the complete genome sequences (5,880 nt) of GZ-GZ18 and HN-CP502 isolates from the Chinese provinces of Guizhou and Hainan, respectively, were cloned, sequenced and characterized. Phylogenetic analysis showed that, among 29 SCYLV isolates described worldwide, the two Chinese isolates clustered together into an independent clade based on the near-complete genome nucleotide (ORF0-ORF5) or amino acid sequences of individual genes, except for the MP protein (ORF4). We propose that the two isolates represent a novel genotype, CHN3, diverging from other genotypes by 1.7-13.6 % nucleotide differences in ORF0-ORF5, and 2.7-28.1 %, 1.8-20.4 %, 0.5-5.1 % and 2.7-15.9 % amino acid differences in P0 (ORF0), RdRp (RNA-dependent RNA polymerase) (ORF1+2), CP (coat protein) (ORF3) and RT (readthrough protein) (ORF3+5), respectively. CHN3 was closely related to the BRA, HAW and PER genotypes, differing by 1.7-3.8 % in the near-complete genome nucleotide sequence. Recombination analysis further identified CHN3 as a new recombinant strain, arising from the major parent CHN-HN1 and the minor parent CHN-GD-WY19. Recombination breakpoints were distributed mostly within the RdRp region in CHN3 and the four significant recombinant genotypes, IND, REU, CUB and BRA. Recombination is considered to contribute significantly to the evolution and emergence of such new SCYLV variants.

Diet and metabolic state are the main factors determining concentrations of perfluoroalkyl substances in female polar bears from Svalbard.

PubMed

Tartu, Sabrina; Bourgeon, Sophie; Aars, Jon; Andersen, Magnus; Lone, Karen; Jenssen, Bjørn Munro; Polder, Anuschka; Thiemann, Gregory W; Torget, Vidar; Welker, Jeffrey M; Routti, Heli

2017-10-01

Perfluoroalkyl substances (PFASs) have been detected in organisms worldwide, including Polar Regions. The polar bear (Ursus maritimus), the top predator of Arctic marine ecosystems, accumulates high concentrations of PFASs, which may be harmful to their health. The aim of this study was to investigate which factors (habitat quality, season, year, diet, metabolic state [i.e. feeding/fasting], breeding status and age) predict PFAS concentrations in female polar bears captured on Svalbard (Norway). We analysed two perfluoroalkyl sulfonates (PFSAs: PFHxS and PFOS) and C 8 -C 13 perfluoroalkyl carboxylates (PFCAs) in 112 plasma samples obtained in April and September 2012-2013. Nitrogen and carbon stable isotope ratios (δ 15 N, δ 13 C) in red blood cells and plasma, and fatty acid profiles in adipose tissue were used as proxies for diet. We determined habitat quality based on movement patterns, capture position and resource selection functions, which are models that predict the probability of use of a resource unit. Plasma urea to creatinine ratios were used as proxies for metabolic state (i.e. feeding or fasting state). Results were obtained from a conditional model averaging of 42 general linear mixed models. Diet was the most important predictor of PFAS concentrations. PFAS concentrations were positively related to trophic level and marine diet input. High PFAS concentrations in females feeding on the eastern part of Svalbard, where the habitat quality was higher than on the western coast, were likely related to diet and possibly to abiotic factors. Concentrations of PFSAs and C 8 -C 10 PFCAs were higher in fasting than in feeding polar bears and PFOS was higher in females with cubs of the year than in solitary females. Our findings suggest that female polar bears that are exposed to the highest levels of PFAS are those 1) feeding on high trophic level sea ice-associated prey, 2) fasting and 3) with small cubs. Copyright © 2017 Elsevier Ltd. All rights reserved.

NOAA Interest in Small Satellite Solutions for Mitigation of Data Gaps

NASA Astrophysics Data System (ADS)

Caulfield, M.; Tewey, K.; John, P.

2016-12-01

The National Oceanic and Atmospheric Administration (NOAA) is undertaking a strategy to achieve satellite constellation robustness by 2023 to maintain continuity of polar satellite observations, which are central to NOAA's weather forecast capability. NOAA's plans include mitigation activities in the event of a loss of polar observations. In 2017, NOAA will begin development of the Earth Observing Nanosatellite - Microwave (EON-MW). EON-MW is a miniature microwave sounder that approximates the atmospheric profiling capabilities of the Advanced Technology Microwave Sounder (ATMS) instrument on the NOAA Joint Polar Satellite System (JPSS). NOAA is collaborating with the Massachusetts Institute of Technology's Lincoln Laboratory (MIT / LL) on EON-MW, which includes 2 years of risk reduction efforts to further define the EON-MW mission and identify and manage key technical risks. These studies will refine designs and evaluate system trades for operational earth observations from a U-class satellite platform, as well as examine microwave sensor concepts and investigated payload architecture to support microwave frequencies for atmospheric remote sensing. Similar to EON-MW, NOAA is also investigating the potential to mitigate against the loss of the JPSS Cross Track Infrared Sounder (CrIS) data with a CubeSat based mid-wave Infrared sounder. NOAA is collaborating with the Jet Propulsion Laboratory (JPL) to design the Earth Observation Nanosatellite-Infrared (EON-IR). EON-IR will leverage the NASA-JPL CubSat based infrared sounder CubSat Infrared Atmospheric Sounder (CIRAS) mission. In FY 2015 NOAA funded a study to analyze the feasibility of meeting the essential requirements of the CrIS from a CubeSat platform and began exploring the basic design of the EON-IR payload and bus. NOAA will continue to study EON-IR in 2016 by examining ways to modify the CIRAS design to better meet NOAA's observational and operational needs. These modifications will aim to increase mission reliability and increase spatial and spectral resolution.

Pattern sampling for etch model calibration

NASA Astrophysics Data System (ADS)

Weisbuch, François; Lutich, Andrey; Schatz, Jirka

2017-06-01

Successful patterning requires good control of the photolithography and etch processes. While compact litho models, mainly based on rigorous physics, can predict very well the contours printed in photoresist, pure empirical etch models are less accurate and more unstable. Compact etch models are based on geometrical kernels to compute the litho-etch biases that measure the distance between litho and etch contours. The definition of the kernels as well as the choice of calibration patterns is critical to get a robust etch model. This work proposes to define a set of independent and anisotropic etch kernels -"internal, external, curvature, Gaussian, z_profile" - designed to capture the finest details of the resist contours and represent precisely any etch bias. By evaluating the etch kernels on various structures it is possible to map their etch signatures in a multi-dimensional space and analyze them to find an optimal sampling of structures to train an etch model. The method was specifically applied to a contact layer containing many different geometries and was used to successfully select appropriate calibration structures. The proposed kernels evaluated on these structures were combined to train an etch model significantly better than the standard one. We also illustrate the usage of the specific kernel "z_profile" which adds a third dimension to the description of the resist profile.

Examining the associations between HIV-related stigma and health outcomes in people living with HIV/AIDS: a series of meta-analyses.

PubMed

Rueda, Sergio; Mitra, Sanjana; Chen, Shiyi; Gogolishvili, David; Globerman, Jason; Chambers, Lori; Wilson, Mike; Logie, Carmen H; Shi, Qiyun; Morassaei, Sara; Rourke, Sean B

2016-07-13

To conduct a systematic review and series of meta-analyses on the association between HIV-related stigma and health among people living with HIV. A structured search was conducted on 6 electronic databases for journal articles reporting associations between HIV-related stigma and health-related outcomes published between 1996 and 2013. Controlled studies, cohort studies, case-control studies and cross-sectional studies in people living with HIV were considered for inclusion. Mental health (depressive symptoms, emotional and mental distress, anxiety), quality of life, physical health, social support, adherence to antiretroviral therapy, access to and usage of health/social services and risk behaviours. 64 studies were included in our meta-analyses. We found significant associations between HIV-related stigma and higher rates of depression, lower social support and lower levels of adherence to antiretroviral medications and access to and usage of health and social services. Weaker relationships were observed between HIV-related stigma and anxiety, quality of life, physical health, emotional and mental distress and sexual risk practices. While risk of bias assessments revealed overall good quality related to how HIV stigma and health outcomes were measured on the included studies, high risk of bias among individual studies was observed in terms of appropriate control for potential confounders. Additional research should focus on elucidating the mechanisms behind the negative relationship between stigma and health to better inform interventions to reduce the impact of stigma on the health and well-being of people with HIV. This systematic review and series of meta-analyses support the notion that HIV-related stigma has a detrimental impact on a variety of health-related outcomes in people with HIV. This review can inform the development of multifaceted, intersectoral interventions to reduce the impact of HIV-related stigma on the health and well-being of people living with HIV. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Three Misconceptions About Radiation — And What We Teachers Can Do to Confront Them

NASA Astrophysics Data System (ADS)

Neumann, Susanne

2014-09-01

During the last few years teaching physics, I have noticed that my students are becoming more and more interested in the topic of radiation. Mobile phones, modern game consoles, and WiFi—all of these devices involving some kind of radiation are part of our students' everyday lives. Students are also frequently confronted in the media with debates relating to different types of radiation: What are the effects of nuclear contamination going to be after the Fukushima accident? Can radiation from mobile phones really cause cancer? Should the use of tanning booths be forbidden for teenagers? Although students seem to be very motivated to learn about the topic of radiation, I have encountered several misconceptions about this topic that my students bring into the physics classroom. Some of these misconceptions might be caused by biased media reports, while others can be attributed to a different usage of the word radiation in everyday language (when compared to the scientific usage of this term). In this paper, I would like to present the most common misconceptions about radiation that I have encountered in my physics courses and I would like to give some ideas how to confront these ideas in teaching. A detailed description of these misconceptions discovered through empirical research can be found in one of my research articles.1

Biased immunoglobulin light chain gene usage in the shark1

PubMed Central

Iacoangeli, Anna; Lui, Anita; Naik, Ushma; Ohta, Yuko; Flajnik, Martin; Hsu, Ellen

2015-01-01

This study of a large family of kappa light (L) chain clusters in nurse shark completes the characterization of its classical immunoglobulin (Ig) gene content (two heavy chain classes, mu and omega, and four L chain isotopes, kappa, lambda, sigma, and sigma-2). The shark kappa clusters are minigenes consisting of a simple VL-JL-CL array, where V to J recombination occurs over a ~500 bp interval, and functional clusters are widely separated by at least 100 kb. Six out of ca. 39 kappa clusters are pre-rearranged in the germline (GL-joined). Unlike the complex gene organization and multistep assembly process of Ig in mammals, each shark Ig rearrangement, somatic or in the germline, appears to be an independent event localized to the minigene. This study examined the expression of functional, non-productive, and sterile transcripts of the kappa clusters compared to the other three L chain isotypes. Kappa cluster usage was investigated in young sharks, and a skewed pattern of split gene expression was observed, one similar in functional and non-productive rearrangements. These results show that the individual activation of the spatially distant kappa clusters is non-random. Although both split and GL-joined kappa genes are expressed, the latter are prominent in young animals and wane with age. We speculate that, in the shark, the differential activation of the multiple isotypes can be advantageously used in receptor editing. PMID:26342033

Biased Immunoglobulin Light Chain Gene Usage in the Shark.

PubMed

Iacoangeli, Anna; Lui, Anita; Naik, Ushma; Ohta, Yuko; Flajnik, Martin; Hsu, Ellen

2015-10-15

This study of a large family of κ L chain clusters in nurse shark completes the characterization of its classical Ig gene content (two H chain isotypes, μ and ω, and four L chain isotypes, κ, λ, σ, and σ-2). The shark κ clusters are minigenes consisting of a simple VL-JL-CL array, where V to J recombination occurs over an ~500-bp interval, and functional clusters are widely separated by at least 100 kb. Six out of ~39 κ clusters are prerearranged in the germline (germline joined). Unlike the complex gene organization and multistep assembly process of Ig in mammals, each shark Ig rearrangement, somatic or in the germline, appears to be an independent event localized to the minigene. This study examined the expression of functional, nonproductive, and sterile transcripts of the κ clusters compared with the other three L chain isotypes. κ cluster usage was investigated in young sharks, and a skewed pattern of split gene expression was observed, one similar in functional and nonproductive rearrangements. These results show that the individual activation of the spatially distant κ clusters is nonrandom. Although both split and germline-joined κ genes are expressed, the latter are prominent in young animals and wane with age. We speculate that, in the shark, the differential activation of the multiple isotypes can be advantageously used in receptor editing. Copyright © 2015 by The American Association of Immunologists, Inc.

IgV(H) and bcl6 somatic mutation analysis reveals the heterogeneity of cutaneous B-cell lymphoma, and indicates the presence of undisclosed local antigens.

PubMed

Franco, Renato; Camacho, Francisca I; Fernández-Vázquez, Amalia; Algara, Patrocinio; Rodríguez-Peralto, José L; De Rosa, Gaetano; Piris, Miguel A

2004-06-01

Our understanding of the ontology of B-cell lymphomas (BCL) has been improved by the study of mutational status of IgV(H) and bcl6 genes, but only a few cases of cutaneous BCL have been examined for this status. We analyzed IgV(H) and bcl6 somatic mutations in 10 cutaneous BCL, classified as follicular (three primary and one secondary), primary marginal zone (two cases), and diffuse large BCL (three primary and one secondary). We observed a lower rate (<2%) of IgV(H) mutation in all marginal zone lymphomas, and a preferential usage of V(H)2-70 (one primary follicular and two primary diffuse large BCL). Fewer than expected replacement mutations in framework regions (FR) were observed in three primary follicular lymphomas (FLs) and in all diffuse large BCL, indicating a negative antigen selection pressure. Ongoing mutations were observed in eight of 10 cases. Only two primary FLs and two diffuse large BCL showed bcl6 somatic mutation. These data support the heterogeneous nature of the different cutaneous BCL, and specifically the distinction between cutaneous follicular and marginal zone lymphomas. The biased usage of V(H)2-70, the low rate of replacement mutation in the FR, and the presence of ongoing mutation imply that local antigens could modulate the growth of primary cutaneous BCL.

Length-dependence of intramolecular electron transfer in σ-bonded rigid molecular rods: an ab initio molecular orbital study

NASA Astrophysics Data System (ADS)

Pati, Ranjit; Karna, Shashi P.

2002-01-01

The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the σ-bonded molecules. The calculated decay constant, β, shows good agreement with previously reported data. For molecular length⩾15 Å, the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.

Measuring quality of care in syncope: case definition affects reported electrocardiogram use but does not bias reporting.

PubMed

Schuur, Jeremiah D; Justice, Amy

2009-01-01

The objective was to calculate agreement between syncope as a reason for visiting (RFV) an emergency department (ED) and as a discharge diagnosis (International Classification of Diseases, Ninth Revision, Clinical Modification [ICD-9]), to determine whether syncope case definition biases reported electrocardiogram (ECG) usage, a national quality measure. The authors analyzed the ED portion of the National Hospital Ambulatory Medical Care Survey (NHAMCS), 1993-2004, for patients age >or=18 years. A visit was defined as being for syncope if it received one of three RFV or ICD-9 codes. Agreement between RFV and ICD-9 codes was calculated, and the percentages of syncope patients (RFV vs. ICD-9) who had an ECG were compared using chi-square and multivariate logistic regression. Raw agreement between syncope as an RFV and as an ICD-9 diagnosis code was 30.1% (95% confidence interval [CI] = 32.6% to 35.5%), representing only moderate agreement beyond chance (kappa = 0.50). ECG utilization was lower among visits defined by RFV (64.1%; 95% CI = 62.0% to 66.3%) than for ICD-9 diagnosis (73.6%; 95% CI = 71.4% to 75.8%). There was no meaningful variation in adjusted ECG use by patient, visit, or hospital characteristics between case definitions. Adjusted ECG use was lower under both case definitions among female patients and discharged patients and increased with age (p < 0.05). Despite only moderate agreement, syncope case definition should not bias reported ECG rate by patient, visit, or hospital characteristics. Among ED patients with syncope, ECG is performed less frequently in women, a potentially important disparity.

SAVINGS BY AND FOR THE POOR: A RESEARCH REVIEW AND AGENDA

PubMed Central

Karlan, Dean; Ratan, Aishwarya Lakshmi; Zinman, Jonathan

2014-01-01

The poor can and do save, but often use formal or informal instruments that have high risk, high cost, and limited functionality. This could lead to undersaving compared to a world without market or behavioral frictions. Undersaving can have important welfare consequences: variable consumption, low resilience to shocks, and foregone profitable investments. We lay out five sets of constraints that may hinder the adoption and effective usage of savings products and services by the poor: transaction costs, lack of trust and regulatory barriers, information and knowledge gaps, social constraints, and behavioral biases. We discuss each in theory, and then summarize related empirical evidence, with a focus on recent field experiments. We then put forward key open areas for research and practice. JEL Codes: D12, D91, G21, O16 PMID:25792764

Role of Alternative Polyadenylation during Adipogenic Differentiation: An In Silico Approach

PubMed Central

Spangenberg, Lucía; Correa, Alejandro; Dallagiovanna, Bruno; Naya, Hugo

2013-01-01

Post-transcriptional regulation of stem cell differentiation is far from being completely understood. Changes in protein levels are not fully correlated with corresponding changes in mRNAs; the observed differences might be partially explained by post-transcriptional regulation mechanisms, such as alternative polyadenylation. This would involve changes in protein binding, transcript usage, miRNAs and other non-coding RNAs. In the present work we analyzed the distribution of alternative transcripts during adipogenic differentiation and the potential role of miRNAs in post-transcriptional regulation. Our in silico analysis suggests a modest, consistent, bias in 3′UTR lengths during differentiation enabling a fine-tuned transcript regulation via small non-coding RNAs. Including these effects in the analyses partially accounts for the observed discrepancies in relative abundance of protein and mRNA. PMID:24143171

ZnO/p-GaN heterostructure for solar cells and the effect of ZnGa2O4 interlayer on their performance.

PubMed

Nam, Seung Yong; Choi, Yong Seok; Lee, Ju Ho; Park, Seong Ju; Lee, Jeong Yong; Lee, Dong Seon

2013-01-01

We report the usage of ZnO material as an alternative for n-GaN for realizing III-nitride based solar cell. The fabricated solar cell shows large turn-on voltage of around 8 volts and a rapid decrease of photocurrent at low bias voltage under darkness and 1-sun illumination conditions, respectively. This phenomenon can be attributed to the formation of high-resistive ultra-thin layers at the ZnO/ p-GaN junction interface during high temperature deposition. Transmission electron microscopy (TEM) studies carried out on the grown samples reveals that the ultra-thin layer consists of ZnGa2O4. It is found that the presence of insulating ZnGa2O4 film is detrimental in the performance of proposed heterostructure for solar cells.

The majority of vitamin A is transported as retinyl esters in the blood of most carnivores.

PubMed

Schweigert, F J; Ryder, O A; Rambeck, W A; Zucker, H

1990-01-01

1. In canines and mustelides total vitamin A was 10-50 times higher compared to other species due to a high amount of retinyl esters (40-99% of total vitamin A) in blood plasma. The dominant vitamin A ester was in most species retinyl stearate. 2. In Ursidae, Procyonidae, Viveridae and Felidae, total vitamin A was much lower. When present, however, retinyl esters also represented 10-65% of total vitamin A in plasma. 3. Only retinol was detected in plasma of the family, Hyaenidae, and the suborder, Pinnipedia. 4. In maned wolf cubs it was found that retinol, retinyl esters and alpha-tocopherol increased with the age of the animals, reaching values comparable to adult animals at the age of 5 months.

The "double panda" sign in Leigh disease.

PubMed

Sonam, Kothari; Bindu, P S; Gayathri, Narayanappa; Khan, Nahid Akhtar; Govindaraju, C; Arvinda, Hanumanthapura R; Nagappa, Madhu; Sinha, Sanjib; Thangaraj, K; Taly, Arun B

2014-07-01

Although the "face of the giant panda" sign on magnetic resonance imaging (MRI) is traditionally considered to be characteristic of Wilson disease, it has also been reported in other metabolic disorders. This study describes the characteristic "giant panda" sign on MRI in a child with Leigh disease. The diagnosis was based on the history of neurological regression; examination findings of oculomotor abnormalities, hypotonia, and dystonia; raised serum lactate levels; and characteristic brain stem and basal ganglia signal changes on MRI. The midbrain and pontine tegmental signal changes were consistent with the "face of the giant panda and her cub" sign. In addition to Wilson disease, metabolic disorders such as Leigh disease should also be considered in the differential diagnosis of this rare imaging finding. © The Author(s) 2013.

A 4 U Laser Heterodyne Radiometer for Methane (CH4) and Carbon Dioxide (CO2) Measurements from an Occultation-Viewing CubSat

NASA Technical Reports Server (NTRS)

Wilson, Emily L.; DiGregorio, A. J.; Riot, Vincent J.; Ammons, Mark S.; Bruner, WIlliam W.; Carter, Darrell; Mao, Jianping; Ramanathan, Anand; Strahan, Susan E.; Oman, Luke D.;

Observations on Gulf of Alaska seamount chains by multi-beam sonar

NASA Astrophysics Data System (ADS)

Smoot, N. Christian

1985-06-01

Geomorphic and age data are presented for the Dellwood, Denson, Dickins, Giacomini, and Ely seamounts, the Tsimshian Seachannel, and the southern Juan de Fuca Ridge with Brown Bear, Bear Cub, Grizzly Bear, and Cobb seamounts. Formational speculations extrapolated to a regional scale allow the strikes and outer limits of the seamount chains to be interpreted. Six of these chains are shown in the Gulf of Alaska, none of which conform to the Pratt-Welker or Kodiak-Bowie in the literature. Different strikes show the chains/plate to have rotated 23° about 17 m.y. ago. Morphology also shows that there are four less guyots in the Gulf than previously thought, and that, at least in the Gulf of Alaska, guyot heights do not necessarily reflect sealevel during erosion.

Geographical distribution of Demodex ursi in black bears from Florida.

PubMed

Foster, G W; Cames, T A; Forrester, D J

1998-01-01

From May 1990 to February 1996, 55 black bears (Ursus americanus floridanus) (38 males, 17 females) from 21 counties in Florida (USA), were examined for Demodex ursi (Acari: Demodecidae). The sample included cubs < 1-yr-old (n = 12), juveniles (1 to < 3 yr, n = 20), and adults (3 to 12 yr, n = 23). Demodex ursi was collected from four bears by deep scrapings of 15 sites on the head and forelimb of each bear. All four bears with demodicosis had crusty, scaly skin lesions, and moderate alopecia. No D. ursi were seen in any of the 750 scrapings from the other 51 bears, nor did any of those bears have signs of demodicosis. Demodicosis was found only in bears from or near the Ocala population in north-central Florida.

Autonomous learning in humanoid robotics through mental imagery.

PubMed

Di Nuovo, Alessandro G; Marocco, Davide; Di Nuovo, Santo; Cangelosi, Angelo

2013-05-01

In this paper we focus on modeling autonomous learning to improve performance of a humanoid robot through a modular artificial neural networks architecture. A model of a neural controller is presented, which allows a humanoid robot iCub to autonomously improve its sensorimotor skills. This is achieved by endowing the neural controller with a secondary neural system that, by exploiting the sensorimotor skills already acquired by the robot, is able to generate additional imaginary examples that can be used by the controller itself to improve the performance through a simulated mental training. Results and analysis presented in the paper provide evidence of the viability of the approach proposed and help to clarify the rational behind the chosen model and its implementation. Copyright © 2012 Elsevier Ltd. All rights reserved.

A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package

PubMed Central

Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M.

2013-01-01

Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs. PMID:24688703

A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package.

PubMed

Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M

2013-01-01

Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs.

Decoding Mechanisms by which Silent Codon Changes Influence Protein Biogenesis and Function

PubMed Central

Bali, Vedrana; Bebok, Zsuzsanna

2015-01-01

Scope Synonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health. Purpose This synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics. Physiological and medical relevance Understanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies. PMID:25817479

Systematic Review of the Use of 3-Dimensional Printing in Surgical Teaching and Assessment.

PubMed

Langridge, Benjamin; Momin, Sheikh; Coumbe, Ben; Woin, Evelina; Griffin, Michelle; Butler, Peter

The use of 3-dimensional (3D) printing in medicine has rapidly expanded in recent years as the technology has developed. The potential uses of 3D printing are manifold. This article provides a systematic review of the uses of 3D printing within surgical training and assessment. A structured literature search of the major literature databases was performed in adherence to PRISMA guidelines. Articles that met predefined inclusion and exclusion criteria were appraised with respect to the key objectives of the review and sources of bias were analysed. Overall, 49 studies were identified for inclusion in the qualitative analysis. Heterogeneity in study design and outcome measures used prohibited meaningful meta-analysis. 3D printing has been used in surgical training across a broad range of specialities but most commonly in neurosurgery and otorhinolaryngology. Both objective and subjective outcome measures have been studied, demonstrating the usage of 3D printed models in training and education. 3D printing has also been used in anatomical education and preoperative planning, demonstrating improved outcomes when compared to traditional educational methods and improved patient outcomes, respectively. 3D printing technology has a broad range of potential applications within surgical education and training. Although the field is still in its relative infancy, several studies have already demonstrated its usage both instead of and in addition to traditional educational methods. Copyright © 2018 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Accuracy-based proficiency testing for testosterone measurements with immunoassays and liquid chromatography-mass spectrometry.

PubMed

Cao, Zhimin Tim; Botelho, Julianne Cook; Rej, Robert; Vesper, Hubert

2017-06-01

Accurate testosterone measurements are needed to correctly diagnose and treat patients. Proficiency Testing (PT) programs using modified specimens for testing can be limited because of matrix effects and usage of non-reference measurement procedure (RMP)-defined targets for evaluation. Accuracy-based PT can overcome such limitations; however, there is a lack of information on accuracy-based PT and feasibility of its implementation in evaluation for testosterone measurements. Unaltered, single-donor human serum from 2 male and 2 female adult donors were analyzed for testosterone by 142 NYSDH-certified clinical laboratories using 16 immunoassays and LC-MS/MS methods. Testosterone target values were determined using an RMP. The testosterone target concentrations for the 4 specimens were 15.5, 30.0, 402 and 498ng/dl. The biases ranged from -17.8% to 73.1%, 3.1% to 21.3%, -24.8% to 8.6%, and -22.1% to 6.8% for the 4 specimens, respectively. Using a total error target of ±25.1%, which was calculated using the minimum allowable bias and imprecision, 73% of participating laboratories had ≥3 of the 4 results within these limits. The variability in total testosterone measurements can affect clinical decisions. Accuracy-based PT can significantly contribute to improving testosterone testing by providing reliable data on accuracy in patient care to laboratories, assay manufacturers, and standardization programs. Copyright © 2017. Published by Elsevier B.V.

The Influence of Safety, Efficacy, and Medical Condition Severity on Natural versus Synthetic Drug Preference.

PubMed

Meier, Brian P; Lappas, Courtney M

2016-11-01

Research indicates that there is a preference for natural v. synthetic products, but the influence of this preference on drug choice in the medical domain is largely unknown. We present 5 studies in which participants were asked to consider a hypothetical situation in which they had a medical issue requiring pharmacological therapy. Participants ( N = 1223) were asked to select a natural, plant-derived, or synthetic drug. In studies 1a and 1b, approximately 79% of participants selected the natural v. synthetic drug, even though the safety and efficacy of the drugs were identical. Furthermore, participants rated the natural drug as safer than the synthetic drug, and as that difference increased, the odds of choosing the natural over synthetic drug increased. In studies 2 and 3, approximately 20% of participants selected the natural drug even when they were informed that it was less safe (study 2) or less effective (study 3) than the synthetic drug. Finally, in study 4, approximately 65% of participants chose a natural over synthetic drug regardless of the severity of a specific medical condition (mild v. severe hypertension), and this choice was predicted by perceived safety and efficacy differences. Overall, these data indicate that there is a bias for natural over synthetic drugs. This bias could have implications for drug choice and usage. © The Author(s) 2015.

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.

PubMed

Aris-Brosou, Stéphane; Bielawski, Joseph P

2006-08-15

A popular approach to examine the roles of mutation and selection in the evolution of genomes has been to consider the relationship between codon bias and synonymous rates of molecular evolution. A significant relationship between these two quantities is taken to indicate the action of weak selection on substitutions among synonymous codons. The neutral theory predicts that the rate of evolution is inversely related to the level of functional constraint. Therefore, selection against the use of non-preferred codons among those coding for the same amino acid should result in lower rates of synonymous substitution as compared with sites not subject to such selection pressures. However, reliably measuring the extent of such a relationship is problematic, as estimates of synonymous rates are sensitive to our assumptions about the process of molecular evolution. Previous studies showed the importance of accounting for unequal codon frequencies, in particular when synonymous codon usage is highly biased. Yet, unequal codon frequencies can be modeled in different ways, making different assumptions about the mutation process. Here we conduct a simulation study to evaluate two different ways of modeling uneven codon frequencies and show that both model parameterizations can have a dramatic impact on rate estimates and affect biological conclusions about genome evolution. We reanalyze three large data sets to demonstrate the relevance of our results to empirical data analysis.

[Linkage of large secondary and registry data sources with data of cohort studies : usage of a dual potential].

PubMed

Jacobs, Svenja; Stallmann, Christoph; Pigeot, Iris

2015-08-01

Cohort studies provide the best evidence of all epidemiological observational studies for the identification of causal relationships between risk factors and diseases. However, this design may lead to drawbacks that may affect the validity and reliability of the results. This follows in particular from systematic errors, such as selection bias or recall bias. One possibility to avoid or counteract some of these drawbacks is to link primary data from cohort studies with secondary and register data. The linkage of these data may also be used for mutual validations. Data that were previously linked with primary data within the context of cohort studies in Germany were obtained from statutory health insurances and pensions as well as data from the Federal Employment Agency and cancer registries. All these data have two features in common: First, they all cover detailed information about a large population and over a long period of time. Second, all sources are in principle able to provide data on an individual level such that an individual data linkage, e.g. with primary data, is possible. However, use and linkage of each of these data sources are restricted by several limitations. These have to be accounted for as well as numerous legal restrictions that exist in Germany to especially prevent the misuse of social data.

External adjustment sensitivity analysis for unmeasured confounding: an application to coronary stent outcomes, Pennsylvania 2004-2008.

PubMed

Huesch, Marco D

2013-06-01

Assessing the real-world comparative effectiveness of common interventions is challenged by unmeasured confounding. To determine whether the mortality benefit shown for drug-eluting stents (DES) over bare metal stents (BMS) in observational studies persists after controls for/tests for confounding. Retrospective observational study involving 38,019 patients, 65 years or older admitted for an index percutaneous coronary intervention receiving DES or BMS in Pennsylvania in 2004-2005 followed up for death through 3 years. Analysis was at the patient level. Mortality was analyzed with Cox proportional hazards models allowing for stratification by disease severity or DES use propensity, accounting for clustering of patients. Instrumental variables analysis used lagged physician stent usage to proxy for the focal stent type decision. A method originating in work by Cornfield and others in 1954 and popularized by Greenland in 1996 was used to assess robustness to confounding. DES was associated with a significantly lower adjusted risk of death at 3 years in Cox and in instrumented analyses. An implausibly strong hypothetical unobserved confounder would be required to fully explain these results. Confounding by indication can bias observational studies. No strong evidence of such selection biases was found in the reduced risk of death among elderly patients receiving DES instead of BMS in a Pennsylvanian state-wide population. © Health Research and Educational Trust.

New options for national population surveys: The implications of internet and smartphone coverage.

PubMed

Couper, Mick P; Gremel, Garret; Axinn, William; Guyer, Heidi; Wagner, James; West, Brady T

2018-07-01

Challenges to survey data collection have increased the costs of social research via face-to-face surveys so much that it may become extremely difficult for social scientists to continue using these methods. A key drawback to less expensive Internet-based alternatives is the threat of biased results from coverage errors in survey data. The rise of Internet-enabled smartphones presents an opportunity to re-examine the issue of Internet coverage for surveys and its implications for coverage bias. Two questions (on Internet access and smartphone ownership) were added to the National Survey of Family Growth (NSFG), a U.S. national probability survey of women and men age 15-44, using a continuous sample design. We examine 16 quarters (4 years) of data, from September 2012 to August 2016. Overall, we estimate that 82.9% of the target NSFG population has Internet access, and 81.6% has a smartphone. Combined, this means that about 90.7% of U.S. residents age 15-44 have Internet access, via either traditional devices or a smartphone. We find some evidence of compensatory coverage when looking at key race/ethnicity and age subgroups. For instance, while Black teens (15-18) have the lowest estimated rate of Internet access (81.9%) and the lowest rate of smartphone usage (72.6%), an estimated 88.0% of this subgroup has some form of Internet access. We also examine the socio-demographic correlates of Internet and smartphone coverage, separately and combined, as indicators of technology access in this population. In addition, we look at the effect of differential coverage on key estimates produced by the NSFG, related to fertility, family formation, and sexual activity. While this does not address nonresponse or measurement biases that may differ for alternative modes, our paper has implications for possible coverage biases that may arise when switching to a Web-based mode of data collection, either for follow-up surveys or to replace the main face-to-face data collection. Copyright © 2018. Published by Elsevier Inc.

The de novo Transcriptome and Its Analysis in the Worldwide Vegetable Pest, Delia antiqua (Diptera: Anthomyiidae)

PubMed Central

Zhang, Yu-Juan; Hao, Youjin; Si, Fengling; Ren, Shuang; Hu, Ganyu; Shen, Li; Chen, Bin

2014-01-01

The onion maggot Delia antiqua is a major insect pest of cultivated vegetables, especially the onion, and a good model to investigate the molecular mechanisms of diapause. To better understand the biology and diapause mechanism of the insect pest species, D. antiqua, the transcriptome was sequenced using Illumina paired-end sequencing technology. Approximately 54 million reads were obtained, trimmed, and assembled into 29,659 unigenes, with an average length of 607 bp and an N50 of 818 bp. Among these unigenes, 21,605 (72.8%) were annotated in the public databases. All unigenes were then compared against Drosophila melanogaster and Anopheles gambiae. Codon usage bias was analyzed and 332 simple sequence repeats (SSRs) were detected in this organism. These data represent the most comprehensive transcriptomic resource currently available for D. antiqua and will facilitate the study of genetics, genomics, diapause, and further pest control of D. antiqua. PMID:24615268

How retellings shape younger and older adults' memories.

PubMed

Barber, Sarah J; Mather, Mara

2014-04-01

The way a story is retold influences the way it is later remembered; after retelling an event in a biased manner people subsequently remember the event in line with their distorted retelling. This study tested the hypothesis that this should be especially true for older adults. To test this, older and younger adults retold a story to be entertaining, to be accurate, or did not complete an initial retelling. Later, all participants recalled the story as accurately as possible. On this final test younger adults were unaffected by how they had previously retold the story. In contrast, older adults had better memory for the story's content and structure if they had previously retold the story accurately. Furthermore, for older adults, greater usage of storytelling language during the retelling was associated with lower subsequent recall. In summary, retellings exerted a greater effect on memory in older, compared with younger, adults.

A generative tool for building health applications driven by ISO 13606 archetypes.

PubMed

Menárguez-Tortosa, Marcos; Martínez-Costa, Catalina; Fernández-Breis, Jesualdo Tomás

2012-10-01

The use of Electronic Healthcare Records (EHR) standards in the development of healthcare applications is crucial for achieving the semantic interoperability of clinical information. Advanced EHR standards make use of the dual model architecture, which provides a solution for clinical interoperability based on the separation of the information and knowledge. However, the impact of such standards is biased by the limited availability of tools that facilitate their usage and practical implementation. In this paper, we present an approach for the automatic generation of clinical applications for the ISO 13606 EHR standard, which is based on the dual model architecture. This generator has been generically designed, so it can be easily adapted to other dual model standards and can generate applications for multiple technological platforms. Such good properties are based on the combination of standards for the representation of generic user interfaces and model-driven engineering techniques.

Expression of recombinant myostatin propeptide pPIC9K-Msp plasmid in Pichia pastoris.

PubMed

Du, W; Xia, J; Zhang, Y; Liu, M J; Li, H B; Yan, X M; Zhang, J S; Li, N; Zhou, Z Y; Xie, W Z

2015-12-28

Myostatin propeptide can inhibit the biological activity of myostatin protein and promote muscle growth. To express myostatin propeptide in vitro with a higher biological activity, we performed codon optimization on the sheep myostatin propeptide gene sequence, and mutated aspartic acid-76 to alanine based on the codon usage bias of Pichia pastoris and the enhanced biological activity of myostatin propeptide mutant. Modified myostatin propeptide gene was cloned into the pPIC9K plasmid to form the recombinant plasmid pPIC9K-Msp. Recombinant plasmid pPIC9K-Msp was transformed into Pichia pastoris GS115 by electrotransformation. Transformed cells were screened, and methanol was used to induce expression. SDS-PAGE and western blotting were used to verify the successful expression of myostatin propeptide with biological activity in Pichia pastoris, providing the basis for characterization of this protein.

Efficient Coproduction of Mannanase and Cellulase by the Transformation of a Codon-Optimized Endomannanase Gene from Aspergillus niger into Trichoderma reesei.

PubMed

Sun, Xianhua; Xue, Xianli; Li, Mengzhu; Gao, Fei; Hao, Zhenzhen; Huang, Huoqing; Luo, Huiying; Qin, Lina; Yao, Bin; Su, Xiaoyun

2017-12-20

Cellulase and mannanase are both important enzyme additives in animal feeds. Expressing the two enzymes simultaneously within one microbial host could potentially lead to cost reductions in the feeding of animals. For this purpose, we codon-optimized the Aspergillus niger Man5A gene to the codon-usage bias of Trichoderma reesei. By comparing the free energies and the local structures of the nucleotide sequences, one optimized sequence was finally selected and transformed into the T. reesei pyridine-auxotrophic strain TU-6. The codon-optimized gene was expressed to a higher level than the original one. Further expressing the codon-optimized gene in a mutated T. reesei strain through fed-batch cultivation resulted in coproduction of cellulase and mannanase up to 1376 U·mL -1 and 1204 U·mL -1 , respectively.

How to manipulate magnetic states of antiferromagnets

NASA Astrophysics Data System (ADS)

Song, Cheng; You, Yunfeng; Chen, Xianzhe; Zhou, Xiaofeng; Wang, Yuyan; Pan, Feng

2018-03-01

Antiferromagnetic materials, which have drawn considerable attention recently, have fascinating features: they are robust against perturbation, produce no stray fields, and exhibit ultrafast dynamics. Discerning how to efficiently manipulate the magnetic state of an antiferromagnet is key to the development of antiferromagnetic spintronics. In this review, we introduce four main methods (magnetic, strain, electrical, and optical) to mediate the magnetic states and elaborate on intrinsic origins of different antiferromagnetic materials. Magnetic control includes a strong magnetic field, exchange bias, and field cooling, which are traditional and basic. Strain control involves the magnetic anisotropy effect or metamagnetic transition. Electrical control can be divided into two parts, electric field and electric current, both of which are convenient for practical applications. Optical control includes thermal and electronic excitation, an inertia-driven mechanism, and terahertz laser control, with the potential for ultrafast antiferromagnetic manipulation. This review sheds light on effective usage of antiferromagnets and provides a new perspective on antiferromagnetic spintronics.

Interval Predictor Models for Data with Measurement Uncertainty

NASA Technical Reports Server (NTRS)

Lacerda, Marcio J.; Crespo, Luis G.

2017-01-01

An interval predictor model (IPM) is a computational model that predicts the range of an output variable given input-output data. This paper proposes strategies for constructing IPMs based on semidefinite programming and sum of squares (SOS). The models are optimal in the sense that they yield an interval valued function of minimal spread containing all the observations. Two different scenarios are considered. The first one is applicable to situations where the data is measured precisely whereas the second one is applicable to data subject to known biases and measurement error. In the latter case, the IPMs are designed to fully contain regions in the input-output space where the data is expected to fall. Moreover, we propose a strategy for reducing the computational cost associated with generating IPMs as well as means to simulate them. Numerical examples illustrate the usage and performance of the proposed formulations.

[Genomics and transcriptomics of the Chinese liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda)].

PubMed

Chelomina, G N

2017-01-01

The review summarizes the results of first genomic and transcriptomic investigations of the liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda). The studies mark the dawn of the genomic era for opisthorchiids, which cause severe hepatobiliary diseases in humans and animals. Their results aided in understanding the molecular mechanisms of adaptation to parasitism, parasite survival in mammalian biliary tracts, and genome dynamics in the individual development and the development of parasite-host relationships. Special attention is paid to the achievements in studying the codon usage bias and the roles of mobile genetic elements (MGEs) and small interfering RNAs (siRNAs). Interspecific comparisons at the genomic and transcriptomic levels revealed molecular differences, which may contribute to understanding the specialized niches and physiological needs of the respective species. The studies in C. sinensis provide a basis for further basic and applied research in liver flukes and, in particular, the development of efficient means to prevent, diagnose, and treat clonorchiasis.

Yeast Kluyveromyces lactis as host for expression of the bacterial lipase: cloning and adaptation of the new lipase gene from Serratia sp.

PubMed

Šiekštelė, Rimantas; Veteikytė, Aušra; Tvaska, Bronius; Matijošytė, Inga

2015-10-01

Many microbial lipases have been successfully expressed in yeasts, but not in industrially attractive Kluyveromyces lactis, which among other benefits can be cultivated on a medium supplemented with whey--cheap and easily available industrial waste. A new bacterial lipase from Serratia sp. was isolated and for the first time expressed into the yeast Kluyveromyces lactis by heterologous protein expression system based on a strong promoter of Kluyveromyces marxianus triosephosphate isomerase gene and signal peptide of Kluyveromyces marxianus endopolygalacturonase gene. In addition, the bacterial lipase gene was synthesized de novo by taking into account a codon usage bias optimal for K. lactis and was expressed into the yeast K. lactis also. Both resulting strains were characterized by high output level of the target protein secreted extracellularly. Secreted lipases were characterized for activity and stability.

Factors associated with good compliance and long-term sustainability in a practitioner-based livestock disease surveillance system.

PubMed

Zurbrigg, Katherine J; Van den Borre, Nicole M

2013-03-01

The Ontario Farm call Surveillance Project (OFSP) was a practitioner-based, syndromic surveillance system for livestock disease. Three data-recording methods (paper, web-based, and handheld electronic) used by participating veterinarians were compared for timeliness (when the report arrived at the OFSP office), completeness of the report, and the usage and costs of incentives offered to veterinarians as compensation for their time to record data. There were no statistically significant differences in these parameters among the 3 data-recording methods. This indicates that different data-recording methods can be used within a single veterinary surveillance program while maintaining data integrity and timely reporting. Factors such as ease of data collection and providing incentives valued by veterinarians ensured high compliance and long-term participation in the project. It also increased the diversity of the participant group, reducing the likelihood of biased data submissions.

Strive toward data harmony of multi sensor aerosol data - Tribute to Dr. Gregory Leptoukh

NASA Astrophysics Data System (ADS)

Wei, J. C.; Lynnes, C.; Kempler, S. J.; Shen, S.

2012-12-01

The Goddard Earth Sciences Data and Information Services Center (GES DISC) has been involved with aerosol data synergy activities and projects over recent years, led by Dr. Gregory Leptoukh. His particular interests centered on issues related to comparison and harmonization of several aspects of aerosol data, such as data quality, bias adjustment, and data provenance. A thorough understanding of these issues is needed to guide multi-sensor data usage and avoid apples-to-oranges inter-comparison and data fusion. In this talk, I will highlight these activities/projects. These would include the tools developed, but also the projects that address specific user needs and innovative services, such as GIOVANNI-MAPSS, AeroStat, NEESPI, MAIRS, ATDD, MDSA, LTA-SWDB, etc. I will also discuss preliminary results from new projects and future goals that build on the ground breaking work, left by Dr. Leptoukh.

How retellings shape younger and older adults’ memories

PubMed Central

Mather, Mara

2014-01-01

The way a story is retold influences the way it is later remembered; after retelling an event in a biased manner people subsequently remember the event in line with their distorted retelling. This study tested the hypothesis that this should be especially true for older adults. To test this, older and younger adults retold a story to be entertaining, to be accurate, or did not complete an initial retelling. Later, all participants recalled the story as accurately as possible. On this final test younger adults were unaffected by how they had previously retold the story. In contrast, older adults had better memory for the story’s content and structure if they had previously retold the story accurately. Furthermore, for older adults, greater usage of storytelling language during the retelling was associated with lower subsequent recall. In summary, retellings exerted a greater effect on memory in older, compared with younger, adults. PMID:25436107

Equation Discovery for Model Identification in Respiratory Mechanics of the Mechanically Ventilated Human Lung

NASA Astrophysics Data System (ADS)

Ganzert, Steven; Guttmann, Josef; Steinmann, Daniel; Kramer, Stefan

Lung protective ventilation strategies reduce the risk of ventilator associated lung injury. To develop such strategies, knowledge about mechanical properties of the mechanically ventilated human lung is essential. This study was designed to develop an equation discovery system to identify mathematical models of the respiratory system in time-series data obtained from mechanically ventilated patients. Two techniques were combined: (i) the usage of declarative bias to reduce search space complexity and inherently providing the processing of background knowledge. (ii) A newly developed heuristic for traversing the hypothesis space with a greedy, randomized strategy analogical to the GSAT algorithm. In 96.8% of all runs the applied equation discovery system was capable to detect the well-established equation of motion model of the respiratory system in the provided data. We see the potential of this semi-automatic approach to detect more complex mathematical descriptions of the respiratory system from respiratory data.

Factors associated with good compliance and long-term sustainability in a practitioner-based livestock disease surveillance system

PubMed Central

Zurbrigg, Katherine J.; Van den Borre, Nicole M.

2013-01-01

The Ontario Farm call Surveillance Project (OFSP) was a practitioner-based, syndromic surveillance system for livestock disease. Three data-recording methods (paper, web-based, and handheld electronic) used by participating veterinarians were compared for timeliness (when the report arrived at the OFSP office), completeness of the report, and the usage and costs of incentives offered to veterinarians as compensation for their time to record data. There were no statistically significant differences in these parameters among the 3 data-recording methods. This indicates that different data-recording methods can be used within a single veterinary surveillance program while maintaining data integrity and timely reporting. Factors such as ease of data collection and providing incentives valued by veterinarians ensured high compliance and long-term participation in the project. It also increased the diversity of the participant group, reducing the likelihood of biased data submissions. PMID:23997260

Gender differences and pain medication.

PubMed

Richardson, Jen; Holdcroft, Anita

2009-01-01

Subtle genetic and psychological variations are increasingly recognized to contribute to pain and analgesic efficacy and safety. The influence of sex on this relationship remains poorly understood, particularly in humans. The issue is complicated by the overlay of gender onto physical sex, and its associated stereotypes and expectations. Women appear to use more pain-relieving medications than men; however, it remains unclear whether these observations represent true differences in analgesic usage patterns, or reporting bias. Differences in analgesic efficacy relating to body composition, metabolism and hormonal profiles have been demonstrated. Psychological and social elements of gender have also been associated with altered pain experiences and analgesic use profiles, albeit with significant individual variations. Intra-group differences may ultimately prove more important than sex differences. Further research may unravel the various threads linking gender and sex effects on analgesia with the aim of individualizing analgesia to optimize pain relief.

Effect of air-blowing duration on the bond strength of current one-step adhesives to dentin.

PubMed

Fu, Jiale; Saikaew, Pipop; Kawano, Shimpei; Carvalho, Ricardo M; Hannig, Matthias; Sano, Hidehiko; Selimovic, Denis

2017-08-01

To evaluate the influence of different air-blowing durations on the micro-tensile bond strength (μTBS) of five current one-step adhesive systems to dentin. One hundred and five caries-free human molars and five current one-step adhesive systems were used: ABU (All Bond Universal, Bisco, Inc.), CUB (CLEARFIL™ Universal Bond, Kuraray), GPB (G-Premio BOND, GC), OBA (OptiBond All-in-one, Kerr) and SBU (Scotchbond Universal, 3M ESPE). The adhesives were applied to 600 SiC paper-flat dentin surfaces according to each manufacturer's instructions and were air-dried with standard, oil-free air pressure of 0.25MPa for either 0s, 5s, 15s or 30s before light-curing. Bond strength to dentin was determined by using μTBS test after 24h of water storage. The fracture pattern on the dentin surface was analyzed by SEM. The resin-dentin interface of untested specimens was visualized by panoramic SEM image. Data from μTBS were analyzed using two-way ANOVA (adhesive vs. air-blowing time), and Games-Howell (a=0.05). Two-way ANOVA revealed a significant effect of materials (p=0.000) and air-blowing time (p=0.000) on bond strength to dentin. The interaction between factors was also significantly different (p=0.000). Maximum bond strength for each system were recorded, OBA/15s (76.34±19.15MPa), SBU/15s (75.18±12.83MPa), CUB/15s (68.23±16.36MPa), GPB/30s (55.82±12.99MPa) and ABU/15s (44.75±8.95MPa). The maximum bond strength of OBA and SUB were significantly higher than that of GPB and ABU (p<0.05). The bond strength of the current one-step adhesive systems is material-dependent (p=0.000), and was influenced by air-blowing duration (p=0.000). For the current one-step adhesive systems, higher bond strengths could be achieved with prolonged air-blowing duration between 15-30s. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Geographical Area and Life History Traits Influence Diet in an Arctic Marine Predator

PubMed Central

2016-01-01

Global changes are thought to affect most Arctic species, yet some populations are more at risk. Today, the Barents Sea ecoregion is suffering the strongest sea ice retreat ever measured; and these changes are suspected to modify food access and thus diet of several species. Biochemical diet tracers enable investigation of diet in species such as polar bears (Ursus maritimus). We examined individual diet variation of female polar bears in Svalbard, Norway, and related it to year, season (spring and autumn), sampling area and breeding status (solitary, with cubs of the year or yearlings). Sampling areas were split according to their ice cover: North-West (less sea ice cover), South-East (larger amplitude in sea ice extent) and North-East/South-West (NESW) as bears from that zone are more mobile among all regions of Svalbard. We measured fatty acid (FA) composition in adipose tissue and carbon (δ13C) and nitrogen (δ15N) stable isotopes in plasma and red blood cells. Females feeding in the North-West area had lower δ15N values than those from the NESW. In South-East females, δ13C values were lower in autumn compared to spring and females seemed less selective in their diet as depicted by large variances in stable isotope values. Considering the differences in FA composition and stable isotope values, we suggest that females from the North-West and South-East could ingest a higher proportion of avian prey. With regard to breeding status, solitary females had higher δ15N values and smaller variance in their stable isotopic values than females with cubs, suggesting that solitary females were more selective and prey on higher trophic level species (i.e. seals). Overall, our results indicate that prey availability for Svalbard polar bears varies according to geographical area and prey selectivity differs according to breeding status. Our findings suggest that complex changes in sea ice and prey availability will interact to affect Svalbard polar bear feeding patterns and associated nutrition. PMID:27196700

Geographical Area and Life History Traits Influence Diet in an Arctic Marine Predator.

PubMed

Tartu, Sabrina; Bourgeon, Sophie; Aars, Jon; Andersen, Magnus; Ehrich, Dorothee; Thiemann, Gregory W; Welker, Jeffrey M; Routti, Heli

2016-01-01

Global changes are thought to affect most Arctic species, yet some populations are more at risk. Today, the Barents Sea ecoregion is suffering the strongest sea ice retreat ever measured; and these changes are suspected to modify food access and thus diet of several species. Biochemical diet tracers enable investigation of diet in species such as polar bears (Ursus maritimus). We examined individual diet variation of female polar bears in Svalbard, Norway, and related it to year, season (spring and autumn), sampling area and breeding status (solitary, with cubs of the year or yearlings). Sampling areas were split according to their ice cover: North-West (less sea ice cover), South-East (larger amplitude in sea ice extent) and North-East/South-West (NESW) as bears from that zone are more mobile among all regions of Svalbard. We measured fatty acid (FA) composition in adipose tissue and carbon (δ13C) and nitrogen (δ15N) stable isotopes in plasma and red blood cells. Females feeding in the North-West area had lower δ15N values than those from the NESW. In South-East females, δ13C values were lower in autumn compared to spring and females seemed less selective in their diet as depicted by large variances in stable isotope values. Considering the differences in FA composition and stable isotope values, we suggest that females from the North-West and South-East could ingest a higher proportion of avian prey. With regard to breeding status, solitary females had higher δ15N values and smaller variance in their stable isotopic values than females with cubs, suggesting that solitary females were more selective and prey on higher trophic level species (i.e. seals). Overall, our results indicate that prey availability for Svalbard polar bears varies according to geographical area and prey selectivity differs according to breeding status. Our findings suggest that complex changes in sea ice and prey availability will interact to affect Svalbard polar bear feeding patterns and associated nutrition.

Exposure to mixtures of organohalogen contaminants and associative interactions with thyroid hormones in East Greenland polar bears (Ursus maritimus).

PubMed

Villanger, Gro D; Jenssen, Bjørn M; Fjeldberg, Rita R; Letcher, Robert J; Muir, Derek C G; Kirkegaard, Maja; Sonne, Christian; Dietz, Rune

2011-05-01

We investigated the multivariate relationships between adipose tissue residue levels of 48 individual organohalogen contaminants (OHCs) and circulating thyroid hormone (TH) levels in polar bears (Ursus maritimus) from East Greenland (1999-2001, n=62), using projection to latent structure (PLS) regression for four groupings of polar bears; subadults (SubA), adult females with cubs (AdF_N), adult females without cubs (AdF_S) and adult males (AdM). In the resulting significant PLS models for SubA, AdF_N and AdF_S, some OHCs were especially important in explaining variations in circulating TH levels: polybrominated diphenylether (PBDE)-99, PBDE-100, PBDE-153, polychlorinated biphenyl (PCB)-52, PCB-118, cis-nonachlor, trans-nonachlor, trichlorobenzene (TCB) and pentachlorobenzene (QCB), and both negative and positive relationships with THs were found. In addition, the models revealed that DDTs had a positive influence on total 3,5,3'-triiodothyronine (TT3) in AdF_S, and that a group of 17 higher chlorinated ortho-PCBs had a positive influence on total 3,5,3',5'-tetraiodothyronine (thyroxine, TT4) in AdF_N. TH levels in AdM seemed less influenced by OHCs because of non-significant PLS models. TH levels were also influenced by biological factors such as age, sex, body size, lipid content of adipose tissue and sampling date. When controlling for biological variables, the major relationships from the PLS models for SubA, AdF_N and AdF_S were found significant in partial correlations. The most important OHCs that influenced TH levels in the significant PLS models may potentially act through similar mechanisms on the hypothalamic-pituitary-thyroid (HPT) axis, suggesting that both combined effects by dose and response addition and perhaps synergistic potentiation may be a possibility in these polar bears. Statistical associations are not evidence per se of biological cause-effect relationships. Still, the results of the present study indicate that OHCs may affect circulating TH levels in East Greenland polar bears, adding to the "weight of evidence" suggesting that OHCs might interfere with thyroid homeostasis in polar bears. Copyright © 2011 Elsevier Ltd. All rights reserved.

Grizzly bear denning chronology and movements in the Greater Yellowstone Ecosystem

USGS Publications Warehouse

Haroldson, Mark A.; Ternent, Mark A.; Gunther, Kerry A.; Schwartz, Charles C.

2002-01-01

Den entrance and emergence dates of grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem are important to management agencies that wish to minimize impacts of human activities on bears. Current estimates for grizzly bear denning events use data that were collected from 1975–80. We update these estimates by including data obtained from 1981–99. We used aerial telemetry data to estimate week of den entry and emergence by determining the midpoint between the last known active date and the first known date denned, as well as the last known date denned and the first known active date. We also investigated post emergence movement patterns relative to den locations. Mean earliest and latest week of den entry and emergence were also determined. Den entry for females began during the fourth week in September, with 90% denned by the fourth week of November. Earliest den entry for males occurred during the second week of October, with 90% denned by the second week of December. Mean week of den entry for known pregnant females was earlier than males. Earliest week of den entry for known pregnant females was earlier than other females and males. Earliest den emergence for males occurred during the first week of February, with 90% of males out of dens by the fourth week of April. Earliest den emergence for females occurred during the third week of March; by the first week of May, 90% of females had emerged. Male bears emerged from dens earlier than females. Denning period differed among classes and averaged 171 days for females that emerged from dens with cubs, 151 days for other females, and 131 days for males. Known pregnant females tended to den at higher elevations and, following emergence, remained at higher elevation until late May. Females with cubs remained relatively close (<3 km) to den sites until the last 2 weeks in May. Timing of denning events was similar to previous estimates for this and other grizzly bear populations in the southern Rocky Mountains. 

Characterization of microstructure and texture across dissimilar super duplex/austenitic stainless steel weldment joint by austenitic filler metal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eghlimi, Abbas, E-mail: a.eghlimi@ma.iut.ac.ir; Shamanian, Morteza; Eskandarian, Masoomeh

The evolution of microstructure and texture across an as-welded dissimilar UNS S32750 super duplex/UNS S30403 austenitic stainless steel joint welded by UNS S30986 (AWS A5.9 ER309LMo) austenitic stainless steel filler metal using gas tungsten arc welding process was evaluated by optical micrography and EBSD techniques. Due to their fabrication through rolling process, both parent metals had texture components resulted from deformation and recrystallization. The weld metal showed the highest amount of residual strain and had large austenite grain colonies of similar orientations with little amounts of skeletal ferrite, both oriented preferentially in the < 001 > direction with cub-on-cube orientationmore » relationship. While the super duplex stainless steel's heat affected zone contained higher ferrite than its parent metal, an excessive grain growth was observed at the austenitic stainless steel's counterpart. At both heat affected zones, austenite underwent some recrystallization and formed twin boundaries which led to an increase in the fraction of high angle boundaries as compared with the respective base metals. These regions showed the least amount of residual strain and highest amount of recrystallized austenite grains. Due to the static recrystallization, the fraction of low degree of fit (Σ) coincident site lattice boundaries, especially Σ3 boundaries, was increased in the austenitic stainless steel heat affected zone, while the formation of subgrains in the ferrite phase increased the content of < 5° low angle boundaries at that of the super duplex stainless steel. - Graphical abstract: Display Omitted - Highlights: • Extensive grain growth in the HAZ of austenitic stainless steel was observed. • Intensification of < 100 > orientated grains was observed adjacent to both fusion lines. • Annealing twins with Σ3 CSL boundaries were formed in the austenite of both HAZ. • Cub-on-cube OR was observed between austenite and ferrite in the weld metal. • Weld metal had the lowest texture intensity and ratio of low angle and CSL boundaries.« less

Benefiting from a migratory prey: spatio-temporal patterns in allochthonous subsidization of an Arctic predator.

PubMed

Giroux, Marie-Andrée; Berteaux, Dominique; Lecomte, Nicolas; Gauthier, Gilles; Szor, Guillaume; Bêty, Joël

2012-05-01

1. Flows of nutrients and energy across ecosystem boundaries have the potential to subsidize consumer populations and modify the dynamics of food webs, but how spatio-temporal variations in autochthonous and allochthonous resources affect consumers' subsidization remains largely unexplored. 2. We studied spatio-temporal patterns in the allochthonous subsidization of a predator living in a relatively simple ecosystem. We worked on Bylot Island (Nunavut, Canada), where arctic foxes (Vulpes lagopus L.) feed preferentially on lemmings (Lemmus trimucronatus and Dicrostonyx groenlandicus Traill), and alternatively on colonial greater snow geese (Anser caerulescens atlanticus L.). Geese migrate annually from their wintering grounds (where they feed on farmlands and marshes) to the Canadian Arctic, thus generating a strong flow of nutrients and energy across ecosystem boundaries. 3. We examined the influence of spatial variations in availability of geese on the diet of fox cubs (2003-2005) and on fox reproductive output (1996-2005) during different phases of the lemming cycle. 4. Using stable isotope analysis and a simple statistical routine developed to analyse the outputs of a multisource mixing model (SIAR), we showed that the contribution of geese to the diet of arctic fox cubs decreased with distance from the goose colony. 5. The probability that a den was used for reproduction by foxes decreased with distance from the subsidized goose colony and increased with lemming abundance. When lemmings were highly abundant, the effect of distance from the colony disappeared. The goose colony thus generated a spatial patterning of reproduction probability of foxes, while the lemming cycle generated a strong temporal variation of reproduction probability of foxes. 6. This study shows how the input of energy owing to the large-scale migration of prey affects the functional and reproductive responses of an opportunistic consumer, and how this input is spatially and temporally modulated through the foraging behaviour of the consumer. Thus, perspectives of both landscape and foraging ecology are needed to fully resolve the effects of subsidies on animal demographic processes and population dynamics. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Risk Factors for Obesity at Age 3 in Alaskan Children, Including the Role of Beverage Consumption: Results from Alaska PRAMS 2005-2006 and Its Three-Year Follow-Up Survey, CUBS, 2008-2009

PubMed Central

Wojcicki, Janet M.; Young, Margaret B.; Perham-Hester, Katherine A.; de Schweinitz, Peter; Gessner, Bradford D.

2015-01-01

Background Prenatal and early life risk factors are associated with childhood obesity. Alaska Native children have one of the highest prevalences of childhood obesity of all US racial/ethnic groups. Methods Using the Pregnancy Risk Assessment Monitoring System (PRAMS) and the follow-up survey at 3 years of age (CUBS), we evaluated health, behavioral, lifestyle and nutritional variables in relation to obesity (95th percentile for body mass index (BMI)) at 3 years of age. Multivariate logistic regression modeling was conducted using Stata 12.0 to evaluate independent risk factors for obesity in non-Native and Alaska Native children. Results We found an obesity prevalence of 24.9% in all Alaskan and 42.2% in Alaska Native 3 year olds. Among Alaska Native children, obesity prevalence was highest in the Northern/Southwest part of the state (51.6%, 95%CI (42.6-60.5)). Independent predictive factors for obesity at age 3 years in Alaska non-Native children were low income (<$10,000 in the year before the child was born (OR 3.94, 95%CI 1.22--17.03) and maternal pre-pregnancy obesity (OR 2.01, 95%CI 1.01-4.01) and longer duration of breastfeeding was protective (OR 0.95, 95%CI 0.91-0.995). Among Alaska Native children, predictive factors were witnessing domestic violence/abuse as a 3 year-old (OR 2.28, 95%CI 1.17-7.60). Among obese Alaska Native children, there was an increased daily consumption of energy dense beverages in the Northern/Southwest region of the state, which may explain higher rates of obesity in this part of the state. Conclusions The high prevalence of obesity in Alaska Native children may be explained by differences in lifestyle patterns and food consumption in certain parts of the state, specifically the Northern/Southwest region, which have higher consumption of energy dense beverages. PMID:25793411

Availability, usage, and factors affecting usage of electrophysical agents by physical therapists: a regional cross-sectional survey

PubMed Central

Abe, Yuichi; Goh, Ah-Cheng; Miyoshi, Kei

2016-01-01

[Purpose] The aim of this study was to investigate the availability, usage, and factors affecting usage of electrophysical agents by physical therapists in Nagano Prefecture, Japan. [Subjects and Methods] Questionnaires were sent to all 1,571 physical therapists working in 245 institutions within Nagano Prefecture. A total of 1,110 questionnaires were returned, out of which 1,099 (70%) questionnaires containing valid responses were analyzed. Frequencies and percentages were calculated for 22 modalities with regards to availability, usage, rate of usage, and confidence level in usage. Factors affecting usage and the relationship between rate of usage and confidence level (Spearman’s rho) were also determined. [Results] The top three responses for the various outcome measures were as follows: (1) hot packs (88%), low frequency stimulators (76%), and ultrasound (68%) for availability; (2) hot packs (72%), ultrasound (61%), and cold packs (59%) for usage; (3) hot packs (75%), cold spray (49%), and ultrasound (44%) for confidence in usage; and (4) equipment availability (80%), past experience (79%), and research evidence (78%) for factors affecting usage. There was a significant positive relationship between confidence and usage for all modalities, except for ultraviolet radiation, iontophoresis, and magnetic field. [Conclusion] Usage was strongly correlated with confidence, with the top three used modalities also being the ones with the highest confidence in usage. PMID:27942126

The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae)

PubMed Central

Salvato, Paola; Simonato, Mauro; Battisti, Andrea; Negrisolo, Enrico

2008-01-01

Background Knowledge of animal mitochondrial genomes is very important to understand their molecular evolution as well as for phylogenetic and population genetic studies. The Lepidoptera encompasses more than 160,000 described species and is one of the largest insect orders. To date only nine lepidopteran mitochondrial DNAs have been fully and two others partly sequenced. Furthermore the taxon sampling is very scant. Thus advance of lepidopteran mitogenomics deeply requires new genomes derived from a broad taxon sampling. In present work we describe the mitochondrial genome of the moth Ochrogaster lunifer. Results The mitochondrial genome of O. lunifer is a circular molecule 15593 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. It contains also 7 intergenic spacers. The gene order of the newly sequenced genome is that typical for Lepidoptera and differs from the insect ancestral type for the placement of trnM. The 77.84% A+T content of its α strand is the lowest among known lepidopteran genomes. The mitochondrial genome of O. lunifer exhibits one of the most marked C-skew among available insect Pterygota genomes. The protein-coding genes have typical mitochondrial start codons except for cox1 that present an unusual CGA. The O. lunifer genome exhibits the less biased synonymous codon usage among lepidopterans. Comparative genomics analysis study identified atp6, cox1, cox2 as cox3, cob, nad1, nad2, nad4, and nad5 as potential markers for population genetics/phylogenetics studies. A peculiar feature of O. lunifer mitochondrial genome it that the intergenic spacers are mostly made by repetitive sequences. Conclusion The mitochondrial genome of O. lunifer is the first representative of superfamily Noctuoidea that account for about 40% of all described Lepidoptera. New genome shares many features with other known lepidopteran genomes. It differs however for its low A+T content and marked C-skew. Compared to other lepidopteran genomes it is less biased in synonymous codon usage. Comparative evolutionary analysis of lepidopteran mitochondrial genomes allowed the identification of previously neglected coding genes as potential phylogenetic markers. Presence of repetitive elements in intergenic spacers of O. lunifer genome supports the role of DNA slippage as possible mechanism to produce spacers during replication. PMID:18627592

Analysis of the use of codon pairs in the HE gene of the ISA virus shows a correlation between bias in HPR codon-pair use and mortality rates caused by the virus

PubMed Central

2013-01-01

Background Segment 6 of the ISA virus codes for hemoagglutinin-esterase (HE). This segment is highly variable, with more than 26 variants identified. The major variation is observed in what is called the high polymorphism region (HPR). The role of the different HPR zones in the viral cycle or evolution remains unknown. However viruses that present the HPR0 are avirulent, while viruses with important deletions in this region have been responsible for outbreaks with high mortality rates. In this work, using bioinformatic tools, we examined the influence of different HPRs on the adaptation of HE genes to the host translational machinery and the relationship to observed virulence. Methods Translational efficiency of HE genes and their HPR were estimated analyzing codon-pair bias (CPB), adaptation to host codon use (codon adaptation index - CAI) and the adaptation to available tRNAs (tAI). These values were correlated with reported mortality for the respective ISA virus and the ΔG of RNA folding. tRNA abundance was inferred from tRNA gene numbers identified in the Salmo salar genome using tRNAScan-SE. Statistical correlation between data was performed using a non-parametric test. Results We found that HPR0 contains zones with codon pairs of low frequency and low availability of tRNA with respect to salmon codon-pair usage, suggesting that HPR modifies HE translational efficiency. Although calculating tAI was impossible because one third of tRNAs (~60.000) were tRNA-ala, translational efficiency measured by CPB shows that as HPR size increases, the CPB value of the HE gene decreases (P = 2x10-7, ρ = −0.675, n = 63) and that these values correlate positively with the mortality rates caused by the virus (ρ = 0.829, P = 2x10-7, n = 11). The mortality associated with different virus isolates or their corresponding HPR sizes were not related with the ΔG of HPR RNA folding, suggesting that the secondary structure of HPR RNA does not modify virulence. Conclusions Our results suggest that HPR size affects the efficiency of gene translation, which modulates the virulence of the virus by a mechanism similar to that observed in production of live attenuated vaccines through deoptimization of codon-pair usage. PMID:23742749

On-board computer progress in development of A 310 flight testing program

NASA Technical Reports Server (NTRS)

Reau, P.

1981-01-01

Onboard computer progress in development of an Airbus A 310 flight testing program is described. Minicomputers were installed onboard three A 310 airplanes in 1979 in order to: (1) assure the flight safety by exercising a limit check of a given set of parameters; (2) improve the efficiency of flight tests and allow cost reduction; and (3) perform test analysis on an external basis by utilizing onboard flight types. The following program considerations are discussed: (1) conclusions based on simulation of an onboard computer system; (2) brief descriptions of A 310 airborne computer equipment, specifically the onboard universal calculator (CUB) consisting of a ROLM 1666 system and visualization system using an AFIGRAF CRT; (3) the ground system and flight information inputs; and (4) specifications and execution priorities for temporary and permanent programs.

Implementation of clinical practice guidelines on lifestyle interventions in Swedish primary healthcare - a two-year follow up.

PubMed

Kardakis, Therese; Jerdén, Lars; Nyström, Monica E; Weinehall, Lars; Johansson, Helene

2018-04-02

Implementation of interventions concerning prevention and health promotion in health care has faced particular challenges resulting in a low frequency and quality of these services. In November 2011, the Swedish National Board of Health and Welfare released national clinical practice guidelines to counteract patients' unhealthy lifestyle habits. Drawing on the results of a previous study as a point of departure, the aim of this two-year follow up was to assess the progress of work with lifestyle interventions in primary healthcare as well as the uptake and usage of the new guidelines on lifestyle interventions in clinical practice. Longitudinal study among health professionals with survey at baseline and 2 years later. Development over time and differences between professional groups were calculated with Pearson chi-square test. Eighteen percent of the physicians reported to use the clinical practice guidelines, compared to 58% of the nurses. Nurses were also more likely to consider them as a support in their work than physicians did. Over time, health professionals usage of methods to change patients' tobacco habits and hazardous use of alcohol had increased, and the nurses worked to a higher extent than before with all four lifestyles. Knowledge on methods for lifestyle change was generally high; however, there was room for improvement concerning methods on alcohol, unhealthy eating and counselling. Forty-one percent reported to possess thorough knowledge of counselling skills. Even if the uptake and usage of the CPGs on lifestyle interventions so far is low, the participants reported more frequent counselling on patients' lifestyle changes concerning use of tobacco and hazardous use of alcohol. However, these findings should be evaluated acknowledging the possibility of selection bias in favour of health promotion and lifestyle guidance, and the loss of one study site in the follow up. Furthermore, this study indicates important differences in physicians and nurses' attitudes to and use of the guidelines, where the nurses reported working to a higher extent with all four lifestyles compared to the first study. These findings suggest further investigations on the implementation process in clinical practice, and the physicians' uptake and use of the CPGs.