bluuebunny/crossref_metadata_2025 huggingface dataset:
Sampling techniques for burbot in a western non‐wadeable river
Authors: Klein Z. B. , Quist M. C. , Rhea D. T. , Senecal A. C.
Published: April 2015

Burbot, Lota lota (L.), populations are declining throughout much of their native distribution. Although numerous aspects of burbot ecology are well understood, less is known about effective sampling techniques for burbot in lotic systems. Occupancy models were used to estimate the probability of detection () for three gears (6.4‐ and 19‐mm bar mesh hoop nets, night electric fishing), within the context of various habitat characteristics. During the summer, night electric fishing had the highest estimated detection probability for both juvenile (, 95% C.I.; 0.35, 0.26–0.46) and adult (0.30, 0.20–0.41) burbot. However, small‐mesh hoop nets (6.4‐mm bar mesh) had similar detection probabilities to night electric fishing for both juvenile (0.26, 0.17–0.36) and adult (0.27, 0.18–0.39) burbot during the summer. In autumn, a similar overlap between detection probabilities was observed for juvenile and adult burbot. Small‐mesh hoop nets had the highest estimated probability of detection for both juvenile and adult burbot (0.46, 0.33–0.59), whereas night electric fishing had a detection probability of 0.39 (0.28–0.52) for juvenile and adult burbot. By using detection probabilities to compare gears, the most effective sampling technique can be identified, leading to increased species detections and more effective management of burbot.
Recording and Accounting for Stakeholder Involvement in Systematic Reviews
Authors: Saan Marieke C. , Boeije Hennie R. , Sattoe Jane N. T. , Bal Marjolijn I. , Missler Marjolein , van Wesel Floryt
Published: April 2015

Objectives

The use of stakeholders in systematic reviews is increasingly valued, but their influence on the systematicity of the review is often unclear. The aim of this study was to describe some of the processes of involvement of stakeholders and to demonstrate a Tool for Recording and Accounting for Stakeholder Involvement (TRASI).

Methods

We demonstrate the TRASI in two worked examples. In one project, the reviewers collaborated with the end‐user and an expert during the literature search. In the other project, experts were consulted to generate keywords before searching the literature.

Results

In the first project, disagreements about keywords to identify studies for the research topic were solved by informal discussion. In the second project, difficulties arose in reaching agreement between experts and reviewers about the core construct and the meaningful keywords associated with it.

Discussion

The TRASI aids researchers to systematically and transparently account for the decisions taken. The TRASI supports information specialists and librarians to shape the search strategy to match the objectives of the review.

Conclusions

We propose the TRASI as a first step in resolving the challenges of detecting and reconstructing stakeholder influences. Potential new applications of the TRASI are discussed.
Parents of children with disabilities in Kuwait: a study of their information seeking behaviour
Authors: Al‐Daihani Sultan M. , Al‐Ateeqi Huda I.
Published: April 2015

Background

Parents of children with disabilities desperately seek information regarding their children's conditions because of the high stakes involved.

Objectives

This study investigates the information needs of parents in Kuwait with special needs children during and after their children's diagnoses. Understanding their information seeking behaviour by identifying their information sources and information seeking barriers will assist librarians and other information professionals in meeting these important information needs.

Methods

A survey was conducted by means of questionnaires administered to 240 participants at a school for children with special needs. The data were analysed using nonparametric Mann–Whitney and Kruskal–Wallis tests.

Results

Most parents needed information at the time of diagnosis, with information about educating the children having the highest mean. Doctors and physicians were the most preferred information sources, followed by books. Online support groups and social media applications were least desirable as information sources. Lack of Arabic resources was identified as the greatest information seeking barrier, followed by lack of information to help parents cope with their child's disability.

Conclusions

Information sources and services for Kuwaiti parents of disabled children need further development and improvement. Librarians and other information professionals can assist by providing parents with information appropriate to their stage in understanding the child's diagnosis and education.
Quantifying dyspigmentation in facial skin ageing: an explorative study
Authors: Dobos G. , Trojahn C. , Lichterfeld A. , D′Alessandro B. , Patwardhan S. V. , Canfield D. , Blume‐Peytavi U. , Kottner J.
Published: April 2015

Synopsis

Objective

The skin melanin system is affected by ageing, resulting in dyspigmentation with associated clinical and psychosocial consequences. In dark skinned phenotypes, broad evidence is available, whereas little is known about pigmentary changes in fair‐skinned Caucasians. The objective of this study was to investigate age‐related changes in facial pigmentation and dyspigmentation in subjects of skin phototypes II–III and to develop and test parameters for quantifying dyspigmentation.

Methods

Twenty‐four skin healthy female subjects were recruited in three distinct age groups (30–40, 50–60, 70–80 years). Skin colour was measured by Mexameter and Chromameter. Skin dyspigmentation was measured by clinical evaluation and newly developed image‐processing parameters on the cheeks and the forehead. The reliability of the clinical evaluation was investigated by intraclass correlation coefficients between three raters, and the validity of the dyspigmentation parameters was analysed by bivariate correlations with related measures.

Results

Skin lightness decreased with increasing age. Clinical dyspigmentation scores showed positive associations with chronological age ranging between 0.452 and 0.606. RBX®‐Brown transformation‐based hyperpigmentation and hypopigmentation indices increased with age, whereas the overall pigmentation intensity decreased with age at the cheeks. The image analysis‐based parameters showed strong associations with the clinical scores and related measurements.

Conclusion

We demonstrated age‐related changes in the facial colour and dyspigmentation of fair‐skinned Caucasian females. An increase in dyspigmentation was found by clinical scoring and the RBX®‐Brown transformation‐based pigmentation indices. The validity of hyper‐ and hypopigmentation indices and overall pigmentation intensity was supported. The RBX® transformation‐based pigmentation indices might be applied in future studies to complement or substitute clinical evaluation.
Sintering Kinetics Across Pore Closure Transition Accounting for Continuous Increase in Grain Coordination with Density
Authors: Delannay Francis
Published: April 2015

The influence of dihedral angle and particle coordination on the evolution of densification rate is investigated throughout the intermediate and final stages of sintering. From a review of literature data, heuristic expressions are proposed for representing different trajectories of evolution of coordination from the onset of skeleton formation up to full density. The influence of dihedral angle and coordination on the threshold density for pore closure is established by revisiting the Plateau–Rayleigh instability criterion. The intermediate and final stages are modeled using representative volume elements that do not restrict coordination to integer values. Computational results enlighten the interplay between coordination and dihedral angle on the evolution of sintering stress, bulk viscosity, and sintering rate. The results allow quantifying the amplitude of the drop of densification rate at pore closure transition. The monotonous increase of coordination with relative density brings about a monotonous increase of sintering rate at constant particle size. Simulations emphasize the beneficial effect of higher initial density and coordination in the green part.
Estimation of indirect genetic effects in group‐housed mink (Neovison vison) should account for systematic interactions either due to kin or sex
Authors: Alemu S.W. , Berg P. , Janss L. , Bijma P.
Published: April 2015

Social interactions among individuals are abundant, both in wild and in domestic populations. With social interactions, the genes of an individual may affect the trait values of other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. Most IGE models assume that individuals interact equally to all group mates irrespective of relatedness. Kin selection theory, however, predicts that an individual will interact differently with family members versus non‐family members. Here, we investigate kin‐ and sex‐specific non‐genetic social interactions in group‐housed mink. Furthermore, we investigated whether systematic non‐genetic interactions between kin or individuals of the same sex influence the estimates of genetic parameters. As a second objective, we clarify the relationship between estimates of the traditional IGE model and a family‐based IGE model proposed in a previous study. Our results indicate that male siblings in mink show different non‐genetic interactions than female siblings in mink and that this may impact the estimation of genetic parameters. Moreover, we have shown how estimates from a family‐based IGE model can be translated to the ordinary direct–indirect model and vice versa. We find no evidence for genetic differences in interactions among related versus unrelated mink.
Palm diversification in two geologically contrasting regions of western Amazonia
Authors: Roncal Julissa , Couderc Marie , Baby Patrice , Kahn Francis , Millán Betty , Meerow Alan W. , Pintaud Jean‐Christophe
Published: April 2015

Aim

The subduction of the Nazca Plate and the eastward propagation of the Andean orogenic wedge in western Amazonia caused the formation of arches or ridges that have influenced the modern configuration of the upper Amazon drainage and the diversification of biota. We used a lineage of 15 palm species (Astrocaryumsect.Huicungo, Arecaceae) to test two biogeographical hypotheses for lowland plants: (1) that vicariance resulted from tectonically mediated geographical barriers (population contraction), and (2) that recurrent dispersal events (population expansion) produced geographical isolation and subsequent speciation.

Location

Rain forests of South America.

Methods

A total of 78 palm individuals were collected in the field, from which five chloroplast and two nuclearDNAfragments were sequenced. We reconstructed a Bayesian dated phylogeny and inferred the demographic history. We used a Bayesian phylogeographical spatial diffusion approach to propose a model of colonization.

Results

We found a phylogeographical break atc. 5° S between two main clades with crown ages ofc. 6.7 and 7.3 Ma located in the Fitzcarrald Arch (FA) and the subsiding northern Amazonian foreland basin (NAFB), respectively. These diversification times were close to the emergence of theFAin the late Miocene, and the coeval development of the transcontinental modern drainage and sedimentation plain of theNAFB. As expected for the recurrent‐dispersal hypothesis, lineage delimitations were spatially inconsistent with the location of rivers or ridges, and we found some evidence of past ancestral population expansion supported particularly by the chloroplast sequences.

Main conclusions

Our results support the biogeographical scenario whereby recurrent dispersal into western Amazonia produced spatial isolation of populations, followed by speciation within two areas of contrasting geological activity: tectonic uplift in theFAversus subsidence in theNAFB. We did not test and cannot rule out ecological speciation within western Amazonia or at finer spatial scales.
Recent climate warming favours more specialized cladoceran taxa in western Canadian Arctic lakes
Authors: Thienpont Joshua R. , Korosi Jennifer B. , Cheng Elisa S. , Deasley Kayla , Pisaric Michael F. J. , Smol John P.
Published: April 2015

Aim

Shifts in the distribution of freshwater algal communities as a result of climate‐related limnological changes are well documented; however, impacts on higher trophic levels have received less attention. For example, little is known about how Cladocera (Crustacea, Branchiopoda), often dominant invertebrates and key ecological indicators, have responded to recent warming on broad spatial and temporal scales. Here, we use lake sediment records to test the hypothesis that recent, intensive warming in the western Canadian Arctic has resulted in consistent shifts in the composition of cladoceran assemblages.

Location

Small, first‐order lakes in the Mackenzie Delta region of the western Canadian Arctic.

Methods

Sediment cores representing the recent past (approximately 150–200 years) were obtained from five lakes spanning a strong climatic gradient. Subfossil remains of Cladocera were identified and enumerated and overall primary production was inferred using spectroscopic techniques. The habitat preferences and feeding strategy of each taxon were compared. Detrended canonical correspondence analysis was used to estimate compositional turnover since 1850, and compared with that of three cladoceran assemblages from Nova Scotia, to place high‐latitude changes in context.

Results

Cladoceran assemblage changes occurred coincident with the timing of known regional warming and were strongly linked to estimated changes in primary production. In the northern and deepest lakes, an increase in the planktonic, filter‐feeding taxon Bosmina spp. coincided with a decrease in the generalist littoral taxa Chydorus cf. brevilabris and Alona circumfimbriata. In the more southern lakes, an increase in macrophyte‐associated scrapers Acroperus harpae and Eurycercus spp. occurred concurrently with decreases in generalist taxa. In one lake, an increase in another specialist, an obligate mud‐dwelling taxon, was observed.

Main conclusions

In the western Canadian Arctic, warming has resulted in an increase in cladoceran taxa occupying more specialized feeding and habitat niches. Generalist taxa capable of occupying multiple habitats and employing diverse feeding strategies have been systematically replaced by more specialist species. This response is analogous to what has been inferred for algal communities across the Northern Hemisphere, and represents the first evidence of consistent cladoceran changes to recent climate warming in high‐latitude regions.
Occurrence and use of an estuarine habitat by giant manta ray Manta birostris
Authors: Medeiros A. M. , Luiz O. J. , Domit C.
Published: April 2015

Based on the knowledge of local artisanal fishermen and on direct observations, this study presents evidence that the giant manta ray Manta birostris uses the Paranaguá estuarine complex in south Brazil, south‐western Atlantic Ocean, in a predictable seasonal pattern. Behavioural observations suggest that the estuary can act as a nursery ground for M. birostris during the summer.
In situ observations of a possible skate nursery off the western Antarctic Peninsula
Authors: Amsler M. O. , Smith K. E. , McClintock J. B. , Singh H. , Thatje S. , Vos S. C. , Brothers C. J. , Brown A. , Ellis D. , Anderson J. , Aronson R. B.
Published: April 2015

A dense aggregation of skate egg cases was imaged during a photographic survey of the sea floor along the western Antarctic Peninsula in November 2013. Egg cases were noted in a narrow band between 394 and 443 m depth. Although some skate species in other oceans are known to utilize restricted areas to deposit eggs in great numbers, such nurseries have not been described in the Southern Ocean.
Deoxynivalenol in chicken feed alters the vaccinal immune response and clinical biochemical serum parameters but not the intestinal and carcass characteristics
Authors: Ghareeb K. , Awad W. A. , Zebeli Q. , Böhm J.
Published: April 2015

This study was conducted to investigate the impacts of deoxynivalenol (DON) feeding either alone or in combination with a microbial feed additive (MFA) on the immune response to a viral vaccine and serum clinical chemical parameters. Forty 1‐day‐old boiler chicks were weighed and randomly divided into four groups, 10 birds in each group: (i) control group fed with basal diet; (ii) DON group fed with basal diet artificially contaminated with 10 mg DON/kg feed; (iii) DON + MFA group fed with basal diet contaminated with 10 mg DON/kg feed and supplemented with 2.5 kg of MFA/ton feed; and (iv) MFA group fed with basal diet supplemented with 2.5 kg of MFA/ton feed. At 35 days of age, birds were slaughtered and blood was collected for investigating the antibody titre against infectious bronchitis virus (IBV) and clinical chemical parameters. The results showed that DON reduced (p = 0.032) the titre against IBV, decreased (p = 0.005) the level of alanine transaminase (ALT) (4.2 ± 0.5 U/l) compared with control birds (6.4 ± 0.5 U/l), increased (p = 0.002) the serum cholesterol concentration (144 ± 6 mg/dl) compared with their control counterparts (123 ± 5 mg/dl) and increased (p = 0.074) the amount of circulating triglycerides (62.25 ± 7.50 mg/dl) compared with controls (39.55 ± 4.74). These results indicate that dietary DON altered the humoral immune response to viral vaccine and affected the serum clinical biochemistry. However, DON in combination with MFA did not affect serum IBV titre. Taken together, DON in the feed of broilers produced an impairment of the success of IBV vaccine and affected the health of birds.
Tissue engineered periodontal products
Authors: Bartold P. M. , Gronthos S. , Ivanovski S. , Fisher A. , Hutmacher D. W.
Published: April 2015

Attainment of periodontal regeneration is a significant clinical goal in the management of advanced periodontal defects arising from periodontitis. Over the past 30 years numerous techniques and materials have been introduced and evaluated clinically and have included guided tissue regeneration, bone grafting materials, growth and other biological factors and gene therapy. With the exception of gene therapy, all have undergone evaluation in humans. All of the products have shown efficacy in promoting periodontal regeneration in animal models but the results in humans remain variable and equivocal concerning attaining complete biological regeneration of damaged periodontal structures. In the early 2000s, the concept of tissue engineering was proposed as a new paradigm for periodontal regeneration based on molecular and cell biology. At this time, tissue engineering was a new and emerging field. Now, 14 years later we revisit the concept of tissue engineering for the periodontium and assess how far we have come, where we are currently situated and what needs to be done in the future to make this concept a reality. In this review, we cover some of the precursor products, which led to our current position in periodontal tissue engineering. The basic concepts of tissue engineering with special emphasis on periodontal tissue engineering products is discussed including the use of mesenchymal stem cells in bioscaffolds and the emerging field of cell sheet technology. Finally, we look into the future to consider what CAD/CAM technology and nanotechnology will have to offer.
Full mouth periodontal debridement with or without adjunctive metronidazole gel in smoking patients with chronic periodontitis: A pilot study
Authors: Bergamaschi C. C. , Santamaria M. P. , Berto L. A. , Cogo‐Müller K. , Motta R. H. L. , Salum E. A. , Nociti F. H. , Goodson J. M. , Groppo F. C.
Published: April 2015

Background and Objective

The evidence of effectiveness of metronidazole (Mtz) as an adjunct therapy to periodontal procedure in the treatment of patients with chronic periodontitis is not conclusive. The aim of this study was to compare the effect of Mtz (delivered locally as a gel or systemically as a tablet) as an adjunctive therapy with full mouth periodontal debridement (1 h of ultrasonic calculus/plaque removal) in smokers with chronic periodontitis.

Material and Methods

This pilot study involved 30 smokers with at least six teeth with a clinical attachment loss of ≥ 5 mm and probing pocket depth (PPD) of ≥ 5 mm. They were randomly assigned into one of three groups (n = 10): (i) 3 g daily of placebo gel applied topically (using a dental tray with the gel overnight) + periodontal debridement; (ii) 3 g daily of a 15% Mtz benzoate gel applied topically (using a dental tray with the gel overnight) + periodontal debridement; and (iii) a daily single dose of 750 mg Mtz (Flagyl®) + periodontal debridement. Clinical parameters (visible plaque index, gingival bleeding index [GBI], relative attachment level and PPD) and quantitative analysis (by real‐time polymerase chain reaction) of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythia were assessed at baseline and at 1, 3 and 6 mo after periodontal debridement.

Results

There was no statistically significant difference in the average GBI and visible plaque index values at baseline between the groups (p ≥ 0.05). There was no significant difference between groups in all parameters evaluated (p ≥ 0.05). Significant reductions in GBI at 3 and 6 mo were observed in all groups (p < 0.05). Significant reductions in both PPD and relative attachment level at 1, 3 and 6 mo were observed in all groups (p < 0.05). Significant reductions in bacterial levels at 7 and 30 d were observed in all groups (p < 0.05).

Conclusion

Adjunctive use of Mtz (gel or tablet) to periodontal debridement had similar clinical and microbiological improvement compared to treatment with placebo + periodontal debridement in smokers with chronic periodontitis up to 6 mo post‐treatment. Further studies are necessary to confirm the clinical relevance of these findings.
Increased physical activity improves sleep and mood outcomes in inactive people with insomnia: a randomized controlled trial
Authors: Hartescu Iuliana , Morgan Kevin , Stevinson Clare D.
Published: April 2015

While high levels of activity and exercise training have been associated with improvements in sleep quality, minimum levels of activity likely to improve sleep outcomes have not been explored. A two‐armed parallel randomized controlled trial (N=41; 30 females) was designed to assess whether increasing physical activity to the level recommended in public health guidelines can improve sleep quality among inactive adults meeting research diagnostic criteria for insomnia. The intervention consisted of a monitored program of ≥150 min of moderate‐ to vigorous‐intensity physical activity per week, for 6 months. The principal end‐point was the Insomnia Severity Index at 6 months post‐baseline. Secondary outcomes included measures of mood, fatigue and daytime sleepiness. Activity and light exposure were monitored throughout the trial using accelerometry and actigraphy. At 6 months post‐baseline, the physical activity group showed significantly reduced insomnia symptom severity (F8,26 = 5.16, P = 0.03), with an average reduction of four points on the Insomnia Severity Index; and significantly reduced depression and anxiety scores (F6,28 = 5.61, P = 0.02; and F6,28 = 4.41, P = 0.05, respectively). All of the changes were independent of daily light exposure. Daytime fatigue showed no significant effect of the intervention (F8,26 = 1.84, P = 0.18). Adherence and retention were high. Internationally recommended minimum levels of physical activity improve daytime and night‐time symptoms of chronic insomnia independent of daily light exposure levels.
New ICA criteria for the diagnosis of acute kidney injury in cirrhotic patients: can we use an imputed value of serum creatinine?
Authors: Rosi Silvia , Piano Salvatore , Frigo Anna C. , Morando Filippo , Fasolato Silvano , Cavallin Marta , Gola Elisabetta , Romano Antonietta , Montagnese Sara , Sticca Antonietta , Gatta Angelo , Angeli Paolo
Published: April 2015

Background & Aims

The new International Club of Ascites diagnostic criteria to diagnose acute kidney injury at hospital admission suggests the possibility of using a presumed baseline serum creatinine, defined as the last of at least two stable creatinine values during the last 3 months. Nevertheless, the possibility of the lack of such a value still remains. In these patients, the KDIGO criteria suggest to use an inverse application of MDRD equation assuming that baseline glomerular filtration rate is 75 ml/min per 1.73 m2 (imputed baseline creatinine). We tested the accuracy of this approach to detect acute kidney injury at admission in patients with decompensated cirrhosis and creatinine <1.5 mg/dl.

Methods

We analysed 213 patients hospitalized for acute decompensation of cirrhosis. At admission, glomerular filtration rate was estimated using creatinine‐based equations and measured by inulin clearance. A diagnosis of acute kidney injury was made using an imputed value of serum creatinine as baseline.

Results

The diagnosis of AKI based on an imputed baseline creatinine identified only 20.1% of patients with measured glomerular filtration rate ≤60 ml/min/1.73 m2 without any predictive value on 90‐day survival.

Conclusions

In patients with cirrhosis and ascites with a creatinine <1.5 mg/dl without a baseline value on their records, the diagnosis of acute kidney injury at admission based on an imputed baseline creatinine is not accurate.
Manganese homeostasis and utilization in pathogenic bacteria
Authors: Juttukonda Lillian J. , Skaar Eric P.
Published: April 2015

Manganese (Mn) is a required cofactor for all forms of life. Given the importance of Mn to bacteria, the host has devised strategies to sequester Mn from invaders. In the macrophage phagosome, NRAMP1 removes Mn and other essential metals to starve intracellular pathogens; in the extracellular space, calprotectin chelates Mn and Zn. Calprotectin‐mediated Mn sequestration is a newly appreciated host defense mechanism, and recent findings are highlighted herein. In order to acquire Mn when extracellular concentrations are low, bacteria have evolved efficient Mn acquisition systems that are under elegant transcriptional control. To counteract Mn overload, some bacteria possess Mn‐specific export systems that are important in vivo, presumably for control of intracellular Mn levels. Mn transporters, their transcriptional regulators and some Mn‐requiring enzymes are necessary for virulence of certain bacterial pathogens, as revealed by animal models of infection. Furthermore, Mn is an important facet of the cellular response to oxidative stress, a host antibacterial strategy. The battle for Mn between host and pathogen is now appreciated to be a major determinant of the outcome of infection. In this MicroReview, the contribution of Mn to the host–pathogen interaction is reviewed, and key questions are proposed for future study.
Balancing drug resistance and growth rates via compensatory mutations in the Plasmodium falciparum chloroquine resistance transporter
Authors: Petersen Ines , Gabryszewski Stanislaw J. , Johnston Geoffrey L. , Dhingra Satish K. , Ecker Andrea , Lewis Rebecca E. , de Almeida Mariana Justino , Straimer Judith , Henrich Philipp P. , Palatulan Eugene , Johnson David J. , Coburn‐Flynn Olivia , Sanchez Cecilia , Lehane Adele M. , Lanzer Michael , Fidock David A.
Published: April 2015

The widespread use of chloroquine to treat Plasmodium falciparum infections has resulted in the selection and dissemination of variant haplotypes of the primary resistance determinant PfCRT. These haplotypes have encountered drug pressure and within‐host competition with wild‐type drug‐sensitive parasites. To examine these selective forces in vitro, we genetically engineered P. falciparum to express geographically diverse PfCRT haplotypes. Variant alleles from the Philippines (PH1 and PH2, which differ solely by the C72S mutation) both conferred a moderate gain of chloroquine resistance and a reduction in growth rates in vitro. Of the two, PH2 showed higher IC50 values, contrasting with reduced growth. Furthermore, a highly mutated pfcrt allele from Cambodia (Cam734) conferred moderate chloroquine resistance and enhanced growth rates, when tested against wild‐type pfcrt in co‐culture competition assays. These three alleles mediated cross‐resistance to amodiaquine, an antimalarial drug widely used in Africa. Each allele, along with the globally prevalent Dd2 and 7G8 alleles, rendered parasites more susceptible to lumefantrine, the partner drug used in the leading first‐line artemisinin‐based combination therapy. These data reveal ongoing region‐specific evolution of PfCRT that impacts drug susceptibility and relative fitness in settings of mixed infections, and raise important considerations about optimal agents to treat chloroquine‐resistant malaria.
ComGA‐RelA interaction and persistence in the Bacillus subtilis K‐state
Authors: Hahn Jeanette , Tanner Andrew W. , Carabetta Valerie J. , Cristea Ileana M. , Dubnau David
Published: April 2015

The bistably expressed K‐state of Bacillus subtilis is characterized by two distinct features; transformability and arrested growth when K‐state cells are exposed to fresh medium. The arrest is manifested by a failure to assemble replisomes and by decreased rates of cell growth and rRNA synthesis. These phenotypes are all partially explained by the presence of the AAA+ protein ComGA, which is also required for the binding of transforming DNA to the cell surface and for the assembly of the transformation pilus that mediates DNA transport. We have discovered that ComGA interacts with RelA and that the ComGA‐dependent inhibition of rRNA synthesis is largely bypassed in strains that cannot synthesize the alarmone (p)ppGpp. We propose that the interaction of ComGA with RelA prevents the hydrolysis of (p)ppGpp in K‐state cells, which are thus trapped in a non‐growing state until ComGA is degraded. We show that some K‐state cells exhibit tolerance to antibiotics, a form of type 1 persistence, and we propose that the bistable expression of both transformability and the growth arrest are bet‐hedging adaptations that improve fitness in the face of varying environments, such as those presumably encountered by B. subtilis in the soil.
COOPERATIVE INTERACTIONS AMONG FRIENDS AND FOES OPERATING WITHIN COLLABORATIVE GOVERNANCE ARRANGEMENTS
Authors: ELGIN DALLAS J.
Published: April 2015

Perhaps nowhere is the inclination to interact with friends over foes more apparent than in the realms of politics and policy, and public managers increasingly operate within collaborative governance arrangements that are highly politicized. To further the existing knowledge on policy‐based interactions, this article examines factors that lead to cooperative interactions between foes. The Advocacy Coalition Framework, Resource Dependence Theory, and Policy Analytical Capacity are utilized to examine effects of resources and beliefs on interactions of climate policy supporters and opponents within Colorado. Despite the contentious nature of climate policy, a majority of individuals interacted equally with friends and foes, with opponents more likely to interact with foes. Extreme beliefs made individuals more likely to interact with friends, while resources had mixed effects. These findings offer an improved understanding of cooperative interactions between foes, which may help public managers operating within collaborative governance arrangements to promote greater cooperation and understanding.
Early Pennsylvanian (Langsettian) fish assemblages from the Joggins Formation, Canada, and their implications for palaeoecology and palaeogeography
Authors: Carpenter David K. , Falcon‐Lang Howard J. , Benton Michael J. , Grey Melissa
Published: April 2015

A review of all available specimens of fossil fishes from the classic Pennsylvanian Joggins locality of Nova Scotia, Canada, reveals the existence of a diverse community of chondrichthyans (xenacanthids, ctenacanthids and the enigmaticAgeleodus), acanthodians (gyracanthids), sarcopterygians (rhizodontids, megalichthyids, rhizodopsids and dipnoans) and actinopterygians (haplolepids). Reassessment of supposed endemic species (Ctenoptychius cristatus,Sagenodus plicatus,Gyracanthus duplicatus) indicates they are invalid, and overall, the assemblage comprises cosmopolitan taxa that were widespread around the coasts of tropical Pangaea. Strontium isotope analysis of fish remains and a critical study of their facies context suggest that these fish communities occupied bodies of water with salinities across the marine–freshwater spectrum. This preponderance of euryhaline forms implies a community structure quite distinct from that of today and might represent a transitory phase prior to the establishment of fully freshwater fish communities. Interpretation of fish ecology provides further evidence that the Joggins Formation was deposited in a paralic setting, and the recognition of one previously undetected brackish incursion strengthens the link between sedimentary cycles at Joggins and Milankovitch‐induced glacio‐eustatic change. Furthermore, interregional correlation of these marine transgressions supports palynostratigraphical arguments for an early Langsettian age for the Joggins Formation. This places tighter constraints on the age of the earliest known crown amniote,Hylonomus lyelli, an important calibration point used in phylogenomic studies.
Transcript profiling of jasmonate‐elicited Taxus cells reveals a β‐phenylalanine‐CoA ligase
Authors: Ramírez‐Estrada Karla , Altabella Teresa , Onrubia Miriam , Moyano Elisabeth , Notredame Cedric , Osuna Lidia , Vanden Bossche Robin , Goossens Alain , Cusido Rosa M. , Palazon Javier
Published: April 2015

Plant cell cultures constitute eco‐friendly biotechnological platforms for the production of plant secondary metabolites with pharmacological activities, as well as a suitable system for extending our knowledge of secondary metabolism. Despite the high added value of taxol and the importance of taxanes as anticancer compounds, several aspects of their biosynthesis remain unknown. In this work, a genomewide expression analysis of jasmonate‐elicited Taxus baccata cell cultures by complementary DNA‐amplified fragment length polymorphism (cDNA‐AFLP) indicated a correlation between an extensive elicitor‐induced genetic reprogramming and increased taxane production in the targeted cultures. Subsequent in silico analysis allowed us to identify 15 genes with a jasmonate‐induced differential expression as putative candidates for genes encoding enzymes involved in five unknown steps of taxane biosynthesis. Among them, the TB768 gene showed a strong homology, including a very similar predicted 3D structure, with other genes previously reported to encode acyl‐CoA ligases, thus suggesting a role in the formation of the taxol lateral chain. Functional analysis confirmed that the TB768 gene encodes an acyl‐CoA ligase that localizes to the cytoplasm and is able to convert β‐phenylalanine, as well as coumaric acid, into their respective derivative CoA esters. β‐phenylalanyl‐CoA is attached to baccatin III in one of the last steps of the taxol biosynthetic pathway. The identification of this gene will contribute to the establishment of sustainable taxol production systems through metabolic engineering or synthetic biology approaches.
Breeding and characterization of soybean Triple Null; a stack of recessive alleles of Kunitz Trypsin Inhibitor, Soybean Agglutinin, and P34 allergen nulls
Authors: Schmidt Monica A. , Hymowitz Theodore , Herman Eliot M.
Published: April 2015

Soybean (Glycine max) seeds contain bioactive proteins with antinutritional and immunological properties that affect metabolism and assimilation of nutrients. The presence of antinutritional proteins requires soybeans to be heat‐treated resulting in input energy costs. Nulls for bioactive seed proteins have been previously isolated from the USDA soybean collection, including Kunitz trypsin inhibitor (TI), soybean agglutinin (LE) and immunodominant soybean allergen P34 protein. Each of these nulls has the potential to partially address the concerns of soybean feed/food consumption. A stack of recessive nulls of TI, LE and P34 was created in a cv ‘Williams 82’ background termed ‘Triple Null’. Triple Null has a slight reduction of total protein compared with ‘Williams 82’ corresponding to aggregate contribution of TI, LE and P34 in the seed proteome. Triple Null's proteome analysis revealed P34 and TI nulls are frame‐shift mutants able to accumulate small amounts of authentic P34 and TI proteins. Triple Null has possible application as a conventional feed/food source and for immunotherapy to mitigate soybean allergenic response.
EST‐SSR analysis provides insights about genetic relatedness, population structure and gene flow in grass pea (Lathyrus sativus)
Authors: Soren Khela R. , Yadav Ashutosh , Pandey Gaurav , Gangwar Priyanka , Parihar Ashok K. , Bohra Abhishek , Dixit Girish P. , Datta Subhojit , Singh Narendra Pratap
Published: April 2015

Grass pea (Lathyrus sativus) is an important food‐legume crop for resource‐poor farmers in the developing world. However, given its cultivation in the most underprivileged regions, the crop has not received appropriate scientific attention particularly from the genomic perspective, thereby giving it a status of genomic orphan. Nevertheless, some recent studies have attempted to develop modern molecular tools to strengthen the genetic and genomic research. In the present investigation, a comprehensive collection comprising 176 accessions was analysed using EST‐simple sequence repeats (SSRs). The SSR analysis revealed existence of a total of 51 alleles with an average polymorphic information content value of 0.35. A moderate level of gene diversity was noticed that ranged from 0.04 to 0.73 with an average of 0.43. Noticeably, two distinct subpopulations were recovered using cluster analysis. In addition, the presence of admixtures in population reflected the strong possibilities of gene flow between the accessions across the geographical boundary. In summary, we provide additional insights about the informativeness of available EST‐SSR markers along with an extended understanding of relatedness, genetic structure and gene flow in an under‐researched legume crop.
Genetic characterization of group A acetylsaponin‐deficient mutants from wild soybean (Glycine soja Sieb. and Zucc.)
Authors: Krishnamurthy Panneerselvam , Lee Jeong‐Dong , Ha Bo‐Keun , Chae Jong‐Hyun , Song Jong Tae , Tsukamoto Chigen , Singh Ram J. , Chung Gyuhwa
Published: April 2015

Group A acetylsaponins are the main causative components for bitter and astringent tastes of soybean (Glycine max). In this study, we examined the genetic nature of the absence of group A acetylsaponins in 12 Korean wild soybean (Glycine soja) accessions. In all 12 accessions, the coding region (1431‐bp) of Sg‐1 locus was identical with Sg‐1a, which adds the xylose sugar moiety at the terminal position of the C‐22 sugar chain of SS‐A, except one nucleotide (G→A change) at +948th position. This point mutation results in change of one amino acid from tryptophan (TGG) to stop codon (TGA). We observed that the mutated Sg‐1 was controlled by a single recessive gene (sg‐10‐a1). This gene was mapped between BARCSOYSSR_07_1561 and BARCSOYSSR_07_1598 on soybean chromosome 7. Our study demonstrated that the mutated Sg‐1 gene in Korean wild soybeans is genetically different from those identified in Japanese soybean cultivar ‘Kinusayaka’ and wild soybean JP‐36121. We believe that the new Sg‐1 mutants can also be utilized to produce a new soybean variety without bitter and astringent properties.
Mind as an Intrinsic Property of Matter
Authors: Jylkkä Jussi
Published: April 2015

This paper argues that the epistemic gap in philosophy of mind stems from the fact that our awareness of our subjective experiences is categorically different from our knowledge of external phenomena. Our knowledge of external objects is always mediated through empirical observation or theoretical descriptions, and does not afford us knowledge of the intrinsic nature of the thing referred to, whereas our awareness of our experiences is immediate and affords us knowledge of the intrinsic nature of our experiences. Finally, it is argued that the thing itself referred to as “neural correlate of consciousness” is constituted by consciousness.
How orthographic transparency affects morphological processing in young readers with and without reading disability
Authors: Lázaro Miguel , García Laura , Burani Cristina
Published: April 2015

This study investigates how orthographic modifications to the stems of complex words affect morphological processing in proficient young Spanish readers and children with reading deficits. In a definition task all children, irrespective of their reading skill, were worse at defining derived words that had an orthographic alteration of the base stem than words with no orthographic alteration. In a go/no‐go lexical decision task, an interaction between base frequency and orthographic alteration was found: base frequency affected derived words with no orthographic alteration more than words with alterations, irrespective of reading skill. Overall, results show that all children benefit from a high frequency base, skilled children outperform children with reading deficits and morphological processing is affected by orthographic alterations similarly in proficient and impaired readers.
The Strategic Use of Noise in Pragmatic Reasoning
Authors: Bergen Leon , Goodman Noah D.
Published: April 2015

We combine two recent probabilistic approaches to natural language understanding, exploring the formal pragmatics of communication on a noisy channel. We first extend a model of rational communication between a speaker and listener, to allow for the possibility that messages are corrupted by noise. In this model, common knowledge of a noisy channel leads to the use and correct understanding of sentence fragments. A further extension of the model, which allows the speaker to intentionally reduce the noise rate on a word, is used to model prosodic emphasis. We show that the model derives several well‐known changes in meaning associated with prosodic emphasis. Our results show that nominal amounts of actual noise can be leveraged for communicative purposes.
Uncertainty and Exploration in a Restless Bandit Problem
Authors: Speekenbrink Maarten , Konstantinidis Emmanouil
Published: April 2015

Decision making in noisy and changing environments requires a fine balance between exploiting knowledge about good courses of action and exploring the environment in order to improve upon this knowledge. We present an experiment on a restless bandit task in which participants made repeated choices between options for which the average rewards changed over time. Comparing a number of computational models of participants’ behavior in this task, we find evidence that a substantial number of them balanced exploration and exploitation by considering the probability that an option offers the maximum reward out of all the available options.
Two Chlamydomonas OPR proteins stabilize chloroplast mRNAs encoding small subunits of photosystem II and cytochrome b6f
Authors: Wang Fei , Johnson Xenie , Cavaiuolo Marina , Bohne Alexandra‐Viola , Nickelsen Joerg , Vallon Olivier
Published: April 2015

In plants and algae, chloroplast gene expression is controlled by nucleus‐encoded proteins that bind to mRNAs in a specific manner, stabilizing mRNAs or promoting their splicing, editing, or translation. Here, we present the characterization of two mRNA stabilization factors of the green alga Chlamydomonas reinhardtii, which both belong to the OctotricoPeptide Repeat (OPR) family. MCG1 is necessary to stabilize the petG mRNA, encoding a small subunit of the cytochrome b6f complex, while MBI1 stabilizes the psbI mRNA, coding for a small subunit of photosystem II. In the mcg1 mutant, the small RNA footprint corresponding to the 5′‐end of the petG transcript is reduced in abundance. In both cases, the absence of the small subunit perturbs assembly of the cognate complex. Whereas PetG is essential for formation of a functional cytochrome b6f dimer, PsbI appears partly dispensable as a low level of PSII activity can still be measured in its absence. Thus, nuclear control of chloroplast gene expression is not only exerted on the major core subunits of the complexes, but also on small subunits with a single transmembrane helix. While OPR proteins have thus far been involved in translation or trans‐splicing of plastid mRNAs, our results expand the potential roles of this repeat family to their stabilization.
A two‐component enzyme complex is required for dolichol biosynthesis in tomato
Authors: Brasher Megan I. , Surmacz Liliana , Leong Bryan , Pitcher Jocelyn , Swiezewska Ewa , Pichersky Eran , Akhtar Tariq A.
Published: April 2015

Dolichol plays an indispensable role in the N‐glycosylation of eukaryotic proteins. As proteins enter the secretory pathway they are decorated by a ‘glycan’, which is preassembled onto a membrane‐anchored dolichol molecule embedded within the endoplasmic reticulum (ER). Genetic and biochemical evidence in yeast and animals indicate that a cis‐prenyltransferase (CPT) is required for dolichol synthesis, but also point to other factor(s) that could be involved. In this study, RNAi‐mediated suppression of one member of the tomato CPT family (SlCPT3) resulted in a ~60% decrease in dolichol content. We further show that the involvement of SlCPT3 in dolichol biosynthesis requires the participation of a distantly related partner protein, designated as CPT‐binding protein (SlCPTBP), which is a close homolog of the human Nogo‐B receptor. Yeast two‐hybrid and co‐immunoprecipitation assays demonstrate that SlCPT3 and its partner protein interact in vivo and that both SlCPT3 and SlCPTBP are required to complement the growth defects and dolichol deficiency of the yeast dolichol mutant, rer2∆. Co‐expression of SlCPT3 and SlCPTBP in yeast and in E. coli confirmed that dolichol synthase activity strictly requires both proteins. Finally, organelle isolation and in vivo localization of fluorescent protein fusions showed that both SlCPT3 and SlCPTBP localize to the ER, the site of dolichol accumulation and synthesis in eukaryotes.
The dynamic loss and gain of introns during the evolution of the Brassicaceae
Authors: Milia Giampiera , Camiolo Salvatore , Avesani Linda , Porceddu Andrea
Published: April 2015

Sequence comparison allows the detailed analysis of evolution at the nucleotide and amino acid levels, but much less information is known about the structural evolution of genes, i.e. how the number, length and distribution of introns change over time. We constructed a parsimonious model for the evolutionary rate of intron loss (IL) and intron gain (IG) within the Brassicaceae and found that IL/IG has been highly dynamic, with substantial differences between and even within lineages. The divergence of the Brassicaceae lineages I and II marked a dramatic change in the IL rate, with the common ancestor of lineage I losing introns three times more rapidly than the common ancestor of lineage II. Our data also indicate a subsequent declining trend in the rate of IL, although in Arabidopsis thaliana introns continue to be lost at approximately the ancestral rate. Variations in the rate of IL/IG within lineage II have been even more remarkable. Brassica rapa appears to have lost introns approximately 15 times more rapidly than the common ancestor of B. rapa and Schenkiella parvula, and approximately 25 times more rapidly than its sister species Eutrema salsugineum. Microhomology was detected at the splice sites of several dynamic introns suggesting that the non‐homologous end‐joining and double‐strand break repair is a common pathway underlying IL/IG in these species. We also detected molecular signatures typical of mRNA‐mediated IL, but only in B. rapa.