bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum
Authors: Bunnik Evelien M , Chung Duk-Won Doug , Hamilton Michael , Ponts Nadia , Saraf Anita , Prudhomme Jacques , Florens Laurence , Le Roch Karine G 
Published: November 2013

Abstract
Background
In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and translational levels.

Results
In this study, we compare steady-state mRNA and polysome-associated mRNA levels of Plasmodium falciparum at different time points during its asexual cell cycle. For more than 30% of its genes, we observe a delay in peak transcript abundance in the polysomal fraction as compared to the steady-state mRNA fraction, suggestive of strong translational control. Our data show that key regulatory mechanisms could include inhibitory activity of upstream open reading frames and translational repression of the major virulence gene family by intronic transcripts. In addition, we observe polysomal mRNA-specific alternative splicing events and widespread transcription of non-coding transcripts.

Conclusions
These different layers of translational regulation are likely to contribute to a complex network that controls gene expression in this eukaryotic pathogen. Disrupting the mechanisms involved in such translational control could provide novel anti-malarial strategies.
An ethics safe harbor for international genomics research?
Authors: Dove Edward S , Knoppers Bartha M , Zawati Ma’n H 
Published: November 2013

Abstract
Background
Genomics research is becoming increasingly globally connected and collaborative, contesting traditional ethical and legal boundaries between global and local research practice. As well, global data-driven genomics research holds great promise for health discoveries. Yet, paradoxically, current research ethics review systems around the world challenge potential improvements in human health from such research and thus undermine respect for research participants. Case reports illustrate that the current system is costly, fragmented, inefficient, inadequate, and inconsistent. There is an urgent need to improve the governance system of ethics review to enable secure and seamless genomic and clinical data sharing across jurisdictions.

Discussion
Building on the international privacy 'safe harbor’ model that was developed following the adoption of the European Privacy Directive, we propose an international infrastructure. The goal is to create a streamlined and harmonized ethics governance system for international, data-driven genomics research projects. The proposed 'Safe Harbor Framework for International Ethics Equivalency’ would consist in part of an agency supporting an International Federation for Ethics Review (IFER), formed by a voluntary agreement among countries, granting agencies, philanthropies, institutions, and healthcare, patient advocacy, and research organizations. IFER would be both a central ethics review body and also a forum for review and follow-up of policies concerning ethics norms for international genomics research projects. It would be built on five principle elements: (1) registration; (2) compliance review; (3) recognition; (4) monitoring and enforcement; and (5) public participation.

Summary
A Safe Harbor Framework for International Ethics Equivalency would create many benefits for researchers, countries, and the general public, and may eventually have application beyond genomics to other areas of biomedical research that increasingly engage in secondary use of data and present only negligible risks. Among the benefits, research participants and patients would have uniform adequate protection, while researchers would be ensured expert ethics review with a reduction in cost, time, administrative hassle, and redundant regulatory hurdles. Most importantly, society would enjoy the maximization of the potential benefits of genomics research.
Conical faults apparent in a 3D seismic image
Authors: Hale Dave , Groshong Richard H. 
Published: November 2013

Map-scale geologic faults with a conical shape are apparent in a public-domain 3D seismic image of block F3 in the Dutch sector of the North Sea. These cone-shaped normal faults exist among many polygonal normal faults in fine-grained clay sediments. The conical faults were discovered using new algorithms for seismic image processing, but they are apparent without that processing. They appear circular in horizontal image slices and have an inverted-V shape in vertical sections for any azimuth through their vertical axes of symmetry. They form horsts bounded by planar strata above and below, with maximum throws of about 35 m roughly halfway between their bases and tops. The bases are up to 1 km wide, and dips of the conical faults are in the range 35º–38º. Because polygonal faults exist elsewhere at or near the seafloor with dips of about 60º, most such faults likely formed close to the depositional interface; the much lower dips of deeply buried faults, such as the faults observed here, are likely due to vertical compaction. We inferred that polygonal and conical fault geometries result from a uniform radial extension stress caused by volumetric contraction, analogous to the formation of mudcracks. Cone-shaped faults have been observed in laboratory experiments on rocks and ceramics, where the conical geometry results from uniaxial compression. In the subsurface, the formation of conical faults implies that stresses and sediments were exceptionally homogeneous. The cone shape suggests a pointlike heterogeneity near the depositional surface, which served as a trigger for downward propagation of the faults, rather unlike the random, in-plane propagation and linking inferred by others for polygonal faults.
Assessing the role of reproduction and stress in the spring emergence of Haematozoan parasites in birds
Authors: Cornelius Jamie , Zylberberg Maxine , Breuner Creagh , Gleiss Adrian C. , Hahn Tom 
Published: November 2013

SummaryA spring emergence of avian haemosporidian infections is nearly universal among temperate zone birds and is often described as a cost of reproductive effort. We take advantage of the opportunistic (i.e., aseasonal) breeding schedule of the red crossbill (Loxia curvirostra) to determine the relative contributions of season vs. host physiology to the timing and intensity of Haemoproteus infections in the temperate zone. Despite breeding activity in both the winter and summer, Haemoproteus infections were highly seasonal- occurring largely from May through September- and measures of host physiology (i.e., reproductive condition and stress parameters) did not explain parasite prevalence. However, within the spring-summer peak, infection intensity (i.e., parasite density) was positively correlated with plasma levels of testosterone and free corticosterone and negatively correlated with corticosterone binding globulin capacity. These data are discussed in terms of the behavioral ecology of host and vector, and suggest that both seasonal increases in vector activity and relapse of latent (i.e., dormant) infections contribute to the spring emergence in birds. Relapse of latent infections does not appear to be induced by reproductive activity or increased allostatic (i.e., energy) load, but rather by a season-specific change in host or parasite physiology (e.g., melatonin or endogenous rhythms).
Mitochondrial uncoupling prevents cold-induced oxidative stress: a case study using UCP1 knock-out mice
Authors: Stier Antoine , Bize Pierre , Habold Caroline , Bouillaud Frédéric , Massemin Sylvie , Criscuolo François 
Published: November 2013

Summary
The relationship between metabolism and reactive oxygen species (ROS) production by the mitochondria has been often (wrongly) viewed as straightforward, with increased metabolism leading to higher pro-oxidants generation. Insights on mitochondrial functioning show that oxygen consumption is either principally coupled with energy conversion as ATP or as heat, depending on whether the ATP-synthase or the mitochondrial uncoupling protein 1 (UCP1) is driving respiration. However, those two processes might greatly differ in terms of oxidative costs. We used a cold challenge to investigate the oxidative stress consequences of an increased metabolism achieved either by the activation of an uncoupled mechanism (i.e. UCP1 activity) in the brown adipose tissue (BAT) of wild-type mice, or by ATP-dependent muscular shivering thermogenesis in mice deficient for UCP1. Although both mouse strains increased by more than twofold their metabolism when acclimatised for 4 weeks to moderate cold (12°C), only mice deficient for UCP1 suffered from elevated levels of oxidative stress. When exposed to cold, mice deficient for UCP1 showed an increase of 20.2% in plasmatic reactive oxygen metabolites, 81.8% in muscular oxidized glutathione and 47.1% in muscular protein carbonyls. In contrast, there was no evidence of elevated levels of oxidative stress in the plasma, muscles or BAT of wild-type mice exposed to cold despite a drastic increase in BAT activity. Our study demonstrates differing oxidative costs linked to the functioning of two highly metabolically active organs during thermogenesis. It urges for careful considerations of mitochondrial functioning when investigating the links between metabolism and oxidative stress. Although both mouse strains increased by more than twofold their energy expenditure when acclimatised for 4 weeks to mild cold (12°C), only mice deficient for UCP1 suffered from elevated levels of oxidative stress. When exposed to cold, mice deficient for UCP1 showed an increase of 20.2% in plasmatic reactive oxygen metabolites, 81.8% in muscular oxidized glutathione and 47.1% in muscular protein carbonyls. In contrast, there was no evidence of elevated levels of oxidative stress in the plasma, muscles or BAT of wild-type mice exposed to cold despite a drastic increase in BAT activity. Our study demonstrates differing oxidative costs linked to the functioning of two highly metabolically active organs during thermogenesis. It urges for careful considerations of mitochondrial functioning when studying/considering the links between energy expenditure and oxidative stress.
Form and metabolic scaling in colonial animals
Authors: Hartikainen Hanna , Humphries Stuart , Okamura Beth 
Published: November 2013

Summary
Benthic colonial organisms exhibit a wide variation in size and shape and provide excellent model systems for testing the predictions of models that describe the scaling of metabolic rate with organism size. We test the hypothesis that colony form will influence metabolic scaling and its derivatives by characterising metabolic and propagule production rates in three species of freshwater bryozoans that vary in morphology and module organisation and which demonstrate two- and three-dimensional growth forms. The results were evaluated with respect to predictions from two models for metabolic scaling. Isometric metabolic scaling in two-dimensional colonies supported predictions of a model based on dynamic energy budget theory (DEB) and not those of a model based on fractally branching supply networks. This metabolic isometry appears to be achieved by equivalent energy budgets of edge and central modules, in one species (Cristatella mucedo) via linear growth and in a second species (Lophopus crystallinus) by colony fission. Allometric scaling characterised colonies of a three-dimensional species (Fredericella sultana), also providing support for the DEB model. Isometric scaling of propagule production rates for C. mucedo and F. sultana suggests that the number of propagules produced in colonies increases directly with the number of modules within colonies. Feeding currents generated by bryozoans function in both food capture and respiration, thus linking metabolic scaling with dynamics of self-shading and resource capture. Metabolic rates fundamentally dictate organismal performance (e.g. growth, reproduction) and, as we show here, are linked with colony form. Metabolic profiles and associated variation in colony form should therefore influence the outcome of biotic interactions in habitats dominated by colonial animals and may drive patterns of macroevolution.
Ultra miniature force plate for measuring triaxial forces in the micro newton range
Authors: Reinhardt Lars , Blickhan Reinhard 
Published: November 2013

SummaryMeasuring the ground reaction forces of the single legs is indispensable to understand the dynamics of legged locomotion. Due to the technical state of the art investigations are limited to animals with a body mass above 1 g. Here we present the design, fabrication, calibration and performance of a novel ultra-miniature force platform at the micro newton level. The sensor was built using the stereolithography technology and had been equipped with semiconductor strain gages. We found a highly linear signal response in the calibrated force range to ± 1300 μN. Individual tests revealed that our force plate still shows a linear response at forces around 4 mN confirming the particular robustness. The sensitivity is above 50 V/N in all directions which makes it possible to resolve forces of 10 μN. Moreover, we demonstrated the suitability of the device on the basis of a typical ground reaction force measurement of Formica polyctena.
Detection and selective avoidance of near ultraviolet radiation by an aquatic annelid: the medicinal leech
Authors: Jellies John 
Published: November 2013

SummaryMedicinal leeches are aquatic predators that inhabit surface waters during daylight and also leave the water where they might be exposed to less screened light. Whereas the leech visual system has been shown to respond to visible light, leeches in the genus Hirudo do not appear to be as negatively phototactic as one might expect in order to avoid potential ultraviolet radiation (UVR) induced damage. I used high intensity LEDs to test the hypothesis that leeches could detect and specifically avoid near UVR (395-405 nM). Groups of unfed juvenile leeches exhibited a robust negative phototaxis to UVR, but had no behavioral response to blue or red and only a slight negative phototaxis to green and white light. Individual leeches also exhibited a vigorous negative phototaxis to UVR; responding in 100% of trials compared to modest negative responses to visible light (responding in about 8% of the trials). The responses in fed and unfed leeches were comparable for UVR stimuli. The responses depended upon the stimulus site: leeches shortened away from UV light to the head, and extended away from UV light to the tail. Electrophysiological nerve recordings showed that the cephalic eyes responded vigorously to UVR. Additionally, individual leech photoreceptors also showed strong responses to UVR, and a higher-order neuron associated with shortening and rapid behavioral responses, the S-cell, was activated by UVR, on both the head and tail. These results demonstrate that the leech can detect UVR and is able to discriminate behaviorally between UVR and visible light.
Visual feedback influences antennal positioning in flying hawk moths
Authors: Krishnan Anand , Sane Sanjay P. 
Published: November 2013

SummaryInsect antennae serve a variety of sensory functions including tactile sensing, olfaction and flight control. For all of these functions, the precise positioning of the antenna is essential to ensure the proper acquisition of sensory feedback. Although antennal movements in diverse insects may be elicited or influenced by multimodal sensory stimuli, the relative effects of these cues and their integration in the context of antennal positioning responses are not well-understood. In previous studies, we have shown that fields of Böhm's bristles located at the base of the antennae provide crucial mechanosensory input for antennal positioning in flying hawk moths. Here, we present electrophysiological and behavioral evidence to show that, in addition to the Böhm's bristles, antennal muscles of hawk moths also respond to bilateral visual input. Moreover, in contrast to the mechanosensory -motor circuit which is entirely contained within the ipsilateral side, visual feedback influences antennal positioning on both contra- and ipsilateral sides. Electromyograms recorded from antennal muscles show that the latency of muscle responses to visual stimulation ranged from 35-60 ms, considerably slower than their responses to mechanosensory stimuli (&lt;10ms). Additionally, the visual inputs received by antennal muscles are both motion-sensitive and direction-selective. We characterized the influence of visual feedback on antennal positioning by presenting open-loop translational and rotational visual stimuli to tethered flying moths. During rotational stimuli, we observed that the antenna contralateral to the direction of the turn moved forward through larger angles than the ipsilateral antenna. These observations suggest that whereas input from the Böhm's bristles mediates rapid corrections of antennal position, visual feedback may be involved in slower, bilaterally coordinated movements of the antenna during visually-guided flight maneuvers. Thus, visual feedback can modulate the set point at which the antenna is held during flight in hawk moths.
Modulation of appetite and feeding behavior of the larval mosquito Aedes aegypti (L.) by the serotonin-selective reuptake inhibitor paroxetine: shifts between distinct feeding modes and the influence of feeding status.
Authors: Kinney Michael P. , Panting Nicholas D. , Clark Thomas M. 
Published: November 2013

Summary
The effects of the serotonin selective reuptake inhibitor paroxetine (2 x 10-5 mol.l-1) on behavior of the larval mosquito Aedes aegypti (L.) are described. Four discrete behavioral states dominate larval behavior, wriggling, two distinct types of feeding, and quiescence. Feeding behaviors consist of foraging along the bottom of the container (substrate browsing), and stationary filter feeding while suspended from the surface film. Fed larvae respond to paroxetine with increased wriggling, and reductions in both feeding behaviors. In contrast, food-deprived larvae treated with paroxetine show no change in the proportion of time spent wriggling or feeding, but shift from stationary filter feeding to substrate browsing. Thus, actions of paroxetine in fed larvae are consistent with suppression of appetite and stimulation of wriggling, whereas paroxetine causes food-deprived larvae to switch from one feeding behavior to another. Further analysis of unfed larvae revealed that paroxetine decreased the power stroke frequency during wriggling locomotion, but had no effect on the swimming velocity during either wriggling or substrate browsing. These data suggest that: (1) serotonergic pathways may trigger shifts between distinct behaviors by actions on higher level (brain) integrating centers where behaviors such as feeding and locomotion are coordinated , (2) these centers in fed and food deprived larvae respond differently to serotonergic stimulation suggesting sensory feedback from feeding status, and (3) serotonergic pathways also modulate central pattern generators of the nerve cord where the bursts of action potentials originate that drive the rhythmic muscle contractions of wriggling.
Divergent strategies for adaptations to stress resistance in two tropical Drosophila species: effects of developmental acclimation for D. bipectinata and the invasive species - D. malerkotliana
Authors: Parkash Ravi , Singh Divya , Lambhod Chanderkala 
Published: November 2013

Summary
Previous studies on two tropical Drosophila species (D. malerkotliana and D. bipectinata) have shown lower resistance to stress related traits but the rapid colonization of D. malerkotliana in the past few decades is not consistent with its sensitivity to desiccation and cold stress. We tested the hypothesis whether developmental acclimation at two growth temperatures (17 & 25 °C) can confer adaptations to desiccation and thermal stresses. We found divergence in developmental plastic effects on cuticular traits i.e. a significant increase of body melanisation (~2 fold) and of cuticular lipid mass (~3 fold) in D. malerkotliana but only 1.5 fold higher cuticular lipid mass in D. bipectinata when grown at 17 °C as compared with 25 °C. A comparison of water budget of these two species showed significantly higher effects of developmental acclimation on body water content, reduced rate of water loss and greater dehydration tolerance to confer higher desiccation resistance in D. malerkotliana as compared with D. bipectinata. Under less warmer growth conditions (17 °C), D. malerkotliana has evidenced greater resistance to cold as well as desiccation stress. In contrast, heat resistance of D. bipectinata is higher than D. malerkotliana when grown at 25 °C. These laboratory observations find support from data on seasonally varying populations. Further, adults acclimated to different stresses showed greater increase in D. malerkotliana as compared with D. bipectinata. Thus, significant increase of stress resistance of D. malerkotliana via developmental acclimation may be responsible for its invasion and ecological success on different continents as compared with D. bipectinata.
Evaluation of the Ion Selectivity of Cyclotriveratrylene Derivatives for Inorganic Ions
Authors: Moriuchi-Kawakami Takayo , Sato Junichi , Shibutani Yasuhiko 
Published: November 2013

Abstract
Four C3-functionalized cyclotriveratrylene (CTV) derivatives 1–4 were synthesized, and the ion selectivity of CTV derivatives for inorganic ions was evaluated. Upon potentiometric measurements, CTV derivatives bearing three quinolinylmethyl or pyridinylmethyl groups (1 or 2) were found to exhibit high selectivity for the Ag+ ion. However, CTV derivatives bearing three benzyl or cyclohexylmethyl groups (3 or 4) exhibited rather high selectivity for the Li+ ion. The aromatic nitrogen and methoxy oxygen atoms in the CTV derivatives were observed to play important roles as effective coordination donor sites for the Ag+ or the Li+ ions.
Synthesis and Thin-film Transistor Characterization of Narrow-gap n-Type Semiconducting Polymers Based on Benzobis(thiadiazole)
Authors: Uemura Taisuke , Mamada Masashi , Teraoka Ryo , Kumaki Daisuke , Tokito Shizuo 
Published: November 2013

Abstract
Solution-processable polymers based on strong acceptor benzobis(thiadiazole) (BBT) units were synthesized to form unipolar n-type organic thin-film transistors (OTFTs) that were electronically characterized. These polymers exhibited a narrow band-gap and low LUMO level, resulting in distinct n-type semiconducting properties within the OTFT devices. The BBT–thiazole polymer material showed better electron transport than BBT–thiophene polymers. The use of electron-deficient units was found to be suitable for the realization of the unipolar n-type semiconducting polymers.
Językoznawstwo ogólne – metodologiczny projekt Ferdynanda de Saussure’a
Authors: Danielewiczowa Magdalena 
Published: November 2013

General linguistics – Ferdinand de Saussure’s methodological project
The article discusses several methodological problems contained in Saussure’s works. General linguistics, a new discipline postulated by the author, was to be founded on linguistic details and at the same time focus on the fundamental and universal mechanisms of speech. Saussure did not consider general linguistics a part of natural sciences or of historical studies; he indicated logic as the discipline that can provide the appropriate tools for an adequate description of language. According to him, the subject of research in linguistics is not given in advance; instead, it depends entirely on the chosen point of view. Internal divisions of the discipline, especially the distinction between the linguistics of “langue” and the linguistics of “parole”, follows, firstly, from the dual nature of language, and secondly, from Saussure’s teaching about the legitimate points of view.