bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage
Authors: Méndez-García Celia , Mesa Victoria , Sprenger Richard R , Richter Michael , Diez María Suárez , Solano Jennifer , Bargiela Rafael , Golyshina Olga V , Manteca Ángel , Ramos Juan Luis , Gallego José R , Llorente Irene , Martins dos Santos Vitor A P , Jensen Ole N , Peláez Ana I , Sánchez Jesús , Ferrer Manuel 
Published: January 2014

Abstract
Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN’ (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN’-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths.
High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments
Authors: Engelhardt Tim , Kallmeyer Jens , Cypionka Heribert , Engelen Bert 
Published: January 2014

Abstract
Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (∼14 Ma old) and the most oligotrophic subsurface sediments of the world’s oceans (South Pacific Gyre (SPG)). The numbers of viruses (104–109 cm−3, counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.
A visible light-driven plasmonic photocatalyst
Authors: Pincella Francesca , Isozaki Katsuhiro , Miki Kazushi 
Published: January 2014

AbstractWe demonstrate a bottom-up approach to fabricating a visible light-driven titania photocatalyst device bearing an embedded two-dimensional (2D) array of gold nanoparticles (AuNPs) as a near-field light-generating layer. The device is a layered structure prepared by depositing a 2D array of AuNPs on a transparent conductive substrate (10 nm indium tin oxide (ITO) layer on quartz), coating the 2D array of AuNPs with a monolayer of trimethoxyoctylsilane (TMOS), and depositing titania nanocrystals on the anchoring molecule (TMOS) layer. The visible light activity of the device was tested using photocatalytic degradation of methylene blue (MB) by illuminating the device with visible light (700 nm light) and ultraviolet (UV) light (250–380 nm). The localized surface plasmon resonance peak of the 36 nm AuNP 2D array is around 700 nm with a full-width at half-maximum of 350 nm. In comparison with other control samples, the device showed the highest photocatalytic activity with visible irradiation, which was 1.7 times higher than that of titania with UV irradiation. The origin of the visible light activity was confirmed by both quadratic incident light power dependency and action spectrum to be plasmon-induced (near-field enhancement by AuNPs) two-photon absorption.
Network Understanding of Herb Medicine via Rapid Identification of Ingredient-Target Interactions
Authors: Zhang Hai-Ping , Pan Jian-Bo , Zhang Chi , Ji Nan , Wang Hao , Ji Zhi-Liang 
Published: January 2014

AbstractToday, herb medicines have become the major source for discovery of novel agents in countermining diseases. However, many of them are largely under-explored in pharmacology due to the limitation of current experimental approaches. Therefore, we proposed a computational framework in this study for network understanding of herb pharmacology via rapid identification of putative ingredient-target interactions in human structural proteome level. A marketing anti-cancer herb medicine in China, Yadanzi (Brucea javanica), was chosen for mechanistic study. Total 7,119 ingredient-target interactions were identified for thirteen Yadanzi active ingredients. Among them, about 29.5% were estimated to have better binding affinity than their corresponding marketing drug-target interactions. Further Bioinformatics analyses suggest that simultaneous manipulation of multiple proteins in the MAPK signaling pathway and the phosphorylation process of anti-apoptosis may largely answer for Yadanzi against non-small cell lung cancers. In summary, our strategy provides an efficient however economic solution for systematic understanding of herbs' power.
Collective behaviour across animal species
Authors: DeLellis Pietro , Polverino Giovanni , Ustuner Gozde , Abaid Nicole , Macrì Simone , Bollt Erik M. , Porfiri Maurizio 
Published: January 2014

AbstractWe posit a new geometric perspective to define, detect and classify inherent patterns of collective behaviour across a variety of animal species. We show that machine learning techniques and specifically the isometric mapping algorithm, allow the identification and interpretation of different types of collective behaviour in five social animal species. These results offer a first glimpse at the transformative potential of machine learning for ethology, similar to its impact on robotics, where it enabled robots to recognize objects and navigate the environment.
Drought impacts on children's respiratory health in the Brazilian Amazon
Authors: Smith Lauren T. , Aragão Luiz E. O. C. , Sabel Clive E. , Nakaya Tomoki 
Published: January 2014

AbstractDrought conditions in Amazonia are associated with increased fire incidence, enhancing aerosol emissions with degradation in air quality. Quantifying the synergic influence of climate and human-driven environmental changes on human health is, therefore, critical for identifying climate change adaptation pathways for this vulnerable region. Here we show a significant increase (1.2%–267%) in hospitalisations for respiratory diseases in children under-five in municipalities highly exposed to drought. Aerosol was the primary driver of hospitalisations in drought affected municipalities during 2005, while human development conditions mitigated the impacts in 2010. Our results demonstrated that drought events deteriorated children's respiratory health particularly during 2005 when the drought was more geographically concentrated. This indicates that if governments act on curbing fire usage and effectively plan public health provision, as a climate change adaptation procedure, health quality would improve and public expenditure for treatment would decrease in the region during future drought events.
Frataxin-bypassing Isu1: characterization of the bypass activity in cells and mitochondria
Authors: Yoon Heeyong , Knight Simon A. B. , Pandey Alok , Pain Jayashree , Zhang Yan , Pain Debkumar , Dancis Andrew 
Published: January 2014

Frataxin is a conserved mitochondrial protein, and deficiency underlies the neurodegenerative disease Friedreich's ataxia. Frataxin interacts with the core machinery for Fe–S cluster assembly in mitochondria. Recently we reported that in frataxin-deleted yeast strains, a spontaneously occurring mutation in one of two genes encoding redundant Isu scaffold proteins, bypassed the mutant phenotypes. In the present study we created strains expressing a single scaffold protein, either Isu1 or the bypass mutant M107I Isu1. Our results show that in the frataxin-deletion strain expressing the bypass mutant Isu1, cell growth, Fe–S cluster protein activities, haem proteins and iron homoeostasis were restored to normal or close to normal. The bypass effects were not mediated by changes in Isu1 expression level. The persulfide-forming activity of the cysteine desulfurase was diminished in the frataxin deletion (∆yfh1 ISU1) and was improved by expression of the bypass Isu1 (∆yfh1 M107I ISU1). The addition of purified bypass M107I Isu1 protein to a ∆yfh1 lysate conferred similar enhancement of cysteine desulfurase as did frataxin, suggesting that this effect contributed to the bypass mechanism. Fe–S cluster-forming activity in isolated mitochondria was stimulated by the bypass Isu1, albeit at a lower rate. The rescuing effects of the bypass Isu1 point to ways that the core defects in Friedreich's ataxia mitochondria can be restored.
Evaporation characteristics of micropores in biomimetic micropump
Authors: Liu Chong , Wang Lei , Li Jingmin , Li Meng , Duan Yajie , Li Tao , Gan Lu 
Published: January 2014

A modified biomimetic micropump based on the stomatal transpiration principle is presented. The micropump is designed to have a layer of SU‐8 microporous membrane and a layer of hydrophilic microporous ceramics, which reflects the natural plant stomata and mesophyll cells. The evaporation characteristics of the different stomata are analysed qualitatively by an established model. There is a positive connection between the stomata evaporation flux and the micropump flow rate. Corresponding experiments on micropump flow rate are conducted. The presented micropump has favourable assembly and reuse properties. The results indicate that the water vapour distribution in the stomata has a trend of edge effect. It also shows that the fluid flow rate in the micropump changes regularly with the stomata size and spacing.
An improved dynamic non-equilibrium wall-model for large eddy simulation
Authors: Park George Ilhwan , Moin Parviz 
Published: January 2014

A non-equilibrium wall-model based on unsteady 3D Reynolds-averaged Navier-Stokes (RANS) equations has been implemented in an unstructured mesh environment. The method is similar to that of the wall-model for structured mesh described by Wang and Moin [Phys. Fluids 14, 2043–2051 (2002)], but is supplemented by a new dynamic eddy viscosity/conductivity model that corrects the effect of the resolved Reynolds stress (resolved turbulent heat flux) on the skin friction (wall heat flux). This correction is crucial in predicting the correct level of the skin friction. Unlike earlier models, this eddy viscosity/conductivity model does not have a stress-matching procedure or a tunable free parameter, and it shows consistent performance over a wide range of Reynolds numbers. The wall-model is validated against canonical (attached) transitional and fully turbulent flows at moderate to very high Reynolds numbers: a turbulent channel flow at Reτ = 2000, an H-type transitional boundary layer up to Reθ = 3300, and a high Reynolds number boundary layer at Reθ = 31 000. Application to a separated flow over a NACA4412 airfoil operating close to maximum lift is also considered to test the performance of the wall-model in complex non-equilibrium flows.
Spatiotemporal pattern of action potential firing in developing inner hair cells of the mouse cochlea
Authors: Sendin Gaston , Bourien Jérôme , Rassendren François , Puel Jean-Luc , Nouvian Régis 
Published: January 2014

Significance
Sensory inner hair cells (IHCs) of the cochlea, the organ of hearing, fire action potentials during development. This presensory activity likely drives refinement of the ascending auditory pathway. Our study shows that the IHCs fire spontaneous bursts of action potentials, which tend to occur at a regular time interval and have a similar length toward the end of the first postnatal week. The spiking behavior does not depend on ATP but, rather, is modulated by the α9α10 nicotinic receptor, which is expressed by the developing IHCs. The firing pattern of the IHCs may therefore convey a temporal signature of the cochlear development to the higher auditory centers.
Patient Blood Management in Elective Total Hip- and Knee-replacement Surgery (Part 2)
Authors: So-Osman Cynthia , Nelissen Rob G. H. H. , Koopman-van Gemert Ankie W. M. M. , Kluyver Ewoud , Pöll Ruud G. , Onstenk Ron , Van Hilten Joost A. , Jansen-Werkhoven Thekla M. , van den Hout Wilbert B. , Brand Ronald , Brand Anneke 
Published: January 2014

Abstract

Background:
Patient blood management is introduced as a new concept that involves the combined use of transfusion alternatives. In elective adult total hip- or knee-replacement surgery patients, the authors conducted a large randomized study on the integrated use of erythropoietin, cell saver, and/or postoperative drain reinfusion devices (DRAIN) to evaluate allogeneic erythrocyte use, while applying a restrictive transfusion threshold. Patients with a preoperative hemoglobin level greater than 13 g/dl were ineligible for erythropoietin and evaluated for the effect of autologous blood reinfusion.

Methods:
Patients were randomized between autologous reinfusion by cell saver or DRAIN or no blood salvage device. Primary outcomes were mean intra- and postoperative erythrocyte use and proportion of transfused patients (transfusion rate). Secondary outcome was cost-effectiveness.

Results:
In 1,759 evaluated total hip- and knee-replacement surgery patients, the mean erythrocyte use was 0.19 (SD, 0.9) erythrocyte units/patient in the autologous group (n = 1,061) and 0.22 (0.9) erythrocyte units/patient in the control group (n = 698) (P = 0.64). The transfusion rate was 7.7% in the autologous group compared with 8.3% in the control group (P = 0.19). No difference in erythrocyte use was found between cell saver and DRAIN groups. Costs were increased by €298 per patient (95% CI, 76 to 520).

Conclusion:
In patients with preoperative hemoglobin levels greater than 13 g/dl, autologous intra- and postoperative blood salvage devices were not effective as transfusion alternatives: use of these devices did not reduce erythrocyte use and increased costs.
Nutritional benefits from domatia inhabitants in an ant–plant interaction: interlopers do pay the rent
Authors: Chanam Joyshree , Sheshshayee Madavalam Sreeman , Kasinathan Srinivasan , Jagdeesh Amaraja , Joshi Kanchan A. , Borges Renee M. 
Published: January 2014

Summary

How a symbiosis originates and is maintained are important evolutionary questions. Symbioses in myrmecophytes (plants providing nesting for ants) are believed to be maintained by protection and nutrients provided by specialist plant‐ants in exchange for nesting spaces (called domatia) and nourishment offered by ant‐plants. However, besides the benefits accrued from housing protective ants, the mechanisms contributing to the fitness advantages of bearing domatia have rarely been examined, especially because the domatia trait is usually constitutively expressed, and many myrmecophytes have obligate mutualisms with single ant species resulting in invariant conditions.

In the unspecialized ant‐plant Humboldtia brunonis (Fabaceae) that offers extrafloral nectar to ants, only some plants produce domatia in the form of hollow internodes. These domatia have a self‐opening slit making them more prone to interlopers and are occupied mostly by non‐protective ants and other invertebrates, especially arboreal earthworms. The protection mutualism with ants is restricted in geographical extent, occurring only at a few sites in the southernmost part of this plant's range in the Western Ghats of India.

We examined nutrient flux from domatia residents to the plant using stable isotopes. We found that between 9% (earthworms) and 17% (protective or non‐protective ants) of nitrogen of plant tissues nearest the domatium came from domatia inhabitants. Therefore, interlopers such as earthworms and non‐protective ants contributed positively to the nitrogen budget of localized plant modules of this understorey tree. 15N‐enriched feeding experiments with protective ants demonstrated that nutrients flowed from domatia inhabitants to nearby plant modules. Fruit set did not differ between paired hand‐pollinated inflorescences on domatia and non‐domatia bearing branches. This was possibly due to the nutrient flux from domatia to adjacent branches without domatia within localized modules.

This study has demonstrated the nutritive role of non‐protective ants and non‐ant invertebrates, hitherto referred to as interlopers, in an unspecialized myrmecophyte. Our study suggests that even before the establishment of a specialized ant–plant protection mutualism, nutritional benefits conferred by domatia inhabitants can explain the fitness benefits of bearing domatia, and thus the maintenance of a trait that facilitates the establishment of a specialized ant–plant symbiosis.
Co‐localization of insect olfactory sensory cells improves the discrimination of closely separated odour sources
Authors: Binyameen Muhammad , Jankuvová Júlia , Blaženec Miroslav , Jakuš Rastislav , Song Liwen , Schlyter Fredrik , Andersson Martin N. 
Published: January 2014

Summary

The sense of smell is crucial for fitness of most animals, enabling them to find mates, food and egg laying sites and to stay away from danger. Hence, odour molecules are detected by sensitive and specific olfactory sensory neurons (OSNs). In insects, the OSNs are stereotypically grouped into olfactory sensilla located mainly on the antennae. The functional significance of this co‐localization principle is poorly understood, but it has been hypothesized that it allows for coincidence detection of odour filaments, improving discrimination of closely separated odour sources.

Using an insect in its natural environment, we conducted the first experimental test of the hypothesis. We manipulated the distance between odour sources of an attractive pheromone and either of two host‐derived attraction antagonists (1,8‐cineole and verbenone) and investigated the effect on trap catches of the bark beetle, Ips typographus (Coleoptera). 1,8‐Cineole is detected by an OSN co‐localized with an OSN for one of the pheromone components, while verbenone is detected by OSNs in other sensilla, not co‐localized with pheromone OSNs.

Consistent with the hypothesis, trap catch increased with distance between odour sources more for 1,8‐cineole than for verbenone. The strongest effect was found among the males, that is the sex that first locates and attacks the host tree.

Our data from the beetle provide, for the first time, direct experimental support for the hypothesis that co‐localization of OSNs in sensilla improves the discrimination of closely separated odour sources. Thus, selection for improved odour source discrimination could well be one of the factors explaining the strict co‐localization of OSNs that is seen across the Insecta class.
A critical examination of indices of dynamic interaction for wildlife telemetry studies
Authors: Long Jed A. , Nelson Trisalyn A. , Webb Stephen L. , Gee Kenneth L. 
Published: January 2014

Summary

Wildlife scientists continue to be interested in studying ways to quantify how the movements of animals are interdependent – dynamic interaction. While a number of applied studies of dynamic interaction exist, little is known about the comparative effectiveness and applicability of available methods used for quantifying interactions between animals.

We highlight the formulation, implementation and interpretation of a suite of eight currently available indices of dynamic interaction. Point‐ and path‐based approaches are contrasted to demonstrate differences between methods and underlying assumptions on telemetry data.

Correlated and biased correlated random walks were simulated at a range of sampling resolutions to generate scenarios with dynamic interaction present and absent. We evaluate the effectiveness of each index at identifying different types of interactive behaviour at each sampling resolution. Each index is then applied to an empirical telemetry data set of three white‐tailed deer (Odocoileus virginianus) dyads.

Results from the simulated data show that three indices of dynamic interaction reliant on statistical testing procedures are susceptible to Type I error, which increases at fine sampling resolutions. In the white‐tailed deer examples, a recently developed index for quantifying local‐level cohesive movement behaviour (the di index) provides revealing information on the presence of infrequent and varying interactions in space and time.

Point‐based approaches implemented with finely sampled telemetry data overestimate the presence of interactions (Type I errors). Indices producing only a single global statistic (7 of the 8 indices) are unable to quantify infrequent and varying interactions through time. The quantification of infrequent and variable interactive behaviour has important implications for the spread of disease and the prevalence of social behaviour in wildlife. Guidelines are presented to inform researchers wishing to study dynamic interaction patterns in their own telemetry data sets. Finally, we make our code openly available, in the statistical software R, for computing each index of dynamic interaction presented herein.