bluuebunny/crossref_metadata_2025_split huggingface dataset:
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
Authors: Coll Francesc , McNerney Ruth , Guerra-Assunção José Afonso , Glynn Judith R. , Perdigão João , Viveiros Miguel , Portugal Isabel , Pain Arnab , Martin Nigel , Clark Taane G. 
Published: September 2014

AbstractStrain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type.
Effective connectivity during animacy perception – dynamic causal modelling of Human Connectome Project data
Authors: Hillebrandt Hauke , Friston Karl J. , Blakemore Sarah-Jayne 
Published: September 2014

AbstractBiological agents are the most complex systems humans have to model and predict. In predictive coding, high-level cortical areas inform sensory cortex about incoming sensory signals, a comparison between the predicted and actual sensory feedback is made and information about unpredicted sensory information is passed forward to higher-level areas. Predictions about animate motion – relative to inanimate motion – should result in prediction error and increase signal passing from lower level sensory area MT+/V5, which is responsive to all motion, to higher-order posterior superior temporal sulcus (pSTS), which is selectively activated by animate motion. We tested this hypothesis by investigating effective connectivity in a large-scale fMRI dataset from the Human Connectome Project. 132 participants viewed animations of triangles that were designed to move in a way that appeared animate (moving intentionally), or inanimate (moving in a mechanical way). We found that forward connectivity from V5 to the pSTS increased and inhibitory self-connection in the pSTS decreased, when viewing intentional motion versus inanimate motion. These prediction errors associated with animate motion may be the cause for increased attention to animate stimuli found in previous studies.
Detection of Volatile Organic Compounds by Weight-Detectable Sensors coated with Metal-Organic Frameworks
Authors: Yamagiwa Hiroki , Sato Seiko , Fukawa Tadashi , Ikehara Tsuyoshi , Maeda Ryutaro , Mihara Takashi , Kimura Mutsumi 
Published: September 2014

AbstractDetection of volatile organic compounds (VOCs) using weight-detectable quartz microbalance and silicon-based microcantilever sensors coated with crystalline metal-organic framework (MOF) thin films is described in this paper. The thin films of two MOFs were grown from COOH-terminated self-assembled monolayers onto the gold electrodes of sensor platforms. The MOF layers worked as the effective concentrators of VOC gases and the adsorption/desorption processes of the VOCs could be monitored by the frequency changes of weight-detectable sensors. Moreover, the MOF layers provided VOC sensing selectivity to the weight-detectable sensors through the size-selective adsorption of the VOCs within the regulated nanospace of the MOFs.
Ultrasonic splicing of polymer optical fibres
Authors: Mizuno Y. , Ohara S. , Hayashi N. , Nakamura K. 
Published: September 2014

A new method of splicing polymer optical fibres by irradiation of megahertz ultrasonic waves is demonstrated. The lowest connection loss of 1.5 dB is obtained at 2 MHz, and a high mechanical strength of 59 N (close to the strength of the base polymer) is achieved at 1 MHz. It is shown that the loss and strength are in a trade‐off relationship, and that the duration of ultrasonic irradiation has a certain optimal value of ∼1 s.
Broadband right‐angle transition from substrate‐integrated waveguide to rectangular waveguide
Authors: Li Teng , Dou Wenbin 
Published: September 2014

A broadband right‐angle transition from a substrate‐integrated waveguide (SIW) to a rectangular waveguide (RWG) is proposed. A coupling aperture etched on the broad wall of the SIW and two stepped ridges embedded in the RWG flange are designed for good matching between both waveguides. A Ka‐band prototype is designed and fabricated. Good agreement between the measured and simulated results is obtained. The measured results show an insertion loss <0.55 dB and a return loss below −15 dB from 31.3 to 38.35 GHz. This broadband transition may be used in microwave and millimetre‐wave circuits and systems.
High‐power VHF tunable filters with high selectivity
Authors: Zhao Zhi‐Yuan , Chen Jiang , Yang Lin , Chen Kun‐He 
Published: September 2014

A tunable helical bandpass filter with high selectivity designed for 30–88 MHz operation is presented. The two‐pole tunable filter is discretely tuned by connecting PIN switched capacitor banks at the terminal ends of the helix. The filter schematic provides two finite transmission zeros located in the lower and upper stopbands, respectively. The experimental filter has an insertion loss between 1.65 and 2.75 dB with its return loss better than 13 dB. The 3‐dB fractional bandwidth of the filter is 3.3%–3.7% and the shape factor (BW30 dB/BW3 dB) is smaller than 5.5 over the entire tuning range. The input power handling capability is greater than 45 dBm. The measured results show good agreement with the simulated ones.
64 × 48 TOF sensor in 0.35 µm CMOS with high ambient light immunity
Authors: Davidovic M. , Seiter J. , Hofbauer M. , Gaberl W. , Schidl S. , Zimmermann H. 
Published: September 2014

A multi‐pixel 64 × 48 time‐of‐flight (TOF) range sensor whose speciality is high immunity against ambient light is presented. The chip was fabricated in a 0.35 µm 1P4M CMOS process, whereby a single pixel occupies an area of 45 × 60 µm2 achieving a fill factor of 50%. The measured distance shows a 1σ deviation below 3.7 mm in the optimum operating range for the sensor. The measurement results show that the sensor successfully acquires the distance even when some parts of the scenery are illuminated with 180 klx ambient light. Furthermore, the most accurate method to characterise particular pixels in a multi‐pixel array is for the first time used in a multi‐pixel TOF sensor.
5 Gbit/s 2‐tap low‐swing voltage‐mode transmitter with least segmented voltage‐mode equalisation
Authors: Kwak Kang‐Sub , Hong Seong‐Kwan , Kwon Oh‐Kyong 
Published: September 2014

A 2‐tap low‐swing voltage‐mode transmitter which compensates the loss of channel at high frequency is proposed. The output driver of the proposed 2‐tap transmitter consists of only two voltage‐mode drivers, and thereby the design complexity of the pre‐driver is greatly reduced compared with that of conventional 2N‐segmented voltage‐mode drivers, where N is the number of equalisation control bits. The output impedance of each voltage‐mode driver is adjusted not only to make the overall output impedance matched with the characteristic impedance of the channel, but also to achieve the desired equalisation coefficient by adopting the proposed calibration circuitry. With a high equalisation coefficient, the proposed output driver consumes less power compared with the hybrid voltage‐mode driver with current‐mode equalisation. The proposed transmitter is implemented using a 90 nm low‐power CMOS process technology and achieves 0.79 pJ/bit without equalisation and 0.98 pJ/bit with 6 dB equalisation, at the data rate of 5 Gbit/s.
Fast Si (100) etching with a smooth surface near the boiling temperature in surfactant‐modified tetramethylammonium hydroxide solutions
Authors: Tang Bin , Sato Kazuo , Zhang De , Cheng Yongsheng 
Published: September 2014

The etching characteristics of the commonly utilised Si (100) facet at high temperatures near the boiling point in surfactant‐modified tetramethylammonium hydroxide (TMAH) solutions are investigated. Solutions of 25 wt% TMAH are selected because of the etching stability and the rate of addition of the surfactant Triton‐X‐100 [C14H22O(C2H4O)n, n = 9–10] ranges from 0.01 to 1% v/v. The etching rates of Si (100) facets close to the boiling point are three to four times higher than those at 80°C in the surfactant‐modified 25 wt% TMAH solutions. In particular, at 115°C, the very near temperature of the boiling point, the silicon sample possessing a high etching rate of 1.45 μm/min and the smooth etched Si (100) surface with an average roughness of about 1 nm is obtained. Moreover, the samples do not demonstrate much undercut difference at the etched convex corners near the boiling point. These results are useful for the fabrication of microelectromechanical systems and indeed provide an efficient etching method for industry products.
Extinction coefficient of water‐based multi‐walled carbon nanotube nanofluids for application in direct‐absorption solar collectors
Authors: Lee Seung‐Hyun , Kim Hyun Jin , Kim Kyu Han , Jang Seok Pil 
Published: September 2014

In this reported work, the extinction coefficient of water‐based nanofluids containing multi‐walled carbon nanotubes (MWNCTs) has been experimentally measured. The MWCNTs were dispersed in deionised water with a surfactant, hexadecyltrimethyl‐ammonium bromide, and they were homogenised by a bath‐type ultrasonicator and a mechanical stirrer. The characteristics of MWCNTs suspended in the nanofluids were examined by transmission electron microscopy and scanning electron microscopy images and their hydrodynamic particle size was measured by a particle size analyser. The extinction coefficient of nanofluids was measured by an in‐house developed apparatus at a single wavelength (632.8 nm) based on the Lambert‐Beer principle. With the experimentally obtained extinction coefficient, the efficiency of a flat‐plate type direct‐absorption solar collector (DASC) was theoretically estimated. For this purpose, a modified analytical solution of the DASC efficiency is presented by assuming that the extinction coefficient is not a function of the wavelength. Finally, the efficiency of DASC is demonstrated according to the nanotube volume fractions. The results show that the DASC concept can further improve the efficiency of the conventional flat‐plate type solar collectors.
Biodegradation characterization and immobilized strains’ potential for quinoline degradation by Brevundimonas sp. K4 isolated from activated sludge of coking wastewater
Authors: Wang Chunrong , Zhang Mengru , Cheng Fanglin , Geng Qi 
Published: September 2014

Abstract
A novel quinoline-degrading strain, named K4, was isolated from activated sludge of a coking wastewater treatment plant and identified as Brevundimonas sp. on the basis of its 16s rDNA gene sequence analysis. Its optimum temperature and pH for quinoline degradation were 30 °C and pH 9.0, respectively, and during the biodegradation process, at 100 mg/L initial quinoline concentration, an inoculation amount of 8% (OD600 of 0.23) was the optimal strain concentration. In addition, the kinetics of free K4 strains for quinoline degradation showed that it followed a zero-order equation. Furthermore, compared with free K4 strains, immobilized K4 strains’ potential for quinoline degradation was investigated by adding both of them into SBR reactors for actual coking wastewater treatment on operation over 15 days. The results showed that bioaugmentation by both free and immobilized K4 strains enhanced quinoline removal efficiency, and especially, the latter could reach its stable removal after a shorter accommodation period, with 94.8% of mean quinoline removal efficiency.
Confucianism: A Very Short Introduction
Authors: Gardner Daniel K. 
Published: September 2014

Abstract
To understand China, it is essential to understand Confucianism. First formulated in the sixth century bce, the teachings of Confucius would come to dominate Chinese society, politics, economics, and ethics. Confucianism: A Very Short Introduction explores the major philosophical ideas of the Confucian tradition, showing their profound impact on state ideology, imperial government, the civil service examination system, domestic life, and social relations over the course of twenty-six centuries. It focuses on two of the Sage's most crucial philosophical problems—what makes for a good person, and what constitutes good government—and demonstrates the enduring significance of these questions today and how the Confucian tradition sits alongside Western ideas and technology.
Evaluation of Shiga toxin 2e‐specific chicken egg yolk immunoglobulin: Production and neutralization activity
Authors: Arimitsu Hideyuki , Sasaki Keiko , Kohda Tomoko , Shimizu Toshiyasu , Tsuji Takao 
Published: September 2014

AbstractChicken egg yolk immunoglobulin (IgY) against Shiga toxin 2e (Stx2e), a major cause of swine edema disease, was prepared to evaluate its possible clinical applications. The titer of Stx2e‐specific IgY in egg yolk derived from three chickens that had been immunized with an Stx2e toxoid increased 2 weeks after primary immunization and remained high until 90 days after this immunization. Anti‐Stx2e IgY was found to neutralize the toxicity of Stx2e by reacting with its A and B subunits, indicating that IgY is a cost‐effective agent to develop for prophylactic foods or diagnosis kits for edema disease.
EDITOR'S CHOICE: REVIEW: Effects of land use on plant diversity – A global meta‐analysis
Authors: Gerstner Katharina , Dormann Carsten F. , Stein Anke , Manceur Ameur M. , Seppelt Ralf 
Published: September 2014

Summary

Plant diversity is globally threatened by anthropogenic land use including management and modification of the natural environment. At regional and local scales, numerous studies world‐wide have examined land use and its effects on plant diversity, but evidence for declining species diversity is mixed. This is because, first, land use comes in many variations, hampering comparisons of studies. Second, land use directly affects the environment, but indirect effects extend beyond the boundaries of the land in use. Third, land‐use effects greatly depend on the environmental, historical and socio‐economic context.

To evaluate the generality and variation of studies’ findings about land‐use effects, we undertook a quantitative synthesis using meta‐analytic techniques.

Using 572 effect sizes from 375 studies distributed globally relating to 11 classes of land use, we found that direct and indirect effects of land use on plant diversity (measured as species richness) are variable and can lead to both local decreases and increases. Further, we found evidence (best AIC model) that land‐use‐specific covariables mostly determine effect‐size variation and that in general land‐use effects differ between biomes.

Synthesis and applications. This extensive synthesis provides the most comprehensive and quantitative overview to date about the effects of the most widespread and relevant land‐use options on plant diversity and their covariables. We found important covariables of specific land‐use classes but little evidence that land‐use effects can be generally explained by their environmental and socio‐economic context. We also found a strong regional bias in the number of studies (i.e. more studies from Europe and North America) and highlight the need for an overarching and consistent land‐use classification scheme. Thereby, our study provides a new vantage point for future research directions.
Effects of riparian forest harvest on streams: a meta‐analysis
Authors: Richardson John S. , Béraud Salomé 
Published: September 2014

SummaryRiparian forest harvesting impacts streams in many ways, from altering temperature regimes, shifting geomorphic structure, increasing sediment fluxes and affecting fish populations. However, we have noted considerable variation in the results between studies that led us to ask whether the effects of forest harvesting on streams were consistent between studies. We used meta‐analysis of 34 replicated studies to address the effects of riparian logging on biological and chemical components of streams in contrast to control sites.We found that the overall effect sizes of several response variables in replicated studies were significantly higher than zero, especially benthic invertebrates, and nitrogen and potassium concentrations. However, there was a very large amount of variation in the effect sizes between studies, and for many measures, the effect sizes from different studies were positive or negative, indicating site‐specific responses.We explored whether stream size, stream gradient and regional potential evapotranspiration could explain some of the effect size variation between studies. Relations with these environmental variables were weak, but suggestive that some of the context‐specific, individual outcomes might be due to underlying environmental differences between sites.Synthesis and applications. Despite relatively low numbers of replicated studies, we found significant overall effects of riparian forest harvesting although the magnitude and direction of responses within individual studies were site specific. This lack of consistency in the direction of effect sizes suggests we need a more context‐dependent approach to the protection of freshwaters from forest management.
FORUM: Do green roofs help urban biodiversity conservation?
Authors: Williams Nicholas S. G. , Lundholm Jeremy , Scott MacIvor J. 
Published: September 2014

Summary

Green roofs are novel ecosystems that are increasingly common in cities. While their hydrologic and energy saving benefits are well‐established, green roofs have also been proposed as having significant value for conserving biodiversity.

We evaluate six hypotheses that describe the purported biodiversity conservation benefits of green roofs. Green roofs largely support generalist species particularly insects, but their conservation value for rare taxa, and other taxonomic groups especially vertebrates, is poorly documented. Further, their ability to replicate biotic communities in the context of ecological restoration is largely untested, as is their potential to connect ground‐level habitats.

Synthesis and applications. Given the evidence, green roof proponents should use restraint in claiming conservation benefits and it is premature for policymakers to consider green roofs equivalent to ground‐level urban habitats. Ecologists need to work with the industry to evaluate green roof biodiversity and help design green roofs based on ecological principles to maximize biodiversity gains.
REVIEW: Do polycultures promote win‐wins or trade‐offs in agricultural ecosystem services? A meta‐analysis
Authors: Iverson Aaron L. , Marín Linda E. , Ennis Katherine K. , Gonthier David J. , Connor‐Barrie Benjamin T. , Remfert Jane L. , Cardinale Bradley J. , Perfecto Ivette 
Published: September 2014

Summary

Agriculture comprises the largest global land use, makes it a leading cause of habitat loss. It is therefore critical to identify how to best construct agricultural systems that can simultaneously provide food and other ecosystem services. This challenge requires that we determine how to maximize win‐win relationships and minimize trade‐offs between services.

Through meta‐analysis, we tested whether within‐field crop diversification (polyculture) can lead to win‐win relationships between two ecosystem services: yield of a focal crop species and biocontrol of crop pests. We selected only studies that recorded both services (N = 26 studies; 301 observations), allowing us to better determine the underlying mechanisms of our principal findings. We calculated log‐response ratios for both ecosystem services in mono‐ and polycultures.

We found win‐win relationships between per‐plant yield of the primary crop and biocontrol in polyculture systems that minimized intraspecific competition via substitutive planting. Additionally, we found beneficial effects on biocontrol with no difference in per‐unit area yield of the primary crop in polyculture fields at high cropping densities (additive planting) where legumes were used as the secondary crop. These results suggest that there is a strong potential for win‐win relationships between biocontrol and per‐unit area yield under certain scenarios. Our findings were consistent across geographical regions and by type of primary crop. We did not find evidence that biocontrol had an effect on yield, but rather, both were independently affected by polycultural cropping.

Synthesis and applications. We show that well‐designed polycultures can produce win‐win outcomes between per‐plant, and potentially per‐unit area, primary crop yield and biocontrol. Biocontrol services are consistently enhanced in polycultures, so polyculture management that focuses on yield optimization is likely to be the best strategy for maximizing both services. In doing so, we suggest that practitioners utilize polycultures that decrease plant–plant competition through a substitution of relatively large quantities of the primary crop for compatibly harvestable secondary crops. Additionally, if planting at high cropping densities, it is important that legumes be the secondary crop.
Tropical rabbitfish and the deforestation of a warming temperate sea
Authors: Vergés Adriana , Tomas Fiona , Cebrian Emma , Ballesteros Enric , Kizilkaya Zafer , Dendrinos Panagiotis , Karamanlidis Alexandros A. , Spiegel David , Sala Enric 
Published: September 2014

Summary

A striking example of climate‐mediated range shifts in marine systems is the intrusion of tropical species into temperate areas world‐wide, but we know very little about the ecological consequences of these range expansions.

In the Mediterranean Sea, the range expansion of tropical rabbitfishes that first entered the basin via the Suez Canal provides a good example of how tropical herbivorous fish can impact the structure of rocky bottoms in temperate seas. Two species of rabbitfishes have now become a dominant component of total fish biomass in the southernmost part of the eastern Mediterranean. Experimental evidence shows these species can profoundly transform benthic communities, turning algal forests into ‘barrens’, but the specific mechanisms that facilitate this shift have not been established.

We surveyed ˜1000 km of coastline in the eastern Mediterranean and identified two clearly distinct areas, a warmer group of regions with abundant tropical rabbitfish and a colder group of regions where these consumers were absent/ extremely rare. In regions with abundant rabbitfish, canopy algae were 65% less abundant, and there was a 60% reduction of overall benthic biomass (algae and invertebrates) and a 40% decrease in total species richness.

Video‐recorded feeding experiments showed that the extensive barrens characteristic of regions with abundant rabbitfish were not due to greater rates of herbivory by these tropical consumers, but rather by functional differences among the herbivores. Temperate herbivorous fish displayed the greatest macroalgae consumption rates overall, but they fed exclusively on established adult macroalgae. In contrast, in regions with abundant rabbitfishes, these consumers fed complementarily on both established macroalgae and on the epilithic algal matrix, which typically contains macroalgal recruits.

Synthesis. Range‐shifting tropical rabbitfish can severely reduce the biomass and biodiversity of temperate reefs at a scale of hundreds of kilometres. A shift from macroalgal dominance to barrens is mediated by the addition of functionally diverse herbivores that characterize tropical reefs. This work highlights the importance of assessing the functional traits of range‐shifting species to determine potential mechanisms of impact on ecological communities.