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In the version of this Article originally published, the author Baran Eren was mistakenly affiliated with the Harbin Institute of Technology, China; it has now been corrected to Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Bimetallic and multi-component catalysts typically exhibit composition-dependent activity and selectivity, and when optimized often outperform single-component catalysts. Here we used ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) and in situ and ex situ transmission electron microscopy (TEM) to elucidate the origin of composition dependence observed in the catalytic activities of monodisperse CoPd bimetallic nanocatalysts for CO oxidation. We found that the catalysis process induced a reconstruction of the catalysts, leaving CoOx on the nanoparticle surface. The synergy between Pd and CoOx coexisting on the surface promotes the catalytic activity of the bimetallic catalysts. This synergistic effect can be optimized by tuning the Co/Pd ratios in the nanoparticle synthesis, and it reaches a maximum at compositions near Co0.24Pd0.76, which achieves complete CO conversion at the lowest temperature. Our combined AP-XPS and TEM studies provide direct observation of the surface evolution of the bimetallic nanoparticles under catalytic conditions and show how this evolution correlates with catalytic properties.

Bimetallic and multi-component catalysts typically exhibit composition-dependent activity and selectivity, and when optimized often outperform single-component catalysts. Here we used ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) and in situ and ex situ transmission electron microscopy (TEM) to elucidate the origin of composition dependence observed in the catalytic activities of monodisperse CoPd bimetallic nanocatalysts for CO oxidation. We found that the catalysis process induced a reconstruction of the catalysts, leaving CoOx on the nanoparticle surface. The synergy between Pd and CoOx coexisting on the surface promotes the catalytic activity of the bimetallic catalysts. This synergistic effect can be optimized by tuning the Co/Pd ratios in the nanoparticle synthesis, and it reaches a maximum at compositions near Co0.24Pd0.76, which achieves complete CO conversion at the lowest temperature. Our combined AP-XPS and TEM studies provide direct observation of the surface evolution of the bimetallic nanoparticles under catalytic conditions and show how this evolution correlates with catalytic properties.

In the version of this Article originally published, the author Baran Eren was mistakenly affiliated with the Harbin Institute of Technology, China; it has now been corrected to Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

On orbital timescales, higher summer insolation is thought to strengthen the continental monsoon while weakening the maritime monsoon in the Northern hemisphere. Through simulations using the Community Earth System Model, we evaluated the relative influence of perihelion precession and high obliquity in the early Holocene during the Asian summer monsoon. The major finding was that precession dominates the atmospheric heating change over the Tibetan Plateau–Himalayas and Maritime Continent, whereas obliquity is responsible for the heating change over the equatorial Indian Ocean. Thus, precession and obliquity can play contrasting roles in driving the monsoons on orbital timescales. In late spring–early summer, interior Asian continental heating drives the South and East Asian monsoons. The broad-scale monsoonal circulation further expands zonally in July–August, corresponding to the development of summer monsoons in West Africa and the subtropical Western North Pacific (WNP) as well as a sizable increase in convection over the equatorial Indian Ocean. Tropical and oceanic heating becomes crucial in late summer. Over South Asia–Indian Ocean (50°E−110°E), the precession maximum intensifies the monsoonal Hadley cell (heating with an inland/highland origin), which is opposite to the meridional circulation change induced by high obliquity (heating with a tropical origin). The existence of the Tibetan Plateau–Himalayas intensifies the precessional impact. During the late-summer phase of the monsoon season, the effect of obliquity on tropical heating can be substantial. In addition to competing with Asian continental heating, obliquity-enhanced heating over the equatorial Indian Ocean also has a Walker-type circulation impact, resulting in suppression of precession-enhanced heating over the Maritime Continent.

On orbital timescales, higher summer insolation is thought to strengthen the continental monsoon while weakening the maritime monsoon in the Northern hemisphere. Through simulations using the Community Earth System Model, we evaluated the relative influence of perihelion precession and high obliquity in the early Holocene during the Asian summer monsoon. The major finding was that precession dominates the atmospheric heating change over the Tibetan Plateau–Himalayas and Maritime Continent, whereas obliquity is responsible for the heating change over the equatorial Indian Ocean. Thus, precession and obliquity can play contrasting roles in driving the monsoons on orbital timescales. In late spring–early summer, interior Asian continental heating drives the South and East Asian monsoons. The broad-scale monsoonal circulation further expands zonally in July–August, corresponding to the development of summer monsoons in West Africa and the subtropical Western North Pacific (WNP) as well as a sizable increase in convection over the equatorial Indian Ocean. Tropical and oceanic heating becomes crucial in late summer. Over South Asia–Indian Ocean (50°E−110°E), the precession maximum intensifies the monsoonal Hadley cell (heating with an inland/highland origin), which is opposite to the meridional circulation change induced by high obliquity (heating with a tropical origin). The existence of the Tibetan Plateau–Himalayas intensifies the precessional impact. During the late-summer phase of the monsoon season, the effect of obliquity on tropical heating can be substantial. In addition to competing with Asian continental heating, obliquity-enhanced heating over the equatorial Indian Ocean also has a Walker-type circulation impact, resulting in suppression of precession-enhanced heating over the Maritime Continent.

We present a general simulation approach for fluid-solid interactions based on the fully Eulerian reference map technique. The approach permits the modelling of one or more finitely deformable continuum solid bodies interacting with a fluid and with each other. A key advantage of this approach is its ease of use, as the solid and fluid are discretized on the same fixed grid, which greatly simplifies the coupling between the phases. We use the method to study a number of illustrative examples involving an incompressible Navier-Stokes fluid interacting with multiple neo-Hookean solids. Our method has several useful features including the ability to model solids with sharp corners and the ability to model actuated solids. The latter permits the simulation of active media such as swimmers, which we demonstrate. The method is validated favourably in the flag-flapping geometry, for which a number of experimental, numerical and analytical studies have been performed. We extend the flapping analysis beyond the thin-flag limit, revealing an additional destabilization mechanism to induce flapping.

The East Asian summer monsoon is unique among summer monsoon systems in its complex seasonality, exhibiting distinct intraseasonal stages. Previous studies have alluded to the downstream influence of the westerlies flowing around the Tibetan Plateau as key to its existence. We explore this hypothesis using an atmospheric general circulation model that simulates the intraseasonal stages with fidelity. Without a Tibetan Plateau, East Asia exhibits only one primary convective stage typical of other monsoons. As the plateau is introduced, the distinct rainfall stages—spring, pre-mei-yu, mei-yu, and midsummer—emerge, and rainfall becomes more intense overall. This emergence coincides with a pronounced modulation of the westerlies around the plateau and extratropical northerlies penetrating northeastern China. The northerlies meridionally constrain the moist southerly flow originating from the tropics, leading to a band of lower-tropospheric convergence and humidity front that produces the rainband. The northward migration of the westerlies away from the northern edge of the plateau leads to a weakening of the extratropical northerlies, which, coupled with stronger monsoonal southerlies, leads to the northward migration of the rainband. When the peak westerlies migrate north of the plateau during the midsummer stage, the extratropical northerlies disappear, leaving only the monsoon low-level circulation that penetrates northeastern China; the rainband disappears, leaving isolated convective rainfall over northeastern China. In short, East Asian rainfall seasonality results from the interaction of two seasonally evolving circulations—the monsoonal southerlies that strengthen and extend northward, and the midlatitude northerlies that weaken and eventually disappear—as summer progresses.

The East Asian summer monsoon is unique among summer monsoon systems in its complex seasonality, exhibiting distinct intraseasonal stages. Previous studies have alluded to the downstream influence of the westerlies flowing around the Tibetan Plateau as key to its existence. We explore this hypothesis using an atmospheric general circulation model that simulates the intraseasonal stages with fidelity. Without a Tibetan Plateau, East Asia exhibits only one primary convective stage typical of other monsoons. As the plateau is introduced, the distinct rainfall stages—spring, pre-mei-yu, mei-yu, and midsummer—emerge, and rainfall becomes more intense overall. This emergence coincides with a pronounced modulation of the westerlies around the plateau and extratropical northerlies penetrating northeastern China. The northerlies meridionally constrain the moist southerly flow originating from the tropics, leading to a band of lower-tropospheric convergence and humidity front that produces the rainband. The northward migration of the westerlies away from the northern edge of the plateau leads to a weakening of the extratropical northerlies, which, coupled with stronger monsoonal southerlies, leads to the northward migration of the rainband. When the peak westerlies migrate north of the plateau during the midsummer stage, the extratropical northerlies disappear, leaving only the monsoon low-level circulation that penetrates northeastern China; the rainband disappears, leaving isolated convective rainfall over northeastern China. In short, East Asian rainfall seasonality results from the interaction of two seasonally evolving circulations—the monsoonal southerlies that strengthen and extend northward, and the midlatitude northerlies that weaken and eventually disappear—as summer progresses.

We present a general simulation approach for fluid-solid interactions based on the fully Eulerian reference map technique. The approach permits the modelling of one or more finitely deformable continuum solid bodies interacting with a fluid and with each other. A key advantage of this approach is its ease of use, as the solid and fluid are discretized on the same fixed grid, which greatly simplifies the coupling between the phases. We use the method to study a number of illustrative examples involving an incompressible Navier-Stokes fluid interacting with multiple neo-Hookean solids. Our method has several useful features including the ability to model solids with sharp corners and the ability to model actuated solids. The latter permits the simulation of active media such as swimmers, which we demonstrate. The method is validated favourably in the flag-flapping geometry, for which a number of experimental, numerical and analytical studies have been performed. We extend the flapping analysis beyond the thin-flag limit, revealing an additional destabilization mechanism to induce flapping.

Ambient-pressure X-ray photoelectron spectroscopy (XPS) was used to investigate the reactions of CO, H2, and their mixtures on Co foils. We found that CO adsorbs molecularly on the clean Co surface and desorbs intact in vacuum with increasing rate until ∼90°C where all CO desorbs in seconds. In equilibrium with 100 mTorr gas, CO dissociates above 120°C, leaving carbide species on the surface but no oxides, because CO efficiently reduces the oxides at temperatures ∼100°C lower than H2. Water as impurities or produced by reaction of CO and H2 efficiently oxidizes Co even at room temperature. Under 97:3 CO/H2 mixture and with increasing temperatures, the Co surface becomes more oxidized and covered by hydroxyl groups until ∼150°C where surface starts to get reduced, accompanied by carbide accumulation indicative of CO dissociation. A similar trend was observed for 9:1 and 1:1 mixtures, but surface reduction begins at higher temperatures. (Figure Presented).

Ambient-pressure X-ray photoelectron spectroscopy (XPS) was used to investigate the reactions of CO, H2, and their mixtures on Co foils. We found that CO adsorbs molecularly on the clean Co surface and desorbs intact in vacuum with increasing rate until ∼90°C where all CO desorbs in seconds. In equilibrium with 100 mTorr gas, CO dissociates above 120°C, leaving carbide species on the surface but no oxides, because CO efficiently reduces the oxides at temperatures ∼100°C lower than H2. Water as impurities or produced by reaction of CO and H2 efficiently oxidizes Co even at room temperature. Under 97:3 CO/H2 mixture and with increasing temperatures, the Co surface becomes more oxidized and covered by hydroxyl groups until ∼150°C where surface starts to get reduced, accompanied by carbide accumulation indicative of CO dissociation. A similar trend was observed for 9:1 and 1:1 mixtures, but surface reduction begins at higher temperatures. (Figure Presented).

Understanding interactions at the interfaces of carbon with ionic liquids (ILs) is crucially beneficial for the diagnostics and performance improvement of electrochemical devices containing carbon as active materials or conductive additives in electrodes and ILs as solvents or additives in electrolytes. The interfacial interactions of three typical imidazolium-based ILs, 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (AMImTFSI) ILs having ethyl (C2), butyl (C4) and octyl (C8) chains in their cations, with highly oriented pyrolytic graphite (HOPG) were studied in-situ by electrochemical scanning tunneling microscopy (EC-STM). The etching of HOPG surface and the exfoliation of graphite/graphene flakes as well as cation intercalation were observed at the HOPG/C2MImTFSI interface. The etching also takes place in C4MImTFSI at −1.5 V vs Pt but only at step edges with a much slower rate, whereas C8MIm+ cations adsorbs strongly on the HOPG surface under similar conditions with no observable etching or intercalation. The EC-STM observations can be explained by the increase in van der Waals interaction between the cations and the graphite surface with increasing length of alkyl chains.

Understanding interactions at the interfaces of carbon with ionic liquids (ILs) is crucially beneficial for the diagnostics and performance improvement of electrochemical devices containing carbon as active materials or conductive additives in electrodes and ILs as solvents or additives in electrolytes. The interfacial interactions of three typical imidazolium-based ILs, 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (AMImTFSI) ILs having ethyl (C2), butyl (C4) and octyl (C8) chains in their cations, with highly oriented pyrolytic graphite (HOPG) were studied in-situ by electrochemical scanning tunneling microscopy (EC-STM). The etching of HOPG surface and the exfoliation of graphite/graphene flakes as well as cation intercalation were observed at the HOPG/C2MImTFSI interface. The etching also takes place in C4MImTFSI at −1.5 V vs Pt but only at step edges with a much slower rate, whereas C8MIm+ cations adsorbs strongly on the HOPG surface under similar conditions with no observable etching or intercalation. The EC-STM observations can be explained by the increase in van der Waals interaction between the cations and the graphite surface with increasing length of alkyl chains.

© 2018, Islamic Azad University (IAU). Emerging contaminants (ECs) are commonly originated from personal care products, cosmetics, pharmaceuticals, pesticides, dioxins, polycyclic aromatic hydrocarbons (PAHs), and alkylphenolic compounds. Due to the huge development of these industries, these ECs have been constantly detected in wastewater, groundwater, and surface water in hazardous quantity. The discharge of these ECs into the environment causes considerable non-esthetic pollution and could be a great threat to the entire ecosystem. The common wastewater treatment plants (WWTPs) which consist of biological, physical, and chemical treatments such as activated sludge, filtration, adsorption, and coagulation are found to be ineffective for desired removal of ECs. In turn, various emerging advanced oxidation processes (AOPs) such as ultrasonic and ultraviolet irradiation with or without the presence of catalyst have raised great attention due to their great potential in remediation of ECs. This paper presents a critical review on types, recent occurrence, sources, environmental impacts, and emerging treatment methods applicable to treat ECs. The current research and applications of ultrasonic, ultraviolet, and combination of both irradiations to treat ECs in wastewater are particularly reviewed. The effect of key parameters on photo-, sono- and, sonophotocatalytic degradation of ECs are commendably accessed such as ultrasonic power, ultrasonic frequency, light intensity, ultraviolet wavelength, solution pH, oxidizing agents, chemical additives, catalyst dosage, and modification of catalyst. The possible reaction mechanisms of ECs degradation process and kinetic model study are also elucidated in detail. Lastly, future research directions and conclusions are proposed to strengthen the understanding on their fate in water. All this information is vital to predict the negative impacts of ECs on the receiving environment effectively.

© 2019 Bouckaert et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

© 2019 Bouckaert et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

The early Holocene climatic optimum is associated with perihelion precession and high obliquity, though most studies emphasize the former over the latter. Asian monsoon proxy records only decisively show the precessional impact. To explore the obliquity effect, four climate simulations are conducted by fixing orbital parameters of present-day (0K), early Holocene (11K), the lowest obliquity (31K), and 11K's precession and eccentricity with 31K's obliquity (11Kp31Ko). We show that high obliquity significantly augments the precessional impact by shifting the Asian monsoon farther north than present. By contrast, the present-day monsoon seasonality can still be identified in the simulations with low obliquity. We argue that the upper tropospheric (South Asian) and lower tropospheric (North Pacific) high-pressure systems are affected by the subtropical atmospheric heating changes responding to obliquity. As a consequence, associated with the changes in meridional gradients of geopotential height and temperature made by the heating, midlatitude transient eddies and monsoon-midlatitude interactions are modulated.

Orbital forcing exerts a strong influence on global monsoon systems, with higher summer insolation leading to stronger summer monsoons in the Northern Hemisphere. However, the associated regional and seasonal changes, particularly the interaction between regional monsoon systems, remain unclear. Simulations using the Community Earth System Model demonstrate that the western North Pacific (WNP) summer monsoon responds to orbital forcing opposite to that of other major Northern Hemisphere monsoon systems. Compared with its current climate state, the simulated WNP monsoon and associated lower-tropospheric trough is absent in the early Holocene when the precession-modulated Northern Hemisphere summer insolation is higher, whereas the summer monsoons in South and East Asia are stronger and shift farther northward. We attribute the weaker WNP monsoon to the stronger diabatic heating of the summer Asian monsoon—in particular over the southern Tibetan Plateau and Maritime Continent—that in turn strengthens the North Pacific subtropical high through atmospheric teleconnections. By contrast, the impact of the midlatitude circulation changes on the WNP monsoon is weaker when the solar insolation is higher. Prior to the present WNP monsoon onset, the upper-tropospheric East Asian jet stream weakens and shifts northward; the monsoon onset is highly affected by the jet-induced high potential vorticity intrusion. In the instance of the extreme perihelion-summer, the WNP monsoon is suppressed despite a stronger midlatitude precursor than present-day, and the midlatitude circulation response to the enhanced South Asian precipitation is considerable. These conditions indicate internal monsoon interactions of an orbital scale, implying a potential mechanistic control of the WNP monsoon.

Orbital forcing exerts a strong influence on global monsoon systems, with higher summer insolation leading to stronger summer monsoons in the Northern Hemisphere. However, the associated regional and seasonal changes, particularly the interaction between regional monsoon systems, remain unclear. Simulations using the Community Earth System Model demonstrate that the western North Pacific (WNP) summer monsoon responds to orbital forcing opposite to that of other major Northern Hemisphere monsoon systems. Compared with its current climate state, the simulated WNP monsoon and associated lower-tropospheric trough is absent in the early Holocene when the precession-modulated Northern Hemisphere summer insolation is higher, whereas the summer monsoons in South and East Asia are stronger and shift farther northward. We attribute the weaker WNP monsoon to the stronger diabatic heating of the summer Asian monsoon—in particular over the southern Tibetan Plateau and Maritime Continent—that in turn strengthens the North Pacific subtropical high through atmospheric teleconnections. By contrast, the impact of the midlatitude circulation changes on the WNP monsoon is weaker when the solar insolation is higher. Prior to the present WNP monsoon onset, the upper-tropospheric East Asian jet stream weakens and shifts northward; the monsoon onset is highly affected by the jet-induced high potential vorticity intrusion. In the instance of the extreme perihelion-summer, the WNP monsoon is suppressed despite a stronger midlatitude precursor than present-day, and the midlatitude circulation response to the enhanced South Asian precipitation is considerable. These conditions indicate internal monsoon interactions of an orbital scale, implying a potential mechanistic control of the WNP monsoon.

The early Holocene climatic optimum is associated with perihelion precession and high obliquity, though most studies emphasize the former over the latter. Asian monsoon proxy records only decisively show the precessional impact. To explore the obliquity effect, four climate simulations are conducted by fixing orbital parameters of present-day (0K), early Holocene (11K), the lowest obliquity (31K), and 11K's precession and eccentricity with 31K's obliquity (11Kp31Ko). We show that high obliquity significantly augments the precessional impact by shifting the Asian monsoon farther north than present. By contrast, the present-day monsoon seasonality can still be identified in the simulations with low obliquity. We argue that the upper tropospheric (South Asian) and lower tropospheric (North Pacific) high-pressure systems are affected by the subtropical atmospheric heating changes responding to obliquity. As a consequence, associated with the changes in meridional gradients of geopotential height and temperature made by the heating, midlatitude transient eddies and monsoon-midlatitude interactions are modulated.

We develop computational methods for the simulation of osmotic swelling phenomena relevant to microscopic vesicles containing transformable solute molecules. We introduce stochastic immersed boundary methods (SIBMs) that can capture osmotically driven fluid transport through semipermeable elastic membranes subject to thermal fluctuations. We also develop numerical methods to handle within SIBMs an elastic shell model for a neo-Hookean material. Our extended SIBM allows for capturing osmotic swelling phenomena driven by concentration changes and interactions between a discrete collection of confined particles while accounting for the thermal fluctuations of the semipermeable membrane and the hydrodynamic transport of solvent. We use our computational methods to investigate osmotic phenomena in regimes that go beyond the classical Van't Hoff theory. We develop statistical mechanics theories for osmotic swelling of vesicles when there are significant interactions between particles that can transform over time. We validate our theoretical results against detailed computational simulations. Our methods are expected to be useful for a wide class of applications allowing for the simulation of osmotically driven flows, thermally fluctuating semipermeable elastic structures, and solute interactions.

We develop computational methods for the simulation of osmotic swelling phenomena relevant to microscopic vesicles containing transformable solute molecules. We introduce stochastic immersed boundary methods (SIBMs) that can capture osmotically driven fluid transport through semipermeable elastic membranes subject to thermal fluctuations. We also develop numerical methods to handle within SIBMs an elastic shell model for a neo-Hookean material. Our extended SIBM allows for capturing osmotic swelling phenomena driven by concentration changes and interactions between a discrete collection of confined particles while accounting for the thermal fluctuations of the semipermeable membrane and the hydrodynamic transport of solvent. We use our computational methods to investigate osmotic phenomena in regimes that go beyond the classical Van't Hoff theory. We develop statistical mechanics theories for osmotic swelling of vesicles when there are significant interactions between particles that can transform over time. We validate our theoretical results against detailed computational simulations. Our methods are expected to be useful for a wide class of applications allowing for the simulation of osmotically driven flows, thermally fluctuating semipermeable elastic structures, and solute interactions.

In nature, animals must contend with the presence of noise, which may limit their ability to detect prey, attract mates and escape predators. Sources of noise vary and may originate from natural (e.g. animal sounds, water) or anthropogenic (e.g. traffic, construction) sources. The vibratory sensory modality has long been overlooked in the study of anthropogenic effects on wildlife. Human-induced environmental changes may introduce noise sources as well as artificial substrates that alter vibratory noise profiles, leading to maladaptive behavioural responses. We conducted field measurements of vibratory noise on various substrate types (natural and artificial) used by animals in human-developed habitats. Next, we conducted laboratory experiments on how vibratory noise affects the prey detection ability of the European garden spider, Araneus diadematus. We tested whether changes in vibratory noise profiles consistent with anthropogenic alterations of vibratory habitats are sufficient to alter the spider's sensitivity to prey cues. We found that overall noise amplitude on artificial substrates was lower and less variable across contexts compared with natural substrates. In experiments with different noise levels, we observed that garden spiders showed noise-dependent changes in sensitivity to prey-mimicking cues, with response thresholds lowest at intermediate noise levels. Experimental levels of intermediate noise consistent with field measurements on natural substrates suggest that spiders' predatory performance is higher when webs are constructed on natural substrates. This suggests that human-introduced substrates may interfere with spiders' predatory performance. As human activities and habitat alteration are widespread, our findings highlight the need to consider the vibratory sensory channel in assessing anthropogenic impacts on wildlife. © 2014 The Association for the Study of Animal Behaviour.

In nature, animals must contend with the presence of noise, which may limit their ability to detect prey, attract mates and escape predators. Sources of noise vary and may originate from natural (e.g. animal sounds, water) or anthropogenic (e.g. traffic, construction) sources. The vibratory sensory modality has long been overlooked in the study of anthropogenic effects on wildlife. Human-induced environmental changes may introduce noise sources as well as artificial substrates that alter vibratory noise profiles, leading to maladaptive behavioural responses. We conducted field measurements of vibratory noise on various substrate types (natural and artificial) used by animals in human-developed habitats. Next, we conducted laboratory experiments on how vibratory noise affects the prey detection ability of the European garden spider, Araneus diadematus. We tested whether changes in vibratory noise profiles consistent with anthropogenic alterations of vibratory habitats are sufficient to alter the spider's sensitivity to prey cues. We found that overall noise amplitude on artificial substrates was lower and less variable across contexts compared with natural substrates. In experiments with different noise levels, we observed that garden spiders showed noise-dependent changes in sensitivity to prey-mimicking cues, with response thresholds lowest at intermediate noise levels. Experimental levels of intermediate noise consistent with field measurements on natural substrates suggest that spiders' predatory performance is higher when webs are constructed on natural substrates. This suggests that human-introduced substrates may interfere with spiders' predatory performance. As human activities and habitat alteration are widespread, our findings highlight the need to consider the vibratory sensory channel in assessing anthropogenic impacts on wildlife. © 2014 The Association for the Study of Animal Behaviour.

The interfaces between electrode and electrolyte play a vital role in various electrochemical systems. However, the understanding of such embedded interfaces and interfacial processes is still limited partly because of the short of proper characterizations tools, especially in-situ/operando techniques. In the past decade, substantial effort has been devoted in the development of in-situ/operando techniques to investigate the solid/liquid interfaces. One successful approach is the combination of in-situ liquid cells and soft x-ray absorption spectroscopy (sXAS). In this review, we showcased several recent examples using such liquid-cell-based in-situ/operando sXAS method to study different aspects of the electrode/electrolyte interface under reaction conditions, including the adsorption and deposition of solute species on electrode surface, morphological and chemical changes of electrode surface, and potential-dependent orientations of interfacial solvent molecules. These examples demonstrated capability of such in-situ/operando sXAS techniques in providing element- and chemical-sensitive interfacial information. This in-situ/operando sXAS technique also opens the way to the investigation of various solid/liquid interfaces in other important heterogeneous reactions.

The interfaces between electrode and electrolyte play a vital role in various electrochemical systems. However, the understanding of such embedded interfaces and interfacial processes is still limited partly because of the short of proper characterizations tools, especially in-situ/operando techniques. In the past decade, substantial effort has been devoted in the development of in-situ/operando techniques to investigate the solid/liquid interfaces. One successful approach is the combination of in-situ liquid cells and soft x-ray absorption spectroscopy (sXAS). In this review, we showcased several recent examples using such liquid-cell-based in-situ/operando sXAS method to study different aspects of the electrode/electrolyte interface under reaction conditions, including the adsorption and deposition of solute species on electrode surface, morphological and chemical changes of electrode surface, and potential-dependent orientations of interfacial solvent molecules. These examples demonstrated capability of such in-situ/operando sXAS techniques in providing element- and chemical-sensitive interfacial information. This in-situ/operando sXAS technique also opens the way to the investigation of various solid/liquid interfaces in other important heterogeneous reactions.

Lithium-sulfur batteries have a theoretical specific energy that is a factor of five greater than that of current lithium-ion batteries, but suffer from consequences of the solubility of lithium polysulfide reaction intermediates that form as the batteries are charged and discharged. These species can react with each other and diffuse out of the cathode, causing battery capacity to fade and ultimately, cell failure. In spite of work that has spanned four decades, fingerprints of polysulfides have not yet been established, precluding a systematic study of lithium-sulfur chemistry. Herein we demonstrate the use of principal component analysis of X-ray absorption spectroscopy (XAS) to obtain fingerprints of lithium polysulfides. This approach enables interpretation of spectral data without any assumptions regarding the origin of the observed spectral features or knowledge of the stability of the polysulfide species of interest.We show that in poly(ethylene oxide)-based solid electrolytes containing polysulfides made by chemically reacting Li2S and elemental sulfur, Li2S2 and Li2S6 spontaneously disproportionate to give binary Li2S/Li2S4 and Li2S4/Li 2S8 mixtures, respectively, while Li2S 4 and Li2S8 exist as single molecular species. XAS fingerprints of Li2S4 and Li2S8 are thus presented. © 2014 The Electrochemical Society.

BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format. This promotes the development of interoperable tools for natural language processing (NLP) of biomedical text. The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format. These contributions included additional implementations of BioC, many new corpora in the format, biomedical NLP tools consuming and producing the format and online services using the format. The ease of use, broad support and rapidly growing number of tools demonstrate the need for and value of the BioC format. Database URL: http://bioc.sourceforge.net/.

Lithium-sulfur batteries have a theoretical specific energy that is a factor of five greater than that of current lithium-ion batteries, but suffer from consequences of the solubility of lithium polysulfide reaction intermediates that form as the batteries are charged and discharged. These species can react with each other and diffuse out of the cathode, causing battery capacity to fade and ultimately, cell failure. In spite of work that has spanned four decades, fingerprints of polysulfides have not yet been established, precluding a systematic study of lithium-sulfur chemistry. Herein we demonstrate the use of principal component analysis of X-ray absorption spectroscopy (XAS) to obtain fingerprints of lithium polysulfides. This approach enables interpretation of spectral data without any assumptions regarding the origin of the observed spectral features or knowledge of the stability of the polysulfide species of interest.We show that in poly(ethylene oxide)-based solid electrolytes containing polysulfides made by chemically reacting Li2S and elemental sulfur, Li2S2 and Li2S6 spontaneously disproportionate to give binary Li2S/Li2S4 and Li2S4/Li 2S8 mixtures, respectively, while Li2S 4 and Li2S8 exist as single molecular species. XAS fingerprints of Li2S4 and Li2S8 are thus presented. © 2014 The Electrochemical Society.

The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance.

A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net