ALBERT

Description: "With so much media and political criticism of their shortcomings and failures, it is easy to overlook the fact that many governments work pretty well much of the time. Great Policy Successes turns the spotlight on instances of public policy that are remarkably successful. It develops a framework for identifying and assessing policy successes, paying attention not just to their programmatic outcomes but also to the quality of the processes by which policies are designed and delivered, the level of support and legitimacy they attain, and the extent to which successful performance endures over time. The bulk of the book is then devoted to 15 detailed case studies of striking policy successes from around the world, including Singapore's public health system, Copenhagen and Melbourne's rise from stilted backwaters to the highly liveable and dynamic urban centres they are today, Brazil's Bolsa Familia poverty relief scheme, the US's GI Bill, and Germany's breakthrough labour market reforms of the 2000s. Each case is set in context, its main actors are introduced, key events and decisions are described, the assessment framework is applied to gauge the nature and level of its success, key contributing factors to success are identified, and potential lessons and future challenges are identified. Purposefully avoiding the kind of heavy theorizing that characterizes many accounts of public policy processes, each case is written in an accessible and narrative style ideally suited for classroom use in conjunction with mainstream textbooks on public policy design, implementation, and evaluation.

Description: The storage concession "Minerbio Stoccaggio" (Bologna, Northern Italy) covers a 69 km 2 area, 65% of hich is located in the Minerbio municipality. Since 1979, a microseismic network for the monitoring of seismicity, eventually induced by gas storage activities, has been installed in this area. The network was operated by Stogit S.p.A, a subsidiary company of Snam, which is the largest storage operator in Italy. In 2016, the microseismic network, consisting of three surface stations and one 100-m-deep borehole sensor with minimum interstation distances of about 3.0 km, was integrated with 12 regional stations installed in an 80 × 80 km 2 area centered on the surface projection of the reservoir. In 2018, the microseismic network was enhanced by adding one surface and three 150-m-deep borehole stations. In this work, we evaluate the detection improvement of the microseismic network, integrated with the regional stations. We define two crustal volumes for earthquake detection: the inner domain of detection, IDD (10 × 10 × 5) km 3 , within which we should ensure the highest network performance, and the extended domain of detection, EDD (22 × 22 × 11) km 3 . By comparing the simulated power spectral density of hypothetical seismic sources located in EDD with the average power spectra of ambient seismic noise observed at each station site, we calculate detection and localization thresholds for the two above-mentioned networks. Under unfavourable noise conditions, we find that the present operative seismic network allows locating earthquakes with M L ≥ 0.8 occurring at the depth of the reservoir and with M L ≥ 1.0 if located within IDD.

Description: Funding information This study received financial support from BComune di Minerbio^ under the grant BSperimentazione ILG Minerbio^ (grant number 0913.010)

Description: Published

Description: 967–977

Description: 3SR TERREMOTI - Attività dei Centri

Description: JCR Journal

Description: This paper presents an original multidisciplinary (geological-structural-geomorphological and seismological) study aimed at investigating the origin of diffused seismic damages affecting several ancient buildings in the Roman port city of Ostia. We also evaluate the possibility to relate these damages to a previously hypothesized ENE-WSW trending fault, bordering the morphological height upon which the Ostia town was founded. Aimed at this scope, we performed seismic noise measures (by using 14 seismic stations) that show no significantly different response and lack of significant ground motion differential amplifications. The coexistence of (i) no local geological heterogeneities and (ii) low amplification of spectral ratios in the recorded seismic signals seems to exclude that the observed seismic damage may be the consequence of significant site effects. When also the large distance from the strongest Apennine’s seismogenic source areas is considered, the possibility that the observed damage may be the consequence of local events should be considered. We discuss the potentiality of the ENE-WSW trending fault as the source of the observed seismic damages, highlighting the supporting evidence as well as the uncertainties of such interpretation.

Description: Published

Description: 833–851

Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica

Description: JCR Journal

Description: This work describes the analysis of the strong-motion data from the Engineering Strong Motion database (ESM, http://esm.mi.ingv.it), aimed at: (1) extract a dataset of accelero- metric waveforms recorded during the 2016–2017 Central Italy seismic sequence; (2) iden- tify the recording stations to be used as reference sites for further seismological analysis; (3) select the records to be used as input for seismic microzonation of higher level at 137 municipalities. Firstly, a residual analysis is carried out on the extracted dataset to perform: (1) the quality check of the waveforms recorded by temporary networks installed soon after the occurrence of the rst main shock (M 6.0, 24 August 2016); (2) the estimation of the site-to-site residual term for each recording station with the aim of recognising potential reference rock sites. Finally, the software REXELite, integrated within the ESM website, is adopted to select suites of spectrum-compatible accelerograms, that will be used as input for calculating site ampli cations through 1D and 2D simulations at sites which suf- fered the greatest damage. The results of this work demonstrate the success of the synergy among Italian institutions. The setup of key infrastructures, such as emergency networks and data repositories, together with the knowledge developed during national projects, turned out to be successful in terms of timely intervention during the emergency phase and the planning of the post-emergency.

Description: Published

Description: 5533–5551

Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica

Description: JCR Journal

Description: We present the analysis of rotational and translational ground motions from earthquakes recorded during October–November 2016, in association with the Central Italy seismic sequence. We use co-located measurements of the vertical ground rotation rate from a large ring laser gyroscope and the three components of ground velocity from a broad-band seismometer. Both instruments are positioned in a deep underground environment, within the Gran Sasso National Laboratories of the Istituto Nazionale di Fisica Nucleare. We collected dozens of events spanning the 3.5–5.9 magnitude range and epicentral distances between 30 and 70 km. This data set constitutes an unprecedented observation of the vertical rotational motions associated with an intense seismic sequence at local distance. Under the plane-wave approximation we process the data set in order to get an experimental estimation of the events backazimuth. Peak values of rotation rate (PRR) and horizontal acceleration (PGA) are markedly correlated, according to a scaling constant which is consistent with previous measurements from different earthquake sequences. We used a prediction model in use for Italy to calculate the expected PGA at the recording site, obtaining consequently predictions for PRR. Within the modelling uncertainties, predicted rotations are consistent with the observed ones, suggesting the possibility of establishing specific attenuation models for ground rotations, like the scaling of peak velocity and peak acceleration in empirical ground-motion prediction relationships. In a second step, after identifying the direction of the incoming wavefield, we extract phase-velocity data using the spectral ratio of the translational and rotational components. This analysis is performed over time windows associated with the P-coda, S-coda and Lg phase. Results are consistent with independent estimates of shear wave velocities in the shallow crust of the Central Apennines

Description: Published

Description: 705-715

Description: 4T. Sismicità dell'Italia

Description: JCR Journal

Description: The purpose of this list of digital platforms is to facilitate the research of scientific data (articles, books, conferences, websites, indexers, etc.) by students of all undergraduate levels. The interface of platforms have similarities and because of this, low degree of difficulty of use. I emphasize that the key to an excellent literature search on digital platforms is to choose the right "keyword".

Description: Our knowledge on distribution, habitats and behavior of Southern Ocean fishes living at water depths beyond scuba-diving limits is still sparse, as it is difficult to obtain quantitative data on these aspects of their biology. Here, we report the results of an analysis of seabed images to investigate species composition, behavior, spatial distribution and preferred habitats of demersal fish assemblages in the southern Weddell Sea. Our study was based on a total of 2736 high-resolution images, covering a total seabed area of 11,317 m2, which were taken at 13 stations at water depths between 200 and 750 m. Fish were found in 380 images. A total of 379 notothenioid specimens were recorded, representing four families (Nototheniidae, Artedidraconidae, Bathydraconidae, Channichthyidae), 17 genera and 25 species. Nototheniidae was the most speciose fam- ily, including benthic species (Trematomus spp.) and the pelagic species Pleuragramma antarctica, which was occasionally recorded in dense shoals. Bathydraconids ranked second with six species, followed by artedidraconids and channichthyids, both with five species. Most abundant species were Trematomus scotti and T. lepidorhinus among nototheniids, and Dol- loidraco longedorsalis and Pagetopsis maculatus among artedidraconids and channichthyids, respectively. Both T. lepi- dorhinus and P. maculatus preferred seabed habitats characterized by biogenous debris and rich epibenthic fauna, whereas T. scotti and D. longedorsalis were frequently seen resting on fine sediments and scattered gravel. Several fish species were recorded to make use of the three-dimensional structure formed by epibenthic foundation species, like sponges, for perching or hiding inside. Nesting behavior was observed, frequently in association with dropstones, in species from various families, including Channichthyidae (Chaenodraco wilsoni and Pagetopsis macropterus) and Bathydraconidae (Cygnodraco mawsoni).

Description: Due to its year-round accessibility and excellent on-site infrastructure, Kongsfjorden and the Ny-Ålesund Research and Monitoring Facility have become established as a primary location to study the impact of environmental change on Arctic coastal ecosystems. Due to its location right at the interface of Arctic and Atlantic oceanic regimes, Kongsfjorden already experiences large amplitudes of variability in physico/chemical conditions and might, thus, be considered as an early warning indicator of future changes, which can then be extrapolated in a pan-Arctic perspective. Already now, Kongsfjorden represents one of the best-studied Arctic fjord systems. However, research conducted to date has concentrated largely on small disciplinary projects, prompting the need for a higher level of integration of future research activities. This contribution, thus, aims at identifying gaps in knowledge and research priorities with respect to ecological and adaptive responses to Arctic ecosystem changes. By doing so we aim to provide a stimulus for the initiation of new international and interdisciplinary research initiatives.

Description: Modern Society needs interactive public discussion to provide an effective way of focusing on hydrological hazards and their consequences. Embracing a holistic Earth system Science approach, we experiment since 2004 different stimulating educational/communicative model which emotionally involves the participants to raise awareness on the social dimension of the disaster hydrogeological risk reduction, pointing out that human behavior is the crucial factor in the degree of vulnerability and the likelihood of disasters taking place. The implementation of strategies for risk mitigation must include educational aspects, as well as economical and societal ones. Education is the bridge between knowledge and understanding and the key to raise risk perception. Children’s involvement might trigger a chain reaction that reinforce and spread the culture of risk. No matter how heavy was the rain that hit our land in the past and recent seasons, we still are not prepared. If on one hand we need to fight against worsening Global Warming that trigger extreme meteorological events, we should also work on sustainable land use and promote landscape preservation. Since science can work on improving knowledge of phenomena, technology can provide modern tool to reduce the impact of disasters, children and adults education is the flywheel to provide the change. We present here two cases selected among the wide range of educational activities that we have tested and to which more than 2,000 students and adults have participated within a period of 12 years. They include learn-by-playing, hands-on, emotional-learning activities, open questions seminars, learning paths, curiosity-driven approaches, special venues and science outreach.

Description: Sendai Partnerships 2015-2025

Description: Published

Description: Ljubljana (Slovenia)

Description: 2TM. Divulgazione Scientifica

Description: The systematic study of biological basis of behavior and of the process involved in economical choices has outlined a new paradigm of research: neuroeconomics. Now the intersection between neuroscience, psychology and economics, neuroeconomics presents itself as an alternative to the neoclassical vision on economics, according to which the homo oeconomicus acts within the bonds of a formalizing rationality tending to the maximization of the anticipated utility. Brain imagining methods have shown that the decision-making processes activate the frontal lobe and the limbic system above all, a big circonvolution running through the callous body on the medial surface of the hemispheres, extending itself down, responsible for the regulation of emotional phenomena. Reinforcing such a tendency, we find the injury paradigm. It was observed that frontal lobe injuries harm the capacity of making advantageous decisions either in one’s own behalf or in others, as well as decisions according to the social conventions. In this paper, we will try to show that if, by the one hand, the neuro visual methods have given us a great amount of data, on the other hand, using them uncritically, with the recurrent confusion between “correlation” and “causal relation”—contemporary microevents indicate only simple correlations, and no cause-effect relation—risks to stress the relevant explanatory gap regarding the abstract ideal of understanding the nature of the brain.

Description: Published

Description: 135-141

Description: 2TM. Divulgazione Scientifica

Description: This paper investigates whether and how depressive disorders affect speech and in particular timing strategies for speech pauses (empty and filled pauses, as well as, phoneme lengthening). The investigation is made exploiting read and spontaneous narratives . The collected data are from 24 subjects, divided into two groups (depressed and control) asked to read a tale, as well as, spontaneously report on their daily activities. Ten different frequency and duration measures for pauses and clauses are proposed and have been collected using the PRAAT software on the speech recordings produced by the participants. A T-Student test for independent samples was applied on the collected frequency and duration measures in order to ascertain whether significant differences between healthy and depressed speech measures are observed. In the “spontaneous narrative” condition, depressed patients exhibited significant differences in: the average duration of their empty pauses, the average frequency, and the average duration of their clauses. In the read narratives, only the average pause’s frequency of the clauses was significantly lower in the depressed subjects with respect to the healthy ones. The results suggest that depressive disorders affect speech quality and speech production through pause and clause durations, as well as, clause quantities. In particular, the significant differences in clause quantities (observed both in the read and spontaneous narratives), suggest a strong general effect of depressive symptoms on cognitive and psychomotor functions. Depressive symptoms produce changes in the planned timing of pauses, even when reading, modifying the timing of pausing strategies.

Description: Published

Description: 73-82

Description: 5TM. Informazione ed editoria

Description: t The role of riverine freshwater inflow on the Central Mediterranean Overturning Circulation (CMOC) was studied using a high-resolution ocean model with a complete distribution of rivers in the Adriatic and Ionian catchment areas. The impact of river runoff on the Adriatic and Ionian Sea basins was assessed by a twin experiment, with and without runoff, from 1999 to 2012. This study tries to show the connection between the Adriatic as a marginal sea containing the downwelling branch of the anti-estuarine CMOC and the large runoff occurring there. It is found that the multiannual CMOC is a persistent anti-estuarine structure with secondary estuarine cells that strengthen in years of large realistic river runoff. The CMOC is demonstrated to be controlled by wind forcing at least as much as by buoyancy fluxes. It is found that river runoff affects the CMOC strength, enhancing the amplitude of the secondary estuarine cells and reducing the intensity of the dominant anti-estuarine cell. A large river runoff can produce a positive buoyancy flux without switching off the antiestuarine CMOC cell, but a particularly low heat flux and wind work with normal river runoff can reverse it. Overall by comparing experiments with, without and with unrealistically augmented runoff we demonstrate that rivers affect the CMOC strength but they can never represent its dominant forcing mechanism and the potential role of river runoff has to be considered jointly with wind work and heat flux, as they largely contribute to the energy budget of the basin. Looking at the downwelling branch of the CMOC in the Adriatic basin, rivers are demonstrated to locally reduce the volume of Adriatic dense water formed in the Southern Adriatic Sea as a result of increased water stratification. The spreading of the Adriatic dense water into the Ionian abyss is affected as well: dense waters overflowing the Otranto Strait are less dense in a realistic runoff regime, with respect to no runoff experiment, and confined to a narrower band against the Italian shelf with less lateral spreading toward the Ionian Sea center. 1

Description: Published

Description: 1675-1703

Description: 4A. Oceanografia e clima

Description: JCR Journal

Description: Humans have very high requirements and expectations when communicating through speech, other than simplicity, flexibility and easiness of interaction. This is because voice interactions do not require cognitive efforts, attention, and memory resources. Voice technologies are however still constrained to use cases and scenarios giving the existing limitations of speech synthesis and recognition systems. Which is the status of nonlinear speech processing techniques and the steps made for cross-fertilization among disciplines? This chapter will provide a short overview trying to answer the above question.

Description: Published

Description: 5-11

Description: 5TM. Informazione ed editoria

Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2015. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.

Description: Mud volcanoes are geological systems often characterized by elevated fluid pressures at depth deviating from hydrostatic conditions. This near-critical state makes mud volcanoes particularly sensitive to external forcing induced by natural or man-made perturbations. We used the Nirano mud volcanic field as a natural laboratory to test pre- and post-seismic effects generated by distant earthquakes.We first characterized the subsurface structure of the Nirano mud volcanic field with a geoelectrical study. Next, we deployed a broad-band seismic station in the area to understand the typical seismic signal generated by the mud volcano. Seismic records show a background noise below 2 s, sometimes interrupted by pulses of drumbeatlike high-frequency signals lasting from several minutes to hours. To date this is the first observation of drumbeat signal observed in mud volcanoes. In 2013 June we recorded a M4.7 earthquake, that occurred approximately 60 km far from our seismic station. According to empirical estimations the Nirano mud volcanic field should not have been affected by the M4.7 earthquake. Yet, before the seismic event we recorded an increasing amplitude of the signal in the 10–20 Hz frequency band. The signal emerged approximately two hours before the earthquake and lasted for about three hours. Our statistical analysis suggests the presence of a possible precursory signal about 10 min before the earthquake.

Description: Published

Description: 907–917

Description: 7A. Geofisica per il monitoraggio ambientale

Description: JCR Journal

Description: Since the past decade, geodetic techniques are widely used to gain important information for the monitoring and modeling of the deformation of the Earth at different length and time scales. Although the GNSS derived estimates of the Earth crust velocity are becoming more and more reliable, advanced data analysis techniques are needed to recognize geophysical features in the GNSS time-series, e.g., non linear behaviors, discontinuities in the signal and in its derivative, i.e., in the velocity. Unfortunately these phenomena are often hidden in the time-series noise and external information, as seismic events, are not always known. The main focus of this work is the detection of signal discontinuities in GNSS time-series through the use of advanced analysis techniques: the wavelets, the Bayesian and the variational methods. The Mumford and Shah (Commun Pure Appl Math 42:577–685, 1989) and the Blake and Zisserman (Visual reconstruction, 1987) variational models for signal segmentation can detect signal discontinuities in an explicitly way. The Blake and Zisserman (Visual reconstruction, 1987) model can also detect discontinuities of the signal first derivative, i.e., velocity abrupt changes can be detected. At first, to prove and assess the capability to detect discontinuities correctly, the methods have been applied to some Cascadia (North America) time-series, characterized by well known aseismic deformations. A second test area has been taken into account: the Calabrian Arc subduction zone, in southern Italy. The analyzed Italian GNSS time-series are characterized by very weak and noisy signals and the geodynamic of the area is mostly unknown. When present, discontinuities are expected to be very small and compatible with the signal noise. This motivates the use of advanced data analysis techniques to investigate the presence of discontinuities. At the moment, the analysis of the Italian time-series has revealed several discontinuities which nature cannot be labeled easily as geophysical or geodetic.

Description: Published

Description: 627-634

Description: 2T. Deformazione crostale attiva

Description: Algorithms based on artificial intelligence (AI) have had a strong development in recent years in different research fields of earth science such as seismology and volcanology. In particular, they have been applied to the study of the volcanic eruptive products of the recent activity of Mount Etna volcano. This work presents an application of the self-organizing map (SOM) neural networks to perform a clustering analysis on petrographic patterns of rocks of Somma–Vesuvius and Campi Flegrei volcanoes, in the Neapolitan area. The goal is to highlight possible affinity between the magmatic reservoirs of these two volcanic complexes. The SOM is known for its ability to cluster data by using intrinsic similarity measures without any previous information about their distribution. Moreover, it allows an easy understandable data visualization by using a two-dimensional map. The SOM has been tested on a geochemical dataset of 271 samples, consisting of 134 samples of Campi Flegrei eruptions (named CF), 24 samples of Somma–Vesuvius effusive eruptions (VF), 73 samples of Somma–Vesuvius explosive eruptions (VX), and finally 40 samples of “foreign” eruptions (ET), included to verify the neural net classification capability. After a pre-processing phase, applied to have a more appropriate data representation as input for the SOM, each sample has been encoded through a vector of 23 features, containing information about major bulk components, trace elements, and Sr isotopic ratio. The resulting SOM identifies three main clusters, and in particular, the foreign patterns (ET) are well separated from the other ones being mainly grouped in a single node. In conclusion, the obtained results suggest the ability of SOM neural network to associate volcanic rock suites on the basis of their geochemical imprint and can be consistent with the hypothesis that there might be a common magma source beneath the whole Neapolitan area.

Description: Published

Description: 55-60

Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici

Description: This paper investigates the ability of adolescents (aged 13–15 years) and young adults (aged 20–26 years) to decode affective bursts culturally situated in a different context (Francophone vs. South Italian). The effects of context show that Italian subjects perform poorly with respect to the Francophone ones revealing a significant native speaker advantage in decoding the selected affective bursts. In addition, adolescents perform better than young adults, particularly in the decoding and intensity ratings of affective bursts of happiness, pain, and pleasure suggesting an effect of age related to language expertise.

Description: Published

Description: 1TM. Formazione

Description: Many marine gastropods show species-specific behavioral responses to different predators, but less is known about the mechanisms influencing differences or similarities in specific responses. Herein, we examined whether two limpet species, Scurria viridula (Lamarck, 1819) and Fissurella latimarginata (Sowerby, 1835), show species- and size-specific similarities or differences in their reaction to predatory seastars and crabs. Both S. viridula and F. latimarginata reacted to their main seastar predators with escape responses. In contrast, both limpets did not flee from common crab predators, but, instead, fastened to the rock. All tested size classes of both limpet species reacted in a similar way, escaping from seastars, but clamping onto the rock in response to crabs. Limpets could reach velocities sufficient to outrun their specific seastar predators, but they were not fast enough to escape crabs. Experiments with limpets of different shell conditions (with and without shell damage) indicated that F. latimarginata with a damaged shell showed “accommodation movements” (slow movements away from stimulus) in response to predatory crabs. In contrast, intact F. latimarginata and all S. viridula (intact and damaged) clamped the shell down to the substratum. The response details suggest that the keyhole limpet F. latimarginata is more sensitive to predators (faster reaction time, longer escape distances, and higher proportion of reacting individuals) than S. viridula, possibly because the morphology of F. latimarginata (the relationship of its shell size and structure to its total body size) makes this species more vulnerable to predation. Our study suggests that chemically mediated effects of seastar and crab predators result in contrasting behavioral responses of both limpet species, independent of their habitat and morphology. Despite the different characteristics of the limpet species and the identity of predators, the limpets react in comparable ways to similar predator types.

Description: Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 115(52), (2018): E12275-E12284. doi: 10.1073/pnas.1805243115.

Description: Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage mechanisms have been previously described: the protein ferritin and vacuolar storage. To investigate the ecological role of these mechanisms among diatoms, iron addition and removal incubations were conducted using natural phytoplankton communities from varying iron environments. We show that among the predominant diatoms, Pseudo-nitzschia were favored by iron removal and displayed unique ferritin expression consistent with a long-term storage function. Meanwhile, Chaetoceros and Thalassiosira gene expression aligned with vacuolar storage mechanisms. Pseudo-nitzschia also showed exceptionally high iron storage under steady-state high and low iron conditions, as well as following iron resupply to iron-limited cells. We propose that bloom-forming diatoms use different iron storage mechanisms and that ferritin utilization may provide an advantage in areas of prolonged iron limitation with pulsed iron inputs. As iron distributions and availability change, this speculated ferritin-linked advantage may result in shifts in diatom community composition that can alter marine ecosystems and biogeochemical cycles.

Description: We thank the captain and crew of the R/V Melville and the CCGS J. P. Tully as well as the participants of the IRNBRU (MV1405) cruise for the California-based data, particularly K. Ellis [University of North Carolina (UNC)], T. Coale (University of California, San Diego), F. Kuzminov (Rutgers), H. McNair [University of California, Santa Barbara (UCSB)], and J. Jones (UCSB). W. Burns (UNC), S. Haines (UNC), and S. Bargu (Louisiana State University) assisted with sample processing and analysis. This work was funded by the National Science Foundation Grants OCE-1334935 (to A.M.), OCE-1334632 (to B.S.T.), OCE-1333929 (to K.T.), OCE-1334387 (to M.A.B.), OCE-1259776 (to K.W.B), and DGE-1650116 (Graduate Research Fellowship to R.H.L).

Description: 2019-06-11

Description: Knowledge on basic biological functions of organisms is essential to understand not only the role they play in the ecosystems but also to manage and protect their populations. The study of biological processes, such as growth, reproduction and physiology, which can be approached in situ or by collecting specimens and rearing them in aquaria, is particularly challenging for deep-sea organisms like cold-water corals. Field experimental work and monitoring of deep-sea populations is still a chimera. Only a handful of research institutes or companies has been able to install in situ marine observatories in the Mediterranean Sea or elsewhere, which facilitate a continuous monitoring of deep-sea ecosystems. Hence, today’s best way to obtain basic biological information on these organisms is (1) working with collected samples and analysing them post-mortem and / or (2) cultivating corals in aquaria in order to monitor biological processes and investigate coral behaviour and physiological responses under different experimental treatments. The first challenging aspect is the collection process, which implies the use of oceanographic research vessels in most occasions since these organisms inhabit areas between ca. 150 m to more than 1000 m depth, and specific sampling gears. The next challenge is the maintenance of the animals on board (in situations where cruises may take weeks) and their transport to home laboratories. Maintenance in the home laboratories is also extremely challenging since special conditions and set-ups are needed to conduct experimental studies to obtain information on the biological processes of these animals. The complexity of the natural environment from which the corals were collected cannot be exactly replicated within the laboratory setting; a fact which has led some researchers to question the validity of work and conclusions drawn from such undertakings. It is evident that aquaria experiments cannot perfectly reflect the real environmental and trophic conditions where these organisms occur, but: (1) in most cases we do not have the possibility to obtain equivalent in situ information and (2) even with limitations, they produce relevant information about the biological limits of the species, which is especially valuable when considering potential future climate change scenarios. This chapter includes many contributions from different authors and is envisioned as both to be a practical “handbook” for conducting cold-water coral aquaria work, whilst at the same time offering an overview on the cold-water coral research conducted in Mediterranean laboratories equipped with aquaria infrastructure. Experiences from Atlantic and Pacific laboratories with extensive experience with cold-water coral work have also contributed to this chapter, as their procedures are valuable to any researcher interested in conducting experimental work with cold-water corals in aquaria. It was impossible to include contributions from all laboratories in the world currently working experimentally with cold-water corals in the laboratory, but at the conclusion of the chapter we attempt, to our best of our knowledge, to supply a list of several laboratories with operational cold-water coral aquaria facilities.

Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2019. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.

Description: The Amatrice–Norcia–Visso sequence is characterized by complex behaviour that is somewhat atypical of main-shock–aftershock sequences, as there were multiple large main shocks that continued for months. In this study we focus on the Amatrice sequence (main shock 2016 August 24, Mw = 5.97) to evaluate the apparent stress values and magnitude-dependent scaling in order to improve our knowledge of processes that control small and large earthquakes within this active region of Italy. Apparent stress is proportional to the ratio of radiated seismic energy and seismic moment, and as such, these stress parameters play an important role in hazard prediction as they have a strong effect on the observed and predicted ground shaking. We analyse 83 events of the sequence from 2016 August 24 to October 16, within a radius of 20 km from the main shock and with an Mw ranging between 5.97 and 2.72. Taking advantage of the averaging nature of coda waves, we analyse coda-envelope-based spectral ratios between neighbouring event pairs.We use equations proposed byWalter et al. to consider stable, low-frequency and high-frequency spectral ratio levelswhich provide measures of the corner frequency and apparent stress ratios of the events within the sequence. The results demonstrate non-self-similar behaviour within the sequence, suggesting a change in dynamics between the largest events and the smaller aftershocks. The apparent stress and corner frequency estimates are compared to those obtained by Malagnini and Munaf`o who utilized hundreds of direct S-wave spectral ratio measurements to obtain their results. Although our analysis is based only on 83 events, our results are in very good agreement, demonstrating once more that the use of coda waves is very stable and provides lower variance measures than those using direct waves. A comparison with recent Central Apennines source scaling models derived from various seismic sequences (1997–1998 Colfiorito, 2002 San Giuliano di Puglia, 2009 L’Aquila) shows that the Amatrice sequence source scaling in this study is well represented by the models proposed by Pacor et al. and Malagnini and Mayeda.

Description: Published

Description: 446-455

Description: 3T. Sorgente sismica

Description: JCR Journal

Description: Here we provide two ArcGIS map packages with georeferenced files on the spatial distribution of sponges and echinoderms in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area (MPA) in the Weddell Sea. Sponges: The map of interpolated occurrence of sponges is based on quantitative abundance data (Gerdes 2014 a - o) and on semi-quantitative data obtained by W. Arntz (retired; formerly AWI) (see Teschke & Brey 2019a for presence / absence records of the latter dataset). The abundance data were classified to be merged with the semi-quantitative data and an inverse distance weighted method was performed on the united dataset. Areas with very common occurrence of sponges occurred on the shelf near Brunt Ice Shelf along Riiser - Larsen Ice Shelf to Ekstrøm Ice Shelf. Echinoderms: A cluster analysis with species x station datasets of asteroids (Teschke & Brey 2019b), ophiuroids (Teschke & Brey 2019c) and holothurians (Gutt et al. 2014) from the Antarctic Weddell Sea indicated a particular cold-water echinoderm fauna on the Filchner shelf. We approximated this potential habitat by bottom temperature ≤ -1°, based on seawater temperature data from the Finite Element Sea Ice - Ocean Model provided by R. Timmermann (AWI). More information on the spatial analysis is given in working paper WG-EMM-16/03 submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (available at https://www.ccamlr.org/en/wg-emm-16).

Description: Here we provide four ArcGIS map packages with georeferenced files on the spatial distribution of demersal and pelagic fishes in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area (MPA) in the Weddell Sea. Antarctic toothfish: The map of Dissostichus mawsoni occurrence probability is based on catch per unit effort (CPUE) data from the database of the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) (data request: 03-08-2016) and on bathymetric data from the International Bathymetric Chart of the Southern Ocean (IBCSO). We fitted a four-parameter Weibull model to the simulated CPUE data per depth interval by means of the R package \textquotesinglefitdistrplus\textquotesingle. The highest D. mawsoni occurrence probability was shown at depths between 1500 and 2000 m and only approximately 20 % of the Antarctic toothfish population occurred deeper than 2000 m. Antarctic silverfish: The map of interpolated abundances of Pleuragramma antarctica was based on pelagic trawl survey data, which were collected during "Polarstern" cruises ANT-I/2, ANT-III/3 and in the context of the Lazarev Sea Krill Survey (LAKRIS) ("Polarstern" cruises ANT-XXI/4, ANT-XXIII/6, ANT-XXIV/2). The first mentioned data were provided by V. Siegel (retired; formerly Th\"unen Institute), the LAKRIS data by H. Flores (AWI). Those data were complemented by benthic trawl survey data, which were collected during seven "Polarstern" cruises between 1996 and 2011 (ANT-XIII/3, ANT-XV/3, ANT-XVII/3, ANT-XIX/5, ANT-XXI/2, ANT-XXIII/8, ANT-XXVII/3) and were provided by R. Knust (AWI) as well as by data on counts of fish species from trawl and dredge samples by Drescher et. (2012), Ekau et al. (2012a, b), Hureau et al. (2012), Kock et al. (2012) and W\"ohrmann et al. (2012). An inverse distance weighted interpolation was performed for a 10 nautical mile radius around each record. Areas with highest numbers of P. antarctica (〉 36 individuals/1000 m²) occurred offshore Riiser -Larsen Ice Shelf and on the southern Weddell Sea continental shelf offshore Filchner Ice Shelf. Demersal fish: The map of predicted habitat suitability for demersal fish is based on data, which were collected during seven "Polarstern" cruises between 1996 and 2011 (ANT-XIII/3, ANT-XV/3, ANT-XVII/3, ANT-XIX/5, ANT-XXI/2, ANT-XXIII/8, ANT-XXVII/3) and were provided by R. Knust (AWI). The habitat suitability model was developed by the use of the modelling package "biomod2". Most suitable habitat conditions for demersal fish in the wider Weddell Sea occurred on the continental shelf between approx. 5° and 30°W, on the shelf west and east of the tip of the Antarctic Peninsula as well as around the South Shetland and South Orkney Islands. Nesting sites of demersal fish: The map on observation of nesting sites of demersal fish is based on data, which were collected during "Polarstern" cruises ANT-XXVII/3, ANT-XXIX/9 and ANT-XXXI/2 and were obtained by T. Lund\"alv (retired; formerly University of Gothenburg), D. Gerdes (retired; formerly AWI) and E. Riginella (University of Padova), respectively. Those data were complemented by a literature research. Most nesting sites were observed west of 25°W, north of the tip of the Antarctic Peninsula and along the west coast of the Antarctic Peninsula. More information is given in the working paper WG-EMM-16/03 submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management CCAMLR (available at https://www.ccamlr.org/en/wg-emm-16). Revised versions of the spatial analysis are described in working paper WG-SAM-17/30 and WS-SM-18/13 submitted to the CCAMLR Working Group on Statistics, Assessments and Modelling and the CCAMLR Workshop on Spatial Management, respectively (available at https://www.ccamlr.org/en/wg-sam-17; https://www.ccamlr.org/en/ws-sm-1

Description: Here, we provided four ArcGIS map packages with georeferenced files on the spatial distribution of Antarctic krill, Euphausia superba, (adults and larvae) and ice krill, Euphausia crystallorophias, in the wider Weddell Sea. The files were created in the context of the development of a marine protected area in the Weddell Sea. Antarctic krill (adults): The map of predicted habitat suitability for adult Antarctic krill was based on krill data from the database KRILLBASE (Atkinson et al., 2017; data request: 26-09-13). Those data were complemented by krill data, which were collected (a) during the Norwegian Antarctic research expedition 1976/77 (M/V "Polarsirkel"), (b) during two Soviet research cruises (RV "Gizhiga", 1977; RV "Volny Vetter", 1983), (c) in the context of the Lazarev Sea Krill Survey ("Polarstern" cruises ANT-XXI/4, ANT-XXIII/2, ANT-XXIII/6, ANT-XXIV/2) as well as (d) during "Polarstern" cruise ANT-XXIX/3. The habitat suitability model was developed by the use of the modelling package "biomod2". As predictor variables, we used (i) dissolved oxygen from the World Ocean Atlas 2013, (ii) ice coverage from AMSR-E sea ice maps, (iii) seawater temperature data from the Finite Element Sea Ice - Ocean Model (FESOM) provided by R. Timmermann (AWI), (iv) bathymetric data from the International Bathymetric Chart of the Southern Ocean (IBCSO) and (v) SeaWiFS chlorophyll-a concentration data. Most suitable habitat conditions for the Antarctic krill seem to occur near the tip of the Antarctic Peninsula, on the continental slope between 15°W and 15°E and on the Maud Rise plateau. Antarctic krill (larvae): The map of interpolated abundances of krill larvae is based on abundance data, which were collected (a) during the Norwegian Antarctic research expeditions 1976/77, 1977/78 and 1979/80 (M/V "Polarsirkel"), (b) in the context of the First International BIOMASS Experiment survey (FIBEX) (Walther Herwig cruise 1981) and the Lazarev Sea Krill Survey (LAKRIS) ("Polarstern" cruises ANT-XXI/4, ANT-XXIII/6) as well as (c) during "Polarstern" cruise ANT-VII/4 and the combined "Polarstern" (ANT-VIII/2) and R.V. "Akademik Fedorova" cruise. An inverse distance weighted (IDW) interpolation was performed for a 30 km radius around each krill larvae record. Areas with highest numbers of E. superba larvae (〉 1000 individuals/m²) occurred west of the Prime Meridian from approximately 65°S to the ice shelf. Ice krill (adults): The map of the potential habitat of E. crystallorophias was approximated by water depth from 0 m to 550 m, using bathymetric data from IBCSO, and mean sea surface temperature ≤ 0°C based on temperature data from FESOM provided by R. Timmermann (AWI). The map of interpolated density of individuals of E. crystallorophias is based on abundance data, which were collected (a) during the Norwegian Antarctic research expedition 1979/80 (M/V "Polarsirkel"), (b) during the German Antarctic research cruise 1975/76 with "Walther Herwig", (c) in the context of the Lazarev Sea Krill Survey ("Polarstern" cruises ANT-XXI/4, ANT-XXIII/2, ANT-XXIII/6, ANT-XXIV/2) as well as (d) during "Polarstern" cruise ANT-V/1-3, ANT-VII/4 and ANT-XXIX/3. An IDW interpolation was performed for a 30 km radius around each record of ice krill. Areas with highest densities of E. crystallorophias individuals occurred on the south-eastern Weddell Sea shelf and near the tip of the Antarctic Peninsula. Volker Siegel (retired; formerly Th\"unen Institute) provided the data for the Antarctic krill and ice krill. More information on the spatial analysis is given in working paper WG-EMM-16/03 submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (available at https://www.ccamlr.org/en/wg-emm-16)

Description: Here we provide four ArcGIS map packages with georeferenced files on the spatial distribution of Antarctic petrels, Ad\'elie penguins (breeders and non-breeders) and Emperor penguins in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area in the Weddell Sea. Antarctic petrel (Thalassoica antarctica): We approximated potential foraging habitats of T. antarctica according to existing literature by ice coverage from AMSR-E sea ice maps, bathymetric data from the International Bathymetric Chart of the Southern Ocean (IBCSO), and seawater temperature data from the Finite Element Sea Ice - Ocean Model (FESOM) provided by R. Timmermann (AWI). Subsequently, we combined our Antarctic petrel model with the kernel utilization distribution model from Descamps et al. (2016). The authors kindly provided us with shape files showing the kernel utilization summer and winter distribution of Antarctic petrel breeding at Svarthamaren. Breeding locations and estimated number of breeding pairs were taken from van Franeker et al. (1999). Favourable habitat conditions for Antarctic petrels were predicted for the Lazarev Sea and along the eastern coast of the Weddell Sea, particularly for the area off the Fimbul Ice Shelf and along the coast between approx. 15°E to 10°W within a water depth range from approx. 500 m to 2500 m. Breeding Ad\'elie penguins (Pygoscelis adeliae): The map of potential foraging habitats of breeding P. adeliae is based on British Antarctic Survey (BAS) Inventory data from Phil Trathan (ID 754) and Mike Dunn and P. Trathan (ID 764, 773, 779), a dataset from BAS (P. Trathan) and Instituto Ant\'artico Argentino (Mercedes Santos) (ID 753) and a dataset from the US AMLR Program from Jefferson Hinke and Wayne Trivelpiece (NOAA) (ID 910), which are stored in the Birdlife International\textquotesingles Seabird Tracking Database (data request: 20-10-2015). Suitable foraging habitats for breeding Ad\'elies from colonies from which no tracking data were not available were approximated by a 50 km buffer and a 50-100 km ring buffer around each colony according to the recommendations of a CCAMLR MPA planning workshop. Breeding locations and estimated abundance of breeding pairs were taken from Lynch and LaRue (2014). The tracking data were processed with a state-space model described by Johnson et al. (2008) and were implemented in the R package crawl (Johnson 2011). Jefferson Hinke (NOAA) kindly provided us with support running the R script. Highly suitable foraging habitats occurred about 50 km away from the colonies on King Georg Island, the colony in Hope Bay (Graham Land) and the colonies on the South Orkney Islands. Non-breeding Ad\'elie penguins (Pygoscelis adeliae): The map of potential foraging habitats of non-breeding P. adeliae is based on British Antarctic Survey (BAS) Inventory data from Phil Trathan (ID 754) and Mike Dunn and P. Trathan (ID 773, 779), a dataset from BAS (P. Trathan) and Instituto Ant\'artico Argentino (Mercedes Santos) (ID 753) and a dataset from the US AMLR Program from Jefferson Hinke and Wayne Trivelpiece (NOAA) (ID 910), which are stored in the Birdlife International\textquotesingles Seabird Tracking Database (data request: 20-10-2015). The tracking data were processed with a state-space model described by Johnson et al. (2008) and were implemented in the R package crawl (Johnson 2011). Jefferson Hinke (NOAA) kindly provided us with support running the R script. Highest habitat utilisation was concentrated in relative small areas (e.g., close to King Georg Island). However, the non-breeding Ad\'elies seemed to roam through large parts of the Weddell Sea. Emperor penguins (Aptenodytes forsteri): The probability map of A. forsteri occurrence was developed as a function of distance to colony and colony size from Fretwell et al. (2012, 2014) as well as from sea ice concentration from AMSR-E sea ice maps. Our model of emperor penguin foraging distribution during breeding season showed that the probability of occurrence is highest at the Halley and Dawson colony near Brunt Ice Shelf and at the Atka colony near Ekstrøm Ice Shelf. More information on the spatial analysis is given in working paper WG-EMM-16/03 and WG-SAM-17/30 (for T. antarctica) submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (EMM) and the CCAMLR Working Group on Statistics, Assessments and Modelling (SAM), respectively (available at https://www.ccamlr.org/en/wg-emm-16 and https://www.ccamlr.org/en/wg-s

Description: Here we provide two ArcGIS map packages with georeferenced files on the spatial distribution of seals in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area in the Weddell Sea. Spatial distribution of seals based on aerial surveys: The map of the spatial distribution of crabeater seals is based on modelled seal abundances from Flores et al. (2008) and Forcada et al. (2012). These modelled abundances were supplemented by abundance data derived from Bester et al. (1995, 2002) and by point data from Pl\"otz et al. (2011a-e), which were translated into abundance values by the count method for line transect data. The calculated data on seal abundances from Pl\"otz et al. (2011a-e) and Bester et al. (1995, 2002) were interpolated using the inverse distance weighted method. The combined data set of modelled and interpolated abundances showed highest absolute seal abundances offshore the Riiser-Larsen Ice Shelf and Quarisen Ice Shelf. Spatial distribution of seals based on tracking data: The map of probability of seal occurrence is based on all tracking data publicly available for the wider Weddell Sea from the MEOP data portal "Marine Mammals Exploring the Oceans Pole to Pole" (data request: 14-11-2016). In addition, we have used MEOP data (UK data: ct27, ct70; German data: ct113, wd06, wd07) for which unconditional sharing is not yet accepted. These data were provided by Lars Boehme (University of St. Andrews) and Horst Bornemann (AWI), respectively. Furthermore, the data from the MEOP data portal were complemented by tracking data sets on southern elephant seals (Tosh et al. 2009, James et al. 2012), Weddell seals (McIntyre et al. 2013) and crabeater seals (Nachtsheim et al. 2016). All tracking data united were processed with a state-space model described by Johnson et al. (2008) and were implemented in the R package crawl (Johnson 2011). The tracking data analysis indicated frequent occurrence of seals in a larger area off the Brunt and Filchner Ice Shelf (approx. 25°W-40°W), and in smaller patches along the eastern Weddell Sea ice shelfs as well as in the region around the tip of the Antarctic Peninsula. More information on the spatial analysis is given in working paper WG-EMM-16/03 and WG-SAM-17/30 submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (EMM) and the CCAMLR Working Group on Statistics, Assessments and Modelling (SAM), respectively (available at https://www.ccamlr.org/en/wg-emm-16 and https://www.ccamlr.org/en/wg-sam-17

Description: Here we provide four ArcGIS map packages with georeferenced files on the spatial distribution of Antarctic petrels, Ad\'elie penguins (breeders and non-breeders) and Emperor penguins in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area in the Weddell Sea. Antarctic petrel (Thalassoica antarctica): We approximated potential foraging habitats of T. antarctica according to existing literature by ice coverage from AMSR-E sea ice maps, bathymetric data from the International Bathymetric Chart of the Southern Ocean (IBCSO), and seawater temperature data from the Finite Element Sea Ice - Ocean Model (FESOM) provided by R. Timmermann (AWI). Subsequently, we combined our Antarctic petrel model with the kernel utilization distribution model from Descamps et al. (2016). The authors kindly provided us with shape files showing the kernel utilization summer and winter distribution of Antarctic petrel breeding at Svarthamaren. Breeding locations and estimated number of breeding pairs were taken from van Franeker et al. (1999). Favourable habitat conditions for Antarctic petrels were predicted for the Lazarev Sea and along the eastern coast of the Weddell Sea, particularly for the area off the Fimbul Ice Shelf and along the coast between approx. 15°E to 10°W within a water depth range from approx. 500 m to 2500 m. Breeding Ad\'elie penguins (Pygoscelis adeliae): The map of potential foraging habitats of breeding P. adeliae is based on British Antarctic Survey (BAS) Inventory data from Phil Trathan (ID 754) and Mike Dunn and P. Trathan (ID 764, 773, 779), a dataset from BAS (P. Trathan) and Instituto Ant\'artico Argentino (Mercedes Santos) (ID 753) and a dataset from the US AMLR Program from Jefferson Hinke and Wayne Trivelpiece (NOAA) (ID 910), which are stored in the Birdlife International\textquotesingles Seabird Tracking Database (data request: 20-10-2015). Suitable foraging habitats for breeding Ad\'elies from colonies from which no tracking data were not available were approximated by a 50 km buffer and a 50-100 km ring buffer around each colony according to the recommendations of a CCAMLR MPA planning workshop. Breeding locations and estimated abundance of breeding pairs were taken from Lynch and LaRue (2014). The tracking data were processed with a state-space model described by Johnson et al. (2008) and were implemented in the R package crawl (Johnson 2011). Jefferson Hinke (NOAA) kindly provided us with support running the R script. Highly suitable foraging habitats occurred about 50 km away from the colonies on King Georg Island, the colony in Hope Bay (Graham Land) and the colonies on the South Orkney Islands. Non-breeding Ad\'elie penguins (Pygoscelis adeliae): The map of potential foraging habitats of non-breeding P. adeliae is based on British Antarctic Survey (BAS) Inventory data from Phil Trathan (ID 754) and Mike Dunn and P. Trathan (ID 773, 779), a dataset from BAS (P. Trathan) and Instituto Ant\'artico Argentino (Mercedes Santos) (ID 753) and a dataset from the US AMLR Program from Jefferson Hinke and Wayne Trivelpiece (NOAA) (ID 910), which are stored in the Birdlife International\textquotesingles Seabird Tracking Database (data request: 20-10-2015). The tracking data were processed with a state-space model described by Johnson et al. (2008) and were implemented in the R package crawl (Johnson 2011). Jefferson Hinke (NOAA) kindly provided us with support running the R script. Highest habitat utilisation was concentrated in relative small areas (e.g., close to King Georg Island). However, the non-breeding Ad\'elies seemed to roam through large parts of the Weddell Sea. Emperor penguins (Aptenodytes forsteri): The probability map of A. forsteri occurrence was developed as a function of distance to colony and colony size from Fretwell et al. (2012, 2014) as well as from sea ice concentration from AMSR-E sea ice maps. Our model of emperor penguin foraging distribution during breeding season showed that the probability of occurrence is highest at the Halley and Dawson colony near Brunt Ice Shelf and at the Atka colony near Ekstrøm Ice Shelf. More information on the spatial analysis is given in working paper WG-EMM-16/03 and WG-SAM-17/30 (for T. antarctica) submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (EMM) and the CCAMLR Working Group on Statistics, Assessments and Modelling (SAM), respectively (available at https://www.ccamlr.org/en/wg-emm-16 and https://www.ccamlr.org/en/wg-s

Description: Here we provide two ArcGIS map packages with georeferenced files on the spatial distribution of seals in the wider Weddell Sea (Antarctica), which were created in the context of the development of a marine protected area in the Weddell Sea. Spatial distribution of seals based on aerial surveys: The map of the spatial distribution of crabeater seals is based on modelled seal abundances from Flores et al. (2008) and Forcada et al. (2012). These modelled abundances were supplemented by abundance data derived from Bester et al. (1995, 2002) and by point data from Pl\"otz et al. (2011a-e), which were translated into abundance values by the count method for line transect data. The calculated data on seal abundances from Pl\"otz et al. (2011a-e) and Bester et al. (1995, 2002) were interpolated using the inverse distance weighted method. The combined data set of modelled and interpolated abundances showed highest absolute seal abundances offshore the Riiser-Larsen Ice Shelf and Quarisen Ice Shelf. Spatial distribution of seals based on tracking data: The map of probability of seal occurrence is based on all tracking data publicly available for the wider Weddell Sea from the MEOP data portal "Marine Mammals Exploring the Oceans Pole to Pole" (data request: 14-11-2016). In addition, we have used MEOP data (UK data: ct27, ct70; German data: ct113, wd06, wd07) for which unconditional sharing is not yet accepted. These data were provided by Lars Boehme (University of St. Andrews) and Horst Bornemann (AWI), respectively. Furthermore, the data from the MEOP data portal were complemented by tracking data sets on southern elephant seals (Tosh et al. 2009, James et al. 2012), Weddell seals (McIntyre et al. 2013) and crabeater seals (Nachtsheim et al. 2016). All tracking data united were processed with a state-space model described by Johnson et al. (2008) and were implemented in the R package crawl (Johnson 2011). The tracking data analysis indicated frequent occurrence of seals in a larger area off the Brunt and Filchner Ice Shelf (approx. 25°W-40°W), and in smaller patches along the eastern Weddell Sea ice shelfs as well as in the region around the tip of the Antarctic Peninsula. More information on the spatial analysis is given in working paper WG-EMM-16/03 and WG-SAM-17/30 submitted to the CCAMLR Working Group on Ecosystem Monitoring and Management (EMM) and the CCAMLR Working Group on Statistics, Assessments and Modelling (SAM), respectively (available at https://www.ccamlr.org/en/wg-emm-16 and https://www.ccamlr.org/en/wg-sam-17

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17934-17942, doi:10.1073/pnas.1910121116.

Description: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.

Description: We are grateful to Martin Kolisko and Fabien Burki for helpful discussion about and comments on the phylogenetic analysis; and Filip Husnik and Vittorio Boscaro for valuable comments on the manuscript. This work was supported by a grant from the National Science Foundation to R.J.G. and P.J.K. (PLR-1341362) and from the Natural Sciences and Engineering Research Council of Canada to P.J.K. (RGPIN-2014-03994).

Description: 2020-02-19

Description: Author Posting. © The Authors, 2019. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 218(3), (2019): 1822-1837, doi: 10.1093/gji/ggz253.

Description: Joint inversion of multiple electromagnetic data sets, such as controlled source electromagnetic and magnetotelluric data, has the potential to significantly reduce uncertainty in the inverted electrical resistivity when the two data sets contain complementary information about the subsurface. However, evaluating quantitatively the model uncertainty reduction is made difficult by the fact that conventional inversion methods—using gradients and model regularization—typically produce just one model, with no associated estimate of model parameter uncertainty. Bayesian inverse methods can provide quantitative estimates of inverted model parameter uncertainty by generating an ensemble of models, sampled proportional to data fit. The resulting posterior distribution represents a combination of a priori assumptions about the model parameters and information contained in field data. Bayesian inversion is therefore able to quantify the impact of jointly inverting multiple data sets by using the statistical information contained in the posterior distribution. We illustrate, for synthetic data generated from a simple 1-D model, the shape of parameter space compatible with controlled source electromagnetic and magnetotelluric data, separately and jointly. We also demonstrate that when data sets contain complementary information about the model, the region of parameter space compatible with the joint data set is less than or equal to the intersection of the regions compatible with the individual data sets. We adapt a trans-dimensional Markov chain Monte Carlo algorithm for jointly inverting multiple electromagnetic data sets for 1-D earth models and apply it to surface-towed controlled source electromagnetic and magnetotelluric data collected offshore New Jersey, USA, to evaluate the extent of a low salinity aquifer within the continental shelf. Our inversion results identify a region of high resistivity of varying depth and thickness in the upper 500 m of the continental shelf, corroborating results from a previous study that used regularized, gradient-based inversion methods. We evaluate the joint model parameter uncertainty in comparison to the uncertainty obtained from the individual data sets and demonstrate quantitatively that joint inversion offers reduced uncertainty. In addition, we show how the Bayesian model ensemble can subsequently be used to derive uncertainty estimates of pore water salinity within the low salinity aquifer.

Description: We gratefully acknowledge funding support from National Science Foundation grants 1458392 and 1459035. We thank the captain and crew of the R.V. Marcus G. Langseth for a successful cruise and the Marine EM Lab at Scripps Institution of Oceanography for providing the instrumentation. We also thank Chris Armerding, Marah Dahn, John Desanto, Jimmy Elsenbeck, Matt Folsom, Keiichi Ishizu, Jeff Pepin, Charlotte Wiman and Georgie Zelenak for participating in the cruise. We gratefully acknowledge Alberto Malinverno for the idea to use a Monte Carlo scheme to estimate the distribution of pore fluid salinity, and William Menke for many constructive conversations and suggestions.

Description: Author Posting. © The Authors, 2019. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 218(3), (2019): 2122-2135, doi: 10.1093/gji/ggz272.

Description: We have conducted the first passive Ocean Bottom Seismograph (OBS) experiment near the Challenger Deep at the southernmost Mariana subduction zone by deploying and recovering an array of 6 broad-band OBSs during December 2016–June 2017. The obtained passive-source seismic records provide the first-ever near-field seismic observations in the southernmost Mariana subduction zone. We first correct clock errors of the OBS recordings based on both teleseismic waveforms and ambient noise cross-correlation. We then perform matched filter earthquake detection using 53 template events in the catalogue of the US Geological Survey and find 〉7000 local earthquakes during the 6-month OBS deployment period. Results of the two independent approaches show that the maximum clock drifting was ∼2 s on one instrument (OBS PA01), while the rest of OBS waveforms had negligible time drifting. After timing correction, we locate the detected earthquakes using a newly refined local velocity model that was derived from a companion active source experiment in the same region. In total, 2004 earthquakes are located with relatively high resolution. Furthermore, we calibrate the magnitudes of the detected earthquakes by measuring the relative amplitudes to their nearest relocated templates on all OBSs and acquire a high-resolution local earthquake catalogue. The magnitudes of earthquakes in our new catalogue range from 1.1 to 5.6. The earthquakes span over the Southwest Mariana rift, the megathrust interface, forearc and outer-rise regions. While most earthquakes are shallow, depths of the slab earthquakes increase from ∼100 to ∼240 km from west to east towards Guam. We also delineate the subducting interface from seismicity distribution and find an increasing trend in dip angles from west to east. The observed along-strike variation in slab dip angles and its downdip extents provide new constraints on geodynamic processes of the southernmost Mariana subduction zone.

Description: We express our appreciation to the science parties and crew members of the R/V Shiyan 3 for deployment and collection of the OBS instruments during the Mariana expeditions. This study is supported by the Hong Kong Research Grant Council Grants (No. 14313816), Faculty of Science at CUHK, Chinese Academy of Sciences (No. Y4SL021001, QYZDY-SSW-DQC005, 133244KYSB20180029), the National Natural Science Foundation of China (No. 41890813, 91628301, 41676042, U1701641, 41576041, 91858207 and U1606401), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100). Generic Mapping Tools (Wessel & Smith 1991) and PSSAC (developed by Prof Lupei Zhu) are used for data analysis and figure preparation in this study. Constructive comments from Dr Lidong Bie and two anonymous reviewers are helpful in improving the manuscript.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Diaz, J. M., Plummer, S., Hansel, C. M., Andeer, P. F., Saito, M. A., & McIlvin, M. R. NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica. Proceedings of the National Academy of Sciences of the United States of America, 116 (33), (2019): 16448-16453, doi: 10.1073/pnas.1821233116.

Description: Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.

Description: This work was supported by a postdoctoral fellowship from the Ford Foundation (to J.M.D.), the National Science Foundation (NSF) under grants OCE 1225801 (to J.M.D.) and OCE 1246174 (to C.M.H.), a Junior Faculty Seed Grant from the University of Georgia Research Foundation (to J.M.D.), and a National Science Foundation Graduate Research Fellowship (to S.P.). The FIRe was purchased through a NSF equipment improvement grant (1624593).The authors thank Melissa Soule for assistance with LC/MS/MS analysis of peptide samples.

Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(27), (2019): 13233-13238, doi: 10.1073/pnas.1904087116.

Description: The overturning circulation of the global ocean is critically shaped by deep-ocean mixing, which transforms cold waters sinking at high latitudes into warmer, shallower waters. The effectiveness of mixing in driving this transformation is jointly set by two factors: the intensity of turbulence near topography and the rate at which well-mixed boundary waters are exchanged with the stratified ocean interior. Here, we use innovative observations of a major branch of the overturning circulation—an abyssal boundary current in the Southern Ocean—to identify a previously undocumented mixing mechanism, by which deep-ocean waters are efficiently laundered through intensified near-boundary turbulence and boundary–interior exchange. The linchpin of the mechanism is the generation of submesoscale dynamical instabilities by the flow of deep-ocean waters along a steep topographic boundary. As the conditions conducive to this mode of mixing are common to many abyssal boundary currents, our findings highlight an imperative for its representation in models of oceanic overturning.

Description: The DynOPO project is supported by the UK Natural Environment Research Council (grants NE/K013181/1 and NE/K012843/1) and the US National Science Foundation (grants OCE-1536453 and OCE-1536779). A.C.N.G. acknowledges the support of the Royal Society and the Wolfson Foundation. S.L. acknowledges the support of award NA14OAR4320106 from the National Oceanic and Atmospheric Administration, US Department of Commerce. The statements, findings, conclusions, and recommendations are those of the authors, and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, or the US Department of Commerce. We are grateful to the scientific party, crew, and technicians on the RRS James Clark Ross for their hard work during data collection.

Description: 2019-12-18

Description: In this paper we describe the macroseismic effects produced by the long and destructive seismic sequence that hit Central Italy from 24 August 2016 to January 2017. Starting from the procedure adopted in the complex field survey, we discuss the characteristics of the building stock and its classification in terms of EMS-98 as well as the issues associated with the intensity assessment due to the evolution of damage caused by multiple shocks. As a result, macroseismic intensity for about 300 localities has been determined; however, most of the intensities assessed for the earthquakes following the first strong shock on 24 August 2016, represent the cumulative effect of damage during the sequence. The earthquake parameters computed from the macroseismic datasets are compared with the instrumental determinations in order to highlight critical issues related to the assessment of macroseismic parameters of strong earthquakes during a seismic sequence. The results also provide indications on how location and magnitude computation can be strongly biased when dealing with historical seismic sequences.

Description: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile (DPC)

Description: Published

Description: 2407–2431

Description: 4T. Sismicità dell'Italia

Description: 1SR TERREMOTI - Sorveglianza Sismica e Allerta Tsunami

Description: 2SR TERREMOTI - Gestione delle emergenze sismiche e da maremoto

Description: 5SR TERREMOTI - Convenzioni derivanti dall'Accordo Quadro decennale INGV-DPC

Description: JCR Journal

Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in ICES Journal of Marine Science 76(4), (2010): 781-786, doi:10.1093/icesjms/fsy194.

Description: Whales are federally protected by the Marine Mammal Protection Act; endangered species, such as the North Atlantic right whale, receive additional protection under the Endangered Species Act. However, their regulations have failed to satisfy conservation and animal welfare concerns. From 1990 to 2011 the North Atlantic right whale (Eubalaena glacialis, NARW) population grew at a mean of 2.8% annually. However, population trends reversed since 2011; the species is in decline, with only ∼100 reproductively active females remaining. This failure is driven by vessel collisions and increasingly fatal and serious entanglement in fixed fishing gear, whose rope strength has increased substantially. Chronic entanglement, drag, and associated morbidity have been linked to poor fecundity. Genuine solutions involve designating areas to be avoided and speed restrictions for ships and removing fishing trap ropes from the water column. A trap fishing closure for NARW habitat in the Cape Cod Bay (U.S.) area has been in place seasonally since 2015. 2017 mortalities in Eastern Canada elicited substantive management changes whereby the 2018 presence of NARW in active trap fishing areas resulted in an effective closure. To avoid these costly closures, the traditional trap fishery model of rope end lines attached to surface marker buoys has to be modified so that traps are marked virtually, and retrieved with gear that does not remain in the water column except during trap retrieval. Consumer demand for genuinely whale-safe products will augment and encourage the necessary regulatory changes so that trap fisheries conserve target and nontarget species.

Description: I thank Mark Baumgartner, Scott Kraus, Tim Werner, Amy Knowlton, Heather Pettis, Scott Landry, Stormy Mayo, Fred Penney, and Beth Casoni for discussions on this topic and Natalie Renier for drawing Figures 5 and 6. Funding was provided by the Woods Hole Oceanographic Institution Independent Research and Development Program.

Description: 2020-01-10

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schwaha, T., Bernhard, J. M., Edgcomb, V. P., & Todaro, M. A. Aethozooides uraniae, a new deep-sea genus and species of solitary bryozoan from the Mediterranean Sea, with a revision of the Aethozoidae. Marine Biodiversity, 49(4), (2019): 1843-1856, doi: 10.1007/s12526-019-00948-w.

Description: Bryozoa is a phylum of about 6000 extant species that are almost exclusively colonial. Few species of the uncalcified Gymnolaemata, the ctenostomes, however, show solitary forms that essentially consist of single zooids. Recently, several specimens of a solitary ctenostome bryozoan were encountered for the first time in the deep Mediterranean Sea, at the edge of an anoxic brine lake. Differences in size, tentacle number, and in the variability of cystid appendages set these specimens apart from all other known solitary species. Moreover, additional morphological autapomorphic traits suggest the erection of a novel genus to allocate the new species. Consequently, the new taxon Aethozooides gen. nov. is proposed in virtue of the general resemblance of the Mediterranean specimens with those of the genus Aethozoon Hayward, 1978. Aethozooides uraniae gen. et sp. nov. shows significant variability in the number and location of cystid appendages that range from two on the basal side to one or two on the zooid mid-peristomial position and/or, rarely, on the terminal frontal side. The polypide possesses a distinct, long tentacle crown always carrying 10 tentacles. The prominent retractor muscle consists of numerous bundles that, in contrast to other known gymnolaemates, attach not only to the lophophoral base but also to various parts of the gut. Distally, the aperture shows a set of four apertural muscles including four parieto-vaginal bands. Reviewing the state and diversity of solitary ctenostomes, we propose a revision of the family Aethozoidae to include the genera Franzenella d’Hondt, 1983, Aethozoon, Aethozooides, and two species currently affiliated to the genus Franzenella (F. monniotae and F. radicans) for which we erected the new taxon Solella gen. nov. Keywords

Description: Open access funding provided by University of Vienna. This study was supported by NSF grants OCE-0849578 to VPE and JMB, OCE-1061391 to JMB and VPE, and The Investment in Science Fund at WHOI.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mitchell, S. J., Houghton, B. F., Carey, R. J., Manga, M., Fauria, K. E., Jones, M. R., Soule, S. A., Conway, C. E., Wei, Z., & Giachetti, T. Submarine giant pumice: A window into the shallow conduit dynamics of a recent silicic eruption. Bulletin of Volcanology, 81(7), (2019): 42, doi:10.1007/s00445-019-1298-5.

Description: Meter-scale vesicular blocks, termed “giant pumice,” are characteristic primary products of many subaqueous silicic eruptions. The size of giant pumices allows us to describe meter-scale variations in textures and geochemistry with implications for shearing processes, ascent dynamics, and thermal histories within submarine conduits prior to eruption. The submarine eruption of Havre volcano, Kermadec Arc, in 2012, produced at least 0.1 km3 of rhyolitic giant pumice from a single 900-m-deep vent, with blocks up to 10 m in size transported to at least 6 km from source. We sampled and analyzed 29 giant pumices from the 2012 Havre eruption. Geochemical analyses of whole rock and matrix glass show no evidence for geochemical heterogeneities in parental magma; any textural variations can be attributed to crystallization of phenocrysts and microlites, and degassing. Extensive growth of microlites occurred near conduit walls where magma was then mingled with ascending microlite-poor, low viscosity rhyolite. Meter- to micron-scale textural analyses of giant pumices identify diversity throughout an individual block and between the exteriors of individual blocks. We identify evidence for post-disruption vesicle growth during pumice ascent in the water column above the submarine vent. A 2D cumulative strain model with a flared, shallow conduit may explain observed vesicularity contrasts (elongate tube vesicles vs spherical vesicles). Low vesicle number densities in these pumices from this high-intensity silicic eruption demonstrate the effect of hydrostatic pressure above a deep submarine vent in suppressing rapid late-stage bubble nucleation and inhibiting explosive fragmentation in the shallow conduit.

Description: This study was funded primarily through an NSF Ocean grant: OCE-1357443 (SJM, BFH and RJC). MM is supported by NSF EAR 1447559. The μXRT analysis was performed at the Lawrence Berkeley National Lab Advanced Light Source beamline 8.3.2 and the large CT scan by SAS at the University of Texas Austin micro-CT facility. Capillary flow porometry and He-pycnometry were assisted by TG and MRJ at the University of Oregon. Microprobe analysis was conducted at the University of Hawai’i at Mānoa. CEC was supported by post-doctoral research fellowship from the Japan Society for the Promotion of Science (JSPS16788). We would like to thank Kenichiro Tani, Takashi Sano, and Eric Hellebrand for their assistance with geochemical data acquisition, JoAnn Sinton and Wagner Petrographic for thin section preparation, Zachary Langdalen for binary processing of BSE images, Warren M. McKenzie for measuring clast densities, and Dula Parkinson for guidance with the μXRT imaging. We further acknowledge the full scientific team, crew and Jason ROV team (Woods Hole Oceanographic Institute) aboard the R/V Roger Revelle (Scripps Institute of Oceanography) during the MESH expedition in 2015, without whom, this study would not have been possible. Finally, we thank Andrew Harris, Katharine Cashman, Lucia Gurioli and an anonymous reviewer for their insightful and helpful reviews of the manuscript.

Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International, 219(1), (2019): 464-478, doi:10.1093/gji/ggz315.

Description: The electromagnetic (EM) field generated by ocean tidal flow is readily detectable in both satellite magnetic field data, and in ocean-bottom measurements of electric and magnetic fields. The availability of accurate charts of tidal currents, constrained by assimilation of modern satellite altimetry data, opens the possibility of using tidal EM fields as a source to image mantle electrical resistivity beneath the ocean basins, as highlighted by the recent success in defining the globally averaged lithosphere–asthenosphere boundary (LAB) with satellite data. In fact, seafloor EM data would be expected to provide better constraints on the structure of resistive oceanic lithosphere, since the toroidal magnetic mode, which can constrain resistive features, is a significant component of the tidal EM field within the ocean, but is absent above the surface (in particular in satellite data). Here we consider this issue in more detail, using a combination of simplified theoretical analysis and 1-D and 3-D numerical modelling to provide a thorough discussion of the sensitivity of satellite and seafloor data to subsurface electrical structure. As part of this effort, and as a step toward 3-D inversion of seafloor tidal data, we have developed a new flexible 3-D spherical-coordinate finite difference scheme for both global and regional scale modelling, with higher resolution models nested in larger scale solutions. We use the new 3-D model, together with Monte Carlo simulations of errors in tidal current estimates, to provide a quantitative assessment of errors in the computed tidal EM signal caused by uncertainty in the tidal source. Over the open ocean this component of error is below 0.01 nT in Bz at satellite height and 0.05 nT in Bx on the seafloor, well below typical signal levels. However, as coastlines are approached error levels can increase substantially. Both analytical and 3-D modelling demonstrate that the seafloor magnetic field is most sensitive to the lithospheric resistance (the product of resistivity and thickness), and is more weakly influenced (primarily in the phase) by resistivity of the underlying asthenosphere. Satellite data, which contain only the poloidal magnetic mode, are more sensitive to the conductive asthenosphere, but have little sensitivity to lithospheric resistance. For both seafloor and satellite data’s changes due to plausible variations in Earth parameters are well above error levels associated with source uncertainty, at least in the ocean interior. Although the 3-D modelling results are qualitatively consistent with theoretical analysis, the presence of coastlines and bathymetric variations generates a complex response, confirming that quantitative interpretation of ocean tidal EM fields will require a 3-D treatment. As an illustration of the nested 3-D scheme, seafloor data at five magnetic and seven electric stations in the northeastern Pacific (41○N, 165○W) are fit with trial-and-error forward modelling of a local domain. The simulation results indicate that the lithospheric resistance is roughly 7 × 108 Ωm2. The phase of the seafloor data in this region are inconsistent with a sharp transition between the resistive lithosphere and conductive asthenosphere.

Description: This work has been supported by National Natural Science Foundation of China grants 41804072 and 41574104, and NSF grant EAR-1447109. Special thanks to Dr Benjamin Murphy who provided the conductivity-depth profile for 1-D earth model, Dr Min Ding who provided valuable discussion about the oceanic lithosphere and Dr Jeffery Love who provided comments on the stylistics of the manuscript.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kelly, M. R., Jr., Neubert, M. G., & Lenhart, S. Marine reserves and optimal dynamic harvesting when fishing damages habitat. Theoretical Ecology, 12(2), (2019): 131-144, doi:10.1007/s12080-018-0399-7.

Description: Marine fisheries are a significant source of protein for many human populations. In some locations, however, destructive fishing practices have negatively impacted the quality of fish habitat and reduced the habitat’s ability to sustain fish stocks. Improving the management of stocks that can be potentially damaged by harvesting requires improved understanding of the spatiotemporal dynamics of the stocks, their habitats, and the behavior of the harvesters. We develop a mathematical model for both a fish stock as well as its habitat quality. Both are modeled using nonlinear, parabolic partial differential equations, and density dependence in the growth rate of the fish stock depends upon habitat quality. The objective is to find the dynamic distribution of harvest effort that maximizes the discounted net present value of the coupled fishery-habitat system. The value derives both from extraction (and sale) of the stock and the provisioning of ecosystem services by the habitat. Optimal harvesting strategies are found numerically. The results suggest that no-take marine reserves can be an important part of the optimal strategy and that their spatiotemporal configuration depends both on the vulnerability of habitat to fishing damage and on the timescale of habitat recovery when fishing ceases.

Description: This manuscript is based upon the work supported by the National Science Foundation under Grant No. DEB-1558904 (to MGN) and also supported by the National Institute for Mathematical and Biological Synthesis, an Institute supported by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aslan, C., Beckman, N. G., Rogers, H. S., Bronstein, J., Zurell, D., Hartig, F., Shea, K., Pejchar, L., Neubert, M., Poulsen, J., HilleRisLambers, J., Miriti, M., Loiselle, B., Effiom, E., Zambrano, J., Schupp, G., Pufal, G., Johnson, J., Bullock, J. M., Brodie, J., Bruna, E., Cantrell, R. S., Decker, R., Fricke, E., Gurski, K., Hastings, A., Kogan, O., Razafindratsima, O., Sandor, M., Schreiber, S., Snell, R., Strickland, C., & Zhou, Y. Employing plant functional groups to advance seed dispersal ecology and conservation. AoB Plants, 11(2), (2019):plz006, doi:10.1093/aobpla/plz006.

Description: Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether single species and entire ecosystems will be resilient to global change. Building on current frameworks, we here posit that seed dispersal ecology should adopt plant functional groups as analytical units to reduce this complexity to manageable levels. Functional groups can be used to distinguish, for their constituent species, whether it matters (i) if seeds are dispersed, (ii) into what context they are dispersed and (iii) what vectors disperse them. To avoid overgeneralization, we propose that the utility of these functional groups may be assessed by generating predictions based on the groups and then testing those predictions against species-specific data. We suggest that data collection and analysis can then be guided by robust functional group definitions. Generalizing across similar species in this way could help us to better understand the population and community dynamics of plants and tackle the complexity of seed dispersal as well as its disruption.

Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio‐Environmental Synthesis Center under the US National Science Foundation Grant DBI‐1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1- 1). Contributions by the authors C.A. led the development of the concepts, writing, and revising of the manuscript with input from N.G.B. and H.S.R. All authors contributed to the development of concepts and are listed in order of contribution and alphabetical order within each level of contribution.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Alexander, H., Johnson, L. K., & Brown, C. T.. Keeping it light: (re)analyzing community-wide datasets without major infrastructure. Gigascience, 8(2),(2019): giy159, doi:10.1093/gigascience/giy159.

Description: DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.

Description: Funding was provided by the Gordon and Betty Moore Foundation (award GBMF4551 to C.T.B.).

Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in , Zakroff, C., Mooney, T.A. & Berumen, M.L. Dose-dependence and small-scale variability in responses to ocean acidification during squid, Doryteuthis pealeii, development. Marine Biology, (2019), 166: 62. doi:10.1007/s00227-019-3510-8.

Description: Coastal squids lay their eggs on the benthos, leaving them to develop in a dynamic system that is undergoing rapid acidification due to human influence. Prior studies have broadly investigated the impacts of ocean acidification on embryonic squid, but have not addressed the thresholds at which these responses occur or their potential variability. We raised squid, Doryteuthis pealeii (captured in Vineyard Sound, Massachusetts, USA: 41° 23.370N 70° 46.418´W), eggs in three trials across the breeding season (May - September, 2013) in a total of six chronic pCO2 exposures (400, 550, 850, 1300, 1900, and 2200 ppm). Hatchlings were counted and subsampled for mantle length, yolk volume, hatching time, hatching success, and statolith morphology. New methods for analysis of statolith shape, rugosity, and surface degradation were developed and are presented (with code). Responses to acidification (e.g., reduced mantle lengths, delayed hatching, and smaller, more degraded statoliths) were evident at ~ 1300 ppm CO2. However, patterns of physiological response and energy management, based on comparisons of yolk consumption and growth, varied among trials. Interactions between pCO2 and hatching day indicated a potential influence of exposure time on responses, while interactions with culture vessel highlighted the substantive natural variability within a clutch of eggs. While this study is consistent with, and expands upon, previous findings of sensitivity of the early life stages to acidification, it also highlights the plasticity and potential for resilience in this population of squid.

Description: This material was based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374 to CZ. This project was funded by National Science Foundation Grant No. 1220034 to TAM.

Description: 2020-04-19

Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(25), (2019):12343-12352, doi:10.1073/pnas.1901080116.

Description: Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.

Description: We thank Dr. David Nes (Texas Tech University) for providing sterols and Dr. Matthieu Legendre and Dr. Chantal Abergel (CNRS, Marseille) for access to the P. celtis sequences. Drs. Irina Arkhipova, Mark Hahn, Judith Luborsky, and Ann Bucklin commented on the manuscript. The research was supported by a USA-UK Fulbright Scholarship and a Royal Society grant (to D.C.L.), the Boston University Superfund Research Program [NIH Grant 5P42ES007381 (to J.J.S. and J.V.G.) and NIH Grant 5U41HG003345 (to J.V.G.)], the European Regional Development Fund and Welsh Government Project BEACON (S.L.K.), the Woods Hole Center for Oceans and Human Health [NIH Grant P01ES021923 and National Science Foundation Grant OCE-1314642 (to J.J.S.)], and NIH Grant R01GM53753 (to T.L.P.).

Description: 2019-12-05

Description: Author Posting. © The Authors, 2019. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 218(3), (2019): 2165-2178, doi: 10.1093/gji/ggz280.

Description: A multitaper estimator is proposed that accommodates time-series containing gaps without using any form of interpolation. In contrast with prior missing-data multitaper estimators that force standard Slepian sequences to be zero at gaps, the proposed missing-data Slepian sequences are defined only where data are present. The missing-data Slepian sequences are frequency independent, as are the eigenvalues that define the energy concentration within the resolution bandwidth, when the process bandwidth is [−1/2,1/2) for unit sampling and the sampling scheme comprises integer multiples of unity. As a consequence, one need only compute the ensuing missing-data Slepian sequences for a given sampling scheme once, and then the spectrum at an arbitrary set of frequencies can be computed using them. It is also shown that the resulting missing-data multitaper estimator can incorporate all of the optimality features (i.e. adaptive-weighting, F-test and reshaping) of the standard multitaper estimator, and can be applied to bivariate or multivariate situations in similar ways. Performance of the missing-data multitaper estimator is illustrated using length of day, seafloor pressure and Nile River low stand time-series.

Description: The length of day utilized in Section 3 are available from http://hpiers.obspm.fr. The pressure data used in Section 4 are available from https://doi.org/10.1029/2018JC014586. A Matlab function MDmwps.m to compute missing-data power spectra is available from the Mathworks file exchange website. The author thanks Jeff Park and editor F.J. Simons for thorough reviews. This work was supported by an Internal Research and Development award at WHOI, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, L. K., Alexander, H., & Brown, C. T. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience, 8(4), (2019): giy158, doi: 10.1093/gigascience/giy158.

Description: Background: De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines,” on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. Results: New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. Conclusions: Given current bioinformatics approaches, there is no single “best” reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.

Description: Funding was provided by the Gordon and Betty Moore Foundation under award number GBMF4551 to C.T.B. Jetstream cloud platform was used with XSEDE allocation TG-BIO160028 [66, 67].

Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17187-17192, doi:10.1073/pnas.1903067116.

Description: Mesoscale eddies are critical components of the ocean’s “internal weather” system. Mixing and stirring by eddies exerts significant control on biogeochemical fluxes in the open ocean, and eddies may trap distinctive plankton communities that remain coherent for months and can be transported hundreds to thousands of kilometers. Debate regarding how and why predators use fronts and eddies, for example as a migratory cue, enhanced forage opportunities, or preferred thermal habitat, has been ongoing since the 1950s. The influence of eddies on the behavior of large pelagic fishes, however, remains largely unexplored. Here, we reconstruct movements of a pelagic predator, the blue shark (Prionace glauca), in the Gulf Stream region using electronic tags, earth-observing satellites, and data-assimilating ocean forecasting models. Based on 〉2,000 tracking days and nearly 500,000 high-resolution time series measurements collected by 15 instrumented individuals, we show that blue sharks seek out the interiors of anticyclonic eddies where they dive deep while foraging. Our observations counter the existing paradigm that anticyclonic eddies are unproductive ocean “deserts” and suggest anomalously warm temperatures in these features connect surface-oriented predators to the most abundant fish community on the planet in the mesopelagic. These results also shed light on the ecosystem services provided by mesopelagic prey. Careful consideration will be needed before biomass extraction from the ocean twilight zone to avoid interrupting a key link between planktonic production and top predators. Moreover, robust associations between targeted fish species and oceanographic features increase the prospects for effective dynamic ocean management.

Description: We thank D. McGillicuddy, G. Lawson, and G. Flierl for helpful discussions while developing this work and 2 anonymous reviewers whose feedback significantly improved the manuscript. We also thank C. Fischer and the OCEARCH team for their support of this research. This work was funded by awards to C.D.B. from the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology; the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution; and the National Aeronatics and Space Administration (NASA) Earth and Space Science Fellowship. C.D.B. and P.G. acknowledge support from the NASA New Investigator Program Award 80NSSC18K0757, and P.G. acknowledges support from NSF Award OCE-1558809. This research is partially supported by funding to S.R.T. as part of the Audacious Project, a collaborative endeavor, housed at TED. We thank donors to the Woods Hole Oceanographic Institution (WHOI) ProjectWHOI crowdfunding campaign: The Secret Lives of Sharks. Computational support was provided by the Amazon Web Services Cloud Credits for Research program. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.

Description: 2020-02-06

Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17207-17212, doi:10.1073/pnas.1900325116.

Description: It has been hypothesized that the overall size of—or efficiency of carbon export from—the biosphere decreased at the end of the Great Oxidation Event (GOE) (ca. 2,400 to 2,050 Ma). However, the timing, tempo, and trigger for this decrease remain poorly constrained. Here we test this hypothesis by studying the isotope geochemistry of sulfate minerals from the Belcher Group, in subarctic Canada. Using insights from sulfur and barium isotope measurements, combined with radiometric ages from bracketing strata, we infer that the sulfate minerals studied here record ambient sulfate in the immediate aftermath of the GOE (ca. 2,018 Ma). These sulfate minerals captured negative triple-oxygen isotope anomalies as low as ∼ −0.8‰. Such negative values occurring shortly after the GOE require a rapid reduction in primary productivity of 〉80%, although even larger reductions are plausible. Given that these data imply a collapse in primary productivity rather than export efficiency, the trigger for this shift in the Earth system must reflect a change in the availability of nutrients, such as phosphorus. Cumulatively, these data highlight that Earth’s GOE is a tale of feast and famine: A geologically unprecedented reduction in the size of the biosphere occurred across the end-GOE transition.

Description: Olivia M. J. Dagnaud assisted during fieldwork. S. V. Lalonde and E. A. Sperling provided helpful comments on an early version of the manuscript. We thank N. J. Planavsky and an anonymous reviewer for their constructive feedback. M.S.W.H. was supported by an NSERC PGS-D and student research grants from National Geographic, the APS Lewis and Clark Fund, Northern Science Training Program, McGill University Graduate Research Enhancement and Travel Awards, Geological Society of America, Mineralogical Association of Canada, and Stanford University. P.W.C. acknowledges support from the University of Colorado Boulder, the Agouron Institute Geobiology postdoctoral Fellowship program, a Natural Sciences and Engineering Council of Canada Postgraduate Scholarship–Doctoral Program scholarship, and the NSTP. Y.P. was supported by the Strategic Priority Research Program of CAS (XDB26000000). T.J.H. thanks Maureen E. Auro for laboratory assistance and the NSF for supporting isotope research in the NIRVANA Labs.

Description: 2020-02-12

Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(45), (2019): 22518-22525, doi:10.1073/pnas.1913714116.

Description: The Ganges–Brahmaputra (G-B) River system transports over a billion tons of sediment every year from the Himalayan Mountains to the Bay of Bengal and has built the world’s largest active sedimentary deposit, the Bengal Fan. High sedimentation rates drive exceptional organic matter preservation that represents a long-term sink for atmospheric CO2. While much attention has been paid to organic-rich fine sediments, coarse sediments have generally been overlooked as a locus of organic carbon (OC) burial. However, International Ocean Discovery Program Expedition 354 recently discovered abundant woody debris (millimeter- to centimeter-sized fragments) preserved within the coarse sediment layers of turbidite beds recovered from 6 marine drill sites along a transect across the Bengal Fan (∼8°N, ∼3,700-m water depth) with recovery spanning 19 My. Analysis of bulk wood and lignin finds mostly lowland origins of wood delivered episodically. In the last 5 My, export included C4 plants, implying that coarse woody, lowland export continued after C4 grassland expansion, albeit in reduced amounts. Substantial export of coarse woody debris in the last 1 My included one wood-rich deposit (∼0.05 Ma) that encompassed coniferous wood transported from the headwaters. In coarse layers, we found on average 0.16 weight % OC, which is half the typical biospheric OC content of sediments exported by the modern G-B Rivers. Wood burial estimates are hampered by poor drilling recovery of sands. However, high-magnitude, low-frequency wood export events are shown to be a key mechanism for C burial in turbidites.

Description: This work was funded by National Science Foundation Grants OCE-1401217 and COL-T354A55 to S.J.F. and OCE-1400805 to V.G. Graduate student participation in the project received support from University of Southern California Provost’s Fellowship to H.L. Samples were provided by the International Ocean Discovery Program. We are grateful for the efforts of the Expedition 354 Science Party, Carl Johnson, and Zongguang Liu. C.F.-L. and A.G. were supported by IODP-France. We thank Colin Osborne and Maria Vorontsova for helpful discussions.

Description: 2020-04-21

Description: The Arctic region is considered to be most sensitive to climate change, with warming in the Arctic occurring considerably faster than the global average due to several positive feedback mechanisms contributing to the “Arctic amplification”. Also the maritime and mountainous climate of Svalbard has undergone changes during the last decades. Here, the focus is set on the current atmospheric boundary conditions for the marine ecosystem in the Kongsfjorden area, discussed in the frame of long-term climatic observations in the larger regional and hemispheric context. During the last century, a general warming is found with temperature increases and precipitation changes varying in strength. During the last decades, a strong seasonality of the warming is observed in the Kongsfjorden area, with the strongest temperature increase occurring during the winter season. The winter warming is related to observed changes in the net longwave radiation. Moreover, changes in the net shortwave are observed during the summer period, attributed to the decrease in reflected radiation caused by the retreating snow cover. Another related aspect of radiation is the intensity of solar ultra-violet radiation that is closely coupled to the abundance of ozone in the column of air overhead. The long term evolution of ozone losses in the Arctic and their connection to climate change are discussed.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17666-17672. doi:10.1073/pnas.1907871116.

Description: The conditions of methane (CH4) formation in olivine-hosted secondary fluid inclusions and their prevalence in peridotite and gabbroic rocks from a wide range of geological settings were assessed using confocal Raman spectroscopy, optical and scanning electron microscopy, electron microprobe analysis, and thermodynamic modeling. Detailed examination of 160 samples from ultraslow- to fast-spreading midocean ridges, subduction zones, and ophiolites revealed that hydrogen (H2) and CH4 formation linked to serpentinization within olivine-hosted secondary fluid inclusions is a widespread process. Fluid inclusion contents are dominated by serpentine, brucite, and magnetite, as well as CH4(g) and H2(g) in varying proportions, consistent with serpentinization under strongly reducing, closed-system conditions. Thermodynamic constraints indicate that aqueous fluids entering the upper mantle or lower oceanic crust are trapped in olivine as secondary fluid inclusions at temperatures higher than ∼400 °C. When temperatures decrease below ∼340 °C, serpentinization of olivine lining the walls of the fluid inclusions leads to a near-quantitative consumption of trapped liquid H2O. The generation of molecular H2 through precipitation of Fe(III)-rich daughter minerals results in conditions that are conducive to the reduction of inorganic carbon and the formation of CH4. Once formed, CH4(g) and H2(g) can be stored over geological timescales until extracted by dissolution or fracturing of the olivine host. Fluid inclusions represent a widespread and significant source of abiotic CH4 and H2 in submarine and subaerial vent systems on Earth, and possibly elsewhere in the solar system.

Description: We are indebted to J. Eckert for his support with FE-EMPA; to K. Aquinho and E. Codillo for providing samples from Zambales; to K. Aquinho for Raman analysis of some of the samples from Zambales and Mt. Dent; to H. Dick for providing access to his thin section collection; to the curators of the IODP core repositories for providing access to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) samples; and to the captains and crews of the many cruises without whom the collection of these samples would not have been possible. Reviews by Peter Kelemen and an anonymous referee greatly improved this manuscript. This study is supported with funds provided by the National Science Foundation (NSF-OCE Award 1634032 to F.K. and J.S.S.).

Description: 2020-02-19

Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(20), (2019):9925-9930, doi:10.1073/pnas.1818349116.

Description: Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (〉30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.

Description: We thank John Baross and Rika Anderson for helpful discussions and feedback on this project. We also thank the chief scientists of the research cruise, Al Devol and Bess Ward, as well as the captain and crew of the R/V Thomas G. Thompson. This work was supported through a NASA Earth and Space Sciences Graduate Research Fellowship to J.K.S. and National Science Foundation Grant OCE-1138368 (to G.R.).

Description: 2019-10-29

Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (24), (2019):11646-11651, doi:10.1073/pnas.1900371116.

Description: Measurements show large decadal variability in the rate of CO2 accumulation in the atmosphere that is not driven by CO2 emissions. The decade of the 1990s experienced enhanced carbon accumulation in the atmosphere relative to emissions, while in the 2000s, the atmospheric growth rate slowed, even though emissions grew rapidly. These variations are driven by natural sources and sinks of CO2 due to the ocean and the terrestrial biosphere. In this study, we compare three independent methods for estimating oceanic CO2 uptake and find that the ocean carbon sink could be responsible for up to 40% of the observed decadal variability in atmospheric CO2 accumulation. Data-based estimates of the ocean carbon sink from pCO2 mapping methods and decadal ocean inverse models generally agree on the magnitude and sign of decadal variability in the ocean CO2 sink at both global and regional scales. Simulations with ocean biogeochemical models confirm that climate variability drove the observed decadal trends in ocean CO2 uptake, but also demonstrate that the sensitivity of ocean CO2 uptake to climate variability may be too weak in models. Furthermore, all estimates point toward coherent decadal variability in the oceanic and terrestrial CO2 sinks, and this variability is not well-matched by current global vegetation models. Reconciling these differences will help to constrain the sensitivity of oceanic and terrestrial CO2 uptake to climate variability and lead to improved climate projections and decadal climate predictions.

Description: We thank Rebecca Wright and Erik Buitenhuis at University of East Anglia, Norwich, for providing updated runs from the NEMO-PlankTOM5 model. T.D. was supported by NSF Grant OCE-1658392. C.L.Q. thanks the UK Natural Environment Research Council for supporting the SONATA Project (Grant NE/P021417/1). P.L. was supported by the Max Planck Society for the Advancement of Science. J.H. was supported under Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys) Grant VH-NG-1301. S.B. and R.S. were supported by the H2020 project CRESCENDO “Coordinated Research in Earth Systems and Climate: Experiments, Knowledge, Dissemination and Outreach,” which received funding from the European Union’s Horizon 2020 research and innovation program under Grant No 641816. SOCAT is an international effort, endorsed by the International Ocean Carbon Coordination Project, the Surface Ocean-Lower Atmosphere Study, and the Integrated Marine Biosphere Research program, to deliver a uniformly quality-controlled surface ocean CO2 database. The many researchers and funding agencies responsible for the collection of data and quality control are thanked for their contributions to SOCAT.

Description: 2019-11-28

Description: The paper presents the results of 5 case studies on complex site e ects selected within the project for the level 3 seismic microzonation of several municipalities of Central Italy dam- aged by the 2016 seismic sequence. The case studies are characterized by di erent geo- logical and morphological con gurations: Monte San Martino is located along a hill slope, Montedinove and Arquata del Tronto villages are located at ridge top whereas Capitignano and Norcia lie in correspondence of sediment- lled valleys. Peculiarities of the sites are constituted by the presence of weathered/jointed rock mass, fault zone, shear wave veloc- ity inversion, complex surface and buried morphologies. These factors make the de ni- tion of the subsoil model and the evaluation of the local response particularly complex and di cult to ascertain. For each site, after the discussion of the subsoil model, the results of site response numerical analyses are presented in terms of ampli cation factors and acceleration response spectra in selected points. The physical phenomena governing the site response have also been investigated at each site by comparing 1D and 2D numerical analyses. Implications are deduced for seismic microzonation studies in similar geological and morphological conditions.

Description: Published

Description: 5741–5777

Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica

Description: JCR Journal

Description: This paper describes the seismological analyses performed within the framework of the seismic microzonation study for the reconstruction of 138 municipalities damaged by the 2016–2017 sequence in Central Italy. Many waveforms were recorded over approximately 15 years at approximately 180 instrumented sites equipped with permanent or temporary stations in an area that includes all the damaged localities. Site response was assessed using earthquake and noise recordings at the selected stations through different parameters, such as spectral amplification curves, fundamental resonance frequencies, site-specific response spectra, and average amplification factors. The present study was a collaboration of many different institutions under the coordination of the Italian Center for Seismic Microzonation and its applications. The results were homogenized and gathered into site-specific forms, which represent the main deliverable for the benefit of Italian Civil Protection. It is remarkable that the bulk of this study was performed in a very short period (approximately 2 months) to provide quantitative information for detailed microzonation and future reconstruction of the damaged municipalities.

Description: Published

Description: 5553–5593

Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica

Description: JCR Journal

Description: Pore water geochemistry and bulk sediment measurements of downcore profiles covering the upper 100 m-long sequence from site 1A, Lake Towuti, Indonesia

Description: Bacteria are surrounded by a protective exoskeleton, peptidoglycan (PG), a cross-linked mesh-like macromolecule consisting of glycan strands interlinked by short peptides. Because PG completely encases the cytoplasmic membrane, cleavage of peptide cross-links is a prerequisite to make space for incorporation of nascent glycan strands for its successful expansion during cell growth. In most bacteria, the peptides consist of l-alanine, d-glutamate, meso-diaminopimelic acid (mDAP) and d-alanine (d-Ala) with cross-links occurring either between d-Ala and mDAP or two mDAP residues. In Escherichia coli, the d-Ala−mDAP cross-links whose cleavage by specialized endopeptidases is crucial for expansion of PG predominate. However, a small proportion of mDAP−mDAP cross-links also exist, yet their role in the context of PG expansion or the hydrolase(s) capable of catalyzing their cleavage is not known. Here, we identified an ORF of unknown function, YcbK (renamed MepK), as an mDAP−mDAP cross-link cleaving endopeptidase working in conjunction with other elongation-specific endopeptidases to make space for efficient incorporation of nascent PG strands into the sacculus. E. coli mutants lacking mepK and another d-Ala−mDAP–specific endopeptidase (mepS) were synthetic sick, and the defects were abrogated by lack of l,d-transpeptidases, enzymes catalyzing the formation of mDAP cross-links. Purified MepK was able to cleave the mDAP cross-links of soluble muropeptides and of intact PG sacculi. Overall, this study describes a PG hydrolytic enzyme with a hitherto unknown substrate specificity that contributes to expansion of the PG sacculus, emphasizing the fundamental importance of cross-link cleavage in bacterial peptidoglycan synthesis.

Description: As monofacial, single-junction solar cells approach their fundamental limits, there has been significant interest in tandem solar cells in the presence of concentrated sunlight or tandem bifacial solar cells with back-reflected albedo. The bandgap sequence and thermodynamic efficiency limits of these complex cell configurations require sophisticated numerical calculation. Therefore, the analyses of specialized cases are scattered throughout the literature. In this paper, we show that a powerful graphical approach called the normalized “Shockley–Queisser (S-Q) triangle” (i.e., imp=1−vmp) is sufficient to calculate the bandgap sequence and efficiency limits of arbitrarily complex photovoltaic (PV) topologies. The results are validated against a wide variety of specialized cases reported in the literature and are accurate within a few percent. We anticipate that the widespread use of the S-Q triangle will illuminate the deeper physical principles and design trade-offs involved in the design of bifacial tandem solar cells under arbitrary concentration and series resistance.

Description: Previous studies have shown that insulin and IGF-1 signaling in the brain, especially the hypothalamus, is important for regulation of systemic metabolism. Here, we develop mice in which we have specifically inactivated both insulin receptors (IRs) and IGF-1 receptors (IGF1Rs) in the hippocampus (Hippo-DKO) or central amygdala (CeA-DKO) by stereotaxic delivery of AAV-Cre into IRlox/lox/IGF1Rlox/loxmice. Consequently, both Hippo-DKO and CeA-DKO mice have decreased levels of the GluA1 subunit of glutamate AMPA receptor and display increased anxiety-like behavior, impaired cognition, and metabolic abnormalities, including glucose intolerance. Hippo-DKO mice also display abnormal spatial learning and memory whereas CeA-DKO mice have impaired cold-induced thermogenesis. Thus, insulin/IGF-1 signaling has common roles in the hippocampus and central amygdala, affecting synaptic function, systemic glucose homeostasis, behavior, and cognition. In addition, in the hippocampus, insulin/IGF-1 signaling is important for spatial learning and memory whereas insulin/IGF-1 signaling in the central amygdala controls thermogenesis via regulation of neural circuits innervating interscapular brown adipose tissue.

Description: The sunflower family, Asteraceae, comprises 10% of all flowering plant species and displays an incredible diversity of form. Asteraceae are clearly monophyletic, yet resolving phylogenetic relationships within the family has proven difficult, hindering our ability to understand its origin and diversification. Recent molecular clock dating has suggested a Cretaceous origin, but the lack of deep sampling of many genes and representative taxa from across the family has impeded the resolution of migration routes and diversifications that led to its global distribution and tremendous diversity. Here we use genomic data from 256 terminals to estimate evolutionary relationships, timing of diversification(s), and biogeographic patterns. Our study places the origin of Asteraceae at ∼83 MYA in the late Cretaceous and reveals that the family underwent a series of explosive radiations during the Eocene which were accompanied by accelerations in diversification rates. The lineages that gave rise to nearly 95% of extant species originated and began diversifying during the middle Eocene, coincident with the ensuing marked cooling during this period. Phylogenetic and biogeographic analyses support a South American origin of the family with subsequent dispersals into North America and then to Asia and Africa, later followed by multiple worldwide dispersals in many directions. The rapid mid-Eocene diversification is aligned with the biogeographic range shift to Africa where many of the modern-day tribes appear to have originated. Our robust phylogeny provides a framework for future studies aimed at understanding the role of the macroevolutionary patterns and processes that generated the enormous species diversity of Asteraceae.

Description: There is a gap between how many scientists communicate and how most people understand and interpret messages. This article argues that the extensive science communications literature needs to be joined by the health literacy literature and anthropological work on cultural variations in hearing and understanding messages. Rapid changes and differences in how people in the United States get information are also discussed. Better understanding of how people get and perceive messages, and how access to information and to health services affects their behavior, should be an iterative and interdisciplinary effort. Community involvement in developing communication strategies is strongly encouraged.

Description: Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.

Description: Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the Tetrahymena doublet microtubule by cryoelectron microscopy. The map demonstrates that the network of microtubule inner proteins weaves into the tubulin lattice and forms an inner sheath. From mass spectrometry data and de novo modeling, we identified Rib43a proteins as the filamentous microtubule inner proteins in the protofilament ribbon region. The Rib43a–tubulin interaction leads to an elongated tubulin dimer distance every 2 dimers. In addition, the tubulin lattice structure with missing microtubule inner proteins (MIPs) by sarkosyl treatment shows significant longitudinal compaction and lateral angle change between protofilaments. These results are evidence that the MIPs directly affect and stabilize the tubulin lattice. It suggests that the doublet microtubule is an intrinsically stressed filament and that this stress could be manipulated in the regulation of ciliary waveforms.

Description: Aberrant MYC oncogene activation is one of the most prevalent characteristics of cancer. By overlapping datasets of Drosophila genes that are insulin-responsive and also regulate nucleolus size, we enriched for Myc target genes required for cellular biosynthesis. Among these, we identified the aminoacyl tRNA synthetases (aaRSs) as essential mediators of Myc growth control in Drosophila and found that their pharmacologic inhibition is sufficient to kill MYC-overexpressing human cells, indicating that aaRS inhibitors might be used to selectively target MYC-driven cancers. We suggest a general principle in which oncogenic increases in cellular biosynthesis sensitize cells to disruption of protein homeostasis.

Description: Organic electrosynthesis can transform the chemical industry by introducing electricity-driven processes that are more energy efficient and that can be easily integrated with renewable energy sources. However, their deployment is severely hindered by the difficulties of controlling selectivity and achieving a large energy conversion efficiency at high current density due to the low solubility of organic reactants in practical electrolytes. This control can be improved by carefully balancing the mass transport processes and electrocatalytic reaction rates at the electrode diffusion layer through pulsed electrochemical methods. In this study, we explore these methods in the context of the electrosynthesis of adiponitrile (ADN), the largest organic electrochemical process in industry. Systematically exploring voltage pulses in the timescale between 5 and 150 ms led to a 20% increase in production of ADN and a 250% increase in relative selectivity with respect to the state-of-the-art constant voltage process. Moreover, combining this systematic experimental investigation with artificial intelligence (AI) tools allowed us to rapidly discover drastically improved electrosynthetic conditions, reaching improvements of 30 and 325% in ADN production rates and selectivity, respectively. This powerful AI-enhanced experimental approach represents a paradigm shift in the design of electrified chemical transformations, which can accelerate the deployment of more sustainable electrochemical manufacturing processes.

Description: In most environments, the visual system is confronted with many relevant objects simultaneously. That is especially true during reading. However, behavioral data demonstrate that a serial bottleneck prevents recognition of more than one word at a time. We used fMRI to investigate how parallel spatial channels of visual processing converge into a serial bottleneck for word recognition. Participants viewed pairs of words presented simultaneously. We found that retinotopic cortex processed the two words in parallel spatial channels, one in each contralateral hemisphere. Responses were higher for attended than for ignored words but were not reduced when attention was divided. We then analyzed two word-selective regions along the occipitotemporal sulcus (OTS) of both hemispheres (subregions of the visual word form area, VWFA). Unlike retinotopic regions, each word-selective region responded to words on both sides of fixation. Nonetheless, a single region in the left hemisphere (posterior OTS) contained spatial channels for both hemifields that were independently modulated by selective attention. Thus, the left posterior VWFA supports parallel processing of multiple words. In contrast, activity in a more anterior word-selective region in the left hemisphere (mid OTS) was consistent with a single channel, showing (i) limited spatial selectivity, (ii) no effect of spatial attention on mean response amplitudes, and (iii) sensitivity to lexical properties of only one attended word. Therefore, the visual system can process two words in parallel up to a late stage in the ventral stream. The transition to a single channel is consistent with the observed bottleneck in behavior.

Description: Genomic analyses of patients with congenital heart disease (CHD) have identified significant contribution from mutations affecting cilia genes and chromatin remodeling genes; however, the mechanism(s) connecting chromatin remodeling to CHD is unknown. Histone H2B monoubiquitination (H2Bub1) is catalyzed by the RNF20 complex consisting of RNF20, RNF40, and UBE2B. Here, we show significant enrichment of loss-of-function mutations affecting H2Bub1 in CHD patients (enrichment 6.01,P= 1.67 × 10−03), some of whom had abnormal laterality associated with ciliary dysfunction. InXenopus, knockdown ofrnf20andrnf40results in abnormal heart looping, defective development of left–right (LR) asymmetry, and impaired cilia motility. Rnf20, Rnf40, and Ube2b affect LR patterning and cilia synergistically. Examination of global H2Bub1 level inXenopusembryos shows that H2Bub1 is developmentally regulated and requires Rnf20. To examine gene-specific H2Bub1, we performed ChIP-seq of mouse ciliated and nonciliated tissues and showed tissue-specific H2Bub1 marks significantly enriched at cilia genes including the transcription factorRfx3. Rnf20 knockdown results in decreased levels ofrfx3mRNA inXenopus, and exogenousrfx3can rescue the Rnf20 depletion phenotype. These data suggest that Rnf20 functions at theRfx3locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.

Description: Plasticity theory aims at describing the yield loci and work hardening of a material under general deformation states. Most of its complexity arises from the nontrivial dependence of the yield loci on the complete strain history of a material and its microstructure. This motivated 3 ingenious simplifications that underpinned a century of developments in this field: 1) yield criteria describing yield loci location; 2) associative or nonassociative flow rules defining the direction of plastic flow; and 3) effective stress–strain laws consistent with the plastic work equivalence principle. However, 2 key complications arise from these simplifications. First, finding equations that describe these 3 assumptions for materials with complex microstructures is not trivial. Second, yield surface evolution needs to be traced iteratively, i.e., through a return mapping algorithm. Here, we show that these assumptions are not needed in the context of sequence learning when using recurrent neural networks, diverting the above-mentioned complications. This work offers an alternative to currently established plasticity formulations by providing the foundations for finding history- and microstructure-dependent constitutive models through deep learning.

Description: Two-dimensional monolayer materials, with thicknesses of up to several atoms, can be obtained from almost every layer-structured material. It is believed that the catalogs of known 2D materials are almost complete, with fewer new graphene-like materials being discovered. Here, we report 2D graphene-like monolayers from monoxides such as BeO, MgO, CaO, SrO, BaO, and rock-salt structured monochlorides such as LiCl, and NaCl using first-principle calculations. Two-dimensional materials containing d-orbital atoms such as HfO, CdO, and AgCl are predicted. Adopting the same strategy, 2D graphene-like monolayers from mononitrides such as scandium nitride (ScN) and monoselenides such as cadmium selenide (CdSe) are discovered. Stress engineering is found to help stabilize 2D monolayers, through canceling the imaginary frequency of phonon dispersion relation. These 2D monolayers show high dynamic, thermal, kinetic, and mechanic stabilities due to atomic hybridization, and electronic delocalization.

Description: Materials that can be switched between low and high thermal conductivity states would advance the control and conversion of thermal energy. Employing in situ time-domain thermoreflectance (TDTR) and in situ synchrotron X-ray scattering, we report a reversible, light-responsive azobenzene polymer that switches between high (0.35 W m−1K−1) and low thermal conductivity (0.10 W m−1K−1) states. This threefold change in the thermal conductivity is achieved by modulation of chain alignment resulted from the conformational transition between planar (trans) and nonplanar (cis) azobenzene groups under UV and green light illumination. This conformational transition leads to changes in the π-π stacking geometry and drives the crystal-to-liquid transition, which is fully reversible and occurs on a time scale of tens of seconds at room temperature. This result demonstrates an effective control of the thermophysical properties of polymers by modulating interchain π-π networks by light.

Description: The Hippo pathway is involved in regulating contact inhibition of proliferation and organ size control and responds to various physical and biochemical stimuli. It is a kinase cascade that negatively regulates the activity of cotranscription factors YAP and TAZ, which interact with DNA binding transcription factors including TEAD and activate the expression of target genes. In this study, we show that the palmitoylation of TEAD, which controls the activity and stability of TEAD proteins, is actively regulated by cell density independent of Lats, the key kinase of the Hippo pathway. The expression of fatty acid synthase and acetyl-CoA carboxylase involved in de novo biosynthesis of palmitate is reduced by cell density in an Nf2/Merlin-dependent manner. Depalmitoylation of TEAD is mediated by depalmitoylases including APT2 and ABHD17A. Palmitoylation-deficient TEAD4 mutant is unstable and degraded by proteasome through the activity of the E3 ubiquitin ligase CHIP. These findings show that TEAD activity is tightly controlled through the regulation of palmitoylation and stability via the orchestration of FASN, depalmitoylases, and E3 ubiquitin ligase in response to cell contact.

Description: Foraging is a goal-directed behavior that balances the need to explore the environment for resources with the need to exploit those resources. InDrosophila melanogaster, distinct phenotypes have been observed in relation to theforaginggene (for), labeled the rover and sitter. Adult rovers explore their environs more extensively than do adult sitters. We explored whether this distinction would be conserved in humans. We made use of a distinction from regulatory mode theory between those who “get on with it,” so-called locomotors, and those who prefer to ensure they “do the right thing,” so-called assessors. In this logic, rovers and locomotors share similarities in goal pursuit, as do sitters and assessors. We showed that genetic variation inPRKG1, the human ortholog offor, is associated with preferential adoption of a specific regulatory mode. Next, participants performed a foraging task to see whether genetic differences associated with distinct regulatory modes would be associated with distinct goal pursuit patterns. Assessors tended to hug the boundary of the foraging environment, much like behaviors seen inDrosophilaadult sitters. In a patchy foraging environment, assessors adopted more cautious search strategies maximizing exploitation. These results show that distinct patterns of goal pursuit are associated with particular genotypes ofPRKG1, the human ortholog offor.

Description: Mutational signatures can reveal properties of underlying mutational processes and are important when assessing signals of selection in cancer. Here, we describe the sequence characteristics of mutations induced by ultraviolet (UV) light, a major mutagen in several human cancers, in terms of extended (longer than trinucleotide) patterns as well as variability of the signature across chromatin states. Promoter regions display a distinct UV signature with reduced TCG 〉 TTG transitions, and genome-wide mapping of UVB-induced DNA photoproducts (pyrimidine dimers) showed that this may be explained by decreased damage formation at hypomethylated promoter CpG sites. Further, an extended signature model encompassing additional information from longer contextual patterns improves modeling of UV mutations, which may enhance discrimination between drivers and passenger events. Our study presents a refined picture of the UV signature and underscores that the characteristics of a single mutational process may vary across the genome.

Description: Drugs that reverse epigenetic silencing, such as the DNA methyltransferase inhibitor (DNMTi) 5-azacytidine (AZA), have profound effects on transcription and tumor cell survival. AZA is an approved drug for myelodysplastic syndromes and acute myeloid leukemia, and is under investigation for different solid malignant tumors. AZA treatment generates self, double-stranded RNA (dsRNA), transcribed from hypomethylated repetitive elements. Self dsRNA accumulation in DNMTi-treated cells leads to type I IFN production and IFN-stimulated gene expression. Here we report that cell death in response to AZA treatment occurs through the 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway. OASs are IFN-induced enzymes that synthesize the RNase L activator 2-5A in response to dsRNA. Cells deficient in RNase L or OAS1 to 3 are highly resistant to AZA, as are wild-type cells treated with a small-molecule inhibitor of RNase L. A small-molecule inhibitor of c-Jun NH2-terminal kinases (JNKs) also antagonizes RNase L-dependent cell death in response to AZA, consistent with a role for JNK in RNase L-induced apoptosis. In contrast, the rates of AZA-induced and RNase L-dependent cell death were increased by transfection of 2-5A, by deficiencies in ADAR1 (which edits and destabilizes dsRNA), PDE12 or AKAP7 (which degrade 2-5A), or by ionizing radiation (which induces IFN-dependent signaling). Finally, OAS1 expression correlates with AZA sensitivity in the NCI-60 set of tumor cell lines, suggesting that the level of OAS1 can be a biomarker for predicting AZA sensitivity of tumor cells. These studies may eventually lead to pharmacologic strategies for regulating the antitumor activity and toxicity of AZA and related drugs.

Description: Analyses of thermal diffusivity data on complex insulators and on strongly correlated electron systems hosted in similar complex crystal structures suggest that quantum chaos is a good description for thermalization processes in these systems, particularly in the high-temperature regime where the many phonon bands and their interactions dominate the thermal transport. Here we observe that for these systems diffusive thermal transport is controlled by a universal Planckian timescale τ∼ℏ/kBT and a unique velocity vE. Specifically, vE≈vph for complex insulators, and vph≲vE≪vF in the presence of strongly correlated itinerant electrons (vph and vF are the phonon and electron velocities, respectively). For the complex correlated electron systems we further show that charge diffusivity, while also reaching the Planckian relaxation bound, is largely dominated by the Fermi velocity of the electrons, hence suggesting that it is only the thermal (energy) diffusivity that describes chaos diffusivity.

Description: SalmonellaTyphimurium can invade and survive within macrophages where the bacterium encounters a range of host environmental conditions. Like many bacteria,S.Typhimurium rapidly responds to changing environments by the use of second messengers such as cyclic di-GMP (c-di-GMP). Here, we generate a fluorescent biosensor to measure c-di-GMP concentrations in thousands of individual bacteria during macrophage infection and to define the sensor enzymes important to c-di-GMP regulation. Three sensor phosphodiesterases were identified as critical to maintaining low c-di-GMP concentrations generated after initial phagocytosis by macrophages. Maintenance of low c-di-GMP concentrations by these phosphodiesterases was required to promote survival within macrophages and virulence for mice. Attenuation ofS. Typhimurium virulence was due to overproduction of c-di-GMP−regulated cellulose, as deletion of the cellulose synthase machinery restored virulence to a strain lacking enzymatic activity of the three phosphodiesterases. We further identified that the cellulose-mediated reduction in survival was constrained to a slow-replicating persister population ofS.Typhimurium induced within the macrophage intracellular environment. As utilization of glucose has been shown to be required forS.Typhimurium macrophage survival, one possible hypothesis is that this persister population requires the glucose redirected to the synthesis of cellulose to maintain a slow-replicating, metabolically active state.