bluuebunny/crossref_metadata_2025 huggingface dataset:
ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data
Authors: Taggart Allison J , Fairbrother William G
Published: July 2018

Background

Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post‐splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read that traverses the lariat branchpoint. This method provides precise branchpoint sequence and position information, but is limited in its ability to quantify abundance of stabilized lariat species in a given RNAseq sample. Bioinformatic tools are needed to better address these emerging biological questions.

Methods

We used an unsupervised machine learning approach on sequencing reads from publicly available ENCODE data to learn to identify and quantify lariats based on RNAseq read coverage shape.

Results

We developed ShapeShifter, a novel approach for identifying and quantifying stable lariat species in RNAseq datasets. We learned a characteristic “lariat” curve from ENCODE RNAseq data and were able to estimate abundances for introns based on read coverage. Using this method we discovered new stable introns in these samples that were not represented using the older, branchpoint‐traversing read method.

Conclusions

ShapeShifter provides a robust approach towards detecting and quantifying stable lariat species.
Acute Spinal Epidural Hematoma as a Complication of Dry Needling: A Case Report
Authors: Berrigan William A. , Whitehair Curtis L. , Zorowitz Richard D.
Published: July 2018

Dry needling is a procedure commonly performed for the relief of myofascial pain disorders. The procedure is generally well tolerated. Adverse events often are mild, but severe complications have been reported. This case report describes an acute spinal epidural hematoma as a complication of dry needling. It is a reminder to the performing physician or therapist to take specific precautions when placing a needle near the spine. Sudden onset of neuropathic pain after needling therapy in and around the spine should prompt emergency assessment with possibly advanced spine imaging to evaluate the integrity of the spinal cord.

Level of Evidence

V
Predictors of Individual Resilience Characteristics Among Individuals Ages 65 and Older in Post-Disaster Settings
Authors: Liddell Jessica , Ferreira Regardt J.
Published: July 2018

Objective

Literature explores which factors most impact resilience and how these factors impact an individual and communities’ ability to cope with disaster. Less research has focused on how age impacts resilience. This research adapts several previous conceptual models used to investigate resilience. To investigate the unique vulnerabilities faced by older individuals in post-disaster settings, this analysis was undertaken to investigate predictors of individual resilience.

Methods

Data for the study were derived from the Centers for Disease Control and Prevention (CDC) Gulf States Population Survey (GSPS). The final sample included 5,713 adult residents from 4 gulf-coast states. Multiple linear regression was used for the analysis.

Results

All models (demographic, health, social, and combined) acted as significant predictors of individual resilience. Health and social resilience models accounted for more of the variance in resilience scores. In all models, age was negatively associated with resilience scores. Being female was protective across all models. The results of the model testing indicate inequitable disaster mitigation, with social and health indicators explaining the most variance in the resilience levels.

Conclusion

This research provides practitioners with the knowledge they need to focus their interventions on the areas where it is most needed to empower resilient individuals. (Disaster Med Public Health Preparedness. 2019;13:256–264)
REAL WORLD PROBLEMS
Authors: Paul L. A. , Quiggin John
Published: July 2018

In the real world, there can be constraints on rational decision-making: there can be limitations on what I can know and on what you can know. There can also be constraints on my ability to deliberate or on your ability to deliberate. It is useful to know what the norms of rational deliberation should be in ideal contexts, for fully informed agents, in an ideal world. But it is also useful to know what the norms of rational deliberation should be in the actual world, in non-ideal contexts, for imperfectly informed agents, especially for big, life-changing decisions. That is, we want to know how to deliberate as best we can, given the real-world limitations on what we can know, and given real-world limitations on how we are able to deliberate. In this paper, our concern is with the norms of rational deliberation in certain, important, non-ideal contexts, where the reasoning occurs from the agent's first person, subjective point of view. The norms governing the process of deliberation for real people in the sorts of non-ideal contexts we'll consider need to reflect the way that real agents, with an incomplete grasp on the facts and an imperfect ability to deliberate, can be expected to proceed. Our central contention is that framing and exploring the deliberative process from the first person perspective allows us to uncover and explore important, real-world constraints on boundedly rational agents deliberating from the subjective perspective.
Richard White, The Republic for Which It Stands: The United States during Reconstruction and the Gilded Age, 1865–1896
Authors: Sklansky Jeffrey
Published: July 2018

The sprawling volumes in the long-running Oxford History of the United States series are intended to serve as comprehensive surveys for a general audience, a task at which Richard White's nearly thousand-page chronicle of the postbellum decades admirably succeeds. But the main interest of such syntheses for historians lies in their reconsideration of the master narratives that organize divergent developments at multiple levels into a cohesive account of American society as a whole in a pivotal period, constructing a framework for past scholarship and a platform for future work. The author's previous field-shaping studies of Native American history, Western history, environmental history, and business history make him well-suited to offer an overarching understanding of an era of climactic upheavals in all of these realms: the age of the last Indian wars and the extensive development of the Great Plains, the slaughter of the buffalo and the industrialization of agriculture, unprecedented class warfare, and the ascendance of big business, along with the meteoric career of Reconstruction and the violent restoration of white supremacy in the New South.
Impact of number of episodes on neurocognitive trajectory in bipolar disorder patients: a 5-year follow-up study
Authors: Sánchez-Morla Eva María , López-Villarreal Ana , Jiménez-López Estela , Aparicio Ana Isabel , Martínez-Vizcaíno Vicente , Roberto Rodriguez-Jimenez , Vieta Eduard , Santos José-Luis
Published: July 2018

Background

The neurocognitive trajectory in bipolar disorder (BD) is variable, with controversial findings, and most evidence come from cross-sectional studies. We aimed to examine the course of neurocognitive functioning in a sample of euthymic BD patients in comparison with a control group during a 5-year follow-up.

Methods

Ninety-nine euthymic bipolar patients and 40 healthy controls were assessed using a comprehensive neurocognitive battery (six neurocognitive domains) at baseline (T1) and then at 5-year follow-up (T2) in a longitudinal study.

Results

No evidence of a progression in neurocognitive dysfunction was found either in cognitive composite index or in any of the neurocognitive domains for the whole cohort. However, there was a negative correlation between number of manic episodes and hospitalisations due to manic episodes and change in neurocognitive composite index (NCI) during the follow-up. Moreover, patients with higher number of manic and hypomanic episodes have a greater decrease in NCI, working memory and visual memory. History of psychotic symptoms was not related to the trajectory of neurocognitive impairment.

Conclusions

Our results suggest that, although the progression of cognitive decline is not a general rule in BD, BD patients who have a greater number of manic or hypomanic episodes may constitute a subgroup characterised by the progression of neurocognitive impairment. Prevention of manic and hypomanic episodes could have a positive impact on the trajectory of cognitive function.
Twenty Years of Double-Star Interferometry and its Lessons
Authors: Finsen W. S.
Published: July 2018

If we may judge by the number of eulogistic review articles to which it gave rise, one of the main talking points among astronomers in the early nineteen-twenties was undoubtedly the application of the interferometer to optical astronomy. It was only natural that interest was focused mainly on the brilliant success of Michelson and Pease (1921} in measuring stellar diameters with the 20-ft beam interferometer on the 100-in Mount Wilson reflector.
Photometrie des Étoiles Doubles
Authors: Muller P.
Published: July 2018

Du point de vue de la photometrie, on peut distinguer tres schematiquement trois sortes d'etoiles doubles:

(1) les couples optiques

(2) les couples physiques sans orbite connue

(3) les couples orbitaux.
Photometric Observations of Visual Double Stars by the Area Scanning Technique
Authors: Franz Otto G.
Published: July 2018

UBV magnitude differences in visual binaries are presented and their accuracy is discussed. Typical observed image profiles of double stars, including sample profiles of Antares, are shown. This contribution will appear jointly with the earlier one (p. 20) in Lowell Obs. Bull., No. 154. The work has been supported by NSF Grant GP-6983.
Intéret de La Caméra Électronique Lallemand Pour La Photométrie des Binaires Visuelles
Authors: Laques P.
Published: July 2018

J'ai montré ultérieurement les résultats des mesures astrométriques d'étoiles doubles, obtenus au moyen de la caméra électronique. Mais il est certain que Ton doit utiliser, en meme temps, les propriétés intrinseques de ce recepteur pour les mesures photométriques des binaires, complément nécessaire des mesures astrométriques.
Plasma beam structure diagnostics in krypton Hall thruster
Authors: Szelecka Agnieszka , Jakubczak Maciej , Kurzyna Jacek
Published: July 2018

Krypton Large Impulse Thruster (KLIMT) project was aimed at incremental development and optimization of a 0.5 kW-class plasma Hall Effect Thruster in which, as a propellant, krypton could be used. The final thermally stable version of the thruster (the third one) was tested in the Plasma Propulsion Satellites (PlaNS) laboratory in the Institute of Plasma Physics and Laser Microfusion (IPPLM) in Warsaw as well as in the European Space Agency (ESA) propulsion laboratory in the European Space Research and Technology Centre (ESTEC).

During final measurement campaign, a wide spectrum of parameters was tested. The plasma potential, electron temperature, electron concentration, and electron energy probability function in the far-field plume of the thruster were measured with a single cylindrical Langmuir probe. Faraday probes were used for recording local values of ion current. Using several collectors in different locations and moving them on the surface of a sphere, the angular distribution of the expelled particles was reconstructed which was a local measure of beam divergence. Angular distribution of ion flux as measured with a central Faraday probe was parameterized with krypton mass flow rate, voltage, coil current ratio, and the cathode mass flow rate. Beam divergence measurements with Faraday probes as well as plasma parameters derived from Langmuir probe seem to be consistent with our understanding of the operating envelope. Obtained results will serve as a baseline in the design of plasma beam structure diagnostics system for the PlaNS laboratory.
Improving Galileo's Carrier-Phase Time Transfer Based on Prior Constraint Information
Authors: Zhang Pengfei , Tu Rui , Gao Yuping , Liu Na , Zhang Rui
Published: July 2018

The Carrier-Phase (CP) technique used in the Global Positioning System (GPS) has proved to be a useful spatial tool for remote precise time transfer. Galileo is a Global Navigation Satellite System like GPS. However, currently, given the low number of satellites at any one observation epoch, Galileo's accuracy and continuity of time transfer leave much to be desired. To achieve better performance of time transfer for Galileo, this study has developed a new approach for Galileo CP time transfer, using prior constraint information such as precise coordinates and troposphere zenith delay constraints. The new approach was applied for precise time transfer in real-time mode and post-processed mode for short baseline and long baseline observations. For the short baseline time link in real-time mode, compared with the standard Galileo CP, the standard deviation improved by 51·4% for the troposphere zenith delay constraint, 47·6% for the station coordinates constraint, and 49·5% when considering both constraints simultaneously. At a 10,000 s time interval, in comparison to the standard CP, the three constraint approaches show stable results as well as improvements of nearly an order of magnitude. In post-processed mode, the constraint approach for Galileo time transfer showed little improvement compared to the standard CP technique for both the short baseline and long baseline time links.
The decline of guilds and their monopoly in English provincial towns, with particular reference to Exeter
Authors: YONEYAMA MASARU
Published: July 2018

This article examines the decline of the craft guilds in early modern England by way of a case-study of the Tuckers’ Company in Exeter. From the 1980s, this case figured prominently in the historiographical debate concerning guild decline; however, it has not been examined recently. The current study reveals the Tuckers’ Company is not a case of decline in guild membership so much as a case of the loss of guild monopoly and a concomitant transition to charitable functions. On the basis of empirical sources, this study also reveals the mechanisms and context of this transformation in the post-Civil War politics of the city of Exeter. Specific attention is given to first, the decline of royal authority bolstering the guild against the city government and secondly, the shift of power in the guild with the ascendance of the merchant fullers. Finally, the historiographical implications of the article's findings are discussed.
Racial Segregation and Southern Lynching
Authors: Cook Lisa D. , Logan Trevon D. , Parman John M.
Published: July 2018

The literature on ethnic fractionalization and conflict has yet to be extended to the American past. In particular, the empirical relationship between racial residential segregation and lynching is unknown. The existing economic, social, and political theories of lynching contain implicit hypotheses about the relationship between racial segregation and racial violence, consistent with more general theories of social conflict. Because Southern lynching occurred in rural and urban areas, traditional urban measures of racial segregation cannot be used to estimate the relationship. Earlier analysis has analyzed the relationship between lynching and racial proportions, a poor proxy for racial segregation. We use a newly developed household-level measure of residential segregation (Logan and Parman 2017) that can distinguish between the effects of increasing racial homogeneity of a location and the tendency to segregate within a location given a particular racial composition to estimate the correlation between racial segregation and lynching in the southern counties of the United States. We find that conditional on racial composition, racially segregated counties were much more likely to experience lynchings. Consistent with the hypothesis that segregation is related to interracial violence, we find that segregation is highly correlated with African American lynching but uncorrelated with white lynching. These results extend the analysis of racial/ethnic conflict into the past and show that the effects of social interactions and interracial proximity in rural areas are as important as those in urban areas.
Modernes Management von Hypophysenadenomen – gegenwärtiger Stand in Diagnostik, Therapie und Nachsorge
Authors: Maldaner Nicolai , Serra Carlo , Tschopp Oliver , Schmid Christoph , Bozinov Oliver , Regli Luca
Published: July 2018

Zusammenfassung. Hypophysenadenome (HA) sind gutartige Tumoren aus parenchymatösen Zellen des Hypopysenvorderlappens. Es wird zwischen endokrin-inaktiven HA und hormonsezernierenden HA differenziert. Die Symptomkonstellation ist abhängig von der hormonellen Über- oder Unterfunktion und dem durch das HA erzeugten Masseneffekt. Neben Kopfschmerzen präsentieren sich HA häufig mit Visusstörungen sowie Gesichtsfeldausfällen als Folge der Kompression des Chiasma opticum. Die chirurgische Resektion über einen transsphenoidalen Zugang ist die bevorzugte Therapieoption für symptomatische oder grössenprogrediente HA. Moderne Techniken wie intraoperative hochauflösende MR-Bildgebung unterstützen den Chirurgen in der maximal sicheren Resektion. Eine Sonderrolle spielen symptomatische Prolaktinome, die in erster Linie medikamentös mit Dopaminagonisten therapiert werden sollten. Aufgrund der Komplexität der Erkrankung ist eine interdisziplinäre Betreuung der Patienten durch Neurochirurgen und Endokrinologen in einem Zentrum mit hohen Fallzahlen empfohlen.
Simulating the Impacts of Irrigation and Dynamic Vegetation Over the North China Plain on Regional Climate
Authors: Wu Liyang , Feng Jinming , Miao Wenhui
Published: July 2018

A dynamic irrigation scheme that considers groundwater processes and dynamic vegetation was constructed and incorporated into Noah land surface model with multiparameterization options coupled with the weather research and forecasting model. Multiple experiments (with and without irrigation) were designed to simulate the impacts of irrigation over the North China Plain (NCP) on regional climate. The simulated irrigation rate of the NCP was close to observations, and its interannual variations were clearly associated with dry or wet years. The groundwater table affected by irrigation varied in the NCP irrigated areas during simulation period but declined overall. The irrigation‐induced increases in green vegetation fraction led to increases in transpiration, indicating that the influences of irrigation on latent heat flux should contain the changes of transpiration besides changes of soil evaporation. The modified surface energy budget caused by irrigation affected surface air temperature (SAT), and the spring and summer SAT in the areas with larger irrigation rate decreased significantly by 0.8–1.6 and 1.2–2.6 °C, respectively. The experiment that considered irrigation showed obvious improvement in simulating several key variables (gross primary productivity, green vegetation fraction, sensible heat flux, and summer SAT). In the NCP, irrigation increased water vapor and caused cooling in boundary layer, which had opposing influences on precipitation, resulting in heterogeneous changes in summer precipitation. The changes of precipitation in nonirrigated areas were related to the influences of irrigation on wind fields. The contribution of direct effects of irrigation to blended influences of irrigation and dynamic vegetation on spring (summer) SAT was 70.9% (63.8%).
Skill of Subseasonal Forecasts in Europe: Effect of Bias Correction and Downscaling Using Surface Observations
Authors: Monhart S. , Spirig C. , Bhend J. , Bogner K. , Schär C. , Liniger M. A.
Published: July 2018

Subseasonal predictions bridge the gap between medium‐range weather forecasts and seasonal climate predictions. This time horizon is of crucial importance for many planning purposes, including energy production and agriculture. The verification of such predictions is normally done for areal averages of upper‐air parameters. Only few studies exist that verify the forecasts for surface parameters with observational stations, although this is crucial for real‐world applications, which often require such predictions at specific surface locations. With this study we provide an extensive station‐based verification of subseasonal forecasts against 1,637 ground based observational time series across Europe. Twenty years of temperature and precipitation reforecasts of the European Centre for Medium‐Range Weather Forecasts Integrated Forecasting System are used to analyze the period of April 1995 to March 2014. A lead time and seasonally dependent bias correction is performed to correct the daily temperature and precipitation forecasts at all stations individually. Two bias correction techniques are compared, a mean debiasing method and a quantile mapping approach. Commonly used skill scores characterizing different aspects of forecast quality are computed for weekly aggregated forecasts with lead times of 5–32 days. Overall, promising skill is found for temperature in all seasons except spring. Temperature forecasts tend to show higher skill in Northern Europe and in particular around the Baltic Sea, and in winter. Bias correction is shown to be essential in enhancing the forecast skill in all four weeks for most of the stations and for both variables with QM generally performing better.
A Kinetic Difference Between 12C‐ and 13C‐Bound Oxygen Exchange Rates Results in Decoupled δ18O and Δ47 Values of Equilibrating DIC Solutions
Authors: Staudigel Philip T. , Swart Peter K.
Published: July 2018

Accurate determination of paleotemperatures using carbonate δ18O and Δ47 values rely upon the assumption that the minerals in question formed close to expected isotopic equilibrium with their environment. If there is insufficient time for dissolved carbonate to equilibrate with water between the production of DIC and mineralization, the mineral may preserve a disequilibrated isotopic state. The equilibrium composition and rate of DIC equilibration are related to the temperature, pH, and salinity of the solution, and these have been quantified in previous studies which investigated this via the quantitative precipitation all dissolved carbonate species (∑DIC) as barium carbonate (BaCO3). Here we present a study wherein the equilibration over time of clumped isotopes (Δ47) is investigated at 5, 15, and 25 °C. Results show a significant non–first‐order behavior for this process, which can be explained with a kinetic isotope effect wherein oxygen bound to 12C will exchange more rapidly than oxygen bound to 13C. This difference in equilibration rates is minor, less than 2%; however, it results in Δ47 values paradoxically becoming initially less equilibrated during initial equilibration. The magnitude and direction of this effect is expected to vary depending on the direction from which δ18O values equilibrate, even in circumstances where the initial and final Δ47 values are identical. The implication of this finding is that carbonates which form rapidly can have decoupled δ18O and Δ47 values. This study presents a mathematical framework wherein this behavior can be described accurately to provide a predictive model for describing equilibrating aqueous systems.
Changes in Extreme Rainfall Over India and China Attributed to Regional Aerosol‐Cloud Interaction During the Late 20th Century Rapid Industrialization
Authors: Lin Lei , Xu Yangyang , Wang Zhili , Diao Chenrui , Dong Wenjie , Xie Shang‐Ping
Published: July 2018

Both mean and extreme rainfall decreased over India and Northern China during 1979–2005 at a rate of 0.2%/decade. The aerosol dampening effects on rainfall has also been suggested as a main driver of mean rainfall shift in India and China. Conflicting views, however, exist on whether aerosols enhance or suppress hazardous extreme heavy rainfall. Using Coupled Model Intercomparison Project phase 5 (CMIP5) multimodel ensemble, here we show that only a subset of models realistically reproduces the late‐20th‐century trend of extreme rainfall for the three major regions in Asia: drying in India and Northern China and wetting in Southern China, all consistent with mean rainfall change. As a common feature, this subset of models includes an explicit treatment of the complex physical processes of aerosol‐cloud interaction (i.e., both cloud‐albedo and cloud‐lifetime effects), while simulation performance deteriorates in models that include only aerosol direct effect or cloud‐albedo effect. The enhanced aerosol pollution during this rapid industrialization era is the leading cause of the spatially heterogeneous extreme rainfall change by dimming surface solar radiation, cooling adjacent ocean water, and weakening moisture transport into the continental region, while GHG warming or natural variability alone cannot explain the observed changes. Our results indicate that the projected intensification of regional extreme rainfall during the early‐to‐mid 21st‐century, in response to the anticipated aerosol reduction, may be underestimated in global climate models without detailed treatment of complex aerosol‐cloud interaction.
The Clustering of Severe Dust Storm Occurrence in China From 1958 to 2007
Authors: Guo Li , Fan Bihang , Zhang Fuqing , Jin Zhao , Lin Henry
Published: July 2018

China is subjected to severe dust storms that deteriorate air quality and cause substantial damages to environment and socioeconomics. Although the annual frequency of severe dust storms in China has been declining since the 1950s, the variability of severe dust storm occurrence in time and space remains inadequately described under the changing climate. Based on the continuous observation at 368 meteorological observation sites across the mainland China over a 50‐year period (1958 to 2007), we found that the temporal clustering of severe dust storm outbreak has intensified after 1985, which exacerbated the irregularity in the monthly distribution of severe dust storms. Moreover, the timing of the clustering has shown a higher interannual variation after 1985. Therefore, the variability of severe dust storm occurrence has increased significantly since the 1980s at the annual and monthly time scales. In addition, the relative probability of experiencing severe dust storms with a large influential range has risen since the 1980s. Spatially, severe dust storm outbreak has receded from spreading across the country in the 1950s to primarily affecting north and northwest China in the 2000s. These findings suggest a relatively higher risk of dust storm disaster in north and northwest China that is associated with the intensified clustering of severe dust storm activity in both time and space. Continuous studies are needed to identify the favorable synoptic system that stimulates the clustering of severe dust storm outbreak. We advocate more efforts to enhance severe dust storm prediction and warning dissemination in north and northwest China.
September 2017's Geoeffective Space Weather and Impacts to Caribbean Radio Communications During Hurricane Response
Authors: Redmon R. J. , Seaton D. B. , Steenburgh R. , He J. , Rodriguez J. V.
Published: July 2018

Between 4 and 10 September 2017, multiple solar eruptions occurred from active region AR12673. NOAA's and NASA's well‐instrumented spacecraft observed the evolution of these geoeffective events from their solar origins, through the interplanetary medium, to their geospace impacts. The 6 September X9.3 flare was the largest to date for the nearly concluded solar cycle 24 and, in fact, the brightest recorded since an X17 flare in September 2005, which occurred during the declining phase of solar cycle 23. Rapid ionization of the sunlit upper atmosphere occurred, disrupting high‐frequency communications in the Caribbean region while emergency managers were scrambling to provide critical recovery services caused by the region's devastating hurricanes. The 10 September west limb eruption resulted in the first solar energetic particle event since 2012 with sufficient flux and energy to yield a ground level enhancement. Spacecraft at L1, including DSCOVR, sampled the associated interplanetary coronal mass ejections minutes before their collision with Earth's magnetosphere. Strong compression and erosion of the dayside magnetosphere occurred, placing geosynchronous satellites in the magnetosheath. Subsequent geomagnetic storms produced magnificent auroral displays and elevated hazards to power systems. Through the lens of NOAA's space weather R‐S‐G storm scales, this event period increased hazards for systems susceptible to elevated “radio blackout” (R3‐strong), “solar radiation storm” (S3‐strong), and “geomagnetic storm” (G4‐severe) conditions. The purpose of this paper is to provide an overview of the September 2017 space weather event, and a summary of its consequences, including forecaster, post‐event analyst, and communication operator perspectives.
Pathogen population structure can explain hospital outbreaks
Authors: Spagnolo Fabrizio , Cristofari Pierre , Tatonetti Nicholas P , Ginzburg Lev R , Dykhuizen Daniel E
Published: July 2018

Hospitalized patients are at risk for increased length of stay, illness, or death due to hospital acquired infections. The majority of hospital transmission models describe dynamics on the level of the host rather than on the level of the pathogens themselves. Accordingly, epidemiologists often cannot complete transmission chains without direct evidence of either host–host contact or a large reservoir population. Here, we propose an ecology-based model to explain the transmission of pathogens in hospitals. The model is based upon metapopulation biology, which describes a group of interacting localized populations and island biogeography, which provides a basis for how pathogens may be moving between locales. Computational simulation trials are used to assess the applicability of the model. Results indicate that pathogens survive for extended periods without the need for large reservoirs by living in localized ephemeral populations while continuously transmitting pathogens to new seed populations. Computational simulations show small populations spending significant portions of time at sizes too small to be detected by most surveillance protocols and that the number and type of these ephemeral populations enable the overall pathogen population to be sustained. By modeling hospital pathogens as a metapopulation, many observations characteristic of hospital acquired infection outbreaks for which there has previously been no sufficient biological explanation, including how and why empirically successful interventions work, can now be accounted for using population dynamic hypotheses. Epidemiological links between temporally isolated outbreaks are explained via pathogen population dynamics and potential outbreak intervention targets are identified.
Spin-induced multiferroicity in the binary perovskite manganite Mn2O3
Authors: Cong Junzhuang , Zhai Kun , Chai Yisheng , Shang Dashan , Khalyavin Dmitry D. , Johnson Roger D. , Kozlenko Denis P. , Kichanov Sergey E. , Abakumov Artem M. , Tsirlin Alexander A. , Dubrovinsky Leonid , Xu Xueli , Sheng Zhigao , Ovsyannikov Sergey V. , Sun Young
Published: July 2018

The ABO3 perovskite oxides exhibit a wide range of interesting physical phenomena remaining in the focus of extensive scientific investigations and various industrial applications. In order to form a perovskite structure, the cations occupying the A and B positions in the lattice, as a rule, should be different. Nevertheless, the unique binary perovskite manganite Mn2O3 containing the same element in both A and B positions can be synthesized under high-pressure high-temperature conditions. Here, we show that this material exhibits magnetically driven ferroelectricity and a pronounced magnetoelectric effect at low temperatures. Neutron powder diffraction revealed two intricate antiferromagnetic structures below 100 K, driven by a strong interplay between spin, charge, and orbital degrees of freedom. The peculiar multiferroicity in the Mn2O3 perovskite is ascribed to a combined effect involving several mechanisms. Our work demonstrates the potential of binary perovskite oxides for creating materials with highly promising electric and magnetic properties.
Optomechanical time-domain reflectometry
Authors: Bashan Gil , Diamandi Hilel Hagai , London Yosef , Preter Eyal , Zadok Avi
Published: July 2018

Optical fibres constitute an exceptional sensing platform. However, standard fibres present an inherent sensing challenge: they confine light to an inner core. Consequently, distributed fibre sensors are restricted to the measurement of conditions that prevail within the core. This work presents distributed analysis of media outside unmodified, standard fibre. Measurements are based on stimulated scattering by guided acoustic modes, which allow us to listen where we cannot look. The protocol overcomes a major difficulty: guided acoustic waves induce forward scattering, which cannot be mapped using time-of-flight. The solution relies on mapping the Rayleigh backscatter contributions of two optical tones, which are coupled by the acoustic wave. Analysis is demonstrated over 3 km of fibre with 100 m resolution. Measurements distinguish between air, ethanol and water outside the cladding, and between air and water outside polyimide-coated fibres. The results establish a new sensor configuration: optomechanical time-domain reflectometry, with several potential applications.
Biodiversity across trophic levels drives multifunctionality in highly diverse forests
Authors: Schuldt Andreas , Assmann Thorsten , Brezzi Matteo , Buscot François , Eichenberg David , Gutknecht Jessica , Härdtle Werner , He Jin-Sheng , Klein Alexandra-Maria , Kühn Peter , Liu Xiaojuan , Ma Keping , Niklaus Pascal A. , Pietsch Katherina A. , Purahong Witoon , Scherer-Lorenzen Michael , Schmid Bernhard , Scholten Thomas , Staab Michael , Tang Zhiyao , Trogisch Stefan , von Oheimb Goddert , Wirth Christian , Wubet Tesfaye , Zhu Chao-Dong , Bruelheide Helge
Published: July 2018

Human-induced biodiversity change impairs ecosystem functions crucial to human well-being. However, the consequences of this change for ecosystem multifunctionality are poorly understood beyond effects of plant species loss, particularly in regions with high biodiversity across trophic levels. Here we adopt a multitrophic perspective to analyze how biodiversity affects multifunctionality in biodiverse subtropical forests. We consider 22 independent measurements of nine ecosystem functions central to energy and nutrient flow across trophic levels. We find that individual functions and multifunctionality are more strongly affected by the diversity of heterotrophs promoting decomposition and nutrient cycling, and by plant functional-trait diversity and composition, than by tree species richness. Moreover, cascading effects of higher trophic-level diversity on functions originating from lower trophic-level processes highlight that multitrophic biodiversity is key to understanding drivers of multifunctionality. A broader perspective on biodiversity-multifunctionality relationships is crucial for sustainable ecosystem management in light of non-random species loss and intensified biotic disturbances under future environmental change.
Facile transformation of imine covalent organic frameworks into ultrastable crystalline porous aromatic frameworks
Authors: Li Xinle , Zhang Changlin , Cai Songliang , Lei Xiaohe , Altoe Virginia , Hong Fang , Urban Jeffrey J. , Ciston Jim , Chan Emory M. , Liu Yi
Published: July 2018

The growing interest in two-dimensional imine-based covalent organic frameworks (COFs) is inspired by their crystalline porous structures and the potential for extensive π-electron delocalization. The intrinsic reversibility and strong polarization of imine linkages, however, leads to insufficient chemical stability and optoelectronic properties. Developing COFs with improved robustness and π-delocalization is highly desirable but remains an unsettled challenge. Here we report a facile strategy that transforms imine-linked COFs into ultrastable porous aromatic frameworks by kinetically fixing the reversible imine linkage via an aza-Diels-Alder cycloaddition reaction. The as-formed, quinoline-linked COFs not only retain crystallinity and porosity, but also display dramatically enhanced chemical stability over their imine-based COF precursors, rendering them among the most robust COFs up-to-date that can withstand strong acidic, basic and redox environment. Owing to the chemical diversity of the cycloaddition reaction and structural tunability of COFs, the pores of COFs can be readily engineered to realize pre-designed surface functionality.
Dynamical coupling between a nuclear spin ensemble and electromechanical phonons
Authors: Okazaki Yuma , Mahboob Imran , Onomitsu Koji , Sasaki Satoshi , Nakamura Shuji , Kaneko Nobu-Hisa , Yamaguchi Hiroshi
Published: July 2018

Dynamical coupling with high-quality factor resonators is essential in a wide variety of hybrid quantum systems such as circuit quantum electrodynamics and opto/electromechanical systems. Nuclear spins in solids have a long relaxation time and thus have the potential to be implemented into quantum memories and sensors. However, state manipulation of nuclear spins requires high-magnetic fields, which is incompatible with state-of-the-art quantum hybrid systems based on superconducting microwave resonators. Here we investigate an electromechanical resonator whose electrically tunable phonon state imparts a dynamically oscillating strain field to the nuclear spin ensemble located within it. As a consequence of the dynamical strain, we observe both nuclear magnetic resonance (NMR) frequency shifts and NMR sidebands generated by the electromechanical phonons. This prototype system potentially opens up quantum state engineering for nuclear spins, such as coherent coupling between sound and nuclei, and mechanical cooling of solid-state nuclei.
Author Correction: Checkpoint blockade immunotherapy reshapes the high-dimensional phenotypic heterogeneity of murine intratumoural neoantigen-specific CD8+ T cells
Authors: Fehlings M. , Simoni Y. , Penny H. L. , Becht E. , Loh C. Y. , Gubin M. M. , Ward J. P. , Wong S. C. , Schreiber R. D. , Newell E. W.
Published: July 2018

The original version of this Article omitted a declaration from the competing interests statement, which should have included the following: ‘R.D.S. is a cofounder, stock holder, and scientific advisory board member of Jounce Therapeutics and Neon Therapeutics, and a member of the scientific advisory boards of BioLegend, Constellation, Lytix, and NGM. He also received research funding from Janssen and Agios.’. This has now been corrected in both the PDF and HTML versions of the Article.
Multi-time quantum correlations with no spatial analog
Authors: Ringbauer Martin , Costa Fabio , Goggin Michael E. , White Andrew G. , Fedrizzi Alessandro
Published: July 2018

Multipartite quantum correlations are a powerful resource that underpins applications from quantum metrology to quantum computing. While most research has focused on spatial correlations, it is now becoming clear that a sequence of measurements on a single quantum system at different points in time reveals a similarly rich, yet fundamentally different structure of multipartite temporal correlations. Here we experimentally observe genuine multi-time correlations in a sequence of three generalized measurements on a single photon. These correlations, manifest by a simultaneous violation of all pairwise Bell inequalities, cannot be reproduced by any spatial quantum state of equal dimension. Our work lays the foundation for the exploration of temporal correlations arising in quantum networks for quantum information applications.
The association between BMI and mortality using early adulthood BMI as an instrumental variable for midlife BMI
Authors: Kjøllesdal Marte K. R. , Smith George Davey , Ariansen Inger , Kinge Jonas Minet , Degerud Eirik , Næss Øyvind
Published: July 2018

The article aims to describe the association between midlife body mass index (BMI) and cardiovascular disease (CVD)- and all-cause mortality, and to use early adulthood BMI as an instrumental variable for midlife BMI, in order to obtain an estimate less distorted by midlife confounders and reverse causality. Data from Norwegian health surveys (1974–2003) (midlife BMI, smoking, blood pressure, total cholesterol, heart rate), Military Conscription Records, National Tuberculosis Screenings (early adulthood BMI), National Educational Registry and Cause of Death Registry were linked. Participants with data on BMI in early adulthood and midlife were included (n = 148.886). Hazard Ratio (HR) for CVD mortality was higher in men with midlife obesity relative to normal weight (HR = 1.46(95% CI 1.25, 1.70). For all-cause mortality, HR was higher in those with obesity or underweight in midlife relative to normal weight (Men:HR = 1.19(95% CI 1.09, 1.29), HR = 2.49(95% CI 1.81, 3.43) Women:HR = 1.33(95% CI 1.13, 1.56), HR = 1.61(95% CI 1.22, 2.13)). In instrumental variable analyses, increased BMI became more strongly associated with CVD and all-cause mortality, and the increased risk of all-cause mortality among the underweight attenuated.
Biochemical and structural characterization of a mannose binding jacalin-related lectin with two-sugar binding sites from pineapple (Ananas comosus) stem
Authors: Azarkan Mohamed , Feller Georges , Vandenameele Julie , Herman Raphaël , El Mahyaoui Rachida , Sauvage Eric , Vanden Broeck Arnaud , Matagne André , Charlier Paulette , Kerff Frédéric
Published: July 2018

A mannose binding jacalin-related lectin from Ananas comosus stem (AcmJRL) was purified and biochemically characterized. This lectin is homogeneous according to native, SDS-PAGE and N-terminal sequencing and the theoretical molecular mass was confirmed by ESI-Q-TOF-MS. AcmJRL was found homodimeric in solution by size-exclusion chromatography. Rat erythrocytes are agglutinated by AcmJRL while no agglutination activity is detected against rabbit and sheep erythrocytes. Hemagglutination activity was found more strongly inhibited by mannooligomannosides than by D-mannose. The carbohydrate-binding specificity of AcmJRL was determined in some detail by isothermal titration calorimetry. All sugars tested were found to bind with low affinity to AcmJRL, with Ka values in the mM range. In agreement with hemagglutination assays, the affinity increased from D-mannose to di-, tri- and penta-mannooligosaccharides. Moreover, the X-ray crystal structure of AcmJRL was obtained in an apo form as well as in complex with D-mannose and methyl-α-D-mannopyranoside, revealing two carbohydrate-binding sites per monomer similar to the banana lectin BanLec. The absence of a wall separating the two binding sites, the conformation of β7β8 loop and the hemagglutinating activity are reminiscent of the BanLec His84Thr mutant, which presents a strong anti-HIV activity in absence of mitogenic activity.
Author Correction: Validation of miRNA prognostic power in hepatocellular carcinoma using expression data of independent datasets
Authors: Nagy Ádám , Lánczky András , Menyhárt Otília , Győrffy Balázs
Published: July 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Randomized effectiveness Trial of the Family Check-Up versus Internet-delivered Parent Training (iComet) for Families of Children with Conduct Problems
Authors: Ghaderi Ata , Kadesjö Christina , Björnsdotter Annika , Enebrink Pia
Published: July 2018

We investigated the effectiveness of the Family Check-Up (FCU) and an Internet-based parent-training program (iComet), along with moderators and mediators of outcome. Families (N = 231) with a child with conduct problems were randomized to one of the conditions for 10 weeks of treatment. The drop-out rate was significantly higher in the iComet (39%) compared to FCU (23%). At post-treatment, both conditions resulted in significant improvement, based on parent-report, but no significant interaction between time and condition, with the exception of conduct problem subscale of the Strengths and Difficulties Questionnaire, slightly favoring the FCU. Neither child, nor teacher reports indicated any significant changes on any of the investigated variables. At 1-, and 2-years follow-up, the gains from the treatment were maintained in both conditions, with basically no significant time X condition interactions. A significantly larger proportion of children in the FCU recovered at post-treatment with regard to opposition defiant behavior, inattention, and conduct problems, compared to the iComet, but almost none of these differences remained significant at 1-, and 2-years follow-up. None of the moderators (child age, parental income or education, or pre-treatment level of motivation) or mediators (limit setting, and appropriate or harsh parenting) of outcome turned out to be significant.
Hypoxia increases neutrophil-driven matrix destruction after exposure to Mycobacterium tuberculosis
Authors: Ong Catherine W. M. , Fox Katharine , Ettorre Anna , Elkington Paul T. , Friedland Jon S.
Published: July 2018

The importance of neutrophils in the pathology of tuberculosis (TB) has been recently established. We demonstrated that TB lesions in man are hypoxic, but how neutrophils in hypoxia influence lung tissue damage is unknown. We investigated the effect of hypoxia on neutrophil-derived enzymes and tissue destruction in TB. Human neutrophils were stimulated with M. tuberculosis (M.tb) or conditioned media from M.tb-infected monocytes (CoMTB). Neutrophil matrix metalloproteinase-8/-9 and elastase secretion were analysed by luminex array and gelatin zymography, gene expression by qPCR and cell viability by flow cytometry. Matrix destruction was investigated by confocal microscopy and functional assays and neutrophil extracellular traps (NETs) by fluorescence assay. In hypoxia, neutrophil MMP-8 secretion and gene expression were up-regulated by CoMTB. MMP-9 activity and neutrophil elastase (NE) secretion were also increased in hypoxia. Hypoxia inhibited NET formation and both neutrophil apoptosis and necrosis after direct stimulation by M.tb. Hypoxia increased TB-dependent neutrophil-mediated matrix destruction of Type I collagen, gelatin and elastin, the main structural proteins of the human lung. Dimethyloxalylglycin (DMOG), which stabilizes hypoxia-inducible factor-1α, increased neutrophil MMP-8 and -9 secretion. Hypoxia in our cellular model of TB up-regulated pathways that increase neutrophil secretion of MMPs that are implicated in matrix destruction.
A Novel Compound, “FA-1” Isolated from Prunus mume, Protects Human Bronchial Epithelial Cells and Keratinocytes from Cigarette Smoke Extract-Induced Damage
Authors: Jang Andrew J. , Lee Ji-Hyeok , Yotsu-Yamashita Mari , Park Joodong , Kye Steve , Benza Raymond L. , Passineau Michael J. , Jeon You-Jin , Nyunoya Toru
Published: July 2018

Extract of the Japanese apricot (JAE) has biological properties as an antioxidant and anti-inflammatory agent. We hypothesized that JAE might exert therapeutic effects on cigarette smoke (CS)-induced DNA damage and cytotoxicity. In this study, we found that concentrated JAE protects against cigarette smoke extract (CSE)-induced cytotoxicity and DNA damage accompanied by increased levels of aldehyde dehydrogenase (ALDH)2, 3A1, and Werner’s syndrome protein (WRN) in immortalized human bronchial epithelial cells (HBEC2) and normal human epidermal keratinocytes (NHEK). Using the centrifugal partition chromatography (CPC) method, we identified an undescribed compound, 5-hydroxymethyl-2-furaldehyde bis(5-formylfurfuryl) acetal (which we named FA-1), responsible for the protective effects against CSE. This chemical structure has not been reported from a natural source to date. Protective effects of isolated FA-1 against CSE were observed in both HBEC2 and NHEK cells. The studies described herein suggest that FA-1 isolated from JAE protects against CSE-induced DNA damage and apoptosis by augmenting multiple isozymes of ALDH and DNA repair and reducing oxidative stress.