bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing Insecticide Effects in Forests: A Tree-Level Approach Using Unmanned Aerial Vehicles
Authors: Leroy Benjamin M L , Gossner Martin M , Lauer Florian P M , Petercord Ralf , Seibold Sebastian , Jaworek Jessica , Weisser Wolfgang W
Published: August 2019

Large-scale field studies on the ecological effects of aerial forest spraying often face methodological challenges, such as insufficient funding, difficult logistics, and legal obstacles. The resulting routine use of underpowered designs could lead to a systematic underestimation of insecticide effects on nontarget arthropod communities. We tested the use of an Unmanned Aerial Vehicles (UAVs) for experimental insecticide applications at tree level to increase replication in cost-efficient way. We assessed the effects of two forestry insecticides, diflubenzuron (DFB) and tebufenozide (TBF), on the oak defoliator, Thaumetopoea processionea (Linnaeus) (Lepidoptera: Thaumetopoeidae), and on nontarget, tree-living Lepidoptera. Individual trees were sprayed with either insecticide or left unsprayed, in a fully factorial design involving 60 trees. Caterpillars fallen from tree crowns were sampled as a measure of mortality, while caterpillar feeding activity was monitored by collecting frass droppings. Both DFB and TBF led to greater mortality of T. processionea and lower Lepidoptera feeding activity than control levels. TBF caused measurable mortality in nontarget groups, affecting Macrolepidoptera more strongly than Microlepidoptera, while there was no significant side effect of DFB. The high treatment efficacy against the target pest indicates that UAV technology is well-suited for the application of insecticide in forests. We detected distinct responses to different insecticides among nontarget groups and suggest there is an influence of application timing and biological traits in these differences, emphasizing the need for more ecologically orientated risk assessment. UAV-supported designs can be used to link laboratory bioassays and large-scale experiments, allowing for more comprehensive assessments of insecticide effects in forest ecosystems.
The Amendments to the Regulations of the Court
Authors: Chaitidou Eleni
Published: August 2019

This article presents and critically discusses the amendments to the Regulations of the International Criminal Court that entered into force in November 2018. The amendments concern the procedural requirements to start an investigation regarding the crime of aggression when a situation has been referred to the Court by a State Party or when the Prosecutor intends to open an investigation proprio motu. In these cases, the Prosecutor must notify the United Nations Security Council and enquire whether it intends to make a determination of an act of aggression. If the Security Council does not make such a determination, the Prosecutor must request the Pre-Trial Chamber to authorize the commencement of the investigation. The amended Regulations aim to ensure that the judges are prepared to entertain such a request relating to the crime of aggression.
Immature Ixodes scapularis (Acari: Ixodidae) Collected From Peromyscus leucopus (Rodentia: Cricetidae) and Peromyscus maniculatus (Rodentia: Cricetidae) Nests in Northern Wisconsin
Authors: Larson Ryan T , Lee Xia , Zembsch Tela , Bron Gebbiena M , Paskewitz Susan M
Published: August 2019

The blacklegged tick, Ixodes scapularis Say, is the primary Lyme disease vector in the eastern United States. Both immature stages of I. scapularis take blood meals from mice belonging to the genus Peromyscus. Mice are active during the night and spend the majority of diel periods in nests. Thus, immature I. scapularis have a greater opportunity to drop from Peromyscus hosts while in nests compared with the forest floor. Here, we collected 11 Peromyscus nests during a 3-mo period during which the immature I. scapularis are known to be active. We then examined nesting materials for the presence of I. scapularis. Immature I. scapularis were detected in 64% of Peromyscus nests examined. Additionally, 55% of the nests contained at least one Dermacentor variabilis Say larva. Eighty-seven percent of all larval ticks found within nests were blood-fed. Because Peromyscus spp. are highly competent reservoirs of numerous tick-borne pathogens, the ticks that detach in their nests may be important for the maintenance of tick-borne diseases. However, further studies are needed to determine the fate of the I. scapularis that detach in Peromyscus nests.
A Comparative Modeling Analysis of Risk-Based Lung Cancer Screening Strategies
Authors: ten Haaf Kevin , Bastani Mehrad , Cao Pianpian , Jeon Jihyoun , Toumazis Iakovos , Han Summer S , Plevritis Sylvia K , Blom Erik F , Kong Chung Yin , Tammemägi Martin C , Feuer Eric J , Meza Rafael , de Koning Harry J
Published: August 2019

Background

Risk-prediction models have been proposed to select individuals for lung cancer screening. However, their long-term effects are uncertain. This study evaluates long-term benefits and harms of risk-based screening compared with current United States Preventive Services Task Force (USPSTF) recommendations.

Methods

Four independent natural history models were used to perform a comparative modeling study evaluating long-term benefits and harms of selecting individuals for lung cancer screening through risk-prediction models. In total, 363 risk-based screening strategies varying by screening starting and stopping age, risk-prediction model used for eligibility (Bach, PLCOm2012, or Lung Cancer Death Risk Assessment Tool [LCDRAT]), and risk threshold were evaluated for a 1950 US birth cohort. Among the evaluated outcomes were percentage of individuals ever screened, screens required, lung cancer deaths averted, life-years gained, and overdiagnosis.

Results

Risk-based screening strategies requiring similar screens among individuals ages 55–80 years as the USPSTF criteria (corresponding risk thresholds: Bach = 2.8%; PLCOm2012 = 1.7%; LCDRAT = 1.7%) averted considerably more lung cancer deaths (Bach = 693; PLCOm2012 = 698; LCDRAT = 696; USPSTF = 613). However, life-years gained were only modestly higher (Bach = 8660; PLCOm2012 = 8862; LCDRAT = 8631; USPSTF = 8590), and risk-based strategies had more overdiagnosed cases (Bach = 149; PLCOm2012 = 147; LCDRAT = 150; USPSTF = 115). Sensitivity analyses suggest excluding individuals with limited life expectancies (<5 years) from screening retains the life-years gained by risk-based screening, while reducing overdiagnosis by more than 65.3%.

Conclusions

Risk-based lung cancer screening strategies prevent considerably more lung cancer deaths than current recommendations do. However, they yield modest additional life-years and increased overdiagnosis because of predominantly selecting older individuals. Efficient implementation of risk-based lung cancer screening requires careful consideration of life expectancy for determining optimal individual stopping ages.
‘Think of Him as The President’: Tabloid Trump and the Political Imaginary, 1980–1999
Authors: Baym Geoffrey
Published: August 2019

Years before Twitter, Fox News, or reality TV, Donald Trump became a public figure through his presence in tabloid media. Much of that focused on sex and spectacle, but early tabloid coverage of Trump was also surprisingly political, with speculation about a possible presidential campaign beginning as early as 1987. Although that coverage has been largely overlooked, this study reveals that tabloid media played a central role in building the foundations of Trump’s political identity. It tracks the early articulation of the Trump character and its simultaneous politicization within a media space outside the ostensibly legitimate arena of institutional public-affairs journalism. In so doing, it reveals the deeper contours of an imagined political world in which a Trump presidency could be conceivable in the first instance—a political imaginary adjacent to the deep assumptions of liberal Democracy, and therefore long invisible to most serious observers of presidential politics.
An unusual cause of bowel ischemia in an intensive care unit patient with herpes simplex virus encephalitis
Authors: Seomangal Karishma , Bashir Yasir , Boland Michael , Neary Paul
Published: August 2019

We present a case of an unexpected cause of bowel ischemia in an intensive care unit patient with herpes simplex virus encephalitis who required an operation. A 79-year-old lady was being worked up and treated for encephalitis with antibiotics and an antiviral. On Day 13, she developed abdominal pain, and an ultrasound showed cholelithiasis but no cholecystitis; thus conservative treatment was advocated. By Day 18, pain localized to the right iliac fossa, and she had an emergency laparotomy that showed bowel ischemia and perforation of the caecum with the cause being a terminal ileal adhesional band. An extended right hemicolectomy and ileostomy was performed. Patients with significant comorbidities who are intensive care unit-dependent may still have unexpected clinical challenges. We advocate an increased clinical vigilance in this cohort for unexpected life-threatening presentations such as bowel ischemia and more specifically the cause of the bowel ischemia.
Ebola virus outbreak in North Kivu and Ituri provinces, Democratic Republic of Congo, and the potential for further transmission through commercial air travel
Authors: Tuite Ashleigh R , Watts Alexander G , Khan Kamran , Bogoch Isaac I
Published: August 2019

Background

The 2018–2019 Ebola virus disease (EVD) outbreak in North Kivu and Ituri provinces, Democratic Republic of Congo (DRC), continues to spread. The recent discovery of cases in Uganda and in Goma, a major city in the eastern DRC, raises concern for potential EVD transmission in distant locales via commercial air travel.

Methods

We examined air travel patterns from the affected region with itinerary-level data from the International Air Transport Association for the year 2018 between July and October, inclusive. We focused on three scenarios: (i) travel from Beni airport, (ii) travel from Beni, Goma and Bunia airports and (iii) travel from Beni, Goma and Bunia, and Kigali airports. We evaluated country-level Infectious Disease Vulnerability Index (IDVI) scores for traveller destinations.

Results

There were 2255 commercial air passengers departing from Beni Airport during the specified time frame, all with domestic destinations, and 55% of which were to Goma. A total of 29 777 passengers travelled from Beni, Bunia and Goma airports during this time frame, with most travel (94.6%) departing from Goma Airport. A total of 72.4% of passengers’ final destination from these three airports were within the DRC, primarily to Kinshasa. There were 166 281 outbound passengers from Beni, Bunia, Goma and Kigali airports with the majority (82.1%) of passengers departing from Kigali. The most frequent destinations from these airports were Nairobi, Kinshasa and Entebbe. Eight of the 10 destinations with greatest passenger volumes are to countries with IDVI scores less than 0.4.

Conclusion

There is little commercial airline connectivity from the current EVD-affected area; however, larger cities in DRC and throughout East Africa should be aware of the low potential for EVD importation through this route. Most countries at greatest risk for EVD importation have limited capacity to manage these cases.
MOS spectroscopy of protocluster candidate galaxies at z = 6.5
Authors: Calvi R , Rodríguez Espinosa J M , Mas-Hesse J M , Chanchaiworawit K , Guzman R , Salvador-Solé E , Gallego J , Herrero A , Manrique A , Marín Franch A
Published: August 2019

The epoch corresponding to a redshift of z ∼ 6.5 is close to full re-ionization of the Universe, and early enough to provide an intriguing environment to observe the early stage of large-scale structure formation. It is also an epoch that can be used to verify the abundance of a large population of low luminosity star-forming galaxies that are deemed responsible for cosmic re-ionization. Here, we present the results of follow-up multi-object spectroscopy using OSIRIS at Gran Telescopio Canarias of 16 Ly α emitter (LAE) candidates discovered in the Subaru/XMM Newton Deep Survey. We have securely confirmed 10 LAEs with sufficient signal-to-noise ratio of the Ly α emission line. The inferred star formation rates of the confirmed LAEs are on the low side, within the range 0.9–4.7 M⊙ yr−1. However, they show relatively high Ly α rest frame equivalent widths. Finally we have shown that the mechanical energy released by the star formation episodes in these galaxies is enough to create holes in the neutral hydrogen medium such that Lyman continuum photons can escape to the intergalactic medium, thus contributing to the re-ionization of the Universe.
Reverse shocks in the relativistic outflows of gravitational wave-detected neutron star binary mergers
Authors: Lamb Gavin P , Kobayashi Shiho
Published: August 2019

The afterglows to gamma-ray bursts (GRBs) are due to synchrotron emission from shocks generated as an ultrarelativistic outflow decelerates. A forward and a reverse shock will form, however, where emission from the forward shock is well studied as a potential counterpart to gravitational wave-detected neutron star mergers the reverse shock has been neglected. Here, we show how the reverse shock contributes to the afterglow from an off-axis and structured outflow. The off-axis reverse shock will appear as a brightening feature in the rising afterglow at radio frequencies. For bursts at ∼100 Mpc, the system should be inclined ≲20° for the reverse shock to be observable at ∼0.1–10 d post-merger. For structured outflows, enhancement of the reverse shock emission by a strong magnetic field within the outflow is required for the emission to dominate the afterglow at early times. Early radio photometry of the afterglow could reveal the presence of a strong magnetic field associated with the central engine.
Deviations from normal distributions in artificial and real time series: a false positive prescription
Authors: Morris Paul J , Chakraborty Nachiketa , Cotter Garret
Published: August 2019

Time-series analysis allows for the determination of the Power Spectral Density (PSD) and Probability Density Function (PDF) for astrophysical sources. The former of these illustrates the distribution of power at various time-scales, typically taking a power-law form, while the latter characterizes the distribution of the underlying stochastic physical processes, with Gaussian and lognormal functional forms both physically motivated. In this paper, we use artificial time series generated using the prescription of Timmer & Koenig to investigate connections between the PDF and PSD. PDFs calculated for these artificial light curves are less likely to be well described by a Gaussian functional form for steep (Γ⪆1) PSD indices due to weak non-stationarity. Using the Fermi LAT monthly light curve of the blazar PKS2155-304 as an example, we prescribe and calculate a false positive rate that indicates how likely the PDF is to be attributed an incorrect functional form. Here, we generate large numbers of artificial light curves with intrinsically normally distributed PDFs and with statistical properties consistent with observations. These are used to evaluate the probabilities that either Gaussian or lognormal functional forms better describe the PDF. We use this prescription to show that PKS2155-304 requires a high prior probability of having a normally distributed PDF, $P(\rm {G})~$ ≥ 0.82, for the calculated PDF to prefer a Gaussian functional form over a lognormal. We present possible choices of prior and evaluate the probability that PKS2155-304 has a lognormally distributed PDF for each.
Radiative transfer distortions of Lyman α emitters: a new Fingers-of-God damping in the clustering in redshift space
Authors: Byrohl Chris , Saito Shun , Behrens Christoph
Published: August 2019

Complex radiative transfer (RT) of the Lyman α photons poses a theoretical challenge to galaxy surveys that infer the large-scale structure with Lyman α emitters (LAEs). Guided by RT simulations, prior studies investigated the impact of RT on the large-scale LAE clustering, and claimed that RT induces a selection effect which results in an anisotropic distortion even in real space but in an otherwise negligible effect in redshift space. However, our previous study, which relies on a full RT code run on the Illustris simulations, shows that the anisotropic selection effect was drastically reduced with higher spatial resolution. Adopting the same simulation framework, we further study the impact of RT on the LAE clustering in redshift space. Since we measure LAE’s radial position through a spectral peak of Lyman α emission, the frequency shift due to RT contaminates the redshift measurement and hence the inferred radial position in redshift space. We demonstrate that this additional RT offset suppresses the LAE clustering along the line of sight, which can be interpreted as a novel Fingers-of-God (FoG) effect. To assess the FoG effect, we develop a theoretical framework modelling the impact of the RT similar to that of the small-scale peculiar velocity which is commonly studied in the context of the redshift space distortion (RSD). Although our findings strongly encourage a more careful RSD modelling in LAE surveys, we also seek a method to mitigate the additional FoG effect due to RT by making use of other information in a Lyman α spectrum.
A young and obscured AGN embedded in the giant radio galaxy Mrk 1498
Authors: Hernández-García L , Panessa F , Bassani L , Bruni G , Ursini F , Chavushyan V , González-Martín O , Cazzoli S , Jiménez-Andrade E F , Arévalo P , Díaz Y , Bazzano A , Ubertini P
Published: August 2019

Mrk 1498 is part of a sample of galaxies with extended emission line regions (extended outwards up to a distance of ∼7 kpc) suggested to be photo-ionized by an AGN that has faded away or that is still active but heavily absorbed. Interestingly, the nucleus of Mrk 1498 is at the center of two giant radio lobes with a projected linear size of 1.1 Mpc. Our multi-wavelength analysis reveals a complex nuclear structure, with a young radio source (Giga-hertz Peaked Spectrum) surrounded by a strong X-ray nuclear absorption, a mid-infrared spectrum that is dominated by the torus emission, plus a circum-nuclear extended emission in the [OIII] image (with radius of ∼ 1 kpc), most likely related to the ionization of the AGN, aligned with the small and large scale radio jet and extended also at X-rays. In addition a large-scale extended emission (up to ∼ 10 kpc) is only visible in [OIII]. These data show conclusive evidence of a heavily absorbed nucleus and has recently restarted its nuclear activity. To explain its complexity, we propose that Mrk 1498 is the result of a merging event or secular processes, such as a minor interaction, that has triggered the nuclear activity and produced tidal streams. The large-scale extended emission that gives place to the actual morphology could either be explained by star formation or outflowing material from the AGN.
NuSTAR and XMM–Newton observations of SXP 59 during its 2017 giant outburst
Authors: Weng Shan-Shan , Ge Ming-Yu , Zhao Hai-Hui
Published: August 2019

The Be X-ray pulsar (BeXRP) SXP 59 underwent a giant outburst in 2017 with a peak X-ray luminosity of 1.1 × 1038 erg s−1. We report on the X-ray behaviour of SXP 59 with the XMM–Newton and NuSTAR observations collected at the outburst peak, decay, and the low luminosity states. The pulse profiles are energy dependent, the pulse fraction increases with the photon energy and saturates at 65 per cent above 10 keV. It is difficult to constrain the change in the geometry of emitting region with the limited data. Nevertheless, because the pulse shape generally has a double-peaked profile at high luminosity and a single peak profile at low luminosity, we prefer the scenario that the source transited from the super-critical state to the sub-critical regime. This result would further imply that the neutron star (NS) in SXP 59 has a typical magnetic field. We confirm that the soft excess revealed below 2 keV is dominated by a cool thermal component. On the other hand, the NuSTAR spectra can be described as a combination of the non-thermal component from the accretion column, a hot blackbody emission, and an iron emission line. The temperature of the hot thermal component decreases with time, while its size remains constant (R ∼ 0.6 km). The existence of the hot blackbody at high luminosity cannot be explained with the present accretion theories for BeXRPs. It means that either more sophisticated spectral models are required to describe the X-ray spectra of luminous BeXRPs, or there is non-dipole magnetic field close to the NS surface.
Helium settling in F stars: constraining turbulent mixing using observed helium glitch signature
Authors: Verma Kuldeep , Silva Aguirre Víctor
Published: August 2019

Recent developments in asteroseismology – due to space-based missions such as CoRoT and Kepler – provide handles on those properties of stars that were either completely inaccessible in the past or only poorly measured. Among several such properties is the surface helium abundance of F and G stars. We used the oscillatory signature introduced by the ionization of helium in the observed oscillation frequencies to constrain the amount of helium settling in F stars. For this purpose, we identified three promising F stars for which the standard models of atomic diffusion predict large settling (or complete depletion) of surface helium. Assuming turbulence at the base of envelope convection zone slows down settling of the helium and heavy elements, we found an envelope mixed mass of approximately 5 × 10−4 M⊙ necessary to reproduce the observed amplitude of helium signature for all the three stars. This is much larger than the mixed mass of the order of 10−6 M⊙ found in the previous studies performed using the measurements of the heavy element abundances. This demonstrates the potential of using the helium signature together with measurements of the heavy element abundances to identify the most important physical processes competing against atomic diffusion, allowing eventually to correctly interpret the observed surface abundances of hot stars, consistent use of atomic diffusion in modelling both hot and cool stars, and shed some light on the long-standing cosmological lithium problem.
Longitudinal wave instability due to rotating beam-plasma interaction in weakly turbulent astrophysical plasmas
Authors: Khorashadizadeh S M , Rostami Sh Abbasi , Niknam A R , Farahani S Vasheghani , Fallah R
Published: August 2019

The aim of this study is to highlight the temporal evolution of the longitudinal wave instability due to the interaction between a rotating electron beam and the magnetoactive plasma region in space plasma structures. The plasma structure which could be either in the solar atmosphere or any active plasma region in space is considered weakly turbulent, where the quasi-linear theory is implemented to enable analytic insight on the wave–particle interaction in the course of the event. It is found that in a weakly turbulent plasma, quasi-linear saturation of the longitudinal wave is accompanied by a significant alteration in the distribution function in the resonant region. In case of a pure electrostatic wave, the wave amplitude experiences elevation due to the energy transfer from the plasma particles. This causes flattening of the bump on tail (BOT) in the electron distribution function. If the gradient of the distribution function is positive, the chance that the beam would excite the wave is probable. In such a situation a plateau on the distribution function (∂f/∂v ≈ 0) is formed that will stop the diffusion of beam particles in the velocity space. Evolution of the electron distribution function experiences a decreases of the instability of the longitudinal wave. It is deduced that the growth rate of the wave instability is inversely proportional to the wave energy. Regarding the Sun, in addition to creating micro-turbulence due to wave–particle interaction, as the wave elevates to higher altitudes it enters a saturated energy state before releasing energy that may be a candidate for the generation of radio bursts.
N-body simulations of terrestrial planet growth with resonant dynamical friction
Authors: Wallace Spencer C , Quinn Thomas R
Published: August 2019

We investigate planetesimal accretion via a direct N-body simulation of an annulus at 1 au orbiting a 1 M$\odot$ star. The planetesimal ring, which initially contains N = 106 bodies is evolved into the oligarchic growth phase. Unlike previous lower resolution studies, we find that the mass distribution of planetesimals develops a bump at intermediate mass after the oligarchs form. This feature marks a boundary between growth modes. The smallest planetesimals are packed tightly enough together to populate mean motion resonances with the oligarchs, which heats the small bodies, enhancing their growth. If we depopulate most of the resonances by decreasing the width of the annulus, this effect becomes weaker. To clearly demonstrate the dynamics driving these growth modes, we also examine the evolution of a planetary embryo embedded in an annulus of collisionless planetesimals. In this case, we find that the resonances push planetesimals away from the embryo, decreasing the surface density of the bodies adjacent to the embryo. This effect only occurs when the annulus is wide enough and the mass resolution of the planetesimals is fine enough to populate the resonances. The bump we observe in the mass distribution resembles the 100 km power-law break seen in the size distribution of asteroid belt objects. Although the bump produced in our simulations occurs at a size larger than 100 km, we show that the bump location is sensitive to the initial planetesimal mass, which implies that this feature is potentially useful for constraining planetesimal formation models.
NUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free Methods
Authors: Roddy Aideen C , Jurek-Loughrey Anna , Souza Jose , Gilmore Alan , O’Reilly Paul G , Stupnikov Alexey , Gonzalez de Castro David , Prise Kevin M , Salto-Tellez Manuel , McArt Darragh G
Published: August 2019

Longitudinal next-generation sequencing of cancer patient samples has enhanced our understanding of the evolution and progression of various cancers. As a result, and due to our increasing knowledge of heterogeneity, such sampling is becoming increasingly common in research and clinical trial sample collections. Traditionally, the evolutionary analysis of these cohorts involves the use of an aligner followed by subsequent stringent downstream analyses. However, this can lead to large levels of information loss due to the vast mutational landscape that characterizes tumor samples.

Here, we propose an alignment-free approach for sequence comparison—a well-established approach in a range of biological applications including typical phylogenetic classification. Such methods could be used to compare information collated in raw sequence files to allow an unsupervised assessment of the evolutionary trajectory of patient genomic profiles.

In order to highlight this utility in cancer research we have applied our alignment-free approach using a previously established metric, Jensen–Shannon divergence, and a metric novel to this area, Hellinger distance, to two longitudinal cancer patient cohorts in glioma and clear cell renal cell carcinoma using our software, NUQA.

We hypothesize that this approach has the potential to reveal novel information about the heterogeneity and evolutionary trajectory of spatiotemporal tumor samples, potentially revealing early events in tumorigenesis and the origins of metastases and recurrences.

Key words: alignment-free, Hellinger distance, exome-seq, evolution, phylogenetics, longitudinal.
Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils
Authors: Patton Austin H , Margres Mark J , Stahlke Amanda R , Hendricks Sarah , Lewallen Kevin , Hamede Rodrigo K , Ruiz-Aravena Manuel , Ryder Oliver , McCallum Hamish I , Jones Menna E , Hohenlohe Paul A , Storfer Andrew
Published: August 2019

Reconstructing species’ demographic histories is a central focus of molecular ecology and evolution. Recently, an expanding suite of methods leveraging either the sequentially Markovian coalescent (SMC) or the site-frequency spectrum has been developed to reconstruct population size histories from genomic sequence data. However, few studies have investigated the robustness of these methods to genome assemblies of varying quality. In this study, we first present an improved genome assembly for the Tasmanian devil using the Chicago library method. Compared with the original reference genome, our new assembly reduces the number of scaffolds (from 35,975 to 10,010) and increases the scaffold N90 (from 0.101 to 2.164 Mb). Second, we assess the performance of four contemporary genomic methods for inferring population size history (PSMC, MSMC, SMC++, Stairway Plot), using the two devil genome assemblies as well as simulated, artificially fragmented genomes that approximate the hypothesized demographic history of Tasmanian devils. We demonstrate that each method is robust to assembly quality, producing similar estimates of Ne when simulated genomes were fragmented into up to 5,000 scaffolds. Overall, methods reliant on the SMC are most reliable between ∼300 generations before present (gbp) and 100 kgbp, whereas methods exclusively reliant on the site-frequency spectrum are most reliable between the present and 30 gbp. Our results suggest that when used in concert, genomic methods for reconstructing species’ effective population size histories 1) can be applied to nonmodel organisms without highly contiguous reference genomes, and 2) are capable of detecting independently documented effects of historical geological events.
Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved
Authors: Ntountoumi Chrysa , Vlastaridis Panayotis , Mossialos Dimitris , Stathopoulos Constantinos , Iliopoulos Ioannis , Promponas Vasilios , Oliver Stephen G , Amoutzias Grigoris D
Published: August 2019

We provide the first high-throughput analysis of the properties and functional role of Low Complexity Regions (LCRs) in more than 1500 prokaryotic and phage proteomes. We observe that, contrary to a widespread belief based on older and sparse data, LCRs actually have a significant, persistent and highly conserved presence and role in many and diverse prokaryotes. Their specific amino acid content is linked to proteins with certain molecular functions, such as the binding of RNA, DNA, metal-ions and polysaccharides. In addition, LCRs have been repeatedly identified in very ancient, and usually highly expressed proteins of the translation machinery. At last, based on the amino acid content enriched in certain categories, we have developed a neural network web server to identify LCRs and accurately predict whether they can bind nucleic acids, metal-ions or are involved in chaperone functions. An evaluation of the tool showed that it is highly accurate for eukaryotic proteins as well.
Functional analysis of Cwc24 ZF-domain in 5′ splice site selection
Authors: Wu Nan-Ying , Cheng Soo-Chen
Published: August 2019

The essential splicing factor Cwc24 contains a zinc-finger (ZF) domain required for its function in splicing. Cwc24 binds over the 5′ splice site after the spliceosome is activated, and its binding prior to Prp2-mediated spliceosome remodeling is important for proper interactions of U5 and U6 with the 5′ splice site sequence and selection of the 5′ splice site. Here, we show that Cwc24 transiently interacts with the 5′ splice site in formation of the functional RNA catalytic core during spliceosome remodeling, and the ZF-motif is required for specific interaction of Cwc24 with the 5′ splice site. Deletion of the ZF domain or mutation of the conserved ZF residues greatly weakened the association of Cwc24 with the spliceosome, and lowered the affinity and specificity of its interaction with the 5′ splice site, resulting in atypical interactions of U5, U6 and Prp8 with the 5′ splice site, and aberrant cleavage at the 5′ splice site. Our results reveal a crucial role of the Cwc24 ZF-motif for defining 5′ splice site selection in the first splicing step.
Alternative ORFs and small ORFs: shedding light on the dark proteome
Authors: Orr Mona Wu , Mao Yuanhui , Storz Gisela , Qian Shu-Bing
Published: August 2019

Traditional annotation of protein-encoding genes relied on assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it is becoming clear that these initial assumptions are incorrect. The findings have led to the realization that genetic information is more densely coded and that the proteome is more complex than previously anticipated. As such, interest in the identification and characterization of the previously ignored ‘dark proteome’ is increasing, though we note that research in eukaryotes and bacteria has largely progressed in isolation. To bridge this gap and illustrate exciting findings emerging from studies of the dark proteome, we highlight recent advances in both eukaryotic and bacterial cells. We discuss progress in the detection of alternative ORFs as well as in the understanding of functions and the regulation of their expression and posit questions for future work.
Dietary fiber and its associations with depression and inflammation
Authors: Swann Olivia G , Kilpatrick Michelle , Breslin Monique , Oddy Wendy H
Published: August 2019

Dietary fiber is a crucial component of a healthy diet, with benefits that can be attributed to processes in the gut microbiota and the resulting by-products. Observational studies support associations between dietary fiber intake and depression and inflammation, but the potential mechanisms are poorly understood. This review examines evidence of the effects of dietary fiber on depression and inflammation and considers plausible mechanisms linking dietary fiber and depression, including microbiota-driven modification of gene expression and increased production of neurotransmitters. Additionally, inflammation may mediate the relationship between dietary fiber intake and depression. A high-fiber diet potentially lowers inflammation by modifying both the pH and the permeability of the gut. The resultant reduction in inflammatory compounds may alter neurotransmitter concentrations to reduce symptoms of depression. Further research into the link between dietary fiber intake and inflammation and depression is essential, as findings could potentially provide guidance for improvement in or prevention of inflammatory and depressive disorders.
A comprehensive classification of monetary policy frameworks in advanced and emerging economies
Authors: Cobham David
Published: August 2019

The paper presents a new classification of monetary policy frameworks that it applies to advanced and emerging economies for the period since the end of the Bretton Woods international monetary system, with a focus on the monetary authorities’ objectives (domestic and external), and on pre-announced targets and actual performance. The classification (available at www.monetaryframeworks.org) also emphasizes the underlying monetary and financial infrastructure that conditions the instruments available to the authorities and, therefore, the coherence of different frameworks. It is constructed mainly from a close reading of IMF Article IV consultation reports. The two major changes revealed by the data are the trends over time towards a heavier focus on inflation, and towards more systematic and coherent monetary arrangements.
Type II Ice-Binding Proteins Isolated from an Arctic Microalga Are Similar to Adhesin-Like Proteins and Increase Freezing Tolerance in Transgenic Plants
Authors: Cho Sung Mi , Kim Sanghee , Cho Hojin , Lee Hyoungseok , Lee Jun Hyuck , Lee Horim , Park Hyun , Kang Seunghyun , Choi Han-Gu , Lee Jungeun
Published: August 2019

Microalgal ice-binding proteins (IBPs) in the polar region are poorly understood at the genome-wide level, although they are important for cold adaptation. Through the transcriptome study with the Arctic green alga Chloromonas sp. KNF0032, we identified six Chloromonas IBP genes (CmIBPs), homologous with the previously reported IBPs from Antarctic snow alga CCMP681 and Antarctic Chloromonas sp. They were organized with multiple exon/intron structures and low-temperature-responsive cis-elements in their promoters and abundantly expressed at low temperature. The biological functions of three representative CmIBPs (CmIBP1, CmIBP2 and CmIBP3) were tested using in vitro analysis and transgenic plant system. CmIBP1 had the most effective ice recrystallization inhibition (IRI) activities in both in vitro and transgenic plants, and CmIBP2 and CmIBP3 had followed. All transgenic plants grown under nonacclimated condition were freezing tolerant, and especially 35S::CmIBP1 plants were most effective. After cold acclimation, only 35S::CmIBP2 plants showed slightly increased freezing tolerance. Structurally, the CmIBPs were predicted to have β-solenoid forms with parallel β-sheets and repeated TXT motifs. The repeated TXT structure of CmIBPs appears similar to the AidA domain-containing adhesin-like proteins from methanogens. We have shown that the AidA domain has IRI activity as CmIBPs and phylogenetic analysis also supported that the AidA domains are monophyletic with ice-binding domain of CmIBPs, and these results suggest that CmIBPs are a type of modified adhesins.
The Impact of Childhood Emotional Abuse on Pain Interference Among People with Chronic Pain who Inject Drugs in Vancouver, Canada
Authors: Prangnell Amy , Shoveller Jean , Voon Pauline , Shulha Hennady , Grant Cameron , Milloy M -J , Kerr Thomas , Hayashi Kanna
Published: August 2019

Objective

High levels of chronic pain interference with daily activities are known to negatively impact quality of life. Although mental health conditions have been associated with pain interference and child abuse, research has been mixed regarding it acting as a mediator, with even less known among people who inject drugs. Therefore, we sought to explore childhood emotional abuse and pain interference among this population.

Methods

Data were derived from two prospective cohort studies of community-recruited people who inject drugs in Vancouver, Canada, between June 2014 and November 2016. We employed multivariable generalized estimating equations to examine the relationship between childhood emotional abuse and pain interference in the past six months. We also conducted a mediation analysis to examine whether mental health disorder diagnoses mediated this association.

Results

Among 822 eligible participants, 341 (41.5%) reported childhood emotional abuse. In a multivariable analysis, experiencing childhood emotional abuse remained independently associated with pain interference (adjusted odds ratio = 1.33, 95% confidence interval [CI] = 1.05–1.70) after adjusting for a range of confounders. Results from the mediation analysis yielded a statistically significant positive average causal mediation effect (β = 0.01, 95% CI = 0.001–0.02). Approximately 12% of the effect was due to mediation.

Conclusions

Our results demonstrate among people who inject drugs with chronic pain, those who experienced childhood emotional abuse were more likely to report pain interference, which was partially mediated by mental health disorder diagnosis history. These findings highlight the importance of incorporating screening and appropriate treatment for mental illness into chronic pain treatment.
Creating a Change Culture in a Police Service: The Role of Police Leadership
Authors: Dubord Neil , Griffiths Curt Taylor
Published: August 2019

Despite the increased emphasis on best practices and evidence-based policing, creating a change culture in police services has remained elusive. Few police agencies have developed the capacity to assess the effectiveness and efficiency of their operations, and there has often been a lack of innovative police leadership to lead reform efforts. This article presents a case study of a municipal police service that transformed the delivery of patrol services and, in so doing, altered the culture of the organization. The role played by an independent review of the department’s patrol division, the service delivery model that was developed, and the strategies used by senior management to secure buy-in from the membership via a department-wide collaborative process are discussed. The discussion concludes with the identification of key requirements for police leaders to create a change culture in their police services and, in so doing, improve the effectiveness and efficiency of the delivery of police services.
6-Year trends in lipids among adults in Shenzhen, China
Authors: Yuan Xueli , Ni Wenqing , Wang Rui , Chi Hongshan , Sun Yuanying , Lv Deliang , Liu Peng , Xu Jian
Published: August 2019

Background

There may be a beneficial effect on lipid levels in Shenzhen in recent years. In this study, we aimed to examine trends in serum lipids in population in Shenzhen between 2009 and 2015.

Methods

We enrolled 2210 adults aged 18–70 years from two independent cross-sectional studies conducted in 2009 and 2015. Blood lipid profiles, such as total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C), were measured. Chi-square test, t-test and multivariate logistic regression analysis were applied for data analysis.

Results

From 2009 to 2015, mean LDL-C declined from 3.05 ± 0.76 mmol/L in 2009 to 2.27 ± 0.75 mmol/L in 2015 (P < 0.001). Similarly, a significant 7.09% decrease in the prevalence of high LDL-C was observed over the same period (P < 0.001). There was an increasing trend in the prevalence of low HDL-C among adults in Shenzhen (P < 0.001). A no-significant increase in prevalence of dyslipidemia was also observed over this 6-year interval (P = 0.139). The prevalence of dyslipidemia was closely related with increasing age, male gender, current smoker, diabetes, obesity and overweight.

Conclusion

This study shows a favourable downward trend in LDL-C concentration in Shenzhen. However, more intense strategies are needed to control dyslipidemia.
What do Workplace Wellness Programs do? Evidence from the Illinois Workplace Wellness Study*
Authors: Jones Damon , Molitor David , Reif Julian
Published: August 2019

Workplace wellness programs cover over 50 million U.S. workers and are intended to reduce medical spending, increase productivity, and improve well-being. Yet limited evidence exists to support these claims. We designed and implemented a comprehensive workplace wellness program for a large employer and randomly assigned program eligibility and financial incentives at the individual level for nearly 5,000 employees. We find strong patterns of selection: during the year prior to the intervention, program participants had lower medical expenditures and healthier behaviors than nonparticipants. The program persistently increased health screening rates, but we do not find significant causal effects of treatment on total medical expenditures, other health behaviors, employee productivity, or self-reported health status after more than two years. Our 95% confidence intervals rule out 84% of previous estimates on medical spending and absenteeism.
The association between benzodiazepine use and falls, and the impact of sleep quality on this association: data from the TILDA study
Authors: Marron L , Segurado R , Kenny R A , McNicholas T
Published: August 2019

Background

Benzodiazepines (BZD) are associated with adverse effects, particularly in older adults.

Aim

This study assesses the association between BZD use and falls, and the impact of sleep quality on this association, in community dwelling adults aged over 50.

Design

Cross-sectional analysis of data from wave 1 of The Irish Longitudinal Study on Ageing.

Methods

Participants were classed as BZD users or non-users and asked if they had fallen in the last year, and whether any falls were unexplained. Sleep quality was assessed via self-reported trouble falling asleep, daytime somnolence and early-rising. Logistic regression assessed for an association between BZD use and falls, and the impact of sleep quality on this association was assessed by categorizing based on BZD use and sleep quality variables.

Results

Of 8175 individuals, 302 (3.69%) reported taking BZDs. BZD use was associated with falls, controlling for confounders [Odds Ratio (OR) 1.40; 1.08, 1.82; P-value 0.012]. There was no significant association between BZDs and unexplained falls, controlling for confounders [OR 1.41; 95% Confidence Interval (CI) 0.95, 2.10; P-value 0.09]. Participants who use BZDs and report daytime somnolence (OR 1.93; 95% CI 1.12, 3.31; P-value 0.017), early-rising (OR 1.93; 95% CI 1.20, 3.11; P-value 0.007) or trouble falling asleep (OR 1.83; 95% CI 1.12, 2.97; P-value 0.015), have an increased odds of unexplained falls.

Conclusion

BZD use is associated with falls, with larger effect size in those reporting poor sleep quality in community dwelling older adults. Appropriate prescription of medications such as BZDs is an important public health issue.
First to “Read” the News: News Analytics and Algorithmic Trading
Authors: von Beschwitz Bastian , Keim Donald B , Massa Massimo
Published: August 2019

Exploiting a unique identification strategy based on inaccurate news analytics, we document an effect of news analytics on the market independent of the informational content of the news. We show that news analytics speed up the stock price and trading volume response to articles, but reduce liquidity. Inaccurate news analytics lead to small price distortions that are corrected quickly. The market impact of news analytics is greatest for press releases, as news analytics exhibit a particular skill in “seeing through” the positive spin of press releases. Furthermore, we provide evidence that high-frequency traders rely on the information from news analytics for directional trading on company-specific news.

Received: May 17, 2018; Editorial decision: June 14, 2019 by Editor: Thierry Foucault. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
(Il)legal Assignments in School Choice
Authors: Ehlers Lars , Morrill Thayer
Published: August 2019

In public school choice, students with strict preferences are assigned to schools. Schools are endowed with priorities over students. Incorporating constraints from different applications, priorities are often modelled as choice functions over sets of students. It has been argued that the most desirable criterion for an assignment is stability; there should not exist any blocking pair: no student shall prefer some school to her assigned school and have higher priority than some student who got into that school or the school has an empty seat. We propose a blocking notion where in addition it must be possible to assign the student to her preferred school. We then define the following stability criterion for a set of assignments: a set of assignments is legal if and only if any assignment outside the set is blocked with some assignment in the set and no two assignments inside the set block each other. We show that under very basic conditions on priorities, there always exists a unique legal set of assignments, and that this set has a structure common to the set of stable assignments: (i) it is a lattice and (ii) it satisfies the rural hospitals theorem. The student-optimal legal assignment is efficient and provides a solution for the conflict between stability and efficiency.