bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep neural networks design and analysis for automatic phase pickers from three-component microseismic recordings
Authors: Zheng Jing , Shen Shuaishuai , Jiang Tianqi , Zhu Weiqiang
Published: October 2019

It is essential to pick P-wave and S-wave arrival times rapidly and accurately for the microseismic monitoring systems. Meanwhile, it is not easy to identify the arrivals at a true phase automatically using traditional picking method. This is one of the reasons that many researchers are trying to introduce deep neural networks to solve these problems. Convolutional neural networks (CNNs) are very attractive for designing automatic phase pickers especially after introducing the fundamental network structure from semantic segmentation field, which can give the probability outputs for every labelled phase at every sample in the recordings. The typical segmentation architecture consists of two main parts: (1) an encoder part trained to extracting coarse semantic features; (2) a decoder part responsible not only for recovering the input resolution at the output but also for obtaining sparse representation of the objects. The fundamental segmentation structure performs well; however, the influence of the parameters in the structure on the pickers has not been investigated. It means that the structure design just depends on experience and tests. In this paper, we solve two main questions to give some guidance on network design. First, we show what sparse features will learn from the three-component microseismic recordings using CNNs. Second, the influence of two key parameters in the network on pickers, namely, the depth of decoder and activation functions, is analysed. Increasing the number of levels for a certain layer in the decoder will increase the burden of demand on trainable parameters, but it is beneficial to the accuracy of the model. Reasonable depth of the decoder can balance prediction accuracy and the demand of labelled data, which is important for microseismic systems because manual labelling process will decrease the real-time performance in monitoring tasks. Standard rectified linear unit (ReLU) and leaky rectified linear unit (Leaky ReLU) with different negative slopes are compared for the analysis. Leaky ReLU with a small negative slope can improve the performance of a given model than ReLU activation function by keeping some information about the negative parts.
Double-difference measurements in global full-waveform inversions
Authors: Örsvuran Rıdvan , Bozdağ Ebru , Modrak Ryan , Lei Wenjie , Ruan Youyi
Published: October 2019

We demonstrate double-difference (DD) tomography, a method involving differential measurements between stations, for 2-D and 3-D adjoint inversions based on realistic source–receiver distributions, with a focus on the global scale. We first present 2-D synthetic inversion results using cross-correlation traveltime and L2 waveform difference objective functions. Introducing a weighting term to DD objective functions based on the number of measurement pairs per station speeds up convergence and reduces bias in the final inverted model due to uneven data coverage. We next demonstrate frequency-dependent multitaper DD measurements in a 3-D experiment with real earthquake data by computing global-scale gradients. At the global scale, careful selection of station pairs is required for differential measurements in terms of geographical distance or geological context. In our technique, if no suitable pairs are found for a particular station, the DD measurement reduces to a classical misfit measurement. Furthermore, we compare 2-D and 3-D DD results with those from corresponding conventional misfits. By exploiting previously unused information in the recorded wavefield, DD tomography shows promise for balancing the gradient and speeding up convergence, especially around dense regional seismic networks.
2. The Social Research Process
Authors: Clark Tom , Foster Liam , Bryman Alan
Published: October 2019

This chapter outlines some of the basic features of social research. It introduces students to the notion that social research is a process, helps to clarify the reasons for reearch, and explores the relationship between theory and research. Using the analogy of a voyage, it demonstrates that specific tasks associated with for carrying out social research tend to be ordered, but not always orderly. There are dynamic points of issue that need to be negotiated to move a dissertation project toward completion, or otherwise there is a risk of being blown off course. By understanding what is meant by the research process, and how theory can be used in social research, readers can begin to explore, describe, and explain the human world with greater confidence.
9. Writing a Research Proposal
Authors: Clark Tom , Foster Liam , Bryman Alan
Published: October 2019

Before starting a dissertation, it is common practice to have to write a research proposal. Not only does a research proposal help make sense of the student’s own project and what it will look like, it also allows he or she to connect research idea to a wider audience so that other people can give advice about whether, and how, it makes ‘research sense’. Often submitted alongside an ethics application, the research proposal is sometimes a requirement of the dissertation process, needing ‘approval’ before undertaking the research project. This chapter details what research proposals look like and why they are important, before outlining the requirements of a typical research proposal.
14. Analysing Qualitative Data
Authors: Clark Tom , Foster Liam , Bryman Alan
Published: October 2019

This chapter discusses the analysis of qualitative material. There are many types of qualitative analysis. Some approaches are related to specific forms of data, whereas others are more generic in nature. There can also be considerable differences between some forms of qualitative analysis to the extent that they have very little in common with one another. Given this diversity, it is not possible adequately to address every type of analysis, or provide highly detailed instructions for the more common techniques. Hence, the chapter introduces the iterative processes of coding and categorization as well as some of the major types of qualitative analysis. It shows how to identify key concepts in data, and how those concepts can be connected to theory.
What are the factors associated with the implementation of a peer-led health promotion program? Insights from a multiple-case study
Authors: Lorthios-Guilledroit A , Filiatrault J , Richard L
Published: October 2019

Peer education is widely used as a health promotion strategy. However, few efforts have been undertaken to understand the implementation of peer-led health promotion programs (HPPs). This multiple-case study identifies factors facilitating the implementation of a peer-led HPP for older adults presenting with fear of falling (Vivre en ï¿½quilibre) and their mechanisms of action. It used a conceptual framework postulating factors that may influence peer-led HPPs implementation and mechanisms through which such factors may generate implementation outcomes. Six independent-living residences for older adults in Quebec (Canada) implemented Vivre en ï¿½quilibre as part of a quasi-experimental study. Implementation factors and outcomes were documented through observation diaries, attendance sheets, peers’ logbooks, questionnaires administered to participants and semi-structured interviews conducted among peers, activity coordinators of residences and a subgroup of participants. The analysis revealed three categories of factors facilitating program implementation, related to individuals, to the program and to the organizational context. Three action mechanisms identified in the framework (interaction, self-organization and adaptation) were facilitated by some of these factors. These findings support the application of the peer-led program implementation conceptual framework used in this study and provide insights for practitioners and researchers interested in implementing peer-led HPPs.
Conditional targeting in mice reveals that hepatic homogentisate 1,2-dioxygenase activity is essential in reducing circulating homogentisic acid and for effective therapy in the genetic disease alkaptonuria
Authors: Hughes Juliette H , Liu Ke , Plagge Antonius , Wilson Peter J M , Sutherland Hazel , Norman Brendan P , Hughes Andrew T , Keenan Craig M , Milan Anna M , Sakai Takao , Ranganath Lakshminarayan R , Gallagher James A , Bou-Gharios George
Published: October 2019

Alkaptonuria is an inherited disease caused by homogentisate 1,2-dioxygenase (HGD) deficiency. Circulating homogentisic acid (HGA) is elevated and deposits in connective tissues as ochronotic pigment. In this study, we aimed to define developmental and adult HGD tissue expression and determine the location and amount of gene activity required to lower circulating HGA and rescue the alkaptonuria phenotype.

We generated an alkaptonuria mouse model using a knockout-first design for the disruption of the HGD gene. Hgd tm1a −/− mice showed elevated HGA and ochronosis in adulthood. LacZ staining driven by the endogenous HGD promoter was localised to only liver parenchymal cells and kidney proximal tubules in adulthood, commencing at E12.5 and E15.5 respectively. Following removal of the gene trap cassette to obtain a normal mouse with a floxed 6th HGD exon, a double transgenic was then created with Mx1-Cre which conditionally deleted HGD in liver in a dose dependent manner. 20% of HGD mRNA remaining in liver did not rescue the disease, suggesting that we need more than 20% of liver HGD to correct the disease in gene therapy.

Kidney HGD activity which remained intact reduced urinary HGA, most likely by increased absorption, but did not reduce plasma HGA nor did it prevent ochronosis. In addition, downstream metabolites of exogenous 13C6-HGA, were detected in heterozygous plasma, revealing that hepatocytes take up and metabolise HGA.

This novel alkaptonuria mouse model demonstrated the importance of targeting liver for therapeutic intervention, supported by our observation that hepatocytes take up and metabolise HGA.
Loss of the nucleoporin Aladin in central nervous system and fibroblasts of Allgrove Syndrome
Authors: Bitetto Giacomo , Ronchi Dario , Bonato Sara , Pittaro Alessandra , Compagnoni Giacomo Monzio , Bordoni Andreina , Salani Sabrina , Frattini Emanuele , Lopez Gianluca , Cribiù Fulvia Milena , Corti Stefania , Comi Giacomo P , Bresolin Nereo , Di Fonzo Alessio
Published: October 2019

Allgrove syndrome (AS) is a rare disease with broad neurological involvement. Neurodegeneration can affect spinal motor neurons, Purkinje cells, striatal neurons and the autonomic system. The mechanisms that lead to neuronal loss are still unclear. Recessive mutations in the AAAS gene affect the encoded protein Aladin, which would normally localize to the cytoplasmic face of the nuclear membrane as part of the nuclear pore complex (NPC). While the NPC is known to be a key factor for nucleocytoplasmic transport, the precise role of Aladin has not been elucidated yet. Here, we explored the consequences of the homozygous AAAS mutation c.464G>A (p.R155H) in central nervous system tissues and fibroblasts of a novel AS patient presenting motor neuron disease, cerebellar ataxia and autonomic dysfunction. Neuropathological analyses showed severe loss of motor neurons and Purkinje cells, with significant reduction in the perinuclear expression of Aladin. A reduced amount of protein was detected in the nuclear membrane fraction of the patient’s brain. RNA analysis revealed a significant reduction of the transcript AAAS-1, while the AAAS-2 transcript was upregulated in fibroblasts. To our knowledge, this is the first study to demonstrate the effects of AAAS mutations in the human central nervous system.
Success of malaria chemoprophylaxis for outbound civil and military travellers in prevention of reintroduction of malaria in Sri Lanka
Authors: Fernando Sumadhya D , Ranaweera Dewanee , Weerasena Methnie S , Booso Rahuman , Wickramasekara Thamara , Madurapperuma Chirath P , Danansuriya Manjula , Rodrigo Chaturaka , Herath Hemantha
Published: October 2019

Background

Sri Lanka was certified as malaria-free in September 2016. However, the continuous presence of the malaria vector poses serious risks of reintroduction of the disease. Chemoprophylaxis and advice on malaria preventive behaviour for international travellers is a key strategy adopted to reduce the risk of imported malaria.

Methods

We conducted an efficiency study of malaria chemoprophylaxis for civilian and military travellers who requested travel advice from the Anti Malaria Campaign (AMC) prior to departure. The AMC is the only agency that can issue malaria chemoprophylaxis to travellers and hence this sample is representative of all such individuals seeking travel advice in Sri Lanka.

Results

A total of 544 (400 civilians and 144 military) travellers were interviewed prior to departure and after return. The majority travelled to African destinations (516/544 [94.8%]) and were prescribed mefloquine (517/544 [95%]). Chemoprophylaxis was well tolerated and discontinuation due to adverse events was minimal. Regular chemoprophylaxis was reported by 505 (92.8%) participants while overseas. The protective efficacy of chemoprophylaxis was 100% among those who complied with the full course.

Conclusions

The compliance with chemoprophylaxis and its protective efficacy were satisfactory in this study. It is an effective tool in preventing imported malaria to post-elimination Sri Lanka.
Policing Reality: Urban Disorder, Failure, and Expert Undoings
Authors: Machold Rhys
Published: October 2019

This article intervenes in discussions about the circulation of policing knowledge and the politics of expertise. As part of a broader conversation about transnational reconfigurations of state power, critical scholars have drawn attention to the influence of global policing “models” and “private” experts in shaping policy. They show how such figures and forms of knowhow symbolically enforce urban order and dispossess marginalized communities under conditions of neoliberal crisis. While incisive, these approaches can unduly portray expert authority as boundless and unassailable. This article argues that a sustained theoretical engagement with questions about controversies and failure opens up fruitful avenues to unsettle the perceived smoothness, inevitability, and omnipotence of experts in relation to politics and governing. Drawing on insights from actor-network theory (ANT), it situates deference to global experts as interventions that seek to enact and police the terms of “reality” concerning urban order. This approach allows us to better understand how such interventions work but also how they misfire and come undone. These claims are developed through a close reading of UK Prime Minister David Cameron's attempt to solicit policy advice from renowned global “supercop” William Bratton in the aftermath of the 2011 England riots.
Mutations that increase expression of the EmrAB-TolC efflux pump confer increased resistance to nitroxoline in Escherichia coli
Authors: Puértolas-Balint Fabiola , Warsi Omar , Linkevicius Marius , Tang Po-Cheng , Andersson Dan I
Published: October 2019

Objectives

To determine the mechanism of resistance to the antibiotic nitroxoline in Escherichia coli.

Methods

Spontaneous nitroxoline-resistant mutants were selected at different concentrations of nitroxoline. WGS and strain reconstruction were used to define the genetic basis for the resistance. The mechanistic basis of resistance was determined by quantitative PCR (qPCR) and by overexpression of target genes. Fitness costs of the resistance mutations and cross-resistance to other antibiotics were also determined.

Results

Mutations in the transcriptional repressor emrR conferred low-level resistance to nitroxoline [nitroxoline MIC (MICNOX) = 16 mg/L] by increasing the expression of the emrA and emrB genes of the EmrAB-TolC efflux pump. These resistant mutants showed no fitness reduction and displayed cross-resistance to nalidixic acid. Second-step mutants with higher-level resistance (MICNOX = 32–64 mg/L) had mutations in the emrR gene, together with either a 50 kb amplification, a mutation in the gene marA, or an IS upstream of the lon gene. The latter mutations resulted in higher-level nitroxoline resistance due to increased expression of the tolC gene, which was confirmed by overexpressing tolC from an inducible plasmid in a low-level resistance mutant. Furthermore, the emrR mutations conferred a small increase in resistance to nitrofurantoin only when combined with an nfsAB double-knockout mutation. However, nitrofurantoin-resistant nfsAB mutants showed no cross-resistance to nitroxoline.

Conclusions

Mutations in different genes causing increased expression of the EmrAB-TolC pump lead to an increased resistance to nitroxoline. The structurally similar antibiotics nitroxoline and nitrofurantoin appear to have different modes of action and resistance mechanisms.
Validity of social media for assessing treatment patterns in oncology patients: a case study in melanoma
Authors: McDonald Laura , Behl Varun , Sundar Vijayarakhavan , Mehmud Faisal , Malcolm Bill , Ramagopalan Sreeram
Published: October 2019

There is a need to understand how patients are managed in the real world to better understand disease burden and unmet need. Traditional approaches to gather these data include the use of electronic medical record (EMR) or claims databases; however, in many cases data access policies prevent rapid insight gathering. Social media may provide a potential source of real-world data to assess treatment patterns, but the limitations and biases of doing so have not yet been evaluated. Here, we assessed whether patient treatment patterns extracted from publicly available patient forums compare to results from more traditional EMR and claims databases. We observed that the 95% confidence intervals of proportions of treatments received at first, second, and third line for advanced/metastatic melanoma generated from unstructured social media data overlapped with 95% confidence intervals from proportions obtained from 1 or more traditional EMR/Claims databases. Social media may offer a valid data option to understand treatment patterns in the real world.
Attraction of Invasive Ambrosia Beetles (Coleoptera: Curculionidae: Scolytinae) to Ethanol-Treated Tree Bolts
Authors: Reding Michael E , Ranger Christopher M
Published: October 2019

Ethanol-treated bolts (tree stem sections) have potential as monitoring and pesticide screening tools for ambrosia beetles (Coleoptera: Curculionidae: Scolytinae). Bolts were infused with ethanol by immersing them for at least 24 h. Attacks on ethanol-treated bolts by Xylosandrus species were compared with captures in ethanol-baited traps. Bolts infused in ethanol were usually as attractive or more attractive to Xylosandrus germanus (Blandford) than ethanol-baited bottle traps. Xylosandrus crassiusculus (Motschulsky) were more attracted to bolts than trap in some experiments, but numbers were low and differences were usually not significant. Two techniques for treating bolts with ethanol were compared. Attraction of ambrosia beetles to ethanol-infused bolts were compared with bolts with a drilled cavity filled with ethanol. Drilled bolts filled with ethanol were attractive to X. germanus and were reliably attacked, but numbers of beetles were often lower than in traps and infused bolts. Aged and fresh ethanol-infused bolts were compared with evaluate residual attractiveness. Bolts aged 7 d usually had fewer X. germanus than fresh bolts and traps, and bolts aged 14 d had no beetles. Ethanol-infused bolts from different species of trees were compared. Xylosandrus germanus attacked all species tested with more attacks usually in red maple (Acer rubrum L.). Anisandrus maiche Stark was attracted to ethanol-infused bolts indicating it may attack trees emitting ethanol. Bolts attracted fewer nontarget species than traps, but residual attraction was much less. The selectivity of ethanol-treated bolts for Xylosandrus species should make them useful for monitoring and screening pesticides against those species.
Spatial Distributions of Thrips (Thysanoptera: Thripidae) in Cotton
Authors: Reay-Jones Francis P F , Greene Jeremy K , Bauer Philip J
Published: October 2019

A 4-yr study was conducted to determine the degree of aggregation of thrips and injury in cotton, Gossypium hirsutum L., and their spatial association with a multispectral vegetation index (normalized difference vegetation index [NDVI]) and soil apparent electrical conductivity (ECa). Using the Spatial Analysis by Distance IndicEs analyses (SADIE), adult thrips were significantly (P < 0.05) aggregated in 4 out of 24 analyses for adult thrips (17%), 4 out of 24 analyses for immature thrips (17%), and 2 out of 15 analyses for injury (13%). The SADIE association tool showed that NDVI values were associated with adult thrips in 2 out of 20 paired datasets (10%), with immature thrips in 3 out of 20 paired datasets (15%), and with thrips injury in 1 out of 14 paired datasets (7.1%). Soil ECa values were generally more associated with thrips variables than NDVI, with shallow ECa positively associated with adult thrips in 6 out of 21 paired datasets (28.6%), with immature thrips in 8 out of 21 paired datasets (40.0%), and with thrips injury in 8 out of 14 paired datasets (57.1%). The greater frequency of positive associations between thrips variables and soil ECa suggests a greater potential for site-specific management, particularly in the Coastal Plain of the southeastern United States, where soil types are highly variable.
Risk factors predicting Candida infective endocarditis in patients with candidemia
Authors: Foong Kap Sum , Sung Abby , Burnham Jason P , Kronen Ryan , Lian Qinghua , Salazar Zetina Ana , Hsueh Kevin , Lin Charlotte , Powderly William G , Spec Andrej
Published: October 2019

Candida infective endocarditis (CIE) is a rare but serious complication of candidemia. Incidence and risk factors associated with CIE among candidemic patients are poorly defined from small cohorts. Identification of clinical predictors associated with this entity may guide more judicious use of cardiac imaging. We conducted a retrospective analysis of all inpatients aged ≥18 years diagnosed with candidemia at our institution. CIE was diagnosed by fulfilling two of the major Duke criteria: specifically a vegetation(s) on echocardiogram and positive blood cultures for Candida spp. We used univariable and multivariable regression analyses to identify risk factors associated with CIE. Of 1,873 patients with candidemia, 47 (2.5%) were identified to have CIE. In our multivariable logistic model, existing valvular heart disease was associated with a higher risk for CIE (adjusted odds ratio [aOR], 7.66; 95% confidence interval [CI], 2.95–19.84). Predictors that demonstrated a decreased risk of CIE included infection with C. glabrata (aOR, 0.17; 95% CI, 0.04–0.69), hematologic malignancy (aOR, 0.09; 95% CI, 0.01–0.68), and receipt of total parenteral nutrition (aOR, 0.38; 95% CI, 0.16–0.91). The 90-day crude mortality for CIE was 48.9%, similar to the overall non-CIE mortality of 41.9% (P = .338). We identified a set of clinical factors that can predict the presence of CIE among patient with candidemia. These findings may reduce the need for unnecessary expensive and invasive imaging studies in a subset of patients with a lower risk profile for endocarditis and alternative infection source.
Numerical simulation of helical jets at active region peripheries
Authors: Wyper Peter F , DeVore C Richard , Antiochos Spiro K
Published: October 2019

Coronal jets are observed above minority-polarity intrusions throughout the solar corona. Some of the most energetic ones occur on the periphery of active regions where the magnetic field is strongly inclined. These jets exhibit a non-radial propagation in the low corona as they follow the inclined field, and often have a broad, helical shape. We present a three-dimensional magnetohydrodynamic simulation of such an active-region-periphery helical jet. We consider an initially potential field with a bipolar flux distribution embedded in a highly inclined magnetic field, representative of the field nearby an active region. The flux of the minority polarity sits below a bald-patch separatrix initially. Surface motions are used to inject free energy into the closed field beneath the separatrix, forming a sigmoidal flux rope that eventually erupts producing a helical jet. We find that a null point replaces the bald patch early in the evolution and that the eruption results from a combination of magnetic breakout and an ideal kinking of the erupting flux rope. We discuss how the two mechanisms are coupled, and compare our results with previous simulations of coronal-hole jets. This comparison supports the hypothesis that the generic mechanism for all coronal jets is a coupling between breakout reconnection and an ideal instability. We further show that our results are in good qualitative and quantitative agreement with observations of active-region-periphery jets.
The evolution of CNO isotopes: the impact of massive stellar rotators
Authors: Romano Donatella , Matteucci Francesca , Zhang Zhi-Yu , Ivison Rob J , Ventura Paolo
Published: October 2019

Chemical abundances and abundance ratios measured in galaxies provide precious information about the mechanisms, modes, and time-scales of the assembly of cosmic structures. Yet, the nucleogenesis and chemical evolution of elements heavier than helium are dictated mostly by the physics of the stars and the shape of the stellar mass spectrum. In particular, estimates of CNO isotopic abundances in the hot, dusty media of high-redshift starburst galaxies offer a unique glimpse into the shape of the stellar initial mass function (IMF) in extreme environments that cannot be accessed with direct observations (star counts). Underlying uncertainties in stellar evolution and nucleosynthesis theory, however, may hurt our chances of getting a firm grasp of the IMF in these galaxies. In this work, we adopt new yields for massive stars, covering different initial rotational velocities. First, we implement the new yield set in a well-tested chemical evolution model for the Milky Way. The calibrated model is then adapted to the specific case of a prototype submillimetre galaxy (SMG). We show that, if the formation of fast-rotating stars is favoured in the turbulent medium of violently star-forming galaxies irrespective of metallicity, the IMF needs to be skewed towards high-mass stars in order to explain the CNO isotopic ratios observed in SMGs. If, instead, stellar rotation becomes negligible beyond a given metallicity threshold, as is the case for our own Galaxy, there is no need to invoke a top-heavy IMF in starbursts.
Coexistence of a planar magnetic structure and an Alfvén wave in the shock-sheath of an interplanetary coronal mass ejection
Authors: Shaikh Zubair I , Raghav Anil , Vichare Geeta
Published: October 2019

The excess speed of coronal mass ejection over the ambient solar wind in interplanetary space generates a highly compressed, heated and turbulent shock-sheath. Here, for the first time, we present in situ observations of a unique and distinct feature of the shock-sheath, which exhibits the characteristics of a planar magnetic structure (PMS) and an Alfvén wave simultaneously. We have used standard techniques to confirm the presence of the PMS as described in Shaikh et al. We have employed the minimum variance analysis technique to estimate the properties of the PMS. The Walén test is used to confirm the presence of the Alfvén wave. Our study unambiguously proves the coexistence of the Alfvén wave and the PMS in the shock-sheath region. Further studies are essential to investigate the origin of such a peculiar shock-sheath and its effect on our view of solar-terrestrial physics.
Timing analysis of 2S 1417-624 observed with NICER and Insight-HXMT
Authors: Ji L , Doroshenko V , Santangelo A , Güngör C , Zhang S , Ducci L , Zhang S-N , Ge M-Y , Qu L J , Chen Y P , Bu Q C , Cao X L , Chang Z , Chen G , Chen L , Chen T X , Chen Y , Chen Y B , Cui W , Cui W W , Deng J K , Dong Y W , Du Y Y , Fu M X , Gao G H , Gao H , Gao M , Gu Y D , Guan J , Guo C C , Han D W , Hu W , Huang Y , Huo J , Jia S M , Jiang L H , Jiang W C , Jin J , Jin Y J , Kong L D , Li B , Li C K , Li G , Li M S , Li T P , Li W , Li X , Li X B , Li X F , Li Y G , Li Z J , Li Z W , Liang X H , Liao J Y , Liu C Z , Liu G Q , Liu H W , Liu S Z , Liu X J , Liu Y , Liu Y N , Lu B , Lu F J , Lu X F , Luo T , Ma X , Meng B , Nang Y , Nie J Y , Ou G , Sai N , Song L M , Song X Y , Sun L , Tan Y , Tao L , Tuo Y L , Wang G F , Wang J , Wang W S , Wang Y S , Wen X Y , Wu B B , Wu M , Xiao G C , Xiong S L , Xu H , Xu Y P , Yang Y R , Yang J W , Yang S , Yang Y J , Zhang A M , Zhang C L , Zhang C M , Zhang F , Zhang H M , Zhang J , Zhang Q , Zhang T , Zhang W , Zhang W C , Zhang W Z , Zhang Y , Zhang Y , Zhang Y F , Zhang Y J , Zhang Z , Zhang Z L , Zhao H S , Zhao J L , Zhao X F , Zheng S J , Zhu Y , Zhu Y X , Zou C L
Published: October 2019

We present a study of timing properties of the accreting pulsar 2S 1417-624 observed during its 2018 outburst, based on Swift/BAT, Fermi/GBM, Insight-HXMT and NICER observations. We report a dramatic change of the pulse profiles with luminosity. The morphology of the profile in the range 0.2-10.0 keV switches from double to triple peaks at ∼2.5 $\rm \times 10^{37}{\it D}_{10}^2\ erg\ s^{-1}$ and from triple to quadruple peaks at ∼7 $\rm \times 10^{37}{\it D}_{10}^2\ erg\ s^{-1}$. The profile at high energies (25-100 keV) shows significant evolutions as well. We explain this phenomenon according to existing theoretical models. We argue that the first change is related to the transition from the sub to the super-critical accretion regime, while the second to the transition of the accretion disc from the gas-dominated to the radiation pressure-dominated state. Considering the spin-up as well due to the accretion torque, this interpretation allows to estimate the magnetic field self-consistently at ∼7 × 1012 G.
Quantifying the thermal Sunyaev–Zel’dovich effect and excess millimetre emission in quasar environments
Authors: Hall Kirsten R , Zakamska Nadia L , Addison Graeme E , Battaglia Nicholas , Crichton Devin , Devlin Mark , Dunkley Joanna , Gralla Megan , Hill J Colin , Hilton Matt , Hubmayr Johannes , Hughes John P , Huffenberger Kevin M , Kosowsky Arthur , Marriage Tobias A , Maurin Loïc , Moodley Kavilan , Niemack Michael D , Page Lyman A , Partridge Bruce , Dünner Planella Rolando , Schillaci Alessandro , Sifón Cristóbal , Staggs Suzanne T , Wollack Edward J , Xu Zhilei
Published: October 2019

In this paper, we probe the hot, post-shock gas component of quasar-driven winds through the thermal Sunyaev–Zel’dovich (tSZ) effect. Combining data sets from the Atacama Cosmology Telescope, the Herschel Space Observatory, and the Very Large Array, we measure average spectral energy distributions of 109 829 optically selected, radio quiet quasars from 1.4 to 3000 GHz in six redshift bins between 0.3 < z < 3.5. We model the emission components in the radio and far-infrared, plus a spectral distortion from the tSZ effect. At z > 1.91, we measure the tSZ effect at 3.8σ significance with an amplitude corresponding to a total thermal energy of 3.1 × 1060 erg. If this energy is due to virialized gas, then our measurement implies quasar host halo masses are ∼6 × 1012 h−1 M⊙. Alternatively, if the host dark matter halo masses are ∼2 × 1012 h−1 M⊙ as some measurements suggest, then we measure a >90 per cent excess in the thermal energy over that expected due to virialization. If the measured SZ effect is primarily due to hot bubbles from quasar-driven winds, we find that $(5^{+1.2}_{-1.3}$) per cent of the quasar bolometric luminosity couples to the intergalactic medium over a fiducial quasar lifetime of 100 Myr. An additional source of tSZ may be correlated structure, and further work is required to separate the contributions. At z ≤ 1.91, we detect emission at 95 and 148 GHz that is in excess of thermal dust and optically thin synchrotron emission. We investigate potential sources of this excess emission, finding that CO line emission and an additional optically thick synchrotron component are the most viable candidates.
A black box for dark sector physics: predicting dark matter annihilation feedback with conditional GANs
Authors: List Florian , Bhat Ishaan , Lewis Geraint F
Published: October 2019

Traditionally, incorporating additional physics into existing cosmological simulations requires re-running the cosmological simulation code, which can be computationally expensive. We show that conditional Generative Adversarial Networks (cGANs) can be harnessed to predict how changing the underlying physics alters the simulation results. To illustrate this, we train a cGAN to learn the impact of dark matter annihilation feedback (DMAF) on the gas density distribution. The predicted gas density slices are visually difficult to distinguish from their real brethren and the peak counts differ by less than 10 per cent for all test samples (the average deviation is <3 per cent). Finally, we invert the problem and show that cGANs are capable of endowing smooth density distributions with realistic substructure. The cGAN does however have difficulty generating new knots as well as creating/eliminating bubble-like structures. We conclude that trained cGANs can be an effective approach to provide mock samples of cosmological simulations incorporating DMAF physics from existing samples of standard cosmological simulations of the evolution of cosmic structure.
Evolution of supernovae-driven superbubbles with conduction and cooling
Authors: El-Badry Kareem , Ostriker Eve C , Kim Chang-Goo , Quataert Eliot , Weisz Daniel R
Published: October 2019

We use spherically symmetric hydrodynamic simulations to study the dynamical evolution and internal structure of superbubbles (SBs) driven by clustered supernovae (SNe), focusing on the effects of thermal conduction and cooling in the interface between the hot bubble interior and cooled shell. Our simulations employ an effective diffusivity to account for turbulent mixing from non-linear instabilities that are not captured in 1D. The conductive heat flux into the shell is balanced by a combination of cooling in the interface and evaporation of shell gas into the bubble interior. This evaporation increases the density, and decreases the temperature, of the SB interior by more than an order of magnitude relative to simulations without conduction. However, most of the energy conducted into the interface is immediately lost to cooling, reducing the evaporative mass flux required to balance conduction. As a result, the evaporation rate is typically a factor of ∼3–30 lower than predicted by the classical similarity solution of (Weaver et al. 1977), which neglects cooling. Blast waves from the first ∼30 SNe remain supersonic in the SB interior because reduced evaporation from the interface lowers the mass they sweep up in the hot interior. Updating the Weaver solution to include cooling, we construct a new analytic model to predict the cooling rate, evaporation rate, and temporal evolution of SBs. The cooling rate, and hence the hot gas mass, momentum, and energy delivered by SBs, is set by the ambient interstellar mass density and the efficiency of non-linear mixing at the bubble–shell interface.
A black hole X-ray binary at ∼100 Hz: multiwavelength timing of MAXI J1820+070 with HiPERCAM and NICER
Authors: Paice J A , Gandhi P , Shahbaz T , Uttley P , Arzoumanian Z , Charles P A , Dhillon V S , Gendreau K C , Littlefair S P , Malzac J , Markoff S , Marsh T R , Misra R , Russell D M , Veledina A
Published: October 2019

We report on simultaneous sub-second optical and X-ray timing observations of the low-mass X-ray binary black hole candidate MAXI J1820+070. The bright 2018 outburst rise allowed simultaneous photometry in five optical bands (ugrizs) with HiPERCAM/GTC (Optical) at frame rates over 100 Hz, together with NICER/ISS observations (X-rays). Intense (factor of 2) red flaring activity in the optical is seen over a broad range of time-scales down to ∼10 ms. Cross-correlating the bands reveals a prominent anticorrelation on time-scales of ∼seconds, and a narrow sub-second correlation at a lag of ≈ +165 ms (optical lagging X-rays). This lag increases with optical wavelength, and is approximately constant over Fourier frequencies of ∼0.3–10 Hz. These features are consistent with an origin in the inner accretion flow and jet base within ∼5000 Gravitational radii. An additional ∼+5 s lag feature may be ascribable to disc reprocessing. MAXI J1820+070 is the third black hole transient to display a clear ∼0.1 s optical lag, which may be common feature in such objects. The sub-second lag variation with wavelength is novel, and may allow constraints on internal shock jet stratification models.
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
Authors: Donath Alexander , Jühling Frank , Al-Arab Marwa , Bernhart Stephan H , Reinhardt Franziska , Stadler Peter F , Middendorf Martin , Bernt Matthias
Published: October 2019

With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases
Authors: Tørresen Ole K , Star Bastiaan , Mier Pablo , Andrade-Navarro Miguel A , Bateman Alex , Jarnot Patryk , Gruca Aleksandra , Grynberg Marcin , Kajava Andrey V , Promponas Vasilis J , Anisimova Maria , Jakobsen Kjetill S , Linke Dirk
Published: October 2019

The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
PhaSepDB: a database of liquid–liquid phase separation related proteins
Authors: You Kaiqiang , Huang Qi , Yu Chunyu , Shen Boyan , Sevilla Cristoffer , Shi Minglei , Hermjakob Henning , Chen Yang , Li Tingting
Published: October 2019

It's widely appreciated that liquid–liquid phase separation (LLPS) underlies the formation of membraneless organelles, which function to concentrate proteins and nucleic acids. In the past few decades, major efforts have been devoted to identify the phase separation associated proteins and elucidate their functions. To better utilize the knowledge dispersed in published literature, we developed PhaSepDB (http://db.phasep.pro/), a manually curated database of phase separation associated proteins. Currently, PhaSepDB includes 2914 non-redundant proteins localized in different organelles curated from published literature and database. PhaSepDB provides protein summary, publication reference and sequence features of phase separation associated proteins. The sequence features which reflect the LLPS behavior are also available for other human protein candidates. The online database provides a convenient interface for the research community to easily browse, search and download phase separation associated proteins. As a centralized resource, we believe PhaSepDB will facilitate the future study of phase separation.
MatrisomeDB: the ECM-protein knowledge database
Authors: Shao Xinhao , Taha Isra N , Clauser Karl R , Gao Yu (Tom) , Naba Alexandra
Published: October 2019

The extracellular matrix (ECM) is a complex and dynamic meshwork of cross-linked proteins that supports cell polarization and functions and tissue organization and homeostasis. Over the past few decades, mass-spectrometry-based proteomics has emerged as the method of choice to characterize the composition of the ECM of normal and diseased tissues. Here, we present a new release of MatrisomeDB, a searchable collection of curated proteomic data from 17 studies on the ECM of 15 different normal tissue types, six cancer types (different grades of breast cancers, colorectal cancer, melanoma, and insulinoma) and other diseases including vascular defects and lung and liver fibroses. MatrisomeDB (http://www.pepchem.org/matrisomedb) was built by retrieving raw mass spectrometry data files and reprocessing them using the same search parameters and criteria to allow for a more direct comparison between the different studies. The present release of MatrisomeDB includes 847 human and 791 mouse ECM proteoforms and over 350 000 human and 600 000 mouse ECM-derived peptide-to-spectrum matches. For each query, a hierarchically-clustered tissue distribution map, a peptide coverage map, and a list of post-translational modifications identified, are generated. MatrisomeDB is the most complete collection of ECM proteomic data to date and allows the building of a comprehensive ECM atlas.
Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria
Authors: Baez William D , Roy Bappaditya , McNutt Zakkary A , Shatoff Elan A , Chen Shicheng , Bundschuh Ralf , Fredrick Kurt
Published: October 2019

In all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine–Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position –3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.
A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
Authors: Leong Ka Wai , Yu Fangyan , Adalsteinsson Viktor A , Reed Sarah , Gydush Gregory , Ladas Ioannis , Li Jiang , Tantisira Kelan G , Makrigiorgos Gerassimos Mike
Published: October 2019

DNA target enrichment via hybridization capture is a commonly adopted approach which remains expensive due in-part to using biotinylated-probe panels. Here we provide a novel isothermal amplification reaction to amplify rapidly existing probe panels without knowledge of the sequences involved, thereby decreasing a major portion of the overall sample preparation cost. The reaction employs two thermostable enzymes, BST-polymerase and duplex-specific nuclease DSN. DSN initiates random ‘nicks’ on double-stranded-DNA which enable BST to polymerize DNA by displacing the nicked-strand. Displaced strands re-hybridize and the process leads to an exponential chain-reaction generating biotinylated DNA fragments within minutes. When starting from single-stranded-DNA, DNA is first converted to double-stranded-DNA via terminal-deoxynucleotidyl-transferase (TdT) prior to initiation of BST–DSN reaction. Biotinylated probes generated by TdT–BST–DSN (TBD) reactions using panels of 33, 190 or 7186 DNA targets are used for hybrid-capture-based target enrichment from amplified circulating-DNA, followed by targeted re-sequencing. Polymerase-nuclease isothermal-chain-reactions generate random amplified probes with no apparent sequence dependence. One round of target-capture using TBD probes generates a modest on-target sequencing ratio, while two successive rounds of capture generate >80% on-target reads with good sequencing uniformity. TBD-reactions generate enough capture-probes to increase by approximately two to three orders-of-magnitude the target-enrichment experiments possible from an initial set of probes.
Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus
Authors: de Groot Arjan , Siponen Marina I , Magerand Romaric , Eugénie Nicolas , Martin-Arevalillo Raquel , Doloy Jade , Lemaire David , Brandelet Géraldine , Parcy François , Dumas Renaud , Roche Philippe , Servant Pascale , Confalonieri Fabrice , Arnoux Pascal , Pignol David , Blanchard Laurence
Published: October 2019

Exposure to harmful conditions such as radiation and desiccation induce oxidative stress and DNA damage. In radiation-resistant Deinococcus bacteria, the radiation/desiccation response is controlled by two proteins: the XRE family transcriptional repressor DdrO and the COG2856 metalloprotease IrrE. The latter cleaves and inactivates DdrO. Here, we report the biochemical characterization and crystal structure of DdrO, which is the first structure of a XRE protein targeted by a COG2856 protein. DdrO is composed of two domains that fold independently and are separated by a flexible linker. The N-terminal domain corresponds to the DNA-binding domain. The C-terminal domain, containing three alpha helices arranged in a novel fold, is required for DdrO dimerization. Cleavage by IrrE occurs in the loop between the last two helices of DdrO and abolishes dimerization and DNA binding. The cleavage site is hidden in the DdrO dimer structure, indicating that IrrE cleaves DdrO monomers or that the interaction with IrrE induces a structural change rendering accessible the cleavage site. Predicted COG2856/XRE regulatory protein pairs are found in many bacteria, and available data suggest two different molecular mechanisms for stress-induced gene expression: COG2856 protein-mediated cleavage or inhibition of oligomerization without cleavage of the XRE repressor.