bluuebunny/crossref_metadata_2025 huggingface dataset:
Can Tolling Help Everyone? Estimating the Aggregate and Distributional Consequences of Congestion Pricing
Authors: Hall Jonathan D
Published: February 2020

Economists have long advocated road pricing as an efficiency-enhancing solution to traffic congestion, yet it has rarely been implemented because it is thought to create losers as well as winners. In theory, a judiciously designed toll applied to a portion of the lanes of a highway can generate a Pareto improvement, even before using the toll revenue. This paper explores the practical relevance of this theoretical possibility by using survey and travel time data, combined with a structural model of traffic congestion, to estimate the joint distribution of agent preferences over three dimensions—value of time, schedule inflexibility, and desired arrival time—and evaluate the effects of adding optimal time-varying tolls. I find that adding tolls on half of the lanes of a highway yields a Pareto improvement. Further, the social welfare gains from doing so are substantial—up to $1,740 per road user per year.
Effects of body size and prior residence on dominance hierarchies in female Asian particolored bats
Authors: Liu Heng , Zhao Xin , Wang Yuze , Liu Ying , Feng Jiang , Jiang Tinglei
Published: February 2020

Social animals may cooperate to gain resources such as food and territory. However, unavoidable conflicts over limited resources frequently occur between group members. Social rank may effectively decrease conflicts within animal social groups, thereby reducing energy consumption and maintaining group stability. In this study, we tested the two factors most often proposed to influence winning a conflict: body size and prior residence. Our results showed that female Asian particolored bats (Vespertilio sinensis) formed near-linear dominance hierarchies. Forearm length was significantly positively correlated with dominance rank in three replicate experiments. In addition, prior residents had significantly higher dominance ranks than intruders of similar body size. These results suggested that both body size and prior residence might affect dominance ranks in female Asian particolored bats.
Survival and persistence of tricolored bats hibernating in Arkansas mines
Authors: Perry Roger W , Jordan Phillip N
Published: February 2020

White-nose syndrome (WNS) has caused large declines in bat populations across eastern North America, making information on demographics of affected species critical to determining their risk for extinction. We used Cormack–Jolly–Seber models to estimate apparent survival rates of hibernating tricolored bats (Perimyotis subflavus) for 5 years in four small abandoned mines in the Ouachita Mountains of Arkansas, located within the WNS endemic area of the United States. Populations in individual mines varied greatly in survival rates, with one mine displaying annual survival rates as high as 0.706 and another as low as 0.101. Differences in survival among bats in different mines could not definitively be attributed to WNS, but may have varied based on a combination of WNS, disturbance, mine climate, and other unknown factors. Further, some hibernacula may have served as temporary winter shelter for young transient males. Sites housing small colonies of hibernating bats may result in high survival rates despite WNS, and protecting these smaller sites may be important for overall species perseverance.
Automated acquisition of vast numbers of electron holograms with atomic-scale phase information
Authors: Takahashi Yoshio , Akashi Tetsuya , Sato Atsuko , Tanigaki Toshiaki , Shinada Hiroyuki , Murakami Yasukazu
Published: February 2020

An automated acquisition system for collecting a large number of electron holograms, to improve the statistical precision of phase analysis, was developed. A technique for shifting the electron beam in combination with stage movement allows data to be acquired over a wide area of a TEM-specimen grid. Undesired drift in the hologram position, which may occur during the hologram acquisition, can be corrected in real time by automated detection of the interference-fringe region in an image. To demonstrate the usefulness of the developed automated hologram acquisition system, gold nanoparticles dispersed on a carbon foil were observed with a 1.2-MV atomic resolution holography electron microscope. The system could obtain 1024 holograms, which provided phase maps for more than 500 nanoparticles with a lateral resolution of 0.14 nm, in just 1 h. The observation results revealed an anomalous increase in mean inner potential for a particle size smaller than 4 nm. The developed automated hologram acquisition system can be applied to improve the precision of phase measurement by averaging many phase images, as demonstrated by single particle analysis for biological entities. Moreover, the system makes it possible to study electrostatic potential of catalysts and other functional nanoparticles at atomic resolution.
A Causal Semantics of IS Generics
Authors: van Rooij Robert , Schulz Katrin
Published: February 2020

The felicity, or acceptability, of IS generics, i.e. generic sentences with indefinite singulars, is considerably more restricted compared to BP generics, generics with bare plurals. The goal of this paper is to account for the limited felicity of IS generics compared to BP generics, on the one hand, while preserving the close similarity between the two types of generics, on the other. We do so by proposing a causal analysis of IS generics, and show that this corresponds closely with a probabilistic analysis of BP generics.
Tracing the Spirit: Christology in Gregory of Nyssa’s Contra Eunomium III
Authors: Abecina Alexander L
Published: February 2020

While Gregory of Nyssa formulated a Spirit-based account of the unity of Christ in Antirrheticus adversus Apolinarium (c.383) I argue that he already held this view when he wrote Ad Eustathium (c.381) and hence when he wrote Contra Eunomium III (c.382). That Gregory makes no explicit reference to Christ’s anointing by the Spirit in Contra Eunomium III is best explained by his need to adapt his Christology to the Eunomian context where any appeal to a Spirit-based Christology would be useless and, worse, self-defeating. I propose criteria for detecting probable traces of a Spirit-based Christology in Contra Eunomium III and analyse two texts found in Parts 3 and 4 that satisfy these criteria. How we understand Gregory’s account of Christ’s unity in Contra Eunomium III therefore needs to be reframed.
On the eccentricity evolution of massive black hole binaries in stellar backgrounds
Authors: Bonetti Matteo , Rasskazov Alexander , Sesana Alberto , Dotti Massimo , Haardt Francesco , Leigh Nathan W C , Arca Sedda Manuel , Fragione Giacomo , Rossi Elena
Published: February 2020

We study the dynamical evolution of eccentric massive black hole binaries (MBHBs) interacting with unbound stars by means of an extensive set of three-body scattering experiments. Compared to previous studies, we extend the investigation down to a MBHB mass ratio of q = m2/m1 = 10−4, where m1 and m2 are the masses of the primary and secondary hole, respectively. Contrary to a simple extrapolation from higher mass ratios, we find that for q ≲ 10−3 the eccentricity growth rate becomes negative, i.e. the binary circularizes as it shrinks. This behaviour is due to the subset of interacting stars captured in metastable counter-rotating orbits; those stars tend to extract angular momentum from the binary, promoting eccentricity growth for q > 10−3, but tend to inject angular momentum into the binary driving it towards circularization for q < 10−3. The physical origin of this behaviour requires a detailed study of the orbits of this subset of stars and is currently under investigation. Our findings might have important consequences for intermediate massive black holes (IMBHs) inspiralling on to MBHs (e.g. a putative $10^3\,\rm M_{\odot }$ black hole inspiralling on to Sgr A*).
Radio and X-ray detections of GX 339–4 in quiescence using MeerKAT and Swift
Authors: Tremou E , Corbel S , Fender R P , Woudt P A , Miller-Jones J C A , Motta S E , Heywood I , Armstrong R P , Groot P , Horesh A , van der Horst A J , Koerding E , Mooley K P , Rowlinson A , Wijers R A M J
Published: February 2020

The radio–X-ray correlation that characterizes accreting black holes at all mass scales – from stellar mass black holes in binary systems to supermassive black holes powering active galactic nuclei – is one of the most important pieces of observational evidence supporting the existence of a connection between the accretion process and the generation of collimated outflows – or jets – in accreting systems. Although recent studies suggest that the correlation extends down to low luminosities, only a handful of stellar mass black holes have been clearly detected, and in general only upper limits (especially at radio wavelengths) can be obtained during quiescence. We recently obtained detections of the black hole X-ray binary (XRB) GX 339–4 in quiescence using the Meer Karoo Array Telescope (MeerKAT) radio telescope and Swift X-ray Telescope instrument on board the Neil Gehrels Swift Observatory, probing the lower end of the radio–X-ray correlation. We present the properties of accretion and of the connected generation of jets in the poorly studied low-accretion rate regime for this canonical black hole XRB system.
Impact of Pictorial Cigarette Warnings Compared With Surgeon General’s Warnings on Understanding of the Negative Health Consequences of Smoking
Authors: Pepper Jessica K , Nguyen Zarndt Anh , Eggers Matthew E , Nonnemaker James M , Portnoy David B
Published: February 2020

Introduction

The Family Smoking Prevention and Tobacco Control Act requires cigarette packages and advertisements to bear health warnings with “color graphics depicting the negative health consequences of smoking.”

Aims and Methods

This study assessed whether new US Food and Drug Administration developed pictorial cigarette warnings (PCW) increased understanding of smoking-related risks relative to the current Surgeon General’s (SG) warnings. In March–May 2019, adolescent and adult smokers and nonsmokers participated in an online experiment with three sessions completed over approximately 2 weeks. Participants viewed 1 of 16 PCW (treatment conditions) or an SG warning (control) on mock cigarette packages and advertisements. Measures assessed whether warnings provided new information, induced thinking about risks, changed smoking-related health beliefs, and were accurately recalled, among other outcomes.

Results

The majority of PCW (≥13 conditions) resulted in greater learning of new information, higher self-reported learning, and greater reports of thinking about smoking risks; they were viewed as more informative, understandable, and attention-drawing compared with the control condition. Most participants believed the warning were factual, although 8 PCW were perceived as less factual than the control. There were changes toward more agreement with health beliefs for 11 PCW between Sessions 1 and 2 and 7 PCW between Sessions 1 and 3. Participants in all treatment conditions were more likely than control condition participants to correctly recall the warning. Across outcomes, PCW related to addiction, death, and quitting did not perform as well as other PCW.

Conclusions

Many of the PCW tested increased understanding of the risks associated with cigarette smoking relative to current SG warnings.

Implications

The Tobacco Control Act requires cigarette packages and advertisements to bear PCW depicting the negative health consequences of smoking. This study tested whether any of 16 newly proposed PCW increased understanding of smoking-related risks relative to existing SG warnings. Results suggest that most PCW tested, particularly those related to less widely known health effects, resulted in greater learning of new information, higher self-reported learning, and greater reports of thinking about smoking risks compared with SG warnings. These results, along with other factors, informed the US Food and Drug Administration’s selection of proposed PCW.
Palivizumab Prophylaxis for infants 29 to 32 weeks gestation at birth: A 10-year audit from Vancouver Island using BC Guidelines
Authors: Taylor Richard S , Baker Margaret H
Published: February 2020

Background

After initially recommending palivizumab (PVZ), a monoclonal antibody against respiratory syncytial virus (RSV) for all infants 29 to 32 weeks at birth if <6 months age at season start, the American Academy of Pediatrics (AAP) and Canadian Paediatric Society (CPS) guidelines were revised. British Columbia was the only jurisdiction in North America to restrict eligibility for this group to those with additional risk factors, long before the change in national recommendations.

Objectives

To determine the risk for first season RSV admission for 29 to 32-week gestational age (GA) infants admitted to Victoria Neonatal Intensive Care Unit (NICU) that either received or were denied PVZ prophylaxis.

Methods

Descriptive cohort study of infants eligible for prophylaxis according to earlier CPS guidelines. Instead, BC guidelines for prophylaxis were applied and data for Vancouver Island infants were collected over 10 consecutive RSV seasons.

Results

We followed 423 infants. Three hundred and thirty-six (79%) did not receive prophylaxis, of which 10 (3.0%; 95% confidence interval [CI] 1.4% to 5.4%) had an RSV hospitalization before the end of April during their first RSV season versus 3 admissions from 87 (3.5%; 95% CI 0.7% to 10%) infants who received prophylaxis.

Conclusions

Our risk factor approach to RSV prophylaxis for infants born at 29 to 32 weeks GA resulted in a low (average incidence=3.1%) rate of RSV hospitalization. Our approach would offer considerable cost savings to RSV prophylaxis programs that continue to offer routine prophylaxis beyond 28/29 weeks GA at birth.
Understanding Clinicians’ Decisions to Assume Prescriptions for Inherited Patients on Long-term Opioid Therapy: A Qualitative Study
Authors: Keller Michelle S , Jusufagic Alma , Nuckols Teryl K , Needleman Jack , Heilemann MarySue
Published: February 2020

Objective

Given the changing political and social climate around opioids, we examined how clinicians in the outpatient setting made decisions about managing opioid prescriptions for new patients already on long-term opioid therapy.

Methods

We conducted in-depth interviews with 32 clinicians in Southern California who prescribed opioid medications in the outpatient setting for chronic pain. The study design, interview guides, and coding for this qualitative study were guided by constructivist grounded theory methodology.

Results

We identified three approaches to assuming a new patient’s opioid prescriptions. Staunch Opposers, mostly clinicians with specialized training in pain medicine, were averse to continuing opioid prescriptions for new patients and often screened outpatients seeking opioids. Cautious and Conflicted Prescribers were wary about prescribing opioids but were willing to refill prescriptions if they perceived the patient as trustworthy and the medication fell within their comfort zone. Clinicians in the first two groups felt resentful about other clinicians “dumping” patients on opioids on them. Rapport Builders, mostly primary care physicians, were the most willing to assume opioid prescriptions and were strategic in their approach to transitioning patients to safer doses.

Conclusions

Clinicians with the most training in pain management were the least willing to assume responsibility for opioid prescriptions for patients already on long-term opioid therapy. In contrast, primary care clinicians were the most willing to assume this responsibility. However, primary care clinicians face barriers to providing high-quality care for patients with complex pain conditions, such as short visit times and less specialized training.
Depth Sensor–Based Assessment of Reachable Work Space for Visualizing and Quantifying Paretic Upper Extremity Motor Function in People With Stroke
Authors: Okuyama Kohei , Kawakami Michiyuki , Tsuchimoto Shohei , Ogura Miho , Okada Kohsuke , Mizuno Katsuhiro , Ushiba Junichi , Liu Meigen
Published: February 2020

Background

Quantitative evaluation of upper extremity (UE) motor function is important in people with hemiparetic stroke. A depth sensor–based assessment of reachable work space (RWS) was applied to visualize and quantify paretic UE motor function.

Objective

The objectives of this study were to examine the characteristics of RWS and to assess its validity, reliability, measurement error, and responsiveness in people with hemiparetic stroke.

Design

This was a descriptive, repeated-measures, observational study.

Methods

Fifty-eight people with stroke participated. RWS was assessed on both paretic and nonparetic UEs, and the RWS ratio was determined by dividing the RWS of the paretic UE by that of the nonparetic UE. The concurrent validity of the RWS was determined by examining the relationship with the Fugl-Meyer Assessment UE motor score. Test-retest reproducibility was examined in 40 participants. Responsiveness was determined by examining the RWS results before and after 3 weeks of intensive training of the paretic UE in 32 participants.

Results

The lower area of RWS bordering shoulder was significantly larger than the upper area, and the medial-lower area of RWS bordering shoulder was significantly larger than the lateral-lower area. The RWS ratio was highly correlated with the Fugl-Meyer Assessment UE motor score (r = 0.81). The RWS ratio showed good intrarater relative reliability (intraclass correlation coefficient = 0.94) and no fixed or proportional bias. The minimal detectable change of the RWS ratio was 16.6. The responsiveness of the RWS ratio was large (standardized response mean = 0.83).

Limitations

Interexaminer reliability was not assessed.

Conclusions

The RWS assessment showed sufficient validity, reliability, and responsiveness in people with hemiparetic stroke. A depth sensor–based RWS evaluation is useful for visualizing and quantifying paretic UE motor function in the clinical setting.
Hazlitt, De Quincey, and the Politics of Slang
Authors: Covelo Roxanne
Published: February 2020

Literary periodicals like the Quarterly Review and Blackwood’s Magazine were the crucible in which Romantic reputations were made and unmade, debated, compared, and sometimes cruelly slandered. Today, it is often the cruellest of these reviews that survive, cited smilingly by modern critics to demonstrate the originality of the authors in question and their reviewers’ ineptitude or resistance to change. The study of William Hazlitt (who receives what is admittedly some of the harshest treatment of the Romantic periodical press) is often approached in this manner. But without sufficient context, the mere recounting of these attacks may elide the subtleties of Romantic-era reviewing and its particular rules of engagement. The present study attempts a more even-handed approach. By focusing on a specific criticism of Hazlitt’s work—namely, his alleged over-use of slang—and by tracing this criticism through its different iterations across magazines, it provides a more nuanced account of Hazlitt’s reception and, by extension, of the professional culture of reviewing. To the same end, the study also considers the writing of Hazlitt’s contemporary and fellow essayist Thomas De Quincey, whose own use of slang is more frequent and more conspicuous than Hazlitt’s but who, for reasons both professional and political, is spared the same critical vitriol.
Follow-up results of myositis patients treated with H. P. Acthar gel
Authors: Saygin Didem , Oddis Chester V , Marder Galina , Moghadam-Kia Siamak , Nandkumar Preeya , Neiman Nicole , Dzanko Sedin , Koontz Diane , Aggarwal Rohit
Published: February 2020

Objectives

Idiopathic inflammatory myopathies (IIM) are a group of autoimmune diseases characterized by proximal muscle weakness. H. P. Acthar gel [repository corticotropin injection (RCI)] is a formulation of adrenocorticotropic hormone and has been approved by Food and Drug Administration for use in IIM; however, literature is limited. In this study, we report longitudinal follow-up of myositis patients treated with RCI.

Methods

Patients with refractory IIM who were enrolled in the prospective, open-label RCI trial were included in this study. The post-trial follow-up period was 6 months with assessments every 2 months, which included myositis core set measures including extra-muscular global, muscle and patient global disease activities, HAQ, and manual muscle testing.

Results

Two patients were lost to follow-up after finalization of the trial, and the remaining eight patients were enrolled in the follow-up study. One patient remained on RCI after the trial. In the follow-up period, four of eight patients had flare at on average 4.1 months after the RCI trial. Among the patients who flared, three required an increase in prednisone. One patient was restarted on RCI at 5.5 months, but had minimal improvement after 3 months. Four patients who remained stable continued to satisfy criteria for the definition of improvement through the 6-month follow-up. However, none showed any further improvement in the primary or secondary efficacy outcomes after the initial RCI trial.

Conclusion

To our knowledge, this is the first study reporting the follow-up results of patients treated with standard dose and duration of Acthar. We believe that our study will provide the basis for the development of future randomized RCI trials in IIM.
Claiming the Narrative Wave With Story Theory
Authors: Liehr Patricia , Smith Mary Jane
Published: February 2020

Over the past few decades, there has been a narrative wave that has advanced and subsided but consistently moved toward acceptance in health care circles. Despite the importance of narrative to nursing practice and research, the discipline has been slow to claim the narrative wave as its own. The purpose of this article is to claim the narrative wave for the discipline of nursing with story theory–guided research and practice and to describe dimensions of the narrative movement in health-related literature. Practical application of story theory is described for both nursing practice and nursing research.
Genomics to personalize care of prostate cancer
Authors: Connors Laurie M.
Published: February 2020

Prostate cancer is one of the most common cancers for men in the United States. Nurse practitioners need to understand oncology care and potential applications of genetic and genomics for men with prostate cancer. Genetic testing options are available to assist in decision making regarding screening for prostate cancer and the treatment of prostate cancer. Translating and integrating genomic test results can assist health care providers, patients, and their families to determine optimal and personalized oncology care in prostate cancer.
Magnetic Resonance Imaging Assessment After Therapy in Prostate Cancer
Authors: Koopman Anna G.M.M. , Jenniskens Sjoerd F.M. , Fütterer Jurgen J.
Published: February 2020

Prostate cancer is the fifth leading cause of death worldwide. A variety of treatment options is available for localized prostate cancer and may range from active surveillance to focal therapy or whole gland treatment, that is, surgery or radiotherapy. Serum prostate-specific antigen levels are an important tool to monitor treatment success after whole gland treatment, unfortunately prostate-specific antigen is unreliable after focal therapy. Multiparametric magnetic resonance imaging of the prostate is rapidly gaining field in the management of prostate cancer and may play a crucial role in the evaluation of recurrent prostate cancer. This article will focus on postprocedural magnetic resonance imaging after different forms of local therapy in patients with prostate cancer.
Identification of Key Therapy Ingredients for SLPs Serving on Multidisciplinary Teams Facilitating Return to Learn for Students With Prolonged Cognitive Effects After Concussion
Authors: Wright Jim , Sohlberg McKay Moore , Watson-Stites Ryann , McCart Melissa
Published: February 2020

Purpose:

This retrospective case series utilized clinical data mining (CDM) to understand the potential key components in an integrated treatment approach delivered by speech–language pathologists (SLPs) treating adolescents experiencing persistent cognitive effects postconcussion. The first purpose was to describe the profiles of students treated in our clinic, how they were treated, and the nature of multidisciplinary communication. The second purpose was to generate testable hypotheses about effective intervention options for this population.

Methods:

Fifteen students aged 13–18 years experiencing prolonged concussion symptoms (PCS) were referred to our SLP graduate training clinic by a local pediatric neuropsychologist for cognitive rehabilitation services. Clinical data mining extracted clinical data in 4 main categories: (a) student characteristics, (b) SLP treatment parameters, (c) clinical outcomes following SLP treatment, and (d) the nature of multidisciplinary communication between practitioners.

Results:

Aligned with risk factors for PCS as reported in the literature, data on student characteristics revealed that the majority of students had sustained multiple previous concussions and reported a history of depression/anxiety. Data on SLP treatment parameters identified metacognitive strategy instruction and the training of assistive technology for cognition as the most frequent interventions selected to address academic goals. Data showing the frequency and type of multidisciplinary communication revealed that SLPs communicated most often with the pediatric neuropsychologist and educational liaison. Clinical outcome data revealed that 12 of the 15 students achieved their academic goals at the time of discharge.

Conclusions:

Overall, CDM results suggested that when working in a multidisciplinary team, SLPs can provide cognitive rehabilitation, support symptom reduction, and deliver psychoeducation potentially effective for students experiencing PCS. Key treatment and outcome measurement issues important for developing testable interventions are discussed.
Word Learning in Aphasia
Authors: Coran Monica , Rodriguez-Fornells Antoni , Ramos-Escobar Neus , Laine Matti , Martin Nadine
Published: February 2020

Objective:

Of current interest in aphasia research is the relevance of what we can learn from studying word learning ability in aphasia. In a preliminary study, we addressed 2 issues related to the novel word learning ability of individuals with aphasia. First, as word learning engages large-scale cognitive-linguistic systems (language skills, verbal short-term memory [STM], other memory and executive functions), we probed whether novel word learning practice in 3 people with aphasia could stimulate these language-related systems. Second, as lesion correlates affecting word learning in aphasia remain unclear, we examined whether the structural integrity of the left arcuate fasciculus (AF) in the same 3 individuals is related to outcomes of novel word learning practice.

Method:

To stimulate word learning systems, our 3 participants practiced for 4 weeks with an explicit novel word—novel referent word learning task, adopted from the Ancient Farming Equipment learning paradigm (Laine & Salmelin, 2010). The participants' progress on receptive and expressive novel word learning was followed up, and their language and verbal STM abilities as well as single-session novel word learning (Learning to Name Aliens by Gupta, Martin, Abbs, Schwartz, & Lipinski, 2006) were tested before and after the practice period. To address the second question, we analyzed the participants' structural magnetic resonance images with respect to the integrity of the left AF and its overlap with the lesion areas.

Results:

All participants showed some receptive word learning in the trained task, as well as improvements in verbal STM span at posttesting. Two of the 3 participants also showed improved performance on some of the language outcome measures. One participant with a partially spared left AF, especially temporoparietal connections, exhibited better word learning performance than the other 2 who had larger damage and disconnection of the AF.

Conclusions:

Although the present results are preliminary, they open the possibility that novel word learning practice in aphasia may stimulate remaining word learning mechanisms in aphasia and thereby influence language and verbal STM abilities. These results also suggest that preservation of novel word learning ability in aphasia in part depends on the integrity of the left arcuate track.
Pseudolysobacter antarcticus gen. nov., sp. nov., isolated from soil in Fildes Peninsula, Antarctica
Authors: Wei Ziyan , Wu Tong , Huang Yao , Zhu Guoxin , Zhang Yumin , Geng Yingchao , Peng Fang
Published: February 2020

A novel strain, designated AQ6-296T, was isolated from a soil sample collected in Fildes Peninsula, Antarctic. Cells were Gram-stain-negative, non-endospore-forming, non-motile, strictly aerobic and rod-shaped. Growth occurred at 4–28 °C (optimum, 20 °C) and at pH 6.0–7.0 (optimum, pH 7.0). NaCl was not obligatory for growth. Colonies were pale yellow after growth for 3 days at 20 °C on Reasoner's 2A agar. The strain was weakly positive for oxidase and the catalase test was negative. The only respiratory quinone was Q-8. The predominant cellular fatty acids were iso-C16 : 0, iso-C15 : 0, iso-C11 : 0 3OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 010-methyl). The major polar lipids were phosphatidylethanolamine, unknown aminolipids, phosphatidylglycerol and diphosphatidylglycerol. The results of phylogenetic analysis based on 16S rRNA gene sequences (the highest similarity at 92.4 % to

Lysobacter dokdonensis

) indicated that strain AQ6-296T is within the family

Xanthomonadaceae

. The DNA G+C content of the type strain was 58.6 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain AQ6-296T is considered to represent a novel genus and species in the family

Xanthomonadaceae

, for which the name Pseudolysobacter antarcticus gen. nov., sp. nov. is proposed. The type strain is AQ6-296T (CCTCC AB 2016313T=KCTC 52744T).
Fast assessment of human receptor-binding capability of 2019 novel coronavirus (2019-nCoV)
Authors: Huang Qiang , Herrmann Andreas
Published: February 2020

The outbreaks of 2002/2003 SARS, 2012/2015 MERS and 2019/2020 Wuhan respiratory syndrome clearly indicate that genome evolution of an animal coronavirus (CoV) may enable it to acquire human transmission ability, and thereby to cause serious threats to global public health. It is widely accepted that CoV human transmission is driven by the interactions of its spike protein (S-protein) with human receptor on host cell surface; so, quantitative evaluation of these interactions may be used to assess the human transmission capability of CoVs. However, quantitative methods directly using viral genome data are still lacking. Here, we perform large-scale protein-protein docking to quantify the interactions of 2019-nCoV S-protein receptor-binding domain (S-RBD) with human receptor ACE2, based on experimental SARS-CoV S-RBD-ACE2 complex structure. By sampling a large number of thermodynamically probable binding conformations with Monte Carlo algorithm, this approach successfully identified the experimental complex structure as the lowest-energy receptor-binding conformations, and hence established an experiment-based strength reference for evaluating the receptor-binding affinity of 2019-nCoV via comparison with SARS-CoV. Our results show that this binding affinity is about 73% of that of SARS-CoV, supporting that 2019-nCoV may cause human transmission similar to that of SARS-CoV. Thus, this study presents a method for rapidly assessing the human transmission capability of a newly emerged CoV and its mutant strains, and demonstrates that post-genome analysis of protein-protein interactions may provide early scientific guidance for viral prevention and control.
Stability of synchronous states in sparse neuronal networks
Authors: Afifurrahman  , Ullner Ekkehard , Politi Antonio
Published: February 2020

The stability of synchronous states is analysed in the context of two populations of inhibitory and excitatory neurons, characterized by different pulse-widths. The problem is reduced to that of determining the eigenvalues of a suitable class of sparse random matrices, randomness being a consequence of the network structure. A detailed analysis, which includes also the study of finite-amplitude perturbations, is performed in the limit of narrow pulses, finding that the stability depends crucially on the relative pulse-width. This has implications for the overall property of the asynchronous (balanced) regime.
Phylogenomics of monitor lizards and the role of competition in dictating body size disparity
Authors: Brennan Ian G. , Lemmon Alan R. , Lemmon Emily Moriarty , Portik Daniel M. , Weijola Valter , Welton Luke , Donnellan Stephen C. , Keogh J.Scott
Published: February 2020

Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragonVaranus komodoensisand the smallest Australian dwarf goannas,Varanuslength and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. We use a phylogenomic approach to estimate the relationships among living and extinct varaniform lizards, incorporating both exon-capture molecular and morphological datasets. Our results suggest that communities of AustralianVaranusshow high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.
Fast Transport of RNA Granules by Direct Interactions with KIF5A/KLC1 Motors Prevents Axon Degeneration
Authors: Fukuda Yusuke , Pazyra-Murphy Maria F. , Tasdemir-Yilmaz Ozge E. , Li Yihang , Rose Lillian , Yeoh Zoe C. , Vangos Nicholas E. , Geffken Ezekiel A. , Seo Hyuk-Soo , Adelmant Guillaume , Bird Gregory H. , Walensky Loren D. , Marto Jarrod A. , Dhe-Paganon Sirano , Segal Rosalind A.
Published: February 2020

Complex neural circuitry requires stable connections formed by lengthy axons. To maintain these functional circuits, fast transport delivers RNAs to distal axons where they undergo local translation. However, the mechanism that enables long distance transport of non-membrane enclosed organelles such as RNA granules is not known. Here we demonstrate that a complex containing RNA and the RNA-binding protein (RBP) SFPQ interacts directly with a tetrameric kinesin containing the adaptor KLC1 and the motor KIF5A. We show that binding of SFPQ to KIF5A/KLC1 motor complex is required for axon survival and is impacted by KIF5A mutations that cause Charcot-Marie-Tooth (CMT) Disease. Moreover, therapeutic approaches that bypass the need for local translation of SFPQ-bound proteins prevent axon degeneration in CMT models. Collectively, these observations show that non-membrane enclosed organelles can move autonomously and that replacing axonally translated proteins provides a therapeutic approach to axonal degenerative disorders.
ConditionalLpar1gene targeting identifies cell types mediating neuropathic pain
Authors: Rivera Richard R. , Lin Mu-En , Bornhop Emily C. , Chun Jerold
Published: February 2020

LPA1is one of the six known receptors (LPA1-6) for lysophosphatidic acid (LPA). ConstitutiveLpar1null mutant mice have been instrumental in identifying roles for LPA-LPA1signaling in neurobiological processes, brain development, and behavior as well as modelling human neurological diseases like neuropathic pain. ConstitutiveLpar1null mutant mice are protected from partial sciatic nerve ligation (PSNL)-induced neuropathic pain, howeverLpar1expressing cell types that are functionally responsible for mediating this protective effect are unknown. Here we report generation of aLpar1flox/floxconditional null mutant mouse that allows cre-mediated conditional deletion combined with its use in a PSNL pain model.Lpar1flox/floxmice were crossed withcretransgenic lines driven by neural gene promoters fornestin(all neural cells),synapsin(neurons), orP0(Schwann cells).CD11b-cretransgenic mice were also used to deleteLpar1in microglia. PSNL-initiated pain responses were reduced following cre-mediatedLpar1deletion with all 3 neural promoters but not the microglial promoter, supporting involvement of Schwann cells and central and/or peripheral neurons in mediating pain. Interestingly, rescue responses that were due to conditional deletion were non-identical, implicating distinct roles forLpar1-expressing cell types. Our results with a newLpar1conditional mouse mutant expand an understanding of LPA1signaling in the PSNL model of neuropathic pain.
Similarities in the behaviour of dance followers among honey bee species suggest a conserved mechanism of dance communication
Authors: George Ebi Antony , Pimplikar Smruti , Thulasi Neethu , Brockmann Axel
Published: February 2020

Group living organisms rely on intra-group communication to adjust individual and collective behavioural decisions. Complex communication systems are predominantly multimodal and combine modulatory and information bearing signals. The honey bee waggle dance, one of the most elaborate forms of communication in invertebrates, stimulates nestmates to search for food and communicates symbolic information about the location of the food source. Previous studies on the dance behaviour in diverse honey bee species demonstrated distinct differences in the combination of visual, auditory, olfactory, and tactile signals produced by the dancer. We now studied the behaviour of the receivers of the dance signals, the dance followers, to explore the significance of the different signals in the communication process. In particular, we ask whether there are differences in the behaviour of dance followers between the 3 major Asian honey bee species,A. florea, A. dorsata and A. cerana, and whether these might correlate with the differences in the signals produced by the dancing foragers. Our comparison demonstrates that the behaviour of the dance followers is highly conserved across all 3 species despite the differences in the dance signals. The highest number of followers was present lateral to the dancer throughout the waggle run, and the mean body orientation of the dance followers with respect to the waggle dancer was close to 90° throughout the run for all 3 species. These findings suggest that dance communication might be more conserved than implied by the differences in the signals produced by the dancer. Along with studies inA. mellifera, our results indicate that all honey bee species rely on tactile contacts between the dancer and follower to communicate spatial information. The cues and signals that differ between the species may be involved in attracting the followers towards the dancer in the different nest environments.
Tumor susceptibility gene-101 regulates glucocorticoid receptor through disorder-mediated allostery
Authors: White Jordan T. , Rives James , Tharp Marla E. , Wrabl James O. , Thompson E. Brad , Hilser Vincent J.
Published: February 2020

Tumor Susceptibility Gene-101 (TSG101) is involved in endosomal maturation and has been implicated in the transcriptional regulation of several steroid hormone receptors (SHRs), although a detailed characterization of such regulation has yet to be conducted. Here we directly measure binding of TSG101 to one SHR, glucocorticoid receptor (GR). Using biophysical and cellular assays, we show that the coiled-coil domain of TSG101; 1) binds and folds the disordered N-terminal domain (NTD) of GR, 2) upon binding, improves DNA-binding of GRin vitro, and 3) enhances the transcriptional activity of GRin vivo. Our findings suggest that TSG101 is abona fidetranscriptional co-regulator of GR.
CRISPR-mediated biocontainment
Authors: Castanon Oscar , Smith Cory J. , Khoshakhlagh Parastoo , Ferreira Raphael , Güell Marc , Said Khaled , Yildiz Ramazan , Dysart Matthew , Wang Stan , Thompson David , Myllykallio Hannu , Church George M.
Published: February 2020

We have exploited the repetitive nature of transposable elements of the human genome to generate synthetic circuits. Transposable elements such as LINE-1 and Alu have successfully replicated in mammalian genomes throughout evolution to reach a copy number ranging from thousands to more than a million. Targeting these repetitive elements with programmable DNA nucleases such as CRISPR-Cas9 rapidly induce extremely high levels of cell death. We use this genotoxic feature to build synthetic biocontainment circuits: CRISPR defense system (CRISPR-DS) capable of preventing CRISPR genome editing, and we introduce the proof-of-concept of CRISPR Safety-Switch, an inducible, stringent and non-leaky kill-switch capable of clearing out cell lines resistant to DNA breaks.
Enhanced stress tolerance through reduction of G3BP and suppression of stress granules
Authors: Lee Anna K. , Klein Jonathon , Tacer Klementina Fon , Lord Tessa , Oatley Melissa J. , Oatley Jon M. , Porter Shaina N. , Pruett-Miller Shondra M. , Tikhonova Elena B. , Karamyshev Andrey L. , Yang Peiguo , Kim Hong Joo , Taylor J. Paul , Potts Patrick Ryan
Published: February 2020

Stress granules (SG) are membrane-less ribonucleoprotein condensates that form in response to various stress stimuli via phase separation. SG act as a protective mechanism to cope with acute stress, but persistent SG have cytotoxic effects that are associated with several age-related diseases. Here, we demonstrate that the testis-specific protein, MAGE-B2, increases cellular stress tolerance by suppressing SG formation through translational inhibition of the key SG nucleator G3BP. MAGE-B2 reduces G3BP protein levels below the critical concentration for phase separation and suppresses SG initiation. Importantly, knockout of the MAGE-B2 mouse ortholog confers hypersensitivity of the male germline to heat stressin vivo. Thus, MAGE-B2 provides cytoprotection to maintain mammalian spermatogenesis, a highly thermo-sensitive process that must be preserved throughout reproductive life. These results demonstrate a mechanism that allows for tissue-specific resistance against stress through fine-tuning phase separation and could aid in the development of male fertility therapies.
Poecivirus is present in individuals with beak deformities in seven species of North American birds
Authors: Zylberberg Maxine , Van Hemert Caroline , Handel Colleen M. , Liu Rachel M. , DeRisi Joseph L.
Published: February 2020

Avian keratin disorder (AKD), a disease characterized by debilitating beak overgrowth but with unknown etiology, has increasingly affected wild bird populations since the 1990s. We previously showed that a novel picornavirus, Poecivirus, is closely correlated with disease status in Black-capped Chickadees (Poecile atricapillus) in Alaska. However, our knowledge of the relationship between Poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of Poecivirus: Mew Gull (Larus canus), Hairy Woodpecker (Picoides villosus), Black-billed Magpie (Pica hudsonia), Northwestern Crow (Corvus caurinus), Red-breasted Nuthatch (Sitta canadensis), and Blackpoll Warbler (Setophaga striata); individuals were sampled in Alaska and Maine (1999-2016). We used targeted PCR followed by Sanger sequencing to test for the presence of Poecivirus in each specimen, and to obtain viral genome sequence from virus-positive host individuals. We detected Poecivirus in all individuals tested, but not in negative controls. Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two Northwestern Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequence from several specimens, including the complete coding region of Poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that Poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that Poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.
Human cytomegalovirus protein pUL36: a dual cell death pathway inhibitor
Authors: Fletcher-Etherington Alice , Nobre Luis , Nightingale Katie , Antrobus Robin , Nichols Jenna , Davison Andrew J. , Stanton Richard J. , Weekes Michael P.
Published: February 2020

Human cytomegalovirus (HCMV) is an important human pathogen and a paradigm of intrinsic, innate and adaptive viral immune evasion. Here, we employed multiplexed tandem mass tag-based proteomics to characterise host proteins targeted for degradation late during HCMV infection. This approach revealed that mixed lineage kinase domain-like protein (MLKL), a key terminal mediator of cellular necroptosis, was rapidly and persistently degraded by the minimally passaged HCMV strain Merlin but not the extensively passaged strain AD169. The strain Merlin viral inhibitor of apoptosis pUL36 was necessary and sufficient both to degrade MLKL and to inhibit necroptosis. Furthermore, mutation of pUL36 Cys131abrogated MLKL degradation and restored necroptosis. As the same residue is also required for pUL36-mediated inhibition of apoptosis by preventing proteolytic activation of pro-caspase 8, we define pUL36 as a multifunctional inhibitor of both apoptotic and necroptotic cell death.

SIGNIFICANCE STATEMENT

Cell death is a key defence against viral infection, preventing spread from infected to uninfected cells. Correspondingly, certain viruses encode inhibitors of apoptotic and necroptotic cell death pathways in order to facilitate their persistence. Human cytomegalovirus (HCMV) is an important human pathogen that can block apoptosis, but hitherto it has been unclear whether or how the virus blocks necroptosis. Here, we used a proteomic screen to identify human proteins targeted for destruction by HCMV, finding that the key necroptosis mediator MLKL is degraded throughout infection. MLKL is targeted for degradation by HCMV protein pUL36, which is also instrumental in inhibiting apoptosis. Thus, pUL36 is a dual cell death pathway inhibitor, and may represent an important therapeutic target.