bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Perfect Storm: Increased Colonization and Failure of Vaccination Leads to Severe Secondary Bacterial Infection in Influenza Virus-Infected Obese Mice
Authors: Karlsson Erik A. , Meliopoulos Victoria A. , van de Velde Nicholas C. , van de Velde Lee-Ann , Mann Beth , Gao Geli , Rosch Jason , Tuomanen Elaine , McCullers Jon , Vogel Peter , Schultz-Cherry Stacey 
Published: September 2017

ABSTRACT

Obesity is a risk factor for developing severe disease following influenza virus infection; however, the comorbidity of obesity and secondary bacterial infection, a serious complication of influenza virus infections, is unknown. To fill this gap in knowledge, lean and obese C57BL/6 mice were infected with a nonlethal dose of influenza virus followed by a nonlethal dose of
Streptococcus pneumoniae
. Strikingly, not only did significantly enhanced death occur in obese coinfected mice compared to lean controls, but also high mortality was seen irrespective of influenza virus strain, bacterial strain, or timing of coinfection. This result was unexpected, given that most influenza virus strains, especially seasonal human A and B viruses, are nonlethal in this model. Both viral and bacterial titers were increased in the upper respiratory tract and lungs of obese animals as early as days 1 and 2 post-bacterial infection, leading to a significant decrease in lung function. This increased bacterial load correlated with extensive cellular damage and upregulation of platelet-activating factor receptor, a host receptor central to pneumococcal invasion. Importantly, while vaccination of obese mice against either influenza virus or pneumococcus failed to confer protection, antibiotic treatment was able to resolve secondary bacterial infection-associated mortality. Overall, secondary bacterial pneumonia could be a widespread, unaddressed public health problem in an increasingly obese population.

IMPORTANCE
Worldwide obesity rates have continued to increase. Obesity is associated with increased severity of influenza virus infection; however, very little is known about respiratory coinfections in this expanding, high-risk population. Our studies utilized a coinfection model to show that obesity increases mortality from secondary bacterial infection following influenza virus challenge through a “perfect storm” of host factors that lead to excessive viral and bacterial outgrowth. In addition, we found that vaccination of obese mice against either virus or bacteria failed to confer protection against coinfection, but antibiotic treatment did alleviate mortality. Combined, these results represent an understudied and imminent public health concern in a weighty portion of the global population.
Picornaviruses and Apoptosis: Subversion of Cell Death
Authors: Croft Sarah N. , Walker Erin J. , Ghildyal Reena 
Published: September 2017

ABSTRACTInfected cells can undergo apoptosis as a protective response to viral infection, thereby limiting viral infection. As viruses require a viable cell for replication, the death of the cell limits cellular functions that are required for virus replication and propagation. Picornaviruses are single-stranded RNA viruses that modify the host cell apoptotic response, probably in order to promote viral replication, largely as a function of the viral proteases 2A, 3C, and 3CD. These proteases are essential for viral polyprotein processing and also cleave cellular proteins.Picornavirusproteases cleave proapoptotic adaptor proteins, resulting in downregulation of apoptosis.Picornavirusproteases also cleave nucleoporins, disrupting the orchestrated manner in which signaling pathways use active nucleocytoplasmic trafficking, including those involved in apoptosis. In addition to viral proteases, the transmembrane 2B protein alters intracellular ion signaling, which may also modulate apoptosis. Overall, picornaviruses, via the action of virally encoded proteins, exercise intricate control over and subvert cell death pathways, specifically apoptosis, thereby allowing viral replication to continue.
Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology
Authors: Tanouchi Yu , Covert Markus W. 
Published: September 2017

ABSTRACT

During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host
Escherichia coli
genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance. Importantly, the new technologies that we developed to enable this study—sequencing secondary sites using next-generation sequencing and then selecting relevant lysogens using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based selection—are broadly applicable to other phage-bacterium systems.

IMPORTANCE
Bacteriophages play an important role in bacterial evolution through lysogeny, where the phage genome is integrated into the host chromosome. While phage integration generally occurs at a specific site in the host chromosome, it is also known to occur at other, so-called secondary sites. In this study, we developed a new experimental technology to comprehensively study secondary integration sites and discovered that phage can integrate into over 300 unique sites in the host genome, resulting in significant genetic diversity in bacteria. We further developed an assay to examine the phenotypic consequence of such diverse integration events and found that phage integration can cause changes in evolutionarily relevant traits such as bacterial motility and increases in antibiotic resistance. Importantly, our method is readily applicable to other phage-bacterium systems.
Economic volatility in childhood and subsequent adolescent mental health problems: a longitudinal population-based study of adolescents
Authors: Bøe Tormod , Skogen Jens Christoffer , Sivertsen Børge , Hysing Mari , Petrie Keith J , Dearing Eric , Zachrisson Henrik Daae 
Published: September 2017

ObjectiveThe aim of the current paper was to investigate the association between the patterns of duration, timing and sequencing of exposure to low family income during childhood, and symptoms of mental health problems in adolescence.SettingSurvey administered to a large population-based sample of Norwegian adolescents.ParticipantsSurvey data from 9154 participants of 16–19 years age (53% participation rate; 52.7% girls) were linked to registry-based information about childhood family income from tax return data.Outcome measuresMental health outcomes were symptoms of emotional, conduct, hyperactivity, peer problems and general mental health problems measured with the Strengths and Difficulties Questionnaire, symptoms of depression measured with Short Mood and Feelings Questionnaire and symptoms of attention-deficit/hyperactivity disorder (ADHD) measured with the Adult ADHD Self-Report Scale.ResultsLatent class analysis and the BCH approach in Mplus were used to examine associations between patterns of poverty exposure and mental health outcomes. Four latent classes of poverty exposure emerged from the analysis. Participants moving into poverty (2.3%), out of poverty (3.5%) or those chronically poor (3.1%) had more symptoms of mental health problems (Cohen’sd=16-.50) than those with no poverty exposure (91.1%). This pattern was, however, not found for symptoms of ADHD. The pattern of results was confirmed in robustness checks using observed data.ConclusionsExposure to poverty in childhood was found to be associated with most mental health problems in adolescence. There was no strong suggestion of any timing or sequencing effects in the patterns of associations.
REACH: study protocol of a randomised trial of rehabilitation very early in congenital hemiplegia
Authors: Boyd Roslyn N , Ziviani Jenny , Sakzewski Leanne , Novak Iona , Badawi Nadia , Pannek Kerstin , Elliott Catherine , Greaves Susan , Guzzetta Andrea , Whittingham Koa , Valentine Jane , Morgan Cathy , Wallen Margaret , Eliasson Ann-Christin , Findlay Lisa , Ware Robert , Fiori Simona , Rose Stephen 
Published: September 2017

ObjectivesCongenital hemiplegia is the most common form of cerebral palsy (CP). Children with unilateral CP show signs of upper limb asymmetry by 8 months corrected age (ca) but are frequently not referred to therapy until after 12 months ca. This study compares the efficacy of infant-friendly modified constraint-induced movement therapy (Baby mCIMT) to infant friendly bimanual therapy (Baby BIM) on upper limb, cognitive and neuroplasticity outcomes in a multisite randomised comparison trial.Methods and analysis150 infants (75 in each group), aged between 3 and 6 months ca, with asymmetric brain injury and clinical signs of upper extremity asymmetry will be recruited. Children will be randomised centrally to receive equal doses of either Baby mCIMT or Baby BIM. Baby mCIMT comprises restraint of the unimpaired hand using a simple restraint (eg, glove, sock), combined with intensive parent implemented practice focusing on active use of the impaired hand in a play-based context. In contrast, Baby BIM promotes active play requiring both hands in a play-based context. Both interventions will be delivered by parents at home with monthly home visits and interim telecommunication support by study therapists. Assessments will be conducted at study entry; at 6, 12 months ca immediately postintervention (primary outcome) and 24 months ca (retention). The primary outcome will be the Mini-Assisting Hand Assessment. Secondary outcomes include the Bayley Scale for Infant and Toddler Development (cognitive and motor domains) and the Hand Assessment of Infants. A subset of children will undertake MRI scans at 24 months ca to evaluate brain lesion severity and brain (re)organisation after intervention.Ethics and disseminationFull ethical approvals for this study have been obtained from the relevant sites. The findings will be disseminated in peer-reviewed publications.Trial registration numberAustralian and New Zealand Clinical Trials Registry: ACTRN12615000180516, Pre results.
Psychological distress and ischaemic heart disease: cause or consequence? Evidence from a large prospective cohort study
Authors: Welsh Jennifer , Korda Rosemary J , Joshy Grace , Butterworth Peter , Brown Alex , Banks Emily 
Published: September 2017

BackgroundIschaemic heart disease (IHD) incidence is elevated in people reporting psychological distress. The extent to which this relationship is causal or related to reverse causality—that is, undiagnosed disease causing distress—is unclear. We quantified the relationship between psychological distress and IHD, with consideration of confounding and undiagnosed disease.MethodsQuestionnaire data (2006–2009) from 151 811 cardiovascular disease-free and cancer-free Australian general population members aged ≥45years (45 and Up Study) were linked to hospitalisation and mortality data, to December 2013. A two-stage approach estimated HRs for incident IHD (IHD-related hospitalisation or death) for low (Kessler-10 scores: 10–<12), mild (12–<16), moderate (16–<22) and high (22–50) psychological distress, adjusting for demographic and behavioural characteristics, and then restricting to those with no/minor functioning limitations (likely free from undiagnosed disease).ResultsOver 859 396 person-years, 5230 incident IHD events occurred (rate: 6.09/1000person-years). IHD risk was increased for mild (age-adjusted and sex-adjusted HR: 1.18, 95% CI 1.11 to 1.26), moderate (1.36, 1.25 to 1.47), and high (1.69, 1.52 to 1.88) versus low distress. HRs attenuated to 1.15 (1.08 to 1.22), 1.26 (1.16 to 1.37) and 1.41 (1.26 to 1.57) after adjustment for demographic and behavioural characteristics and were further attenuated by 35%–41% in those with no/minor limitations, leaving a significant but relatively weak dose-response relationship: 1.11 (1.02 to 1.20), 1.21 (1.08 to 1.37) and 1.24 (1.02 to 1.51) for mild, moderate and high versus low distress, respectively. The observed adjustment-related attenuation suggests measurement error/residual confounding likely contribute to the remaining association.ConclusionA substantial part of the distress-IHD association is explained by confounding and functional limitations, an indicator of undiagnosed disease. Emphasis should be on psychological distress as a marker of healthcare need and IHD risk, rather than a causative factor.
Towards laboratory detection of topological vortices in superfluid phases of QCD
Authors: Das Arpan , Dave Shreyansh S. , De Somnath , Srivastava Ajit M. 
Published: September 2017

Topological defects arise in a variety of systems, e.g. vortices in superfluid helium to cosmic strings in the early universe. There is an indirect evidence of neutron superfluid vortices from the glitches in pulsars. One also expects that the topological defects may arise in various high baryon density phases of quantum chromodynamics (QCD), e.g. superfluid topological vortices in the color flavor locked (CFL) phase. Though vastly different in energy/length scales, there are universal features in the formation of all these defects. Utilizing this universality, we investigate the possibility of detecting these topological superfluid vortices in laboratory experiments, namely heavy-ion collisions (HICs). Using hydrodynamic simulations, we show that vortices can qualitatively affect the power spectrum of flow fluctuations. This can give an unambiguous signal for superfluid transition resulting in vortices, allowing for the check of defect formation theories in a relativistic quantum field theory system, and the detection of superfluid phases of QCD. Detection of nucleonic superfluid vortices in low energy HICs will give opportunity for laboratory controlled study of their properties, providing crucial inputs for the physics of pulsars.
Holocene source rock deposition in the Black Sea, insights from a dropcore study offshore Bulgaria
Authors: Fallah M. , Mayer J. , Tari G. , Baur J. 
Published: September 2017

Abstract
One of the main issues in source rock evaluation has always been the availability of thermally immature samples, which would represent the same source rock quality and facies as the mature source rock within the deeper parts of the basin. Forty dropcore sample locations from shallow depths beneath the present-day seafloor were selected and analysed for mineral composition and bulk geochemical parameters. The water depths of the samples range from shelfal to bathyal environments. The quartz content of the samples clearly decreases with increasing distance from sedimentary input sources (e.g. river deltas), whereas clay content increases towards the distal areas. Mass movements (e.g. slides and debris flows) along the present-day shelf are recognizable on the bathymetry, as well as in the mineral content. Bulk geochemical parameters show that currently only poor to fair gas-prone source rocks are deposited within the study area. This lack of source rock quality, as well as organic content, is attributed to the fine-grained sedimentary input from the Danube river. These fine-grained sediments decrease the organic productivity due to dulling (decrease in the thickness of the photic zone) of the water column, and dilute the currently deposited source rock with low TOC sediments. These effects decrease with distance from the Danube delta, as indicated by published data from outside the study area. Additionally mass movements along the present-day shelf rework possible source rocks. The results of this study clearly show that anoxic conditions alone are not sufficient for source rock deposition. Distance from major sedimentary input and basin geometry are of major importance, and should be considered in basin modelling.
Interacting with Recommenders—Overview and Research Directions
Authors: Jugovac Michael , Jannach Dietmar 
Published: September 2017

Automated recommendations have become a ubiquitous part of today’s online user experience. These systems point us to additional items to purchase in online shops, they make suggestions to us on movies to watch, or recommend us people to connect with on social websites. In many of today’s applications, however, the only way for users to interact with the system is to inspect the recommended items. Often, no mechanisms are implemented for users to give the system feedback on the recommendations or to explicitly specify preferences, which can limit the potential overall value of the system for its users.
Academic research in recommender systems is largely focused on algorithmic approaches for item selection and ranking. Nonetheless, over the years a variety of proposals were made on how to design more interactive recommenders. This work provides a comprehensive overview on the existing literature on user interaction aspects in recommender systems. We cover existing approaches for preference elicitation and result presentation, as well as proposals that consider recommendation as an interactive process. Throughout the work, we furthermore discuss examples of real-world systems and outline possible directions for future works.
Electronic Social Capital for Self-Organising Multi-Agent Systems
Authors: Petruzzi Patricio E. , Pitt Jeremy , Busquets Dídac 
Published: September 2017

It is a recurring requirement in open systems, such as networks, distributed systems, and socio-technical systems, that a group of agents must coordinate their behaviour for the common good. In those systems—where agents are heterogeneous—unexpected behaviour can occur due to errors or malice. Agents whose practices free-ride the system can be accepted to a certain level; however, not only do they put the stability of the system at risk, but they also compromise the agents that behave according to the system’s rules.In social systems, it has been observed thatsocial capitalis an attribute of individuals that enhances their ability to solve collective action problems. Sociologists have studied collective action through human societies and observed that social capital plays an important role in maintaining communities though time as well as in simplifying the decision-making in them. In this work, we explore the use of Electronic Social Capital for optimising self-organised collective action.We developed a context-independent Electronic Social Capital framework to test this hypothesis. The framework comprises a set of handlers that capture events from the system and update three different forms of social capital: trustworthiness, networks, and institutions. Later, a set of metrics are generated by the forms of social capital and used for decision-making. The framework was tested in different scenarios such as two-player games,n-player games, and public goods games. The experimental results show that social capital optimises the outcomes (in terms of long-term satisfaction and utility), reduces the complexity of decision-making, and scales with the size of the population.This work proposes an alternative solution using Electronic Social Capital to represent and reason with qualitative, instead of traditional quantitative, values. This solution could be embedded into socio-technical systems to incentivise collective action without commodifying the resources or actions in the system.
Nonuniform surround suppression of visual responses in mouse V1
Authors: Samonds Jason M. , Feese Berquin D. , Lee Tai Sing , Kuhlman Sandra J. 
Published: September 2017

Complex receptive field characteristics, distributed across a population of neurons, are thought to be critical for solving perceptual inference problems that arise during motion and image segmentation. For example, in a class of neurons referred to as “end-stopped,” increasing the length of stimuli outside of the bar-responsive region into the surround suppresses responsiveness. It is unknown whether these properties exist for receptive field surrounds in the mouse. We examined surround modulation in layer 2/3 neurons of the primary visual cortex in mice using two-photon calcium imaging. We found that surround suppression was significantly asymmetric in 17% of the visually responsive neurons examined. Furthermore, the magnitude of asymmetry was correlated with orientation selectivity. Our results demonstrate that neurons in mouse primary visual cortex are differentially sensitive to the addition of elements in the surround and that individual neurons can be described as being either uniformly suppressed by the surround, end-stopped, or side-stopped. NEW & NOTEWORTHY Perception of visual scenes requires active integration of both local and global features to successfully segment objects from the background. Although the underlying circuitry and development of perceptual inference is not well understood, converging evidence indicates that asymmetry and diversity in surround modulation are likely fundamental for these computations. We determined that these key features are present in the mouse. Our results support the mouse as a model to explore the neural basis and development of surround modulation as it relates to perceptual inference.
Coupling of synaptic inputs to local cortical activity differs among neurons and adapts after stimulus onset
Authors: Wright Nathaniel C. , Hoseini Mahmood S. , Yasar Tansel Baran , Wessel Ralf 
Published: September 2017

Cortical activity contributes significantly to the high variability of sensory responses of interconnected pyramidal neurons, which has crucial implications for sensory coding. Yet, largely because of technical limitations of in vivo intracellular recordings, the coupling of a pyramidal neuron’s synaptic inputs to the local cortical activity has evaded full understanding. Here we obtained excitatory synaptic conductance ( g) measurements from putative pyramidal neurons and local field potential (LFP) recordings from adjacent cortical circuits during visual processing in the turtle whole brain ex vivo preparation. We found a range of g-LFP coupling across neurons. Importantly, for a given neuron, g-LFP coupling increased at stimulus onset and then relaxed toward intermediate values during continued visual stimulation. A model network with clustered connectivity and synaptic depression reproduced both the diversity and the dynamics of g-LFP coupling. In conclusion, these results establish a rich dependence of single-neuron responses on anatomical, synaptic, and emergent network properties. NEW & NOTEWORTHY Cortical neurons are strongly influenced by the networks in which they are embedded. To understand sensory processing, we must identify the nature of this influence and its underlying mechanisms. Here we investigate synaptic inputs to cortical neurons, and the nearby local field potential, during visual processing. We find a range of neuron-to-network coupling across cortical neurons. This coupling is dynamically modulated during visual processing via biophysical and emergent network properties.