bluuebunny/crossref_metadata_2025 huggingface dataset:
Spinal Cord Stimulator Infection: Approach to Diagnosis, Management, and Prevention
Authors: Esquer Garrigos Zerelda , Farid Saira , Bendel Markus A , Sohail M Rizwan
Published: October 2019

Spinal cord stimulation (SCS) is the most utilized invasive electrical neuromodulation treatment for the management of refractory chronic pain syndromes. Infection is one of the most dreaded complications related to SCS implantation and may prevent patients from receiving adequate pain treatment, adding to the initial cost and disability. Most SCS infections present as generator pocket infection. However, delay in diagnosis may lead to complications such as meningitis, epidural abscess, and/or vertebral osteomyelitis. Early recognition of SCS-related infections and associated complications is based on clinical suspicion, laboratory testing, and appropriate diagnostic imaging. While superficial surgical site infection following SCS implant may be treated with antibiotic therapy alone, deep infection involving implant warrants device removal to achieve cure. Duration of antimicrobial therapy depends on severity of clinical presentation and presence or absence of associated complications. Several preventive strategies can be incorporated in surgical practice to reduce the risk of SCS infection.
Resistance of IID Noise in Differentially Private Schemes for Trajectory Publishing
Authors: Wang Hao , Li Kaiju
Published: October 2019

Although analyzing and mining user’s trajectory data can provide outstanding benefit, data owners may not be willing to upload their trajectory data because of privacy concerns. Recently, differential privacy technology has achieved a good trade-off between data utility and privacy preserving by publishing noisy outputs, and relevant schemes have been proposed for trajectory release. However, we experimentally find that a relatively accurate estimate of the true data value can still be obtained from the noisy outputs by means of a posterior estimation. But there are no practical mechanisms against current schemes to verify their effectiveness and resistance. To fill this gap, we propose a solution to evaluate the resistance performance of differential privacy on trajectory data release, including a notion of correlation-distinguishability filtering (CDF) and a privacy quantification measurement. Specifically, taking advantage of the principle of filtering that independent noise can be filtered out from correlated sequence, CDF is proposed to sanitize the noise added into the trajectory. To conduct this notion in practice, we attempt to apply a Kalman/particle filter to filter out the corresponding Gaussian/Laplace noise added by differential privacy schemes. Furthermore, to quantify the distortion of privacy strength before and after filtering, an entropy-based privacy quantification metric is proposed, which is used to measure the lost uncertainty of the true locations for an adversary. Experimental results show that the resistance performance of current approaches has a degradation to varying degrees under the filtering attack model in our solution. Moreover, the privacy quantification metric can be regarded as a unified criterion to measure the privacy strength introduced by the noise that does not conform to the form required by differential privacy.
Computing Grounded Extensions Of Abstract Argumentation Frameworks
Authors: Nofal Samer , Atkinson Katie , Dunne Paul E
Published: October 2019

An abstract argumentation framework is a directed graph $(V,E)$ such that the vertices of $V$ denote abstract arguments and $E \subseteq V \times V$ represents the attack relation between them. We present a new ad hoc algorithm for computing the grounded extension of an abstract argumentation framework. We show that the new algorithm runs in $\mathcal{O}(|V|+|E|)$ time. In contrast, the existing state-of-the-art algorithm runs in $\mathcal{O}(|V|+|S||E|)$ time where $S$ is the grounded extension of the input graph.
Sender and receiver experience alters the response of fish to disturbance cues
Authors: Goldman Jack A , Feyten Laurence E A , Ramnarine Indar W , Brown Grant E
Published: October 2019

Predation is a pervasive selection pressure, shaping morphological, physiological, and behavioral phenotypes of prey species. Recent studies have begun to examine how the effects of individual experience with predation risk shapes the use of publicly available risk assessment cues. Here, we investigated the effects of prior predation risk experience on disturbance cue production and use by Trinidadian guppies Poecilia reticulata under laboratory conditions. In our first experiment, we demonstrate that the response of guppies from a high predation population (Lopinot River) was dependent upon the source of disturbance cue senders (high vs. low predation populations). However, guppies collected from a low predation site (Upper Aripo River) exhibited similar responses to disturbance cues, regardless of the sender population. In our second experiment, we used laboratory strain guppies exposed to high versus low background risk conditions. Our results show an analogous response patterns as shown for our first experiment. Guppies exposed to high background risk conditions exhibited stronger responses to the disturbance cues collected from senders exposed to high (vs. low) risk conditions and guppies exposed to low risk conditions were not influenced by sender experience. Combined, our results suggest that experience with background predation risk significantly impacts both the production of and response to disturbance cues in guppies.
The haemodynamic basis of lung congestion during exercise in heart failure with preserved ejection fraction
Authors: Reddy Yogesh N V , Obokata Masaru , Wiley Brandon , Koepp Katlyn E , Jorgenson Caitlin C , Egbe Alexander , Melenovsky Vojtech , Carter Rickey E , Borlaug Barry A
Published: October 2019

Aims 

Increases in extravascular lung water (EVLW) during exercise contribute to symptoms, morbidity, and mortality in patients with heart failure and preserved ejection fraction (HFpEF), but the mechanisms leading to pulmonary congestion during exercise are not well-understood.

Methods and results 

Compensated, ambulatory patients with HFpEF (n = 61) underwent invasive haemodynamic exercise testing using high-fidelity micromanometers with simultaneous lung ultrasound, echocardiography, and expired gas analysis at rest and during submaximal exercise. The presence or absence of EVLW was determined by lung ultrasound to evaluate for sonographic B-line artefacts. An increase in EVLW during exercise was observed in 33 patients (HFpEFLW+, 54%), while 28 (46%) did not develop EVLW (HFpEFLW−). Resting left ventricular function was similar in the groups, but right ventricular (RV) dysfunction was two-fold more common in HFpEFLW+ (64 vs. 31%), with lower RV systolic velocity and RV fractional area change. As compared to HFpEFLW−, the HFpEFLW+ group displayed higher pulmonary capillary wedge pressure (PCWP), higher pulmonary artery (PA) pressures, worse RV-PA coupling, and higher right atrial (RA) pressures during exercise, with increased haemoconcentration indicating greater loss of water from the vascular space. The development of lung congestion during exercise was significantly associated with elevations in PCWP and RA pressure as well as impairments in RV-PA coupling (area under the curve values 0.76–0.84).

Conclusion 

Over half of stable outpatients with HFpEF develop increases in interstitial lung water, even during submaximal exercise. The acute development of lung congestion is correlated with increases in pulmonary capillary hydrostatic pressure that favours fluid filtration, and systemic venous hypertension due to altered RV-PA coupling, which may interfere with fluid clearance.

Clinical trial registration 

NCT02885636.
Emergence of Lyme disease as a social problem: analysis of discourse using the media content
Authors: Pascal Clélia , Arquembourg Jocelyne , Vorilhon Philippe , Lesens Olivier
Published: October 2019

Background

Chronic Lyme disease (LD) is a matter of debate worldwide and has emerged as a social problem. We aim to analyze the media content and describe the transformation process of a collective pain into a social problem in France.

Methods

Using social science methodology, a corpus of articles from 20 newspapers and videos from seven major TV stations from 1987 to 2017 were analyzed for discourse content. The speaking times and the frequency of interventions between doctors supporting the official guidelines and those against them were compared using the Mann–Whitney test and the Chi-square test, respectively.

Results

In France, the media discourse is carried through testimonials from patient organizations and a professor of infectiology who acted as a whistleblower (WB). We showed that the emergence of the LD alert in the media corresponds to the process described by social sciences as ‘naming, blaming, claiming’. Since his first article in 2014, the WB has featured in 24% (22/89) of newspaper articles compared with 20% (18/89) for doctors defending the official guidelines (P = 0.52). Since his first appearance on a TV newscast in 2014, the WB has appeared in 45% (22/49) of news reports on LD with 24% of the speaking time compared with 22% (11/49) for doctors defending the official guidelines (P = 0.018).

Conclusions

Media coverage of LD has been unbalanced since 2014 and promotes associations as well as the WB, who seems to be better identified than any of the different doctors defending the official guidelines.
Social determinants of sleep disturbance in safety-net primary care: unmet needs, classist discrimination, and anxiety
Authors: Tan Joseph S , Cariello Annahir N , Pugh Mickeal , Henry Richard S , Perrin Paul B , Dautovich Natalie D , Rybarczyk Bruce
Published: October 2019

Background

The 3P model proposes that predisposing, precipitating, and perpetuating factors all play a role in sleep disturbance.

Objective

The purpose of the current study is to investigate social determinants of sleep disturbance by applying the 3P model to a safety-net primary care setting, specifically by evaluating the role of classism and unmet needs as precipitating factors for sleep disturbance, and anxiety as a perpetuating factor for sleep disturbance.

Methods

Participants (N = 210) were a convenience sample of racially/ethnically diverse adults over the age of 18 (age M = 44.7 years) recruited from a safety-net primary care clinic in an urban area. The study employed a cross-sectional design. Participants completed a survey assessing sleep disturbances, anxiety, unmet needs, classism, social support, and a researcher-generated demographic form.

Results and Conclusions

The unmet need for affordable long-term housing and greater experiences of classism were associated with more sleep disturbance, suggesting that both acted as precipitating factors. In a structural equation model with adequate fit indices, anxiety mediated the relationships with sleep disturbance for both the unmet need for affordable long-term housing and classism, suggesting that it serves as a perpetuating factor. Medical providers are recommended to explore these potential needs in safety-net primary care when patients present with sleep disturbance or anxiety. Assisting with connections to long-term housing and helping patients counteract and cope with classist discrimination may be effective in improving sleep in safety-net primary care.
Health literacy among Malawian HIV-positive youth: a qualitative needs assessment and conceptualization
Authors: Uwamahoro Nadege Sandrine , Ngwira Bagrey , Vinther-Jensen Kirsten , Rowlands Gill
Published: October 2019

Despite growing evidence of the significance of health literacy in managing and coping with acquired immune deficiency syndrome (HIV), it is not yet an integrated part of HIV/AIDS-related health promotion research and practice in Africa. This article contributes to addressing the gap in research on health literacy and HIV in Sub-Saharan Africa. We aimed to assess health literacy-related needs of young people living with HIV (YPLHIV) and adapt existing health literacy frameworks to the context of HIV/AIDS in Malawi. We used focus group discussions to collect data from a sample of the membership of the national association of YPLHIV. Twenty-four HIV-positive youth (18–29 years) participated in focus group discussions. Participants came from three regions of Malawi. Additionally, we conducted three in-depth interviews with key informants. We used a thematic framework approach to analyse data in MAXQDA. We contextualized definitions of four dimensions of health literacy: functional, interactive, critical and distributed health literacy, which we used as an a priori analytical framework. To further contextualize the framework, we revised it iteratively throughout the analysis process. We identified the need for comprehensive information about HIV and sexual reproductive health, skills to interact with healthcare providers and navigate the health system, and skills to appraise information from different sources, among others. The identified needs were translated into nine action recommendations for the national association of YPLHIV, and with relevance within the wider HIV sector in Malawi and beyond. We found that the dimensions in our analytical framework operate on the individual, system and public policy levels.
Hookah is the enemy of health campaign: a campaign for prevention of hookah smoking among youth
Authors: Sadeghi Reza , Mazloomy Mahmoodabad Seyed Saeed , Fallahzadeh Hossein , Rezaeian Mohsen , Bidaki Reza , Khanjani Narges
Published: October 2019

Hookah smoking is now a serious health threat especially for adolescents. Implementation of planned interventions can help reduce hookah smoking. This study was conducted to investigate the effect of a campaign Hookah is the Enemy of Health Campaign (HEHC) based on the protection motivation theory to prevent hookah smoking among the youth in Sirjan city, in 2018. This was a pre- and post-intervention study. Participants were 280 male and female youth who were selected randomly through the health centers of Sirjan. The educational campaign was conducted during 3 months and participants were trained through interpersonal, group, organizational and community channels and mass media. Data were collected by filling out a questionnaire (containing 64 questions) by the participant before the intervention and 3 months after. Data were analyzed by descriptive statistics (frequency and percentage), chi-square and Wilcoxon signed-rank test by SPSS20 software. The prevalence of hookah smoking was 44.3% in the target group. There was a significant change in the mean scores of knowledge and perceived susceptibility, perceived severity, response efficiency, self-efficacy, rewards, fear and protection motivation after the HEHC (p < 0.05), but there was no significant difference in the structure of perceived cost (p > 0.05). Also, the prevalence of hookah smoking among the target group for those who had ever consumed decreased from 8.9 to 4% and for those who used it occasionally decreased from 35 to 19.4%. The HEHC was effective in reducing hookah smoking, raising knowledge and improving the constructs of the protection motivation theory among the youth of Sirjan.
Why staff at European schools abstain from enforcing smoke-free policies on persistent violators
Authors: Schreuders Michael , Linnansaari Anu , Lindfors Pirjo , van den Putte Bas , Kunst Anton E
Published: October 2019

Secondary schools in European countries increasingly implement comprehensive smoke-free school policies (SFSPs) that prohibit most or even all adolescents from smoking during school hours. Consistent enforcement of SFSPs is essential for realizing optimum effectiveness. A main challenge represents adolescents who persistently violate the rules. We studied how staff in European countries respond to these persistent violators and why they may turn a blind eye. We used interview transcripts from 69 staff members at 22 schools in 6 European countries to identify cases in which staff turned a blind eye. We then applied thematic analysis for identifying the considerations as to why they turn a blind eye. Turning a blind eye on persistent violators happened among school staff in all six countries. Three considerations were identified. First, staff believe their primary role and duty is to support all adolescents to develop into well-functioning adults, and sometimes it is best to accept smoking. Second, staff expect that applying stricter disciplinary measures will not stop persistent violators and is more likely to create more severe problems. Third, staff do not feel supported by relevant actors in society (e.g. parents) in influencing adolescent smoking. We conclude that staff’s considerations stress the need to support school staff in enforcing the increasingly comprehensive rules on the most persistent smokers.
Elmod3 knockout leads to progressive hearing loss and abnormalities in cochlear hair cell stereocilia
Authors: Li Wu , Feng Yong , Chen Anhai , Li Taoxi , Huang Sida , Liu Jing , Liu Xianlin , Liu Yalan , Gao Jiangang , Yan Denise , Sun Jie , Mei Lingyun , Liu Xuezhong , Ling Jie
Published: October 2019

ELMOD3, an ARL2 GTPase-activating protein, is implicated in causing hearing impairment in humans. However, the specific role of ELMOD3 in auditory function is still far from being elucidated. In the present study, we used the CRISPR/Cas9 technology to establish an Elmod3 knockout mice line in the C57BL/6 background (hereinafter referred to as Elmod3−/− mice) and investigated the role of Elmod3 in the cochlea and auditory function. Elmod3−/− mice started to exhibit hearing loss from 2 months of age, and the deafness progressed with aging, while the vestibular function of Elmod3−/− mice was normal. We also observed that Elmod3−/− mice showed thinning and receding hair cells in the organ of Corti and much lower expression of F-actin cytoskeleton in the cochlea compared with wild-type mice. The deafness associated with the mutation may be caused by cochlear hair cells dysfunction, which manifests with shortening and fusion of inner hair cells stereocilia and progressive degeneration of outer hair cells stereocilia. Our finding associates Elmod3 deficiencies with stereocilia dysmorphologies and reveals that they might play roles in the actin cytoskeleton dynamics in cochlear hair cells, and thus relate to hearing impairment.
A genome-wide association study implicates multiple mechanisms influencing raised urinary albumin–creatinine ratio
Authors: Casanova Francesco , Tyrrell Jessica , Beaumont Robin N , Ji Yingjie , Jones Samuel E , Hattersley Andrew T , Weedon Michael N , Murray Anna , Shore Angela C , Frayling Timothy M , Wood Andrew R
Published: October 2019

Raised albumin–creatinine ratio (ACR) is an indicator of microvascular damage and renal disease. We aimed to identify genetic variants associated with raised ACR and study the implications of carrying multiple ACR-raising alleles with metabolic and vascular-related disease. We performed a genome-wide association study of ACR using 437 027 individuals from the UK Biobank in the discovery phase, 54 527 more than previous studies, and followed up our findings in independent studies. We identified 62 independent associations with ACR across 56 loci (P < 5 × 10–8), of which 20 were not previously reported. Pathway analyses and the identification of 20 of the 62 variants (at r2 > 0.8) coinciding with signals for at least 16 related metabolic and vascular traits, suggested multiple pathways leading to raised ACR levels. After excluding variants at the CUBN locus, known to alter ACR via effects on renal absorption, an ACR genetic risk score was associated with a higher risk of hypertension, and less strongly, type 2 diabetes and stroke. For some rare genotype combinations at the CUBN locus, most individuals had ACR levels above the microalbuminuria clinical threshold. Contrary to our hypothesis, individuals carrying more CUBN ACR-raising alleles, and above the clinical threshold, had a higher frequency of vascular disease. The CUBN allele effects on ACR were twice as strong in people with diabetes—a result robust to an optimization-algorithm approach to simulating interactions, validating previously reported gene–diabetes interactions (P ≤ 4 × 10–5). In conclusion, a variety of genetic mechanisms and traits contribute to variation in ACR.
When Polls Disagree: How Competitive Results and Methodological Quality Shape Partisan Perceptions of Polls and Electoral Predictions
Authors: Kuru Ozan , Pasek Josh , Traugott Michael W
Published: October 2019

This study leverages a survey experiment in the lead up to the 2016 U.S. presidential election to evaluate how partisan biases, poll results, and their methodological quality interact to shape people’s assessments of polling accuracy and electoral expectations. In a nationally representative sample, we find that individuals disproportionately find polls more credible when their preferred candidate is leading. Partisan biases are mitigated when the polls themselves vary in objective indicators of quality: while more educated respondents are more likely to identify high-quality polls accurately, low education respondents’ bias was reduced when they encountered polls with varying methodological quality. Finally, these moderators influence respondents’ electoral expectations as well. We discuss the implications for journalistic coverage of polls, public opinion, and political polarization.
The Influence of Behavioral, Social, and Environmental Factors on Reproducibility and Replicability in Aquatic Animal Models
Authors: Lieggi Christine , Kalueff Allan V , Lawrence Christian , Collymore Chereen
Published: October 2019

The publication of reproducible, replicable, and translatable data in studies utilizing animal models is a scientific, practical, and ethical necessity. This requires careful planning and execution of experiments and accurate reporting of results. Recognition that numerous developmental, environmental, and test-related factors can affect experimental outcomes is essential for a quality study design. Factors commonly considered when designing studies utilizing aquatic animal species include strain, sex, or age of the animal; water quality; temperature; and acoustic and light conditions. However, in the aquatic environment, it is equally important to consider normal species behavior, group dynamics, stocking density, and environmental complexity, including tank design and structural enrichment. Here, we will outline normal species and social behavior of 2 commonly used aquatic species: zebrafish (Danio rerio) and Xenopus (X. laevis and X. tropicalis). We also provide examples as to how these behaviors and the complexity of the tank environment can influence research results and provide general recommendations to assist with improvement of reproducibility and replicability, particularly as it pertains to behavior and environmental complexity, when utilizing these popular aquatic models.
Randomized, Blinded, Dose-Ranging Trial of an Ebola Virus Glycoprotein Nanoparticle Vaccine With Matrix-M Adjuvant in Healthy Adults
Authors: Fries Louis , Cho Iksung , Krähling Verena , Fehling Sarah K , Strecker Thomas , Becker Stephan , Hooper Jay W , Kwilas Steven A , Agrawal Sapeckshita , Wen Judy , Lewis Maggie , Fix Amy , Thomas Nigel , Flyer David , Smith Gale , Glenn Gregory
Published: October 2019

Background

Ebola virus (EBOV) epidemics pose a major public health risk. There currently is no licensed human vaccine against EBOV. The safety and immunogenicity of a recombinant EBOV glycoprotein (GP) nanoparticle vaccine formulated with or without Matrix-M adjuvant were evaluated to support vaccine development.

Methods

A phase 1, placebo-controlled, dose-escalation trial was conducted in 230 healthy adults to evaluate 4 EBOV GP antigen doses as single- or 2-dose regimens with or without adjuvant. Safety and immunogenicity were assessed through 1-year postdosing.

Results

All EBOV GP vaccine formulations were well tolerated. Receipt of 2 doses of EBOV GP with adjuvant showed a rapid increase in anti-EBOV GP immunoglobulin G titers with peak titers observed on Day 35 representing 498- to 754-fold increases from baseline; no evidence of an antigen dose response was observed. Serum EBOV-neutralizing and binding antibodies using wild-type Zaire EBOV (ZEBOV) or pseudovirion assays were 3- to 9-fold higher among recipients of 2-dose EBOV GP with adjuvant, compared with placebo on Day 35, which persisted through 1 year.

Conclusions

Ebola virus GP vaccine with Matrix-M adjuvant is well tolerated and elicits a robust and persistent immune response. These data suggest that further development of this candidate vaccine for prevention of EBOV disease is warranted.
The growing nostalgia for past regulatory misadventures and the risk of repeating these mistakes with Big Tech
Authors: Wilson Christine S , Klovers Keith
Published: October 2019

Digital markets are increasingly described as the ‘railroads’ of the 21st century. Extending that metaphor, some commentators argue we should revive stale railroad-era economic regulations and adapt them to the digital age. This enthusiasm appears to be buoyed by both a sudden nostalgia for railroad and airline regulations once administered by the Interstate Commerce Commission (ICC) and the Civil Aeronautics Board (CAB) and an equally sudden amnesia of the enormous harm those regulations caused to consumers. ICC and CAB regulations are indeed an apt metaphor, as they illustrate perfectly how sectoral regulations sold to the public as simple, clear, and cheap can go awry. Ultimately, a bipartisan consensus emerged to disband those agencies and deregulate those industries. After deregulation, prices fell, output expanded, and firms innovated. Proposals to regulate Big Tech today in a similar fashion forget these important lessons. We should know better than to do the same thing again today and expect a different result.
Trickle-Round Signals: When Low Status Is Mixed with High
Authors: Bellezza Silvia , Berger Jonah
Published: October 2019

Trickle-down theories suggest that status symbols and fashion trends originate from the elites and move downward, but some high-end restaurants serve lowbrow food (e.g., potato chips, macaroni and cheese), and some high-status individuals wear downscale clothing (e.g., ripped jeans, duct-taped shoes). Why would high-status actors adopt items traditionally associated with low-status groups? Using a signaling perspective to explain this phenomenon, the authors suggest that elites sometimes adopt items associated with low-status groups as a costly signal to distinguish themselves from middle-status individuals. As a result, signals sometimes trickle round, moving directly from the lower to the upper class, before diffusing to the middle class. Furthermore, consistent with a signaling perspective, the presence of multiple signaling dimensions facilitates this effect, enabling the highs to mix and match high and low signals and differentiate themselves. These findings deepen the understanding of signaling dynamics, support a trickle-round theory of fashion, and shed light on alternative status symbols.
Prognosis viewing for nasopharyngeal carcinoma treated with intensity-modulated radiation therapy: application of nomogram and decision curve analysis
Authors: Fei Zhaodong , Qiu Xiufang , Li Mengying , Chen Chuanben , Li Yi , Huang Yingying
Published: October 2019

Objective

To view and evaluate the prognosis factors in patients with nasopharyngeal carcinoma (NPC) treated with intensity modulated radiation therapy using nomogram and decision curve analysis (DCA).

Methods

Based on a primary cohort comprising consecutive patients with newly confirmed NPC (n = 1140) treated between January 2014 and December 2015, we identified independent prognostic factors of overall survival (OS) to establish a nomogram. The model was assessed by bootstrap internal validation and external validation in an independent validation cohort of 460 patients treated between January 2013 and December 2013. The predictive accuracy and discriminative ability were measured by calibration curve, concordance index (C-index) and risk-group stratification. The clinical usefulness was assessed by DCA.

Results

The nomogram incorporated T-stage, N-stage, age, concurrent chemotherapy and primary tumour volume (PTV). The calibration curve presented good agreement for between the nomogram-predicted OS and the actual measured survival probability in both the primary and validation cohorts. The model showed good discrimination with a C-index of 0.741 in the primary cohort and 0.762 in the validation cohort. The survival curves of different risk-groups were separated clearly. Decision curve analysis demonstrated that the nomogram provided a higher net benefit (NB) across a wider reasonable range of threshold probabilities for predicting OS.

Conclusion

This study presents a predictive nomogram model with accurate prediction and independent discrimination ability compared with combination of T-stage and N-stage. The results of DCA supported the point that PTV can help improve the prognostic ability of T-stage and should be added to the TNM staging system.
Application of focused ion-beam sampling for sidewall-roughness measurement of free-standing sub-μm objects by atomic force microscopy
Authors: Nagatomi Takaharu , Nakao Tatsuya , Fujimoto Yoko
Published: October 2019

In the present study, a free-standing object-sampling technique for microelectromechanical systems (MEMS) is developed to measure their sidewall surface roughnesses by atomic force microscopy (AFM). For this purpose, a conventional focused ion beam (FIB) sampling technique widely used for cross-sectional transmission electron microscope specimen preparation was applied. The sub-nm-order roughness parameters were quantitatively measured for sidewalls of Si-bridge test samples. The roughness parameters were compared before and after H2 annealing treatment, which induced smoothing of the surface by migration of the Si atoms. The reduction in the surface roughness by a factor of approximately one-third with 60-s H2 annealing was quantitatively evaluated by AFM. The present study confirms that the developed FIB–AFM technique is one potential approach for quantitatively evaluating the surface-roughness parameters on the oblique faces of free-standing objects in MEMS devices.
Modelling the post-reionization neutral hydrogen (H i) 21-cm bispectrum
Authors: Sarkar Debanjan , Majumdar Suman , Bharadwaj Somnath
Published: October 2019

Measurements of the post-reionization 21-cm bispectrum $B_{{\rm H\,{\small I}}\, }(\boldsymbol {k_1},\boldsymbol {k_2},\boldsymbol {k_3})$ using various upcoming intensity mapping experiments hold the potential for determining the cosmological parameters at a high level of precision. In this paper, we have estimated the 21-cm bispectrum in the z range 1 ≤ z ≤ 6 using seminumerical simulations of the neutral hydrogen (H i) distribution. We determine the k and z range where the 21-cm bispectrum can be adequately modelled using the predictions of second-order perturbation theory, and we use this to predict the redshift evolution of the linear and quadratic H i bias parameters b1 and b2, respectively. The b1 values are found to decrease nearly linearly with decreasing z, and are in good agreement with earlier predictions obtained by modelling the 21-cm power spectrum $P_{{\rm H\,{\small I}}\, }(k)$. The b2 values fall sharply with decreasing z, becomes zero at z ∼ 3 and attains a nearly constant value b2 ≈ −0.36 at z < 2. We provide polynomial fitting formulas for b1 and b2 as functions of z. The modelling presented here is expected to be useful in future efforts to determine cosmological parameters and constrain primordial non-Gaussianity using the 21-cm bispectrum.
Beyond second-order convergence in simulations of magnetized binary neutron stars with realistic microphysics
Authors: Most E R , Papenfort L Jens , Rezzolla L
Published: October 2019

We investigate the impact of using high-order numerical methods to study the merger of magnetized neutron stars with finite-temperature microphysics and neutrino cooling in full general relativity. By implementing a fourth-order accurate conservative finite-difference scheme we model the inspiral together with the early post-merger and highlight the differences to traditional second-order approaches at the various stages of the simulation. We find that even for finite-temperature equations of state, convergence orders higher than second order can be achieved in the inspiral and post-merger for the gravitational-wave phase. We further demonstrate that the second-order scheme overestimates the amount of proton-rich shock-heated ejecta, which can have an impact on the modelling of the dynamical part of the kilonova emission. Finally, we show that already at low resolution the growth rate of the magnetic energy is consistently resolved by using a fourth-order scheme.
Common envelope to explosion delay time of Type Ia supernovae
Authors: Soker Noam
Published: October 2019

I study the rate of Type Ia supernovae (SNe Ia) within about a million years after the assumed common envelope evolution (CEE) that forms the progenitors of these SNe Ia, and find that the population of SNe Ia with short CEE to explosion delay (CEED) time is ≈few × 0.1 of all SNe Ia. I also claim for an expression for the rate of these SNe Ia that occur at short times after the CEE ($t_{\rm CEED} \lesssim 10^6 {~\rm yr}$), which is different from that of the delay time distribution (DTD) billions of years after star formation. This tentatively hints that the physical processes that determine the short CEED time distribution (CEEDTD) are different (at least to some extent) from those that determine the DTD at billions of years. To reach these conclusions I examine SNe Ia that interact with a circumstellar matter (CSM) within months after explosion, so-called SNe Ia-CSM, and the rate of SNe Ia that on a time-scale of tens to hundreds of years interact with a CSM that might have been a planetary nebula, so-called SNe Ia inside a planetary nebula (SNIPs). I assume that the CSM in these populations results from a CEE, and hence this study is relevant mainly to the core-degenerate (CD) scenario, the double-degenerate (DD) scenario, the double-detonation (DDet) scenario with white dwarf companions, and to the CEE-wind channel of the single-degenerate (SD) scenario.
A DECam view of the diffuse dwarf galaxy Crater II: the colour–magnitude diagram
Authors: Walker A R , Martínez-Vázquez C E , Monelli M , Vivas A K , Bono G , Gallart C , Cassisi S , Andreuzzi G , Bernard E J , Dall’Ora M , Fiorentino G , Nidever D L , Olsen K , Pietrinferni A , Stetson P B
Published: October 2019

We present a deep Blanco/DECam colour–magnitude diagram (CMD) for the large but very diffuse Milky Way satellite dwarf galaxy Crater II. The CMD shows only old stars with a clearly bifurcated subgiant branch (SGB) that feeds a narrow red giant branch. The horizontal branch (HB) shows many RR Lyrae and red HB stars. Comparing the CMD with [Fe/H] = −2.0 and [α/Fe] = + 0.3 alpha-enhanced BaSTI isochrones indicates a mean age of 12.5 Gyr for the main event and a mean age of 10.5 Gyr for the brighter SGB. With such multiple star formation events Crater II shows similarity to more massive dwarfs that have intermediate age populations, however for Crater II there was early quenching of the star formation and no intermediate age or younger stars are present. The spatial distribution of Crater II stars overall is elliptical in the plane of the sky, the detailed distribution shows a lack of strong central concentration, and some inhomogeneities. The 10.5 Gyr subgiant and upper main-sequence stars show a slightly higher central concentration when compared to the 12.5 Gyr population. Matching to Gaia DR2 we find the proper motion of Crater II: μαcos δ = −0.14 ± 0.07, μδ = −0.10 ± 0.04 mas yr−1, approximately perpendicular to the semimajor axis of Crater II. Our results provide constraints on the star formation and chemical enrichment history of Crater II, but cannot definitively determine whether or not substantial mass has been lost over its lifetime.
Impact of X-rays on CO emission from high-z galaxies
Authors: Vallini L , Tielens A G G M , Pallottini A , Gallerani S , Gruppioni C , Carniani S , Pozzi F , Talia M
Published: October 2019

We study the impact of active galactic nuclei (AGNs) on the CO spectral line energy distribution (SLED) of high-z galaxies. In particular, we want to assess if the CO SLED can be used as a probe of AGN activity. To this purpose, we develop a semi-analytical model that takes into account the radiative transfer and the clumpy structure of giant molecular clouds where the CO lines are excited, their distribution in the galaxy disc, and the torus obscuration of the AGN radiation. We study the joint effect on the CO SLED excitation of (i) the X-ray luminosity from the AGNs (LX), (ii) the size of the molecular disc, (iii) the inclination angle (Ω) of the torus with respect to the molecular disc, and (iv) the Giant Molecular Cloud (GMC) mean density. We also discuss the possibility of an enhanced cosmic ray ionization rate (CRIR). We find that the X-ray-dominated region (XDR) generated by the AGNs in every case enhances the CO SLED for J > 5, with increasing excitation of high-J CO lines for increasing X-ray luminosity. Because high-z galaxies are compact, the XDR typically encloses the whole disc, thus its effect can be more important with respect to lower redshift objects. The impact of the XDR can be disentangled from an enhanced CRIR either if $L_\mathrm{ X}\,\gt\, 10^{44} \rm \, erg\, s^{-1}$, or if Ω ≥ 60°. We finally provide predictions on the CO(7–6)/[C ii] and CO(17–16)/[C ii] ratios as a function of LX, which can be relevant for ALMA follow-up of galaxies and quasars previously detected in [C ii].
ProCarbDB: a database of carbohydrate-binding proteins
Authors: Copoiu Liviu , Torres Pedro H M , Ascher David B , Blundell Tom L , Malhotra Sony
Published: October 2019

Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein–carbohydrate interfaces. In order to better understand protein–carbohydrate interactions, we have developed an open-access database, ProCarbDB, which, unlike the Protein Data Bank (PDB), clearly distinguishes between the complete carbohydrate ligands and their monomeric units. ProCarbDB is a comprehensive database containing over 5200 3D X-ray crystal structures of protein–carbohydrate complexes. In ProCarbDB, the complete carbohydrate ligands are annotated and all their interactions are displayed. Users can also select any protein residue in the proximity of the ligand to inspect its interactions with the carbohydrate ligand and with other neighbouring protein residues. Where available, additional curated information on the binding affinity of the complex and the effects of mutations on the binding have also been provided in the database. We believe that ProCarbDB will be an invaluable resource for understanding protein–carbohydrate interfaces. The ProCarbDB web server is freely available at http://www.procarbdb.science/procarb.
Transcriptome visualization and data availability at the Saccharomyces Genome Database
Authors: Ng Patrick C , Wong Edith D , MacPherson Kevin A , Aleksander Suzi , Argasinska Joanna , Dunn Barbara , Nash Robert S , Skrzypek Marek S , Gondwe Felix , Jha Sagar , Karra Kalpana , Weng Shuai , Miyasato Stuart , Simison Matt , Engel Stacia R , Cherry J Michael
Published: October 2019

The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.
Controlling aggregation of cholesterol-modified DNA nanostructures
Authors: Ohmann Alexander , Göpfrich Kerstin , Joshi Himanshu , Thompson Rebecca F , Sobota Diana , Ranson Neil A , Aksimentiev Aleksei , Keyser Ulrich F
Published: October 2019

DNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure–function relationship of membrane-interfacing DNA constructs — a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.
PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation
Authors: Sun Hong , Guo Yangfan , Lan Xiaoping , Jia Jia , Cai Xiaoshu , Zhang Guoqing , Xie Jingjing , Liang Qian , Li Yixue , Yu Guangjun
Published: October 2019

From clinical observations to large-scale sequencing studies, the phenotypic impact of genetic modifiers is evident. To better understand the full spectrum of the genetic contribution to human disease, concerted efforts are needed to construct a useful modifier resource for interpreting the information from sequencing data. Here, we present the PhenoModifier (https://www.biosino.org/PhenoModifier), a manually curated database that provides a comprehensive overview of human genetic modifiers. By manually curating over ten thousand published articles, 3078 records of modifier information were entered into the current version of PhenoModifier, related to 288 different disorders, 2126 genetic modifier variants and 843 distinct modifier genes. To help users probe further into the mechanism of their interested modifier genes, we extended the yeast genetic interaction data and yeast quantitative trait loci to the human and we also integrated GWAS data into the PhenoModifier to assist users in evaluating all possible phenotypes associated with a modifier allele. As the first comprehensive resource of human genetic modifiers, PhenoModifier provides a more complete spectrum of genetic factors contributing to human phenotypic variation. The portal has a broad scientific and clinical scope, spanning activities relevant to variant interpretation for research purposes as well as clinical decision making.
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
Authors: Alcock Brian P , Raphenya Amogelang R , Lau Tammy T Y , Tsang Kara K , Bouchard Mégane , Edalatmand Arman , Huynh William , Nguyen Anna-Lisa V , Cheng Annie A , Liu Sihan , Min Sally Y , Miroshnichenko Anatoly , Tran Hiu-Ki , Werfalli Rafik E , Nasir Jalees A , Oloni Martins , Speicher David J , Florescu Alexandra , Singh Bhavya , Faltyn Mateusz , Hernandez-Koutoucheva Anastasia , Sharma Arjun N , Bordeleau Emily , Pawlowski Andrew C , Zubyk Haley L , Dooley Damion , Griffiths Emma , Maguire Finlay , Winsor Geoff L , Beiko Robert G , Brinkman Fiona S L , Hsiao William W L , Domselaar Gary V , McArthur Andrew G
Published: October 2019

The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD’s Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.
Individual Responsibilities in Partial Compliance: Skilled Health Worker Emigration from Under-Served Regions
Authors: Yuksekdag Yusuf
Published: October 2019

One of the ways to address the effects of skilled worker emigration is to restrict the movement of skilled workers. However, even if skilled workers have responsibilities to assist their compatriots, what if other parties, such as affluent countries or source country governments, do not fulfil their fair share of responsibilities? This discussion raises an interesting problem about how to think of individual responsibilities under partial compliance where other agents (including affluent countries, developing states, or other individuals) do not fulfil their fair share of responsibilities. What is fair to expect from them? Taking health worker emigration as a case in point, I discuss whether the individual health workers’ fair share of responsibilities to address basic health care needs decreases or increases when the other parties do not fulfil their share. First, I review the responsibilities that different stakeholders may hold. Second, I argue that there are strong reasons against increasing or decreasing health workers’ fair share of responsibilities in a situation of partial compliance. I also argue that it is unfair for non-complier states to enforce health workers to fulfil their fair share or take up the slack.