bluuebunny/crossref_metadata_2025 huggingface dataset:
The large genome of Synechococcus moorigangaii CMS01 isolated from a mangrove ecosystem- evidences of motility and adaptive features
Authors: Ghosh Anwesha , Bhadury Punyasloke
Published: December 2020

The whole genome of Synechococcus moorigangaii CMS01 isolated from Indian Sundarbans mangroves of Bay of Bengal is about 5.5 Mbp in size and contains approximately 0.5 Mbp plasmids. Genome annotation revealed total of 5806 genes out of which 5701 were CDSs. Of these, 5616 coding genes with 5616 protein coding CDSs were found. Along with genes coding for essential metabolic proteins, transport proteins and other cellular apparatus, genome also codes for proteins involved in flagella and pilus formation which has not been widely reported before in any coastal species of Synechococcus. The genome contains one incomplete prophage sequence. The genome analysis revealed adaptive features of S. moorigangaii CMS01 and establishes its ubiquitous distribution in coastal water of Bay of Bengal.
GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest
Authors: Wu Qing-Wen , Xia Jun-Feng , Ni Jian-Cheng , Zheng Chun-Hou
Published: December 2020

Predicting disease-related long non-coding RNAs (lncRNAs) is beneficial to finding of new biomarkers for prevention, diagnosis and treatment of complex human diseases. In this paper, we proposed a machine learning techniques-based classification approach to identify disease-related lncRNAs by graph auto-encoder (GAE) and random forest (RF) (GAERF). First, we combined the relationship of lncRNA, miRNA and disease into a heterogeneous network. Then, low-dimensional representation vectors of nodes were learned from the network by GAE, which reduce the dimension and heterogeneity of biological data. Taking these feature vectors as input, we trained a RF classifier to predict new lncRNA-disease associations (LDAs). Related experiment results show that the proposed method for the representation of lncRNA-disease characterizes them accurately. GAERF achieves superior performance owing to the ensemble learning method, outperforming other methods significantly. Moreover, case studies further demonstrated that GAERF is an effective method to predict LDAs.
LDpred2: better, faster, stronger
Authors: Privé Florian , Arbel Julyan , Vilhjálmsson Bjarni J
Published: December 2020

Motivation

Polygenic scores have become a central tool in human genetics research. LDpred is a popular method for deriving polygenic scores based on summary statistics and a matrix of correlation between genetic variants. However, LDpred has limitations that may reduce its predictive performance.

Results

Here, we present LDpred2, a new version of LDpred that addresses these issues. We also provide two new options in LDpred2: a ‘sparse’ option that can learn effects that are exactly 0, and an ‘auto’ option that directly learns the two LDpred parameters from data. We benchmark predictive performance of LDpred2 against the previous version on simulated and real data, demonstrating substantial improvements in robustness and predictive accuracy compared to LDpred1. We then show that LDpred2 also outperforms other polygenic score methods recently developed, with a mean AUC over the 8 real traits analyzed here of 65.1%, compared to 63.8% for lassosum, 62.9% for PRS-CS and 61.5% for SBayesR. Note that LDpred2 provides more accurate polygenic scores when run genome-wide, instead of per chromosome.

Availability and implementation

LDpred2 is implemented in R package bigsnpr.

Supplementary information

Supplementary data are available at Bioinformatics online.
Shiga toxin-producing Escherichia coli diagnosed by Stx PCR: assessing the public health risk of non-O157 strains
Authors: Carroll K.J , Jenkins C , Harvey-Vince L , Mohan K , Balasegaram S
Published: December 2020

Background

The implementation by diagnostic laboratories in England of polymerase chain reaction (PCR) to screen faecal specimens for Shiga toxin-producing Escherichia coli (STEC) has resulted in a significant increase in notifications mainly due to non-O157 strains. The purpose of this study was to develop an approach to public health risk assessment that prioritizes follow-up to cases caused by haemolytic uraemic syndrome (HUS) associated E. coli (HUSEC) strains and minimizes unnecessary actions.

Methods

Epidemiological and microbiological data were prospectively collected from 1 November 2013 to 31 March 2017 and used to compare three risk assessment approaches.

Results

A history of HUS/bloody diarrhoea/age under 6 years and faecal specimens positive for stx-predicted HUSEC with a diagnostic accuracy of 84% (95% CI; 81–88%). STEC isolated by Gastrointestinal Bacteria Reference Unit (GBRU) and stx2 and eae positive predicted HUSEC with a diagnostic accuracy of 99% (95% CI; 98–100%). Risk assessment combining these two tests predicts the most efficient use of resources, predicting that 18% (97/552) of cases would be eligible for follow-up at some stage, 16% (86/552) following local stx PCR results, 1% (7/552) following GBRU results of stx2 and eae status and 0.7% (4/552) following whole-genome sequencing. Follow-up could be stopped in 78% (76/97) of these cases, 97% (74/76) following second stage risk assessment.

Conclusions

This three-stage risk assessment approach prioritizes follow-up to HUSEC and minimizes unnecessary public health actions. We developed it into the algorithm for public health actions included in the updated PHE Guidance for management of STEC published in August 2018.
Divergences in the Control of Mitochondrial Respiration Are Associated With Life-Span Variation in Marine Bivalves
Authors: Rodríguez Enrique , Hakkou Mohammed , Hagen Tory M , Lemieux Hélène , Blier Pierre U
Published: December 2020

The role played by mitochondrial function in the aging process has been a subject of intense debate in the past few decades, as part of the efforts to understand the mechanistic basis of longevity. The mitochondrial oxidative stress theory of aging suggests that a progressive decay of this organelle’s function leads to an exacerbation of oxidative stress, with a deleterious impact on mitochondrial structure and DNA, ultimately promoting aging. Among the traits suspected to be associated with longevity is the variation in the regulation of oxidative phosphorylation, potentially affecting the management of oxidative stress. Longitudinal studies using the framework of metabolic control analysis have shown age-related differences in the flux control of respiration, but this approach has seldom been taken on a comparative scale. Using 4 species of marine bivalves exhibiting a large range of maximum life span (from 28 years to 507 years), we report life-span-related differences in flux control at different steps of the electron transfer system. Increased longevity was characterized by a lower control by NADH (complex I-linked) and Succinate (complex II-linked) pathways, while respiration was strongly controlled by complex IV when compared to shorter-lived species. Complex III exerted strong control over respiration in all species. Furthermore, high longevity was associated with higher citrate synthase activity and lower ATP synthase activity. Relieving the control exerted by the electron entry pathways could be advantageous for reaching higher longevity, leading to increased control by complex IV, the final electron acceptor in the electron transfer system.
Relationship Between Dietary Variety and Frailty in Older Japanese Women During the Period of Restriction on Outings Due to COVID-19
Authors: Otaki Naoto , Yano Megumu , Yokoro Miyuki , Tanino Norikazu , Fukuo Keisuke
Published: December 2020

Objectives

To investigate the relationship between diet and frailty in community-dwelling older adults during the period of restriction on outings due to novel coronavirus disease 2019 (COVID-19).

Method

A mail survey targeting adults aged 65 years or older, including questions on sex, age, height, weight, and social participation, was conducted in May 2020. The participants’ dietary variety score and frailty score were then calculated.

Results

Overall, 322 women aged 65 years or older and who were living in the community were recruited for the study; 253 were finally analyzed. The mean age of the 253 participants was 80.0 ± 6.4 years. The dietary variety score and frailty scores were significantly correlated in the linear regression analysis (β: −0.224, p < .001). In the multivariate regression analysis, these factors remained significantly correlated in Model 1, which was adjusted for age (β: −0.229, p < .001), and Model 2, which was adjusted for age, body mass index, and other confounding factors (β: −0.208, p = .001).

Discussion

Diet was correlated with frailty in older adults living in the community during the period of restriction on outings due to COVID-19.
Remote triggering in Iran: large peak dynamic stress is not the main driver of triggering
Authors: Bansal Abhey Ram , Ghods Abdolreza
Published: December 2020

The study of the dynamic triggering of earthquakes and tremors during large earthquakes at faraway distances is an active area of research. This type of remote dynamic triggering is often found in subduction zones. The Iranian plateau is part of the Alpine–Himalayan orogenic system and hosts different collision styles of deformation and significant strike-slip faults. Using 13 yr (26 December 2004–8 September 2017) of continuous data of Iranian National Seismic Network (INSN) and some dense temporary networks, for the first time we carried a systematic study of dynamic triggering in Iran during 47 recent large earthquakes with magnitude and depth ranges of 6.4–9.1 and 8–90 km, respectively. We explored the local catalogue of 124 805 events with a magnitude of completeness (Mc) of 1.8 for the study of dynamic triggering but did not find any convincing evidence of dynamic triggering from the catalogue. The waveform data of 24 hr duration around the main events were analysed to find possible dynamic triggering through manual analysis of the waveform, STA/LTA, and beta statistics and found the triggering. We found dynamic triggering in Iran during Sumatra, 26 December 2004, Mw 9.1; Tohoku-Oki, 11 March 2011, Mw 9.1; Indian Ocean, 11 April 2012, Mw8.6 and Baluchistan, 24 September 2013 earthquakes and also possible triggering during Sumatra, 12 September 2007, Mw8.5. Only ∼10 per cent of the analysed earthquakes produced dynamic triggering. The triggering initiates during the passage of high amplitude Love waves and continues through the passage of the Rayleigh waves. We found north, central and eastern regions are more probable for triggering than Zagros and Makran regions. The instances of triggering were not restricted to only a small region, but instead, occurred at multiple locations. We find the onset of tremor correlates with very small stress changes, on the order of 1 kPA. However, the amplitude of the dynamic stresses is not a sufficient condition since some of the areas with considerably larger dynamic stresses are not triggered any seismicity in the region. The backazimuth angle of ∼50° and ∼120° seems to play an important role in the triggering. Teleseismic waves most probable for triggering local earthquakes within NW and central Iran include incoming surface waves with an incident angle of ∼60°–90° with respect to the local fault fabric.
Does tricuspid valve detachment improve outcomes compared with the non-tricuspid valve detachment approach in ventricular septal defect closure?
Authors: Ling Yunfei , Bian Xiaohui , Wang Yue , Qian Yongjun
Published: December 2020

A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was whether the tricuspid valve detachment (TVD) approach to ventricular septal defect repair provides superior outcomes compared with the non-TVD approach. Altogether more than 54 papers were found using the reported search, of which 10 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. A total of 2059 participants were enrolled in the 10 studies, including 2 prospective studies and 8 retrospective studies. Six studies demonstrated a longer cardiopulmonary bypass time or aortic clamp time in the TVD group, whereas 4 studies showed no difference. Only 1 study reported a lower incidence of trivial tricuspid regurgitation in the TVD group, whereas the other 9 studies showed no significant difference. One study showed that a higher incidence of residual shunting occurred in those patients who had indications for TVD but did not perform detachment during surgery. No difference in postoperative residual shunting was demonstrated in the other 9 studies. We conclude that surgeons should be reassured that if TVD is required to repair the ventricular septal defect, although it may lead to longer cardiopulmonary bypass time and cross-clamp times, outcomes are equivalent in terms of the degree of tricuspid regurgitation and incidence of the residual ventricular septal defect.
Clinical Switching Strategies of Various Antidepressants to Vortioxetine in the PREDDICT Trial
Authors: Mills Natalie T , Sampson Emma , Fourrier Célia , Baune Bernhard T
Published: December 2020

Background

Partial response to antidepressant medication as well as relapse and treatment resistance are common in major depressive disorder (MDD). Therefore, for most patients with MDD, there will be a need to consider changing antidepressant medication at some stage during the course of the illness. The PREDDICT study investigates the efficacy of augmenting vortioxetine with celecoxib.

Methods

We describe the method used in the PREDDICT study to change participants, who were already taking antidepressant medication at the time of the screening visit, to vortioxetine. We used a cross-titration to change study participants to vortioxetine.

Results

Of a total of 122 study participants who were randomized to receive vortioxetine plus celecoxib or vortioxetine plus placebo at the study baseline visit, 82 were taking antidepressant medication (other than vortioxetine) prior to randomization. These medications were selective serotonin reuptake inhibitors, serotonin noradrenaline reuptake inhibitors, tricyclic antidepressants, mirtazapine, or agomelatine. Eighty of these 82 participants completed the changeover to vortioxetine as well as the study baseline visit. We found side effects were generally mild during this changeover period. In addition, there was a reduction in mean total Montgomery-Åsberg Depression Rating Scale score of 2.5 (SD 6.0) from study baseline to week 2 and a further reduction in mean total Montgomery-Åsberg Depression Rating Scale of 2.5 (SD 5.9) from week 2 to week 4.

Conclusion

Changing other antidepressants to vortioxetine can be done safely and was generally well-tolerated. However, there are some antidepressant classes, in particular monoamine oxidase inhibitors that require a washout period, which were not represented in this study.

Trial registration

Australian New Zealand Clinical Trials Registry (ANZCTR); ID number 12617000527369p; http://www.anzctr.org.au/ACTRN12617000527369p.aspx
Effectiveness of Palivizumab Against Respiratory Syncytial Virus Hospitalization Among Preterm Infants in a Setting With Year-Round Circulation
Authors: Yeo Kee Thai , Yung Chee Fu , Khoo Poh Choo , Saffari Seyed Ehsan , Sng Jane Swee Peng , How Mee See , Quek Bin Huey
Published: December 2020

Background

The year-round respiratory syncytial virus (RSV) circulation in tropical regions leads to different transmission patterns and burden of disease among infants born very preterm.

Methods

We conducted a retrospective cohort study to estimate the effectiveness of palivizumab in preventing RSV hospitalization at 6 and 12 months after discharge, among infants born at <32 weeks’ gestation in our tropical setting.

Results

A total of 109 infants (26.3%) received palivizumab at discharge, of 415 who were eligible. All patients received ≥4 doses, with 105 infants (96.3%) completing 5 doses. Within 1 year after discharge, there were 35 RSV-associated admissions (3 [2.8%] in the palivizumab vs 32 [10.5%] in the nonpalivizumab group; P = .02). After adjustment for confounders, the effectiveness of palivizumab against RSV hospitalization was estimated to be 90% (95% confidence interval, 10%–99%) up to 6 months after discharge. The median time to RSV hospitalization was shorter in the nonpalivizumab than in the palivizumab group (median [range], 155 [15–358] vs 287 [145–359] days, respectively; P = .11). Five infants (14.3%), all from the nonpalivizumab group, required admission to the intensive care unit.

Conclusions

In our setting with year-round RSV circulation, palivizumab prophylaxis was effective in reducing RSV hospitalization among high-risk preterm infants of <32 weeks’ gestation within the initial 6 months after discharge.
Evaluation of electronic health record-integrated digital health tools to engage hospitalized patients in discharge preparation
Authors: Dalal Anuj K , Piniella Nicholas , Fuller Theresa E , Pong Denise , Pardo Michael , Bessa Nathaniel , Yoon Catherine , Lipsitz Stuart , Schnipper Jeffrey L
Published: December 2020

Objective

To evaluate the effect of electronic health record (EHR)-integrated digital health tools comprised of a checklist and video on transitions-of-care outcomes for patients preparing for discharge.

Materials and Methods

English-speaking, general medicine patients (>18 years) hospitalized at least 24 hours at an academic medical center in Boston, MA were enrolled before and after implementation. A structured checklist and video were administered on a mobile device via a patient portal or web-based survey at least 24 hours prior to anticipated discharge. Checklist responses were available for clinicians to review in real time via an EHR-integrated safety dashboard. The primary outcome was patient activation at discharge assessed by patient activation (PAM)-13. Secondary outcomes included postdischarge patient activation, hospital operational metrics, healthcare resource utilization assessed by 30-day follow-up calls and administrative data and change in patient activation from discharge to 30 days postdischarge.

Results

Of 673 patients approached, 484 (71.9%) enrolled. The proportion of activated patients (PAM level 3 or 4) at discharge was nonsignificantly higher for the 234 postimplementation compared with the 245 preimplementation participants (59.8% vs 56.7%, adjusted OR 1.23 [0.38, 3.96], P = .73). Postimplementation participants reported 3.75 (3.02) concerns via the checklist. Mean length of stay was significantly higher for postimplementation compared with preimplementation participants (10.13 vs 6.21, P < .01). While there was no effect on postdischarge outcomes, there was a nonsignificant decrease in change in patient activation within participants from pre- to postimplementation (adjusted difference-in-difference of −16.1% (9.6), P = .09).

Conclusions

EHR-integrated digital health tools to prepare patients for discharge did not significantly increase patient activation and was associated with a longer length of stay. While issues uncovered by the checklist may have encouraged patients to inquire about their discharge preparedness, other factors associated with patient activation and length of stay may explain our observations. We offer insights for using PAM-13 in context of real-world health-IT implementations.

Trial Registration

NIH US National Library of Medicine, NCT03116074, clinicaltrials.gov
Ziada v. Gantz and Eshel
Authors: Clark Kate
Published: December 2020

Civilians who bring claims against powerful states or their officials, for harm resulting from the conduct of war, face challenges that no single legal procedure can possibly overcome. Certain codified international laws outline specific protections for civilians, but this protective infrastructure stands in the shadow of two creatures of uncodified international customary law: state sovereignty and the immunity of states and their officials. The subject of this case note is a civil claim before a Dutch domestic court, against powerful officials of the state of Israel. The claimant, a Palestinian Dutch national, is attempting to sue the officials for the unlawful killing of six members of his family in the intentional bombing of their home in Gaza in 2014. In January 2020, he set out to establish the Dutch court’s jurisdiction based on an exceptional provision of the Dutch Code of Civil Procedure. This contribution argues that the Dutch court erred in allowing the asserted ‘functional immunity’ of the foreign officials to counter its own jurisdiction.
Dual Nationality and International Criminal Court Jurisdiction
Authors: Wolman Andrew
Published: December 2020

The International Criminal Court (ICC) can exercise jurisdiction over nationals of states parties. However, it has never been clear whether the Court will automatically recognize a nationality that has been conferred by a state party under its domestic law, nor what criteria it would use to evaluate that nationality should it not be automatically accepted. In December 2019, the Office of the Prosecutor made its first formal pronouncement on the question, finding that the ICC does not have jurisdiction over North Koreans, despite their being South Korean nationals under South Korean law, because North Koreans are not able to exercise their rights as South Koreans until accepted as such by application, and on occasion their applications might be refused. In this article, I reject the Prosecutor’s analysis as misguided. I also reject the other main approaches to nationality recognition suggested by scholars, namely a ‘genuine link’ requirement, a deferral to municipal law, and a deferral to municipal law except where a conferral of nationality violates international law. Instead, I propose a functional approach that would respect municipal conferral of nationality unless that conferral unreasonably interferes with the sovereign interests of a non-state party.
A Prospective Evaluation of Xpert MTB/RIF Ultra for Childhood Pulmonary Tuberculosis in Uganda
Authors: Jaganath Devan , Wambi Peter , Reza Tania F , Nakafeero Jascent , Aben Ernest O , Kiconco Emma , Nannyonga Gertrude , Nsereko Moses , Sekadde Moorine P , Mudiope Mary , Kato-Maeda Midori , Starke Jeffrey , Andama Alfred , Mohanty Swomitra , Wobudeya Eric , Cattamanchi Adithya
Published: December 2020

Background

Xpert MTB/RIF Ultra (Xpert Ultra) has improved the sensitivity to detect pulmonary tuberculosis (TB) in adults. However, there have been limited prospective evaluations of its diagnostic accuracy in children.

Methods

We enrolled children undergoing assessment for pulmonary TB in Kampala, Uganda, over a 12-month period. Children received a complete TB evaluation and were classified as Confirmed, Unconfirmed, or Unlikely TB. We calculated the sensitivity and specificity of Xpert Ultra among children with Confirmed vs Unlikely TB. We also determined the diagnostic accuracy with clinical, microbiological, and extended microbiological reference standards (MRSs).

Results

Of the 213 children included, 23 (10.8%) had Confirmed TB, 88 (41.3%) had Unconfirmed TB, and 102 (47.9%) had Unlikely TB. The median age was 3.9 years, 13% were HIV-positive, and 61.5% were underweight. Xpert Ultra sensitivity was 69.6% (95% confidence interval [CI]: 47.1-86.8) among children with Confirmed TB and decreased to 23.4% (95% CI: 15.9-32.4) with the clinical reference standard. Specificity was 100% (95% CI: 96.4-100) among children with Unlikely TB and decreased to 94.7% (95% CI: 90.5-97.4) with a MRS. Sensitivity was 52.9% (95% CI: 35.1-70.2) and specificity 95.5% (95% CI: 91.4-98.1) with the extended MRS. Of the 26 positive Xpert Ultra results, 6 (23.1%) were “Trace-positive,” with most (5/6) occurring in children with Unconfirmed TB.

Conclusions

Xpert Ultra is a useful tool for diagnosing pulmonary TB in children, but there remains a need for more sensitive tests to detect culture-negative TB.
A machine-learning approach to correcting atmospheric seeing in solar flare observations
Authors: Armstrong John A , Fletcher Lyndsay
Published: December 2020

Current post-processing techniques for the correction of atmospheric seeing in solar observations – such as Speckle interferometry and Phase Diversity methods – have limitations when it comes to their reconstructive capabilities of solar flare observations. This, combined with the sporadic nature of flares meaning observers cannot wait until seeing conditions are optimal before taking measurements, means that many ground-based solar flare observations are marred with bad seeing. To combat this, we propose a method for dedicated flare seeing correction based on training a deep neural network to learn to correct artificial seeing from flare observations taken during good seeing conditions. This model uses transfer learning, a novel technique in solar physics, to help learn these corrections. Transfer learning is when another network already trained on similar data is used to influence the learning of the new network. Once trained, the model has been applied to two flare data sets: one from AR12157 on 2014 September 6 and one from AR12673 on 2017 September 6. The results show good corrections to images with bad seeing with a relative error assigned to the estimate based on the performance of the model. Further discussion takes place of improvements to the robustness of the error on these estimates.
Exomoon candidates from transit timing variations: eight Kepler systems with TTVs explainable by photometrically unseen exomoons
Authors: Fox Chris , Wiegert Paul
Published: December 2020

If a transiting exoplanet has a moon, that moon could be detected directly from the transit it produces itself, or indirectly via the transit timing variations (TTVs) it produces in its parent planet. There is a range of parameter space where the Kepler Space Telescope is sensitive to the TTVs exomoons might produce, though the moons themselves would be too small to detect photometrically via their own transits. The Earth’s Moon, for example, produces TTVs of 2.6 min amplitude by causing our planet to move around their mutual centre of mass. This is more than Kepler’s short-cadence interval of 1 min and so nominally detectable (if transit timings can be measured with comparable accuracy), even though the Moon’s transit signature is only 7 per cent that of Earth’s, well below Kepler’s nominal photometric threshold. Here, we examine several Kepler systems, exploring the hypothesis that an exomoon could be detected solely from the TTVs it induces on its host planet. We compare this with the alternate hypothesis that the TTVs are caused by an non-transiting planet in the system. We examine 13 Kepler systems and find 8 where both hypotheses explain the observed TTVs equally well. Though no definitive exomoon detection can be claimed on this basis, the observations are nevertheless completely consistent with a dynamically stable moon small enough to fall below Kepler’s photometric threshold for transit detection, and these systems warrant further observation and analysis.
Explicit symplectic-like integration with corrected map for inseparable Hamiltonian
Authors: Luo Junjie , Lin Weipeng , Yang Lili
Published: December 2020

Symplectic algorithms are widely used for long-term integration of astrophysical problems. However, this technique can only be easily constructed for separable Hamiltonian, as preserving the phase-space structure. Recently, for inseparable Hamiltonian, the fourth-order extended phase-space explicit symplectic-like methods have been developed by using the Yoshida’s triple product with a mid-point map, where the algorithm is more effective, stable and also more accurate, compared with the sequent permutations of momenta and position coordinates, especially for some chaotic case. However, it has been found that, for the cases such as with chaotic orbits of spinning compact binary or circular restricted three-body system, it may cause secular drift in energy error and even more the computation break down. To solve this problem, we have made further improvement on the mid-point map with a momentum-scaling correction, which turns out to behave more stably in long-term evolution and have smaller energy error than previous methods. In particular, it could obtain a comparable phase-space distance as computing from the eighth-order Runge–Kutta method with the same time-step.
Cosmological constraints from higher redshift gamma-ray burst, H ii starburst galaxy, and quasar (and other) data
Authors: Cao Shulei , Ryan Joseph , Khadka Narayan , Ratra Bharat
Published: December 2020

We use higher redshift gamma-ray burst (GRB), H ii starburst galaxy (H iiG), and quasar angular size (QSO-AS) measurements to constrain six spatially flat and non-flat cosmological models. These three sets of cosmological constraints are mutually consistent. Cosmological constraints from a joint analysis of these data sets are largely consistent with currently accelerating cosmological expansion and with cosmological constraints derived from a combined analysis of Hubble parameter (H(z)) and baryon acoustic oscillation (BAO, with Planck-determined baryonic matter density) measurements. A joint analysis of the H(z) + BAO + QSO-AS + H iiG + GRB data provides fairly model-independent determinations of the non-relativistic matter density parameter $\Omega _{\rm m_0}=0.313\pm 0.013$ and the Hubble constant $H_0=69.3\pm 1.2\, \rm {km \, s^{-1} \, Mpc^{-1}}$. These data are consistent with the dark energy being a cosmological constant and with spatial hypersurfaces being flat, but they do not rule out mild dark energy dynamics or a little spatial curvature. We also investigate the effect of including quasar flux measurements in the mix and find no novel conclusions.
GG Carinae: orbital parameters and accretion indicators from phase-resolved spectroscopy and photometry
Authors: Porter Augustus , Grant David , Blundell Katherine , Lee Steven
Published: December 2020

B[e] supergiants are a rare and unusual class of massive and luminous stars, characterized by opaque circumstellar envelopes. GG Carinae is a binary whose primary component is a B[e] supergiant and whose variability has remained unsatisfactorily explained. Using photometric data from ASAS, OMC, and ASAS-SN and spectroscopic data from the Global Jet Watch and FEROS to study visible emission lines, we focus on the variability of the system at its ∼31-d orbital period and constrain the stellar parameters of the primary. There is one photometric minimum per orbital period and, in the emission line spectroscopy, we find a correlation between the amplitude of radial velocity variations and the initial energy of the line species. The spectral behaviour is consistent with the emission lines forming in the primary’s wind, with the variable amplitudes between line species being caused by the less energetic lines forming at larger radii on average. By modelling the atmosphere of the primary, we are able to model the radial velocity variations of the wind lines in order to constrain the orbit of the binary. We find that the binary is even more eccentric than previously believed (e = 0.5 ± 0.03). Using this orbital solution, the system is brightest at periastron and dimmest at apastron, and the shape of the photometric variations at the orbital period can be well described by the variable accretion by the secondary of the primary’s wind. We suggest that the evolutionary history of GG Carinae may need to be re-evaluated in a binary context.
“We Need to Taper.” Interviews with Clinicians and Pharmacists About Use of a Pharmacy-Led Opioid Tapering Program
Authors: Firemark Alison J , Schneider Jennifer L , Kuntz Jennifer L , Papajorgji-Taylor Dea , Dickerson John F , Thorsness Lou Ann , Reese Katherine R , Sullivan Mark D , Debar Lynn L , Smith David H
Published: December 2020

Objective

To identify factors that influence or interfere with referrals by primary care providers (PCPs) to a pharmacist-led telephone-based program to assist patients undergoing opioid tapering. The Support Team Onsite Resource for Management of Pain (STORM) program provides individualized patient care and supports PCPs in managing opioid tapers.

Design

Qualitative interviews were conducted with referring PCPs and STORM staff. Interview guides addressed concepts from the RE-AIM framework, focusing on issues affecting referral to the STORM program.

Setting

An integrated healthcare system (HCS) in the Northwest United States.

Subjects

Thirty-five interviews were conducted with 20 PCPs and 15 STORM staff.

Methods

Constant comparative analysis was used to identify key themes from interviews. A codebook was developed based on interview data and a qualitative software program was used for coding, iterative review, and content analysis. Representative quotes illustrate identified themes.

Results

Use of the STORM opioid tapering program was influenced by PCP, patient, and HCS considerations. Factors motivating use of STORM included lack of PCP time to support chronic pain patients requiring opioid tapering and the perception that STORM is a valued partner in patient care. Impediments to referral included PCP confidence in managing opioid tapering, patient resistance to tapering, forgetting about program availability, and PCP resistance to evolving guidelines regarding opioid tapering goals.

Conclusions

PCPs recognized that STORM supported patient safety and reduced clinician burden. Utilization of the program could be improved through ongoing PCP education about the service and consistent co-location of STORM pharmacists within primary care clinics.
Evaluation of the Impact of the COVID-19 Lockdown in the Clinical Course of Migraine
Authors: Gonzalez-Martinez Alicia , Planchuelo-Gómez Álvaro , Guerrero Ángel L , García-Azorín David , Santos-Lasaosa Sonia , Navarro-Pérez María Pilar , Odriozola-González Paula , Irurtia María Jesús , Quintas Sonia , de Luis-García Rodrigo , Gago-Veiga Ana Beatriz
Published: December 2020

Objective

Previous studies have demonstrated that emotional stress, changes in lifestyle habits and infections can worsen the clinical course of migraine. We hypothesize that changes in habits and medical care during coronavirus disease 2019 (COVID-19) lockdown might have worsened the clinical course of migraine.

Design

Retrospective survey study collecting online responses from migraine patients followed-up by neurologists at three tertiary hospitals between June and July 2020.

Methods

We used a web-based survey that included demographic data, clinical variables related with any headache (frequency) and migraine (subjective worsening, frequency, and intensity), lockdown, and symptoms of post-traumatic stress.

Results

The response rate of the survey was 239/324 (73.8%). The final analysis included 222 subjects. Among them, 201/222 (90.5%) were women, aged 42.5 ± 12.0 (mean±SD). Subjective improvement of migraine during lockdown was reported in 31/222 participants (14.0%), while worsening in 105/222 (47.3%) and was associated with changes in migraine triggers such as stress related to going outdoors and intake of specific foods or drinks. Intensity of attacks increased in 67/222 patients (30.2%), and it was associated with the subjective worsening, female sex, recent insomnia, and use of acute medication during a headache. An increase in monthly days with any headache was observed in 105/222 patients (47.3%) and was related to symptoms of post-traumatic stress, older age and living with five or more people.

Conclusions

Approximately half the migraine patients reported worsening of their usual pain during the lockdown. Worse clinical course in migraine patients was related to changes in triggers and the emotional impact of the lockdown.
Microscopic derivation of density functional theory for superfluid systems based on effective action formalism
Authors: Yokota Takeru , Kasuya Haruki , Yoshida Kenichi , Kunihiro Teiji
Published: December 2020

A density-functional theory for superfluid systems is developed in the framework of the functional renormalization group based on the effective action formalism. We introduce the effective action for the particle-number and non-local pairing densities and demonstrate that the Hohenberg–Kohn theorem for superfluid systems is established in terms of the effective action. The flow equation for the effective action is then derived, where the flow parameter runs from $0$ to $1$, corresponding to the non-interacting and interacting systems. From the flow equation and the variational equation that the equilibrium density satisfies, we obtain the exact expression for the Kohn–Sham potential generalized to include the pairing potentials. The resultant Kohn–Sham potential has a nice feature in that it expresses the microscopic formulae of the external, Hartree, pairing and exchange–correlation terms separately. It is shown that our Kohn–Sham potential gives the ground-state energy of the Hartree–Fock–Bogoliubov theory by neglecting the correlations. An advantage of our exact formalism lies in the fact that it provides ways to improve the correlation part systematically.
The renormalization group and the diffusion equation
Authors: Matsumoto Masami , Tanaka Gota , Tsuchiya Asato
Published: December 2020

We study the relationship between the renormalization group and the diffusion equation. We consider the exact renormalization group equation for a scalar field that includes an arbitrary cutoff function and an arbitrary quadratic seed action. As a generalization of the result obtained by Sonoda and Suzuki, we find that the correlation functions of diffused fields with respect to the bare action agree with those of bare fields with respect to the effective action, where the diffused field obeys a generalized diffusion equation determined by the cutoff function and the seed action and agrees with the bare field at the initial time.
Morse Theory without Non-Degeneracy
Authors: Kirwan Frances , Penington Geoffrey
Published: December 2020

We describe an extension of Morse theory to smooth functions on compact Riemannian manifolds, without any non-degeneracy assumptions except that the critical locus must have only finitely many connected components.
Ontogeny and variation of the pachycephalosaurine dinosaurSphaerotholus buchholtzae, and its systematics within the genus
Authors: Woodruff D Cary , Goodwin Mark B , Lyson Tyler R , Evans David C
Published: December 2020

The ontogeny and taxonomy of the dome-headed pachycephalosaurs are topics of continued debate. Pachycephalosaurid diversity in the Maastrichtian of North America is particularly controversial, and the validity and composition within the genus Sphaerotholus remains unresolved. While the type species, S. goodwini, is generally considered valid, debate has centred around the validity and taxonomy of S. buchholtzae and S. edmontonensis. Here we employ morphometrics, histology and phylogenetic analysis to resolve these issues.

An ontogenetic assessment of S. buchholtzae (N > 20) confirms previously observed ontogenetic morphologies: inflation of the frontoparietal dome, obliteration of tesserate surface texture, blunting of the peripheral nodes and decreasing void space within the dome. While linear bivariate analysis finds S. edmontonensis nested within S. buchholtzae, three-dimensional geometric morphometrics supports S. edmontonensis and S. buchholtzae as distinct species. Phylogenetic analysis recovers a Sphaerotholus lineage with S. goodwini as sister-taxon to a clade formed by S. edmontonensis and S. buchholtzae.

The stratigraphic, phylogenetic, morphometric and ontogenetic data support the validity of both S. edmontonensis and S. buchholtzae, and their placement within the genus Sphaerotholus. The morphological similarities of S. edmontonensis to immature S. buchholtzae, and the slightly older geological age of S. edmontonensis, suggest that S. edmontonensis and S. buchholtzae may be part of an anagenetic lineage.
Comparative Gene Expression Analysis Reveals Mechanism of Pinus contorta Response to the Fungal Pathogen Dothistroma septosporum
Authors: Lu Mengmeng , Feau Nicolas , Vidakovic Dragana Obreht , Ukrainetz Nicholas , Wong Barbara , Aitken Sally N. , Hamelin Richard C. , Yeaman Sam
Published: December 2020

Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight, a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two D. septosporum isolates and analyzed the differentially expressed genes (DEGs), differential exon usage, and coexpressed gene modules using RNA-sequencing data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one D. septosporum isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene module–identified genes to the reference plant-pathogen interaction pathway deposited in the Kyoto Encyclopedia of Genes and Genomes database. These genes are present in PAMP-triggered and effector-triggered immunity pathways. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to D. septosporum effectors. Taken together, our results show that gene expression response to D. septosporum infection in lodgepole pine varies both among tree genotypes and pathogen strains and involves both known candidate genes and a number of genes with previously unknown functions.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Expansion of the Cassava Brown Streak Disease Epidemic in Eastern Democratic Republic of Congo
Authors: Casinga C. M. , Shirima R. R. , Mahungu N. M. , Tata-Hangy W. , Bashizi K. B. , Munyerenkana C. M. , Ughento H. , Enene J. , Sikirou M. , Dhed’a B. , Monde G. , Kumar P. L. , Legg J. P.
Published: December 2020

Cassava plays a key role in ensuring food security and generating income for smallholder farmers throughout Central Africa, particularly in the Democratic Republic of Congo (DRC). This status is threatened, however, by cassava brown streak disease (CBSD), which has expanded its incidence and range in eastern DRC. The study described here comprises the first extensive assessment of temporal change in the occurrence of CBSD and its causal viruses in DRC, based on surveys conducted during 2016 and 2018. Cassava fields were inspected in Ituri, Nord-Kivu, Sud-Kivu, Tanganyika, and Haut-Katanga provinces within eastern DRC to record foliar incidence and severity of CBSD. Leaf samples were collected for virus detection and species-level identification. New occurrences of CBSD, confirmed by virus diagnostic tests, were recorded in two provinces (Haut-Katanga and Sud-Kivu) and nine previously unaffected territories, covering an area of >62,000 km2, and at up to 900 km from locations of previously published reports of CBSD in DRC. Overall, average CBSD incidence within fields was 13.2% in 2016 and 16.1% in 2018. In the new spread zone of Haut-Katanga, incidence increased from 1.7 to 15.9%. CBSD is now present in provinces covering 321,000 km2, which is approximately 14% of the total area of DRC. This represents a major expansion of the CBSD epidemic, which was only recorded from one province (Nord-Kivu) in 2012. Both Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus were detected in Ituri, Nord-Kivu, and Sud-Kivu, but only CBSV was detected in Haut-Katanga. Overall, these results confirm the increasing threat that CBSD poses to cassava production in DRC and describe an important expansion in the African pandemic of CBSD.
Genome Assembly and Annotation ofBotryosphaeria dothideasdau11-99, a Latent Pathogen of Apple Fruit Ring Rot in China
Authors: Yu Chengming , Diao Yufei , Lu Quan , Zhao Jiaping , Cui Shengnan , Peng Cheng , He Bangling , Liang Yuancun , Liu Huixiang
Published: December 2020

Botryosphaeria dothidea is a latent and important fungal pathogen on a wide range of woody plants. Fruit ring rot caused by B. dothidea is a major disease in China on apple. This study establishes a high-quality, nearly complete, and well-annotated genome sequence of B. dothidea strain sdau11-99. The findings of this research provide a reference genome resource for further research on the apple fruit ring rot pathogen on apple and other hosts.
Editing miR482b and miR482c Simultaneously by CRISPR/Cas9 Enhanced Tomato Resistance toPhytophthora infestans
Authors: Hong Yuhui , Meng Jun , He Xiaoli , Zhang Yuanyuan , Liu Yarong , Zhang Chengwei , Qi Hongyan , Luan Yushi
Published: December 2020

Late blight, caused by Phytophthora infestans, is severely damaging to the global tomato industry. Micro-RNAs (miRNAs) have been widely demonstrated to play vital roles in plant resistance by repressing their target genes. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) method has been continuously improved and extensively applied to edit plant genomes. However, editing multiplex miRNAs by CRISPR/Cas9 in tomato has not been studied yet. We knocked out miR482b and miR482c simultaneously in tomato through the multiplex CRISPR/Cas9 system. Two transgenic plants with silenced miR482b and miR482c simultaneously and one transgenic line with silenced miR482b alone were obtained. Compared with wild-type plants, the disease symptoms of three transgenic plants upon infection were reduced, accompanied by increased expression of their common target nucleotide binding site-leucine-rich repeat genes and decreased levels of reactive oxygen species. Furthermore, silencing miR482b and miR482c simultaneously was more resistant than silencing miR482b alone in tomato. More importantly, we found that knocking out miR482b and miR482c can elicit expression perturbation of other miRNAs, suggesting cross-regulation between miRNAs. Our study demonstrated that editing miR482b and miR482c simultaneously with CRISPR/Cas9 is an efficient strategy for generating pathogen-resistant tomatoes, and cross-regulation between miRNAs may reveal the novel mechanism in tomato–P. infestans interactions.
Percutaneous left atrial appendage occlusion
Authors: Mohammed Moghniuddin , Ranka Sagar , Reddy Madhu
Published: December 2020

Purpose of review

To review recent evidence evaluating the long-term safety and efficacy outcomes of left atrial appendage occlusion (LAAO), current guideline recommendations for LAAO use, performance of LAAO in comparison with direct oral anticoagulants (DOAC) and recently approved LAAO device.

Recent findings

The last 18 months have been marked with increasing evidence of the utility of LAAO in patients who are not candidates for long-term oral anticoagulation (OAC). Long-term data from two continued access registries to PROTECT-AF and PREVAIL support LAAO as a safe and effective long-term anticoagulation therapy. This new evidence led to class IIb recommendation for LAAO in nonvalvular atrial fibrillation (NVAF) patients not eligible for long-term OAC. PRAGUE-17 randomized controlled trial showed LAAO is noninferior to DOAC lending support to use of this modality in current era. PINNACLE FLX trial showed improved implant success and adequate closure rate which led to the device's Food and Drug Administration approval.

In conclusion, percutaneous LAAO appears to be a promising option for NVAF patients who are not candidates for long-term OAC in the current era. Further evidence guiding optimal patient selection and periprocedural antithrombotic regimen will help identify the patients who would benefit the most from this procedure.