bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability and instability of breathers in the U(1) Sasa–Satsuma and nonlinear Schrödinger models*
Authors: Alejo Miguel A , Fanelli Luca , Muñoz Claudio
Published: May 2021

We consider the Sasa–Satsuma (SS) and nonlinear Schrödinger (NLS) equations posed along the line, in 1 + 1 dimensions. Both equations are canonical integrable U(1) models, with solitons, multi-solitons and breather solutions Yang (2010 SIAM Mathematical Modeling and Computation). For these two equations, we recognize four distinct localized breather modes: the Sasa–Satsuma for SS, and for NLS the Satsuma–Yajima, Kuznetsov–Ma and Peregrine breathers. Very little is known about the stability of these solutions, mainly because of their complex structure, which does not fit into the classical soliton behavior Grillakis et al (1987 J. Funct. Anal.
74 160–97). In this paper we find the natural H
2 variational characterization for each of them. This seems to be the first known variational characterization for these solutions; in particular, the first one obtained for the famous Peregrine breather. We also prove that Sasa–Satsuma breathers are H
2 nonlinearly stable, improving the linear stability property previously proved by Pelinovsky and Yang (2005 Chaos
15 037115). Moreover, in the SS case, we provide an alternative understanding of the SS solution as a breather, and not only as an embedded soliton. The method of proof is based in the use of a H
2 based Lyapunov functional, in the spirit of Alejo and Muñoz (2013 Commun. Math. Phys.
324 233–62), extended this time to the vector-valued case. We also provide another rigorous justification of the instability of the remaining three nonlinear modes (Satsuma–Yajima, Peregrine and Kuznetsov–Ma), based in the study of their corresponding linear variational structure (as critical points of a suitable Lyapunov functional), and complementing the instability results recently proved e.g. in Muñoz (2017 Proyecciones (Antofagasta) 36 653–83).
How modular structure determines operational resilience of power grids
Authors: Kim Heetae
Published: May 2021

The synchronization stability has been analyzed as one of the important dynamical characteristics of power grids. In this study, we bring the operational perspective to the synchronization stability analysis by counting not only full but also partial synchronization between nodes. To do so, we introduce two distinct measures that estimate the operational resilience of power-grid nodes: functional secureness centrality and functional robustness centrality. We demonstrate the practical applicability of the measures in a model network motif and an IEEE test power grid. As a case study of German power grid, we reveal that the modular structure of a power grid and particular unidirectional current flow determine the distribution of the operational resilience of power-grid nodes. Reproducing our finding on clustered benchmark networks, we validate the modular effect on power grid stability and confirm that our measures can be the insightful tools to understand the power grids’ synchronization dynamics.
Oscillon collapse to black holes
Authors: Nazari Zainab , Cicoli Michele , Clough Katy , Muia Francesco
Published: May 2021

Using numerical relativity simulations we study the dynamics of pseudo-topological objects called oscillons for a class of models inspired by axion-monodromy. Starting from free field solutions supported by gravitational attractions, we investigate the effect of adding self-interactions, and contrast this with the effect of adding self-interactions whilst removing gravitational support. We map out regions of the parameter space where the initial conditions rapidly collapse to black holes, and other regions where they remain pseudo-stable or disperse.
Computational ghost imaging with deep compressed sensing*
Authors: Zhang Hao , Xia Yunjie , Duan Deyang
Published: May 2021

Computational ghost imaging (CGI) provides an elegant framework for indirect imaging, but its application has been restricted by low imaging performance. Herein, we propose a novel approach that significantly improves the imaging performance of CGI. In this scheme, we optimize the conventional CGI data processing algorithm by using a novel compressed sensing (CS) algorithm based on a deep convolution generative adversarial network (DCGAN). CS is used to process the data output by a conventional CGI device. The processed data are trained by a DCGAN to reconstruct the image. Qualitative and quantitative results show that this method significantly improves the quality of reconstructed images by jointly training a generator and the optimization process for reconstruction via meta-learning. Moreover, the background noise can be eliminated well by this method.
The SPIRAL1 charge breeder: key points for a high-performance 1+ beam injection
Authors: Maunoury L. , Kamalou O. , Cam J.F. , Damoy S. , Delahaye P. , Dubois M. , Frigot R. , Hormigos S. , Vandamme C.
Published: May 2021

The SPIRAL1 charge breeder is now under operation. Radioactive beam has already been delivered [1] to physicists for performing experiments. Although charge breeding efficiencies demonstrated high performances for stable ion beams, efficiencies regarding radioactive ion beams were found to be lower than expected in the first experiment. The beam optics, prior to the injection of the 1+ ions into the SPIRAL1 charge breeder, is of prime importance [2] for reaching such high efficiencies. Moreover, the intensities of the radioactive ion beams are so low that it is very difficult to tune the charge breeder. The tuning of the charge breeder for radioactive ion beams requires a particular procedure often referred to as “blind tuning”. A stable beam with a similar Brho (within a few percent) is required to find the set of optic parameters before tuning the radioactive ion beam. Hence, it has been decided to focus our efforts on this procedure in order to get control of the 1+ beam optics leading to high charge breeding efficiencies whatever the 1+ mass, energy and Target Ion Source System (TISS) used. Knowing that each TISS provides ion beams with a specific energy spread ΔE, and given that the energy acceptance window of the charge breeder is rather narrow, this parameter must also play an important role in determining the overall charge breeding efficiency.

This contribution will show the strategy undertaken to overcome the difficulties encountered in the charge breeding tuning with 1+ radioactive ion beams from the different ion sources, and the results already obtained. A series of experiments have been done to record beam parameters as well as beam profiles in two modes: “shooting through” and 1+/N+. Simulations have been developed to replicate the measurements: for this purpose a combination of SIMION and TraceWin software was used. The final goal is to define a set of beam optics reliable enough for operation covering a large range of 1+ mass, energy and emittance; applying the resulting set of parameters must eventually allow to approach the expected optimal charge breeder performances while producing a radioactive ion beam.
Dissolved and gaseous nitrogen losses in forests controlled by soil nutrient stoichiometry
Authors: Oulehle Filip , Goodale Christine L , Evans Christopher D , Chuman Tomáš , Hruška Jakub , Krám Pavel , Navrátil Tomáš , Tesař Miroslav , Ač Alexandr , Urban Otmar , Tahovská Karolina
Published: May 2021

Global chronic nitrogen (N) deposition to forests can alleviate ecosystem N limitation, with potentially wide ranging consequences for biodiversity, carbon sequestration, soil and surface water quality, and greenhouse gas emissions. However, the ability to predict these consequences requires improved quantification of hard-to-measure N fluxes, particularly N gas loss and soil N retention. Here we combine a unique set of long-term catchment N budgets in the central Europe with ecosystem 15N data to reveal fundamental controls over dissolved and gaseous N fluxes in temperate forests. Stream leaching losses of dissolved N corresponded with nutrient stoichiometry of the forest floor, with stream N losses increasing as ecosystems progress towards phosphorus limitation, while soil N storage increased with oxalate extractable iron and aluminium content. Our estimates of soil gaseous losses based on 15N stocks averaged 2.5 ± 2.2 kg N ha−1 yr−1 and comprised 20% ± 14% of total N deposition. Gaseous N losses increased with forest floor N:P ratio and with dissolved N losses. Our relationship between gaseous and dissolved N losses was also able to explain previous 15N-based N loss rates measured in tropical and subtropical catchments, suggesting a generalisable response driven by nitrate (NO3
−) abundance and in which the relative importance of dissolved N over gaseous N losses tended to increase with increasing NO3
− export. Applying this relationship globally, we extrapolated current gaseous N loss flux from forests to be 8.9 Tg N yr−1, which represent 39% of current N deposition to forests worldwide.
A quantitative genetics approach to validate lab- versus field-based behavior in novel environments
Authors: Mouchet Alexia , Dingemanse Niels J
Published: May 2021

Conclusions about the adaptive nature of repeatable variation in behavior (i.e., “personality”) are often derived from laboratory-based assays. However, the expression of genetic variation differs between laboratory and field. Laboratory-based behavior might not predict field-based behavior thus, cross-context validation is required. We estimated the cross-context correlation between behavior expressed by wild great tits (Parus major) in established laboratory versus field novel environment assays. Both assays have been used as proxies for “exploration tendency.” Behavior in both contexts had similar repeatability (R = 0.35 vs. 0.37) but differed in heritability (h2 = 0.06 vs. 0.23), implying differences in selection pressures. Unexpectedly, there was no cross-context correlation. Laboratory- and field-based behavior thus reflected expressions of two distinct underlying characters. Post hoc simulations revealed that sampling bias did not explain the lack of correlation. Laboratory-based behavior may reflect fear and exploration, but field-based behavior may reflect escape behavior instead, though other functional interpretations cannot be excluded. Thus, in great tits, activity expressed in laboratory versus field novel environment assays is modulated by multiple quasi-independent characters. The lack of cross-context correlation shown here may also apply to other setups, other repeatable behaviors, and other taxa. Our study thus implies care should be taken in labeling behaviors prior to firm validation studies.
Motor cortex stimulation for chronic neuropathic pain: results of a double-blind randomized study
Authors: Hamani Clement , Fonoff Erich T , Parravano Daniella C , Silva Valquiria A , Galhardoni Ricardo , Monaco Bernardo A , Navarro Jessie , Yeng Lin T , Teixeira Manoel J , de Andrade Daniel Ciampi
Published: May 2021

Motor cortex stimulation via surgically implanted electrodes has been used as an off-label treatment for chronic neuropathic pain, but its efficacy has not been fully established. We aimed to objectively study the efficacy of motor cortex stimulation and characterize potential predictors of response.

In this randomized, double-blind, sham-controlled, single centre trial, we recruited 18 patients with chronic neuropathic pain who did not adequately respond to conventional treatment and had a numerical pain rating scale (NRS) score ≥6. Patients were initially assigned to receive 3 months of active (‘on’) or sham (‘off’) stimulation in a double-blind cross-over phase. This was followed by a 3-month single-blind phase, and 6 months of open-label follow-up. A meaningful response in our trial was defined as a ≥30% or 2-point reduction in NRS scores during active stimulation.

Using Bayesian statistics, we found a 41.4% probability of response towards on versus off motor cortex stimulation. The probability of improvement during active stimulation (double-blind, single-blind and open-label phases) compared to baseline was 47.2–68.5%. Thirty nine per cent of the patients were considered long-term responders, 71.4% of whom had facial pain, phantom limb pain or complex regional pain syndrome. In contrast, 72.7% of non-responders had either post-stroke pain or pain associated with brachial plexus avulsion. Thirty-nine per cent of patients had a substantial postoperative analgesic effect after electrode insertion in the absence of stimulation. Individuals with diagnoses associated with a good postoperative outcome or those who developed an insertional effect had a near 100% probability of response to motor cortex stimulation.

In summary, we found that ∼40% of patients responded to motor cortex stimulation, particularly those who developed an insertional effect or had specific clinical conditions that seemed to predict an appropriate postoperative response.
Classification of Cortical Neurons by Spike Shape and the Identification of Pyramidal Neurons
Authors: Lemon Roger N , Baker Stuart N , Kraskov Alexander
Published: May 2021

Many investigators who make extracellular recordings from populations of cortical neurons are now using spike shape parameters, and particularly spike duration, as a means of classifying different neuronal sub-types. Because of the nature of the experimental approach, particularly that involving nonhuman primates, it is very difficult to validate directly which spike characteristics belong to particular types of pyramidal neurons and interneurons, as defined by modern histological approaches. This commentary looks at the way antidromic identification of pyramidal cells projecting to different targets, and in particular, pyramidal tract neurons (PTN), can inform the utility of spike width classification. Spike duration may provide clues to a diversity of function across the pyramidal cell population, and also highlights important differences that exist across species. Our studies suggest that further electrophysiological and optogenetic approaches are needed to validate spike duration as a means of cell classification and to relate this to well-established histological differences in neocortical cell types.
Coronavirus Disease 2019 (COVID-19) Disease Severity: Pregnant vs Nonpregnant Women at 82 Facilities
Authors: Hsu Albert L , Ohler Adrienne M , Goldstein Andrea , Truong Sarah , Tang Cynthia Y , Wan Xiu-Feng , McElroy Jane A
Published: May 2021

Background

Pregnancy has been reported to be a risk factor for severe COVID-19. We evaluated the impact of pregnancy on severe COVID-19 and mortality in an electronic medical record (EMR) database that enabled exclusion of labor and delivery (L&D) encounters.

Methods

In this retrospective cohort study, EMRs from 82 healthcare facilities in the Cerner COVID-19 Datamart were analyzed. The study comprised 38 106 individuals aged 18–45 years old with COVID-19 who had emergency department, urgent care, or inpatient encounters from December 2019 to September 2020. Subgroups were balanced through propensity score weights for age, race, smoking status, and number of comorbidities. The primary outcome was COVID-19–related mortality; secondary outcomes were markers of severe COVID-19: intubations, mechanical ventilation, use of vasopressors, diagnosis of sepsis, and diagnosis of acute respiratory distress syndrome.

Results

In comparing pregnant and nonpregnant women, no statistical differences were found for markers of severe COVID-19, after adjusting for age, smoking, race, and comorbidities. The adjusted odds of an inpatient encounter were higher for pregnant vs nonpregnant women (adjusted odds ratio [aOR], 13.2; 95% confidence interval [CI], 11.6–15.3; P < .001), but notably lower after excluding L&D encounters (aOR, 2.3; 95% CI, 1.89–2.88; P < .001). In comparison to women without L&D encounters, hospitalization was significantly more likely for men.

Conclusions

We did not find an increased risk of severe COVID-19 or mortality in pregnancy. Hospitalization does not necessarily indicate severe COVID-19 in pregnancy, as half of pregnant patients with COVID-19 were admitted for L&D encounters in this study.
State Continuity in the Absence of Government: The Underlying Rationale in International Law
Authors: Rim Yejoon
Published: May 2021

The traditional criteria for statehood assume that a state must have a government that enables state effectiveness. In the absence of a separate criterion for state continuity, the ‘constitutive elements’ for state creation have been regarded as also ‘continuative elements’ that preserve a state from extinction. However, practice has shown that a state can continue to exist even in the absence of government, which implies that simple assumptions on state continuity, paralleling rationale developed in the discourse of state creation, are inadequate as an explanatory framework for the situation and should thus be reconsidered. To this end, the article examines the underlying rationale for state continuity in the absence of a government, drawing a distinction between constitutive and continuative elements of statehood. Further, it suggests reframing the element of government as an entitlement belonging to the people and apprehending the state as a legally framed concept that cannot be simply determined by its effectiveness. In so doing, the article explores the role of international law in supporting the legal continuity of the state beyond effectiveness.
The Associations of Handgrip Strength and Leg Extension Power Asymmetry on Incident Recurrent Falls and Fractures in Older Men
Authors: McGrath Ryan , Blackwell Terri L , Ensrud Kristine E , Vincent Brenda M , Cawthon Peggy M
Published: May 2021

Background

Evaluating asymmetries in muscle function could provide important insights for fall risk assessments. We sought to determine the associations of (i) handgrip strength (HGS) asymmetry and (ii) leg extension power (LEP) asymmetry on risk of incident recurrent falls and fractures in older men.

Method

There were 5 730 men with HGS asymmetry data and 5 347 men with LEP asymmetry data from the Osteoporotic Fractures in Men (MrOS) study. A handgrip dynamometer measured HGS and a Nottingham Power Rig ascertained LEP. Percent difference in maximal HGS between hands was calculated, and asymmetric HGS was defined as men in the highest quartile of dissimilarity for HGS between hands. The same approach was used to determine asymmetric LEP. Participants self-reported falls every 4 months after the baseline exam, and persons with ≥2 falls in the first year were considered recurrent fallers. Fractures and their dates of occurrence were self-reported and confirmed with radiographic reports.

Results

Older men in the highest HGS asymmetry quartile had a 1.20 (95% confidence interval [CI]: 1.01–1.43) relative risk for incident recurrent falls. Likewise, men in the highest HGS asymmetry quartile had a higher risk for incident fractures: 1.41 (CI: 1.02–1.96) for hip, 1.28 (CI: 1.04–1.58) for major osteoporotic, and 1.24 (CI: 1.06–1.45) for nonspine. There were no significant associations between LEP asymmetry and recurrent falls or fractures.

Conclusions

Asymmetric HGS could be a novel risk factor for falls and fractures that is more feasible to measure than LEP. Fall risk assessments should consider evaluating muscle function, including HGS asymmetry.
Metabolomic Changes Are Predictive of Aging in Laying Hens
Authors: Bendikov-Bar Inna , Malitsky Sergey , Itkin Maxim , Rusal Mark , Sagi Dror
Published: May 2021

Aging in vertebrates is an extremely complex process that is still poorly understood. One confining factor to studying vertebrate aging is the lack of appropriate models. The laying hen is a good model to study vertebrate aging, as it can be maintained under standard housing conditions, its breeds are genetically well defined and it exhibits significant aging phenotypes at around 18 months of age. Furthermore, laying hens are maintained in a challenging realistic environment and possess a fully functional immune system. Here we used, for the first time, metabolomic profiling of laying hens’ blood for identifying biomarkers of aging. Random forest classifier was used to quantify the quality of the markers and found that the markers can predict the correct age group of individuals with 90% accuracy. Animals under time-restricted feeding, a condition known to increase health span, appeared younger under the markers, indicating that the aging biomarkers can also predict the effectiveness of environmental treatments. Additionally, we found that noise, defined as the ratio between the standard deviation and the mean, is an exceptionally robust and universal biomarker of aging, as metabolomic noise increases significantly with age in laying hens, humans, and mice. Our study suggests the laying hen as a useful model to study aging in vertebrates and establishes metabolomic noise as a novel, universal biomarker of aging.
A minimal sequon sufficient for O-linked glycosylation by the versatile oligosaccharyltransferase PglS
Authors: Knoot Cory J , Robinson Lloyd S , Harding Christian M
Published: May 2021

Bioconjugate vaccines, consisting of polysaccharides attached to carrier proteins, are enzymatically generated using prokaryotic glycosylation systems in a process termed bioconjugation. Key to bioconjugation are a group of enzymes known as oligosaccharyltransferases (OTases) that transfer polysaccharides to engineered carrier proteins containing conserved amino acid sequences known as sequons. The most recently discovered OTase, PglS, has been shown to have the broadest substrate scope, transferring many different types of bacterial glycans including those with glucose at the reducing end. However, PglS is currently the least understood in terms of the sequon it recognizes. PglS is a pilin-specific O-linking OTase that naturally glycosylates a single protein, ComP. In addition to ComP, we previously demonstrated that an engineered carrier protein containing a large fragment of ComP is also glycosylated by PglS. Here we sought to identify the minimal ComP sequon sufficient for PglS glycosylation. We tested >100 different ComP fragments individually fused to Pseudomonas aeruginosa exotoxin A (EPA), leading to the identification of an 11-amino acid sequence sufficient for robust glycosylation by PglS. We also demonstrate that the placement of the ComP sequon on the carrier protein is critical for stability and subsequent glycosylation. Moreover, we identify novel sites on the surface of EPA that are amenable to ComP sequon insertion and find that Cross-Reactive Material 197 fused to a ComP fragment is also glycosylated. These results represent a significant expansion of the glycoengineering toolbox as well as our understanding of bacterial O-linking sequons.
Testing predictions on supplier governance from the global value chains literature
Authors: Van Biesebroeck Johannes , Schmitt Alexander
Published: May 2021

A vast empirical literature analyzes the determinants of the make-or-buy decision. How to organize supplier relationships when the buy option is chosen has received much less attention. The global value chains framework provides testable predictions on the nature of buyer–supplier collaboration. We use a unique transaction-level dataset of outsourced automotive components to study carmakers’ choices between four distinct types of supplier governance: market, captive, relational, or modular. The theory formulates predictions based on three characteristics: the complexity or contractibility of a transaction, the capabilities in the supply base, and how objectively codifiable performance requirements are. Our results illustrate that sourcing relationships vary systematically and that the effects of proxies for the three characteristics are in line with the theory.
Decision and coordination of low-carbon supply chain under the trend of new retailing
Authors: Wu Xinjian , Yu Chao
Published: May 2021

Considering the supply chains consisting of a single manufacturer, a single new retailer and a traditional retailer and assuming that demands were affected by the manufacturer’s reduction of carbon emission, the new retailer’s service and the traditional retailer’s promotion, new retailing channel preference coefficient is defined and the supply chain decision models under different contract mechanisms are developed. The inference of how the manufacturer improves reduction of carbon emission, how the new retailer improves service and how the traditional retailer improves promotion through effective coordination mechanism is analyzed. The research results show that the cost sharing will make supply chain have a Pareto improvement to a considerable degree. The greater the marginal profit of the supplier is, the worse the coordination effect of the cooperative emission reduction mode will be. The comparative advantage of the cooperative service coordination and cooperative promotion coordination depends on the influence of service and promotion on channel demand. The greater the impact of reduction of carbon emission on channel demand is, the higher its rate should be shared by the channel retailer. The profit of supply chain is positively related to a new retailing channel preference; this indicates that opening up the ‘new retailing’ is beneficial for improving supply chain profits.
Antibiotic prescribing for respiratory tract infection in patients with suspected and proven COVID-19: results from an antibiotic point prevalence survey in Scottish hospitals
Authors: Seaton R Andrew , Cooper Lesley , Gibbons Cheryl L , Malcolm William , Choo-Kang Brian , Griffith David , Dundas Stephanie , Brittain Suzanne , Hamilton Kayleigh , Jeffreys Danielle , McKinney Rachel , Guthrie Debbie , Sneddon Jacqueline
Published: May 2021

Background

Bacterial co-infection is infrequently observed with SARS-CoV-2/COVID-19 infection outside of critical care, however, antibiotics are commonly prescribed.

Objectives

To examine factors associated with antibiotic prescribing for suspected respiratory tract infection (RTI) and evaluate the nature and dynamics of prescribing in hospitalized patients with suspected and proven COVID-19 infection.

Methods

An antibiotic point prevalence survey in hospitalized adult patients was conducted in designated COVID-19 clinical areas (including critical care) in 15 Scottish hospitals. Antibiotics prescribed for RTI and factors associated with prescribing were investigated.

Results

Of 820 surveyed patients, 272 (prevalence 33.3%) received antibiotics for suspected RTI on the survey day and 58.8% were SARS-CoV-2 positive. Antibiotics were empirical in 91.9% and amoxicillin (24.6%), doxycycline (20.5%) and co-amoxiclav (15%) were most frequently prescribed. Oral antibiotics were prescribed in 54.5% and duration was recorded in 76.7% on wards for a median of 5 days. IV to oral switch occurred after a median of 2 days. Prescribing for RTI was independently and positively associated with COPD/chronic lung disease, purulent/bloody sputum, abnormal chest X-ray, and CRP ≥ 100 mg/L. Probable and definite hospital-acquired COVID-19 and diabetes were associated with a lower odds of receiving an antibiotic for RTI.

Conclusions

Antibiotic prescribing for suspected RTI was commonly observed and predominantly empirical in suspected or proven COVID-19. Initiatives to reinforce stewardship principles including clinical review, effective use of microbiological diagnostics and better understanding of the role of biomarkers are central to further limit unnecessary antibiotic therapy in COVID-19.
Psychosocial Functioning Among Caregivers of Childhood Cancer Survivors Following Treatment Completion
Authors: Quast Lauren F , Williamson Lewis Rebecca , Lee Jennifer L , Blount Ronald L , Gilleland Marchak Jordan
Published: May 2021

Objective

To inform efforts to better support caregivers of children with cancer during the transition from treatment to survivorship, this study sought to characterize caregiver mental health-related quality of life (HRQOL) and anxiety, and examine the influence of family psychosocial risk and caregiver problem-solving on these outcomes.

Method

Participants included 124 caregivers (child age M = 10.05 years; SD = 4.78), 12–19 months from the conclusion of cancer-directed treatment. Participants’ self-reported mental HRQOL, anxiety, and problem-solving were compared with community norms using t-tests. Correlations and hierarchical multiple regressions examined the influence of psychosocial risk and problem-solving on caregiver mental HRQOL and anxiety.

Results

Overall, caregivers reported HRQOL and anxiety within normal limits. Caregivers also reported more adaptive patterns of problem-solving than community norms. Subsets of caregivers reported clinical levels of psychosocial risk (11%) and at-risk levels of mental HRQOL (2.5%) and anxiety (5.7%). Females reported greater anxiety than males. Psychosocial risk and negative problem orientation (NPO) were both related to poorer mental HRQOL and greater anxiety (r = .40–.51, p’s < .001). Positive problem orientation related to better mental HRQOL and lower anxiety (r = .18–.21, p’s < .05). Impulsivity/carelessness and avoidance were associated with greater anxiety (r = .19–.25, p’s < .05). Only NPO accounted for additional variance in mental HRQOL and anxiety, over and above psychosocial risk and demographic characteristics.

Conclusions

The majority of caregivers appear to be resilient and experience limited distress during the off therapy period. Targeting negative cognitive appraisals (NPO) through cognitive-behavioral therapy or problem-solving skills training may further improve caregiver psychosocial functioning.
Eosinophilic meningomyelitis caused by Toxocara spp. in a migrant coming from La Reunion
Authors: Faure Guillaume , Goulenok Tiphaine , Lariven Sylvie , Dossier Antoine , Henry-Feugeas Marie-Cécile , Argy Nicolas , Papo Thomas
Published: May 2021

A young man coming from La Reunion presented with headache, back pain, progressive urinary incontinence and gait instability. Blood cells count and cerebrospinal fluid (CSF) analysis showed eosinophilia. Magnetic resonance imaging (MRI) confirmed thoracic myelitis. CSF and serum serodiagnosis for Toxocara were both positive. Eosinophilic meningomyelitis secondary to a toxocariasis was diagnosed.
Establishment method affects rice root plasticity in response to drought and its relationship with grain yield stability
Authors: Xie Xiaobing , Quintana Marinell R , Sandhu Nitika , Subedi Sushil R , Zou Yingbin , Rutkoski Jessica Elaine , Henry Amelia
Published: May 2021

By responding to the variable soil environments in which they are grown, the roots of rice crops are likely to contribute to yield stability across a range of soil moistures, nutrient levels, and establishment methods. In this study, we explored different approaches to quantification of root plasticity and characterization of its relationship with yield stability. Using four different statistical approaches (plasticity index, slope, AMMI, and factor analytic) on a set of 17 genotypes including several recently-developed breeding lines targeted to dry direct-seeding, we identified only very few direct relationships between root plasticity and yield stability. However, genotypes identified as having combined yield stability and root plasticity showed higher grain yields across trials. Furthermore, root plasticity was expressed to a greater degree in puddled transplanted trials rather than under dry direct-seeding. Significant interactions between nitrogen and water resulted in contrasting relationships between nitrogen-use efficiency and biomass stability between puddled-transplanted and direct-seeded conditions. These results reflect the complex interaction between nitrogen, drought, and even different types of drought (as a result of the establishment method) on rice root growth, and suggest that although rice root plasticity may confer stable yield across a range of environments, it might be necessary to more narrowly define the targeted environments to which it will be most beneficial.
Fundamental Identifiability Limits in Molecular Epidemiology
Authors: Louca Stilianos , McLaughlin Angela , MacPherson Ailene , Joy Jeffrey B , Pennell Matthew W
Published: May 2021

Viral phylogenies provide crucial information on the spread of infectious diseases, and many studies fit mathematical models to phylogenetic data to estimate epidemiological parameters such as the effective reproduction ratio (Re) over time. Such phylodynamic inferences often complement or even substitute for conventional surveillance data, particularly when sampling is poor or delayed. It remains generally unknown, however, how robust phylodynamic epidemiological inferences are, especially when there is uncertainty regarding pathogen prevalence and sampling intensity. Here, we use recently developed mathematical techniques to fully characterize the information that can possibly be extracted from serially collected viral phylogenetic data, in the context of the commonly used birth-death-sampling model. We show that for any candidate epidemiological scenario, there exists a myriad of alternative, markedly different, and yet plausible “congruent” scenarios that cannot be distinguished using phylogenetic data alone, no matter how large the data set. In the absence of strong constraints or rate priors across the entire study period, neither maximum-likelihood fitting nor Bayesian inference can reliably reconstruct the true epidemiological dynamics from phylogenetic data alone; rather, estimators can only converge to the “congruence class” of the true dynamics. We propose concrete and feasible strategies for making more robust epidemiological inferences from viral phylogenetic data.
Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci
Authors: Mongiardino Koch Nicolás
Published: May 2021

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
pegIT - a web-based design tool for prime editing
Authors: Anderson Mads Valdemar , Haldrup Jakob , Thomsen Emil Aagaard , Wolff Jonas Holst , Mikkelsen Jacob Giehm
Published: May 2021

Prime editing (PE) is a novel CRISPR-derived genome editing technique facilitating precision editing without double-stranded DNA breaks. PE, mediated by a Cas9-reverse transcriptase fusion protein, is based on dual-functioning prime editing guide RNAs (pegRNAs), serving both as guide molecules and as templates carrying the desired edits. Due to such diverse functions, manual pegRNA design is a subject to error and not suited for large-scale setups. Here, we present pegIT, a user-friendly web tool for rapid pegRNA design for numerous user-defined edits, including large-scale setups. pegIT is freely available at https://pegit.giehmlab.dk.
Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs
Authors: Weinberg Christina E , Olzog V Janett , Eckert Iris , Weinberg Zasha
Published: May 2021

Self-cleaving ribozymes are catalytic RNAs that cut themselves at a specific inter-nucleotide linkage. They serve as a model of RNA catalysis, and as an important tool in biotechnology. For most of the nine known structural classes of self-cleaving ribozymes, at least hundreds of examples are known, and some are present in multiple domains of life. By contrast, only four unique examples of the hairpin ribozyme class are known, despite its discovery in 1986. We bioinformatically predicted 941 unique hairpin ribozymes of a different permuted form from the four previously known hairpin ribozymes, and experimentally confirmed several diverse predictions. These results profoundly expand the number of natural hairpin ribozymes, enabling biochemical analysis based on natural sequences, and suggest that a distinct permuted form is more biologically relevant. Moreover, all novel hairpins were discovered in metatranscriptomes. They apparently reside in RNA molecules that vary both in size—from 381 to 5170 nucleotides—and in protein content. The RNA molecules likely replicate as circular single-stranded RNAs, and potentially provide a dramatic increase in diversity of such RNAs. Moreover, these organisms have eluded previous attempts to isolate RNA viruses from metatranscriptomes—suggesting a significant untapped universe of viruses or other organisms hidden within metatranscriptome sequences.
Role of non-alcoholic fatty liver disease in the evolution of renal function in patients with diabetes mellitus
Authors: Aubert Lucía , Sandino Justo , Gutiérrez-Solís Elena , García-Martín Florencio , Segura Julián , Porrini Esteban , Morales Enrique
Published: May 2021

Background

The increasing prevalence of type 2 diabetes mellitus (T2DM) has influenced in an increasing prevalence of chronic kidney disease (CKD). Little is known about the influence of non-alcoholic fatty liver disease (NAFLD) on the progression of CKD. The aim of this study was to analyse the role of NAFLD and its severity in the progression of renal function in patients with T2DM.

Methods

We conducted a retrospective and observational study including patients with T2DM and estimated glomerular filtration rate (eGFR) >30 mL/min/1.73 m2. NAFLD was defined as the presence of compatible ultrasonography and/or the presence of fibrosis using the NAFLD score. Patients were classified into three groups according to the NAFLD score: Group 1: <−1.85; Group 2: −1.85–0.18 and Group 3: >0.18.

Results

A total of 102 patients were included [67.6% males, median age 59 years [interquartile range (IQR) 53–64)], with a median time of T2DM evolution of 70 months (IQR 39–131). Group 3 had lower eGFR (84.8 ± 40.4 versus 71.4 ± 30.6 mL/min/1.73 m2; P = 0.03) and higher proteinuria at baseline (0.56 ± 0.77 versus 1.59 ± 2.70 g/24 h; P = 0.05). After a follow-up time of 75.8 ± 23.9 months, Group 3 had a significant decrease in eGFR (66.6 ± 33.3 versus 36.8 ± 23.1 mL/min/1.73 m2; P ≤ 0.01) and a higher risk of CKD progression [odds ratio 7.50 (95% confidence interval 2.76–20.35); P ≤ 0.001] defined as a decrease in eGFR of >50%.

Conclusions

The presence of NAFLD with high-risk fibrosis confers higher risk of CKD progression in patients with T2DM. Therefore NAFLD should be a risk factor evaluated in these patients to optimize treatment.
High-Quality Genome Assembly of Pseudopestalotiopsis theae, the Pathogenic Fungus Causing Tea Gray Blight
Authors: Zheng Shiqin , Chen Ruiqi , Wang Zhe , Liu Juan , Cai Yan , Peng Minghui , Zhang Tian , Li Yunxi , Wang Baohua , Bao Jiandong , Zhang Dongmei , Wang Zonghua , Hu Hongli
Published: May 2021

Tea gray blight is one of the most serious foliar diseases of tea tree, caused by the plant-pathogenic fungus Pseudopestalotiopsis theae, which can affect production and quality of tea worldwide. We generated a highly contiguous, 50.41-Mbp genome assembly (N50 = 1.30 Mbp) of P. theae strain CYF27 by combining PacBio long-read and Illumina short-read sequencing technologies. We identified a total of 15,626 gene models, of which 1,038 genes encode putative secreted proteins. The high-quality genome assembly and annotation resource reported here will be useful for the study of fungal infection mechanisms and pathogen–host interaction.
A Qualitative Analysis of Ostomy-Related Patient Education Videos on YouTube
Authors: Basim Pelin , Argun Derya
Published: May 2021

OBJECTIVE

To analyze the content, reliability, and quality of the most viewed YouTube videos targeting patients with ostomies intending to learn about ostomy care (OC).

METHODS

Using the keywords “stoma care,” “colostomy care,” and “ileostomy care,” researchers assessed the publicly visible English-language ostomy patient education videos available on YouTube. A total of 84 videos were independently analyzed by two physicians experienced in OC. Data on video characteristics, source, content, reliability, and quality were collected and recorded for each video separately.

RESULTS

Of the 84 videos analyzed, 49 were classified as useful (58.33%) and 35 as misleading (41.66%). There were statistically significant differences between the groups in terms of the time elapsed since upload (P < .017), reliability (P < .001), comprehensiveness (P < .001), Global Quality Scale scores (P < .001), source (P < .001), and lecturer types (P < .011). The reliability, comprehensiveness, and Global Quality Scale scores were statistically higher for videos uploaded by universities, professional healthcare communities, and nonprofit physicians (P < .001). However, the popularity of the OC videos posted on YouTube was not related to their reliability, comprehensiveness, or quality.

CONCLUSIONS

The open-access nature of the YouTube platform may impair patient education video quality and accuracy. YouTube may be an additional educational tool for OC, but clinicians need to be familiar with specific and reliable resources to guide and educate new patients with ostomies to achieve the best outcomes.
Reliability of the Patient and Observer Scar Assessment Scale in Evaluating Linear Scars after Thyroidectomy
Authors: Chung Jae-Ho , Kwon Sang-Ho , Kim Ki-Jae , Lee Jae-Min , Yoon Jeong-Min , Cheon Jeong-Hyun , Yoon Eul-Sik , Park Seung-Ha
Published: May 2021

OBJECTIVE

To compare the reliability of the Patient and Observer Scar Assessment Scale (POSAS) with the Vancouver Scar Scale (VSS) in evaluating thyroidectomy scars.

METHODS

At 6 months after the operation, 112 patients who underwent thyroid surgery via collar neck incision were evaluated by two blinded plastic surgeons and two senior residents using the VSS and the observer component of the POSAS. In addition, the observer-reported VAS score and patient-reported Likert score were evaluated. Internal consistency, interobserver reliability, and correlations between the patient- and observer-reported outcomes were examined.

RESULTS

The observer component of POSAS scores demonstrated higher internal consistency and interobserver reliability than the VSS. However, the correlations between the observer-reported VAS score and the patient-reported Likert score (0.450) and between the total sum of patient and observer component scores (0.551) were low to moderate.

CONCLUSIONS

The POSAS is more consistent over repeated measurements; accordingly, it may be considered a more objective and reliable scar assessment tool than the VSS. However, a clinician’s perspective may not exactly match the patient’s perception of the same scar.
8. ASSOCIATION OF NOCTURNAL BLOOD PRESSURE DIPPING PATTERN WITH CARDIOVASCULAR EVENTS AND ALL-CAUSE MORTALITY IN PATIENTS WITH HYPERTENSION: A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Willim Herick Alvenus , Cipta Harie
Published: May 2021

Background:

Hypertension remains a main contributor to morbidity and mortality worldwide. Studies have found that ambulatory blood pressure (BP) monitoring is superior to clinic BP in predicting prognosis in patients with hypertension. Assessment of nocturnal BP dipping pattern during ambulatory BP monitoring can provide additional prognostic significance and guide treatment decisions.

Objective:

To conduct a systematic review and meta-analysis of the association of nocturnal BP dipping pattern with cardiovascular events and all-cause mortality in patients with hypertension.

Methods:

Relevant literature was identified using PubMed, ProQuest, Cochrane Library, Embase, and Google Scholar. Subjects were categorized as dippers or non-dippers according to systolic dipping pattern by ambulatory BP monitoring. Dippers was defined as decreased in systolic BP from day to night of ≥10%. Non-dippers was defined as decreased in systolic BP from day to night of <10%. The outcomes were cardiovascular events and all-cause mortality. Meta analysis was performed using Review Manager 5.3 software.

Results:

Eight cohort studies involving a total of 5260 hypertensive patients were included, of which 6 studies reported data on cardiovascular events and 4 studies reported data on all-cause mortality. On pooled analysis, hypertensive patients classified as non-dippers had significant increased risk of cardiovascular events compared with dippers (risk ratio [RR] 1.82; 95% confidence interval [CI] 1.55–2.14; p < 0.00001; I
2 = 50%). Similarly, non-dippers had significant increased risk of all-cause mortality compared with dippers (RR 2.49; 95% CI 1.82–3.41; p < 0.00001; I
2 = 10%).

Conclusion:

In patients with hypertension, the non-dipper pattern was significantly associated with increased risk of cardiovascular events and all-cause mortality.
17. THE FACTORS AFFECTING INTRADIALYTIC HYPERTENSION IN ROUTINE HEMODIALYSIS PATIENT AT BALI HUSADA CIPTA CANTI DENPASAR
Authors: Wicaksana A.A. Gede Oka Suta , Erawan I Gusti Ngurah Agung Tresna
Published: May 2021

Background:

Intradialytic hypertension (IDH) define as a condition where an increase blood pressure (BP) in hemodialysis patient from pre- to post- hemodialysis. Fluctuations in BP are one of the most common complications among hemodialysis. IDH prevalence was variably reported from 10–15%. IDH has been recently identified as an independent mortality risk factor.

Objective:

This study was aimed to determine the prevalence and risk factor of IDH among hemodialysis patient in Bali Husada Cipta Canti Clinic (BHCC), Denpasar.

Method:

This is an analytic cross-sectional study conducted in BHCC, Denpasar. The data collected from medical record from all dialytic patient on December 2020. Patient with inclusion criteria were collected. Patient with incomplete data was excluded. BP measurements perform before and after hemodialysis. Patient defines with IDH if the difference of systolic blood pressure before and after hemodialysis was more than 10 mmHg in 2 times hemodialysis sequentially.

Result:

Our study involved 100 patients with male patient was 60 (60%) and mean age is 53.66 years (±10.88 SD). The IDH prevalence was 51% (n = 51). We found no significant differences in ages, body mass index (BMI), oral antihypertensive usage, diabetes status, hemoglobin, erythropoietin usage, quick of blood (QB) between IDH and non-IDH group. There was significant different in ultrafiltration between IDH and non IDH group (p = 0.045; OR 0.443; IK95% 0.199–0.987).

Conclusion:

IDH in BHCC have a higher prevalence (51%) than previous studies. There was significant different in ultrafiltration between IDH and non-IDH group. Patient with higher ultrafiltration have protective risk for IDH.