bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative phylogenomics of ESBL-, AmpC- and carbapenemase-producing Klebsiella pneumoniae originating from companion animals and humans
Authors: Garcia-Fierro Raquel , Drapeau Antoine , Dazas Melody , Saras Estelle , Rodrigues Carla , Brisse Sylvain , Madec Jean-Yves , Haenni Marisa 
Published: February 2022

Abstract

Background
WHO considers ESBL- and carbapenemase-producing Klebsiella pneumoniae a major global concern. In animals, ESBL- and carbapenemase-producing K. pneumoniae of human-related ST11, ST15 and ST307 have been reported, but not in the context of large WGS-based One Health investigations.

Objectives
To perform comparative phylogenomics on a large collection of multidrug-resistant (MDR) K. pneumoniae recovered from diseased companion animals and humans.

Methods
MDR K. pneumoniae (n = 105) recovered from companion animals in France during 2010–18 were phenotypically characterized. All isolates were whole-genome sequenced using the NovaSeq technology and phylogenomic analysis across animal and human K. pneumoniae was performed using appropriate pipelines.

Results
bla CTX-M-15, blaDHA-1 and blaOXA-48 were strongly associated with IncFIIk, IncR and IncL plasmids, respectively. When compared with human K. pneumoniae genomes, four groups of closely related French human and animal isolates belonging to ST11, ST15 and ST307 were detected, suggesting the circulation of clones between the human and animal sectors at country level. A large cluster of 31 ST11-KL105 animal isolates from France and Switzerland suggested it corresponds to a sub-lineage that is particularly well-adapted to the animal host.

Conclusions
This study demonstrates the spread of blaCTX-M-15-carrying ST15 and ST307, and blaDHA-1-carrying ST11 K. pneumoniae clones in animal populations. ST11 was the main vector of blaOXA-48/IncL, despite the absence of carbapenem use in French animals. Comparative phylogenomics suggests cross-transmission of K. pneumoniae sub-lineages more prone than others to colonize/infect the animal host. Our data also evidenced the emergence of convergent hypervirulent and MDR K. pneumoniae in animals.
Systematic review and narrative synthesis of computerized audit and feedback systems in healthcare
Authors: Tsang Jung Yin , Peek Niels , Buchan Iain , van der Veer Sabine N , Brown Benjamin 
Published: February 2022

AbstractObjectives(1) Systematically review the literature on computerized audit and feedback (e-A&F) systems in healthcare. (2) Compare features of current systems against e-A&F best practices. (3) Generate hypotheses on how e-A&F systems may impact patient care and outcomes.MethodsWe searched MEDLINE (Ovid), EMBASE (Ovid), and CINAHL (Ebsco) databases to December 31, 2020. Two reviewers independently performed selection, extraction, and quality appraisal (Mixed Methods Appraisal Tool). System features were compared with 18 best practices derived from Clinical Performance Feedback Intervention Theory. We then used realist concepts to generate hypotheses on mechanisms of e-A&F impact. Results are reported in accordance with the PRISMA statement.ResultsOur search yielded 4301 unique articles. We included 88 studies evaluating 65 e-A&F systems, spanning a diverse range of clinical areas, including medical, surgical, general practice, etc. Systems adopted a median of 8 best practices (interquartile range 6–10), with 32 systems providing near real-time feedback data and 20 systems incorporating action planning. High-confidence hypotheses suggested that favorable e-A&F systems prompted specific actions, particularly enabled by timely and role-specific feedback (including patient lists and individual performance data) and embedded action plans, in order to improve system usage, care quality, and patient outcomes.Conclusionse-A&F systems continue to be developed for many clinical applications. Yet, several systems still lack basic features recommended by best practice, such as timely feedback and action planning. Systems should focus on actionability, by providing real-time data for feedback that is specific to user roles, with embedded action plans.Protocol RegistrationPROSPERO CRD42016048695.
Health informatics interventions to minimize out-of-pocket medication costs for patients: what providers want
Authors: Kiessling Karalyn A , Iott Bradley E , Pater Jessica A , Toscos Tammy R , Wagner Shauna R , Gottlieb Laura M , Veinot Tiffany C 
Published: February 2022

AbstractObjectiveTo explore diverse provider perspectives on: strategies for addressing patient medication cost barriers; patient medication cost information gaps; current medication cost-related informatics tools; and design features for future tool development.Materials and MethodsWe conducted 38 semistructured interviews with providers (physicians, nurses, pharmacists, social workers, and administrators) in a Midwestern health system in the United States. We used 3 rounds of qualitative coding to identify themes.ResultsProviders lacked access to information about: patients’ ability to pay for medications; true costs of full medication regimens; and cost impacts of patient insurance changes. Some providers said that while existing cost-related tools were helpful, they contained unclear insurance information and several questioned the information’s quality. Cost-related information was not available to everyone who needed it and was not always available when needed. Fragmentation of information across sources made cost-alleviation information difficult to access. Providers desired future tools to compare medication costs more directly; provide quick references on costs to facilitate clinical conversations; streamline medication resource referrals; and provide centrally accessible visual summaries of patient affordability challenges.DiscussionThese findings can inform the next generation of informatics tools for minimizing patients’ out-of-pocket costs. Future tools should support the work of a wider range of providers and situations and use cases than current tools do. Such tools would have the potential to improve prescribing decisions and better link patients to resources.ConclusionResults identified opportunities to fill multidisciplinary providers’ information gaps and ways in which new tools could better support medication affordability for patients.
Genetic diversity and population structure of invasive and native populations of Erigeron canadensis L.
Authors: Bhattacharya Saurav , Hernández Fernando , Alves Mariana Ferreira , Machado Raquel Moura , Sun Yan-Yan , Wang Meng-Ru , Zhang Chao-Bin , Hao Jian-Hua 
Published: February 2022

Abstract
Invasive alien plants threaten biodiversity across the world. Erigeron canadensis (horseweed) is one of the most problematic agricultural weeds and represents a classic example of intercontinental invasion. Here, we studied the genetic diversity and population structure of invasive alien populations from the Jiangsu and Zhejiang Provinces in China and native populations from Alabama, in the USA. We used 10 polymorphic SSR loci to genotype 312 individuals from 5 native and 5 invasive populations to estimate the genetic diversity and structure. Invasive populations from Jiangsu and Zhejiang Provinces showed, on average, similar genetic diversity to native populations from Alabama, indicating no severe genetic bottlenecks during the invasion. STRUCTURE revealed that low population differentiation occurred, and that only two genetic groupings were detected in both native and invaded ranges. The high diversity observed in the invasive populations suggested multiple introductions and/or the introduction of genetically diverse propagules during initial colonization. Our study provides new insights toward understanding the invasion dynamics of this globally noxious weed in Eastern China. Preventing gene flow via seed dispersal between invasive and native populations should be examined to prevent the introduction and dispersal of herbicide-resistant individuals and inform management practices.
Attenuation of opioid tolerance by ETA receptor antagonist, BQ123, administered intravenously in mice
Authors: Bhalla Shaifali , Lyne Jaimee , Gulati Anil , Andurkar Shridhar V 
Published: February 2022

Abstract

Objectives
Intracerebroventricular injection of endothelin-A receptor antagonist BQ123 potentiates opioid analgesia and reverses analgesic tolerance. This study explores whether these effects can be replicated by injecting BQ123 intravenously.

Methods
Male Swiss-Webster mice were used. Morphine tolerance was induced using 3- or 7-day dosing. Intravenous BQ123 (8 mg/kg) was injected only once on Day 1, 2, 3 or 4 (3-day studies), and on Day 4, 6 or 8 (7-day studies). On Day 4 or 8, respectively, tail-flick and hot-plate latencies were measured following a morphine challenge dose.

Key findings
Intravenous BQ123 increased the potency and duration of morphine antinociceptive responses. In the 3-day study, the antinociceptive response was unaffected by BQ123 given on Days 1 or 2. BQ123 treatment on Day 3 or 4 (Day 4, BQ123 given 15-min before morphine) significantly potentiated antinociceptive response versus vehicle-treated tolerant mice. In 7-day studies, the antinociceptive response was unaffected by BQ123 given on Day 4. BQ123 given on Day 6 or 8 (Day 8, BQ123 given 15-min before morphine) produced a &gt;100% increase in antinociceptive response versus vehicle-treated tolerant mice for at least 48 h.

Conclusions
Intravenous administration of BQ123 is effective in potentiating morphine analgesia and restoring antinociceptive response in morphine-tolerant mice.
The VMC survey – XLVII. Turbulence-controlled hierarchical star formation in the Large Magellanic Cloud
Authors: Miller Amy E , Cioni Maria-Rosa L , de Grijs Richard , Sun Ning-Chen , Bell Cameron P M , Choudhury Samyaday , Ivanov Valentin D , Marconi Marcella , Oliveira Joana M , Petr–Gotzens Monika , Ripepi Vincenzo , van Loon Jacco Th 
Published: February 2022

ABSTRACT
We perform a statistical clustering analysis of upper main-sequence stars in the Large Magellanic Cloud (LMC) using data from the Visible and Infrared Survey Telescope for Astronomy survey of the Magellanic Clouds. We map over 2500 young stellar structures at 15 significance levels across ∼120 square degrees centred on the LMC. The structures have sizes ranging from a few parsecs to over 1 kpc. We find that the young structures follow power-law size and mass distributions. From the perimeter–area relation, we derive a perimeter–area dimension of 1.44 ± 0.20. From the mass–size relation and the size distribution, we derive two-dimensional fractal dimensions of 1.50 ± 0.10 and 1.61 ± 0.20, respectively. We find that the surface density distribution is well represented by a lognormal distribution. We apply the Larson relation to estimate the velocity dispersions and crossing times of these structures. Our results indicate that the fractal nature of the young stellar structures has been inherited from the gas clouds from which they form and that this architecture is generated by supersonic turbulence. Our results also suggest that star formation in the LMC is scale-free from 10 to 700 pc.
Rotation measure and synchrotron emission signatures in simulations of magnetized galactic discs
Authors: Rappaz Yoan , Schober Jennifer , Girichidis Philipp 
Published: February 2022

ABSTRACT
We analyse observational signatures of magnetic fields for simulations of a Milky Way-like disc with supernova-driven interstellar turbulence and self-consistent chemical processes. In particular, we post-process two simulations data sets of the SILCC Project for two initial amplitudes of the magnetic field, B0 = 3 and 6 μG, to study the evolution of Faraday rotation measures (RM) and synchrotron luminosity. For calculating the RM, three different models of the electron density ne are considered. A constant electron density, and two estimations based on the density of ionized species and the fraction of the total gas, respectively. Our results show that the RM profiles are extremely sensitive to the ne models, which assesses the importance of accurate electron distribution observations/estimations for the magnetic fields to be probed using Faraday RMs. As a second observable of the magnetic field, we estimate the synchrotron luminosity in the simulations using a semi-analytical cosmic ray model. We find that the synchrotron luminosity decreases over time, which is connected to the decay of magnetic energy in the simulations. The ratios between the magnetic, the cosmic ray, and the thermal energy density indicate that the assumption of equipartition does not hold for most regions of the ISM. In particular, for the ratio of the cosmic ray to the magnetic field energy the assumption of equipartition could lead to a wrong interpretation of the observed synchrotron emission.
Urea levels and cardiovascular disease in patients with chronic kidney disease
Authors: Laville Solène M , Couturier Aymeric , Lambert Oriane , Metzger Marie , Mansencal Nicolas , Jacquelinet Christian , Laville Maurice , Frimat Luc , Fouque Denis , Combe Christian , Robinson Bruce M , Stengel Bénédicte , Liabeuf Sophie , Massy Ziad A ,   the CKD-REIN study collaborators, Ayav Carole , Briançon Serge , Cannet Dorothée , Combe Christian , Fouque Denis , Frimat Luc , Herpe Yves-Edouard , Jacquelinet Christian , Laville Maurice , Massy Ziad A , Pascal Christophe , Robinson Bruce M , Stengel Bénédicte , Lange Céline , Legrand Karine , Liabeuf Sophie , Metzger Marie , Speyer Elodie , Hannedouche Thierry , Moulin Bruno , Mailliez Sébastien , Lebrun Gaétan , Magnant Eric , Choukroun Gabriel , Deroure Benjamin , Lacraz Adeline , Lambrey Guy , Philippe Jean , Bourdenx  , Essig Marie , Lobbedez Thierry , Azar Raymond , Sekhri Hacène , Smati Mustafa , Jamali Mohamed , Klein Alexandre , Delahousse Michel , Combe Christian , Martin Séverine , Landru Isabelle , Thervet Eric , Massy Ziad A , Lang Philippe , Belenfant Xavier , Urena Pablo , Vela Carlos , Frimat Luc , Chauveau Dominique , Panescu Viktor , Noel Christian , Glowacki François , Hoffmann Maxime , Hourmant Maryvonne , Besnier Dominique , Testa Angelo , Kuentz François , Zaoui Philippe , Chazot Charles , Juillard Laurent , Burtey Stéphane , Keller Adrien , Kamar Nassim , Fouque Denis , Laville Maurice 
Published: February 2022

ABSTRACT

Background
Elevated serum urea levels are common in moderate-to-advanced chronic kidney disease (CKD). Several studies have shown that urea is a direct and indirect uraemic toxin, especially with regard to cardiovascular disease. We sought to determine whether serum urea levels are associated with adverse cardiovascular events and death before renal replacement therapy (RRT) in patients with CKD.

Methods
CKD-REIN is a prospective cohort of CKD nephrology outpatients not receiving maintenance dialysis. The 2507 patients included in the analysis were divided into three groups according to the baseline serum urea level (T1 &lt;10.5, T2 10.5–15.1 and T3 ≥15.1 mmol/L). Cox proportional hazard models were used to estimate hazard ratios (HRs) for first atheromatous or non-atheromatous cardiovascular (CV) events and all-cause mortality before RRT. The models were adjusted for baseline comorbidities, laboratory data and medications.

Findings
Of the 2507 included patients {median [interquartile range (IQR)] age: 69 [61–77]; mean (standard deviation) estimated glomerular filtration rate (eGFR) 33.5 (11.6) mL/min/1.73 m²}, 54% had a history of cardiovascular disease. After multiple adjustments for CV risk factors (including eGFR), patients in T3 had a higher risk of atheromatous and non-atheromatous CV events than patient in T1 (n events = 451, HR [95% CI]: 1.93 [1.39; 2.69]). The adjusted HRs for death before RRT (n events = 407) were 1.31 [0.97; 1.76] and 1.73 [1.22; 2.45] for patients T2 and those in T3, respectively.

Interpretation
Our data suggested that urea is a predictor of CV outcomes beyond CV risk factors including eGFR.
Insights into polyamine metabolism: homospermidine is double-oxidized in two discrete steps by a single copper-containing amine oxidase in pyrrolizidine alkaloid biosynthesis
Authors: Zakaria Mahmoud M , Stegemann Thomas , Sievert Christian , Kruse Lars H , Kaltenegger Elisabeth , Girreser Ulrich , Çiçek Serhat S , Nimtz Manfred , Ober Dietrich 
Published: February 2022

Abstract
Polyamines are important metabolites in plant development and abiotic and biotic stress responses. Copper-containing amine oxidases (CuAOs) are involved in the regulation of polyamine levels in the cell. CuAOs oxidize primary amines to their respective aldehydes and hydrogen peroxide. In plants, aldehydes are intermediates in various biosynthetic pathways of alkaloids. CuAOs are thought to oxidize polyamines at only one of the primary amino groups, a process frequently resulting in monocyclic structures. These oxidases have been postulated to be involved in pyrrolizidine alkaloid (PA) biosynthesis. Here, we describe the identification and characterization of homospermidine oxidase (HSO), a CuAO of Heliotropium indicum (Indian heliotrope), involved in PA biosynthesis. Virus-induced gene silencing of HSO in H. indicum leads to significantly reduced PA levels. By in vitro enzyme assays after transient in planta expression, we show that this enzyme prefers Hspd over other amines. Nuclear magnetic resonance spectroscopy and mass spectrometry analyses of the reaction products demonstrate that HSO oxidizes both primary amino groups of homospermidine (Hspd) to form a bicyclic structure, 1-formylpyrrolizidine. Using tracer feeding, we have further revealed that 1-formylpyrrolizidine is an intermediate in the biosynthesis of PAs. Our study therefore establishes that HSO, a canonical CuAO, catalyzes the second step of PA biosynthesis and provides evidence for an undescribed and unusual mechanism involving two discrete steps of oxidation that might also be involved in the biosynthesis of complex structures in other alkaloidal pathways.
Strengthening systematic reviews in public health: guidance in the Cochrane Handbook for Systematic Reviews of Interventions, 2nd edition
Authors: Cumpston Miranda S , McKenzie Joanne E , Welch Vivian A , Brennan Sue E 
Published: February 2022

Abstract

Aims
Decision makers in public health practice and policy rely on access to trustworthy, relevant, synthesized evidence. The second edition of the Cochrane Handbook for Systematic Reviews of Interventions (‘the Handbook’) reflects a major revision in guidance for authors of systematic reviews, incorporating a decade of methodological development and a number of significant changes to previous recommendations. This paper aims to highlight new guidance that addresses a number of key methodological challenges for authors of systematic reviews in public health.

Results
The revised Handbook includes guidance on framing public health research questions for synthesis, considering equity, intervention complexity, risk of bias assessment and synthesis methods other than meta-analysis. Reviews of public health interventions frequently encounter the types of methodological complexity addressed in this new guidance.

Conclusion
We hope that readers will find that the Cochrane Handbook includes detailed and thoughtful guidance on both conceptualizing and executing systematic reviews relevant to public health questions. Considering the available methods guidance will, we hope, provide support for authors of public health reviews to tackle the challenges they encounter, strengthen their analysis and provide useful answers to the important questions asked by stakeholders and users of public health evidence.
A retrospective comparison of COVID-19 and seasonal influenza mortality and outcomes in the ICUs of a French university hospital
Authors: de Marignan Donatien , Vacheron Charles-Hervé , Ader Florence , Lecocq Maxime , Richard Jean Christophe , Frobert Emilie , Casalegno Jean Sebastien , Couray-Targe Sandrine , Argaud Laurent , Rimmele Thomas , Aubrun Frédéric , Dailler Frédéric , Fellahi Jean Luc , Bohe Julien , Piriou Vincent , Allaouchiche Bernard , Friggeri Arnaud , Wallet Florent 
Published: February 2022

BACKGROUND
SARS-Cov-2 (COVID-19) has become a major worldwide health concern since its appearance in China at the end of 2019.

OBJECTIVE
To evaluate the intrinsic mortality and burden of COVID-19 and seasonal influenza pneumonia in ICUs in the city of Lyon, France.

DESIGN
A retrospective study.

SETTING
Six ICUs in a single institution in Lyon, France.

PATIENTS
Consecutive patients admitted to an ICU with SARS-CoV-2 pneumonia from 27 February to 4 April 2020 (COVID-19 group) and seasonal influenza pneumonia from 1 November 2015 to 30 April 2019 (influenza group). A total of 350 patients were included in the COVID-19 group (18 refused to consent) and 325 in the influenza group (one refused to consent). Diagnosis was confirmed by RT-PCR. Follow-up was completed on 1 April 2021.

MAIN OUTCOME(S) AND MEASURE(S)
Differences in 90-day adjusted-mortality between the COVID-19 and influenza groups were evaluated using a multivariable Cox proportional hazards model.

RESULTS
COVID-19 patients were younger, mostly men and had a higher median BMI, and comorbidities, including immunosuppressive condition or respiratory history were less frequent. In univariate analysis, no significant differences were observed between the two groups regarding in-ICU mortality, 30, 60 and 90-day mortality. After Cox modelling adjusted on age, sex, BMI, cancer, sepsis-related organ failure assessment (SOFA) score, simplified acute physiology score SAPS II score, chronic obstructive pulmonary disease and myocardial infarction, the probability of death associated with COVID-19 was significantly higher in comparison to seasonal influenza [hazard ratio 1.57, 95% CI (1.14 to 2.17); P = 0.006]. The clinical course and morbidity profile of both groups was markedly different; COVID-19 patients had less severe illness at admission (SAPS II score, 37 [28 to 48] vs. 48 [39 to 61], P < 0.001 and SOFA score, 4 [2 to 8] vs. 8 [5 to 11], P < 0.001), but the disease was more severe considering ICU length of stay, duration of mechanical ventilation, PEEP level and prone positioning requirement.

CONCLUSION
After ICU admission, COVID-19 was associated with an increased risk of death compared with seasonal influenza. Patient characteristics, clinical course and morbidity profile of these diseases is markedly different.
Clinical outcomes of slow-coagulation continuous-wave transscleral cyclophotocoagulation laser for treatment of glaucoma
Authors: Khodeiry Mohamed M. , Liu Xiangxiang , Lee Richard K. 
Published: February 2022

Purpose of review
The complications and inadequate efficacy of prior cyclodestructive procedures limited their role in glaucoma management. Recent advances in treatment techniques and parameters for laser cyclophotocoagulation has expanded its role in today's glaucoma practice. In this review, we discuss the treatment outcomes of slow-coagulation continuous-wave transscleral cyclophotocoagulation (CW-TSCPC) as a glaucoma surgical procedure for multiple types of glaucoma in lowering intraocular pressure (IOP).

Recent findings
Slow-coagulation TSCPC is a relatively new technique for CW-TSCPC that, unlike the ‘pop’ power titration technique of laser energy delivery, aims to avoid the production of the ‘pop’ sound that signals explosive inflammatory energy delivery to the ciliary body and nearby tissue. In slow-coagulation TSCPC, laser energy is applied in a fixed and lower amount over a longer duration, compared with the conventional pop technique. This laser energy approach leads to more stable, reliable, titratable, and selective ciliary body ablation for control of IOP, especially relative to the controversial current use of micropulse TSCPC.

Summary
Slow-coagulation CW-TSCPC can be used safely, efficiently, reproducibly, and efficaciously in wide range of glaucoma types including those with no history of incisional surgeries, good visual acuity, and medically refractory glaucomas.