bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infection With the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta Variant Is Associated With Higher Recovery of Infectious Virus Compared to the Alpha Variant in Both Unvaccinated and Vaccinated Individuals
Authors: Huai Luo Chun , Paul Morris C , Sachithanandham Jaiprasath , Amadi Adannaya , Gaston David C , Li Maggie , Swanson Nicholas J , Schwartz Matthew , Klein Eili Y , Pekosz Andrew , Mostafa Heba H 
Published: December 2021

Abstract

Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VOC) B.1.617.2 (Delta) displaced B.1.1.7 (Alpha) and is associated with increases in coronavirus disease 2019 (COVID-19) cases, greater transmissibility, and higher viral RNA loads, but data are lacking regarding the infectious virus load and antiviral antibody levels in the nasal tract.

Methods
Whole genome sequencing, cycle threshold (Ct) values, infectious virus, anti-SARS-CoV-2 immunoglobulin G (IgG) levels, and clinical chart reviews were combined to characterize SARS-CoV-2 lineages circulating in the National Capital Region between January and September 2021 and differentiate infections in vaccinated and unvaccinated individuals by the Delta, Alpha, and B.1.2 (the predominant lineage prior to Alpha) variants.

Results
The Delta variant displaced the Alpha variant to constitute 99% of the circulating lineages in the National Capital Region by August 2021. In Delta infections, 28.5% were breakthrough cases in fully vaccinated individuals compared to 4% in the Alpha infected cohort. Breakthrough infections in both cohorts were associated with comorbidities, but only Delta infections were associated with a significant increase in the median days after vaccination. More than 74% of Delta samples had infectious virus compared to &lt;30% from the Alpha cohort. The recovery of infectious virus with both variants was associated with low levels of local SARS-CoV-2 IgG.

Conclusions
Infection with the Delta variant was associated with more frequent recovery of infectious virus in vaccinated and unvaccinated individuals compared to the Alpha variant but was not associated with an increase in disease severity in fully vaccinated individuals. Infectious virus was correlated with the presence of low amounts of antiviral IgG in the nasal specimens.
Limited Evidence for Use of a Black Race Modifier in eGFR Calculations: A Systematic Review
Authors: Marzinke Mark A , Greene Dina N , Bossuyt Patrick M , Chambliss Allison B , Cirrincione Lauren R , McCudden Christopher R , Melanson Stacy E F , Noguez Jaime H , Patel Khushbu , Radix Asa E , Takwoingi Yemisi , Winston-McPherson Gabrielle , Young Bessie A , Hoenig Melanie P 
Published: December 2021

Abstract

Background
Commonly used estimated glomerular filtration rate (eGFR) equations include a Black race modifier (BRM) that was incorporated during equation derivation. Race is a social construct, and a poorly characterized variable that is applied inconsistently in clinical settings. The BRM results in higher eGFR for any creatinine concentration, implying fundamental differences in creatinine production or excretion in Black individuals compared to other populations. Equations without inclusion of the BRM have the potential to detect kidney disease earlier in patients at the greatest risk of chronic kidney disease (CKD), but also has the potential to over-diagnose CKD or impact downstream clinical interventions. The purpose of this study was to use an evidence-based approach to systematically evaluate the literature relevant to the performance of the eGFR equations with and without the BRM and to examine the clinical impact of the use or removal.

Content
PubMed and Embase databases were searched for studies comparing measured GFR to eGFR in racially diverse adult populations using the Modification of Diet in Renal Disease or the 2009-Chronic Kidney Disease Epidemiology Collaboration-creatinine equations based on standardized creatinine measurements. Additionally, we searched for studies comparing clinical use of eGFR calculated with and without the BRM. Here, 8632 unique publications were identified; an additional 3 studies were added post hoc. In total, 96 studies were subjected to further analysis and 44 studies were used to make a final assessment.

Summary
There is limited published evidence to support the use of a BRM in eGFR equations.
Smash the Thing: William Kentridge, Classical Antiquity, and hisRefusal of TimeinO Sentimental Machine
Authors: Agbamu Samuel 
Published: December 2021

AbstractThis article examines a 2018 exhibition of William Kentridge’s work, entitled O Sentimental Machine, at the Liebieghaus Skulpturensammlung in Frankfurt. This exhibition placed the South African artist’s work in confrontation with the museum’s collections, which offer an overview of sculpture from antiquity to early modernity. The exhibition draws together themes explored in Kentridge’s sustained engagement with Greek and Roman antiquity: critiques of triumphant narratives of history; questions of memorialization and ruination; and the probing of narratives of enlightenment, which begin with Plato’s allegory of the cave (Rep. 514a–521b). The first half of the article considers Kentridge’s dialogues with Greek and Roman antiquity in his wider works before turning to his Triumphs and Laments (2016), a series of images telling the story of Rome, imprinted on the embankment walls of the Tiber. The second half focuses on O Sentimental Machine, paying particular attention to The Refusal of Time, a piece presented at the exhibition. The article argues that this piece offers a compelling challenge to narratives of ‘civilisation’, at the centre of which lie hegemonic notions of time, underpinned by constructions of the classical tradition. Kentridge thus offers a vision for emancipatory engagements with Greek and Roman antiquity.
Cognitive Skills and Economic Preferences in the Fund Industry
Authors: Farago Adam , Holmén Martin , Holzmeister Felix , Kirchler Michael , Razen Michael 
Published: December 2021

AbstractWe investigate the impact of cognitive skills and economic preferences on fund managers' professional decisions by running a battery of experiments with them. First, we find that fund managers’ risk tolerance positively correlates with fund risk when accounting for fund benchmark, fund category and other controls. Second, we show that fund managers’ ambiguity tolerance positively correlates with the funds’ tracking error from the benchmark. Finally, we report that cognitive skills do not explain fund performance in terms of excess returns. However, we do find that fund managers with high cognitive reflection abilities compose funds at lower risk.
Illegal: The Recourse to Force to Recover Occupied Territory and the Second Nagorno-Karabakh War
Authors: Ruys Tom , Silvestre Felipe Rodríguez 
Published: December 2021

Abstract
The Second Nagorno-Karabakh War, and its lingering aftermath, have put the fundamental and largely unsettled question of the jus ad bellum in the spotlight: when part of one state’s territory is occupied by another state for a prolonged duration, can the former state have lawful recourse to military force to recover its land? Prior to the 2020 conflict, the Nagorno-Karabakh region was widely regarded as belonging de jure to Azerbaijan, but as being unlawfully occupied – for more than 25 years – by Armenia. Accordingly, was Azerbaijan entitled to claim self-defence to lawfully recover it, even though the pre-2020 territorial status quo in the region had existed for more than a quarter of a century? In addition, could Azerbaijan invoke self-defence again in the near or distant future to recover those remaining parts of territory that continue to be outside of its control now that a new ceasefire is being enforced in the region? The answers to these questions have ramifications that extend far beyond the Caucasus, being of relevance for a wide range of pending conflicts around the globe. Upon closer scrutiny, the present authors believe that a negative answer is in order.
The year in cardiovascular medicine 2021: dyslipidaemia
Authors: Tokgozoglu Lale , Orringer Carl , Ginsberg Henry N. , Catapano Alberico L. 
Published: December 2021

AbstractThe past year was an exciting time for clinical lipidology when we learnt more about existing therapies as well as therapies targeting novel pathways discovered through genetic studies. LDL cholesterol remained the main target and a variety of drugs to lower LDL cholesterol through different mechanisms were explored. Emerging evidence on the atherogenity of triglyceride-rich lipoproteins led to renewed interest in lowering them with new treatments. Lp(a) was back in focus with evidence on causality and new targeted therapeutics which dramatically lower Lp(a) levels. We will be able to personalise lipid lowering therapy further with this enriched armamentarium once we have the results of the cardiovascular outcome studies with some of these new agents.
The year in cardiovascular medicine 2021: interventional cardiology
Authors: Escaned Javier , Jaffer Farouc A. , Mehilli Julinda , Mehran Roxana 
Published: December 2021

Abstract
Since last year’s report in the European Heart Journal, we have witnessed substantial progress in all aspects of interventional cardiology. Of note, the practice of interventional cardiology took place amidst successive waves of the COVID-19 pandemic, which continues to be a major burden for all healthcare professionals around the globe. In our yearly review, we shall revisit the developments in percutaneous coronary intervention (PCI), structural heart interventions, and adjunctive pharmacotherapy.
The year in cardiovascular medicine 2021: heart failure and cardiomyopathies
Authors: Bauersachs Johann , de Boer Rudolf A. , Lindenfeld JoAnn , Bozkurt Biykem 
Published: December 2021

Abstract
In the year 2021, the universal definition and classification of heart failure (HF) was published that defines HF as a clinical syndrome with symptoms and/or signs caused by a cardiac abnormality and corroborated by elevated natriuretic peptide levels or objective evidence of cardiogenic congestion. This definition and the classification of HF with reduced ejection fraction (HFrEF), mildly reduced, and HF with preserved ejection fraction (HFpEF) is consistent with the 2021 ESC Guidelines on HF. Among several other new recommendations, these guidelines give a Class I indication for the use of the sodium–glucose co-transporter 2 (SGLT2) inhibitors dapagliflozin and empagliflozin in HFrEF patients. As the first evidence-based treatment for HFpEF, in the EMPEROR-Preserved trial, empagliflozin reduced the composite endpoint of cardiovascular death and HF hospitalizations. Several reports in 2021 have provided novel and detailed analyses of device and medical therapy in HF, especially regarding sacubitril/valsartan, SGLT2 inhibitors, mineralocorticoid receptor antagonists, ferric carboxymaltose, soluble guanylate cyclase activators, and cardiac myosin activators. In patients hospitalized with COVID-19, acute HF and myocardial injury is quite frequent, whereas myocarditis and long-term damage to the heart are rather uncommon.
Impact of sodium-glucose co-transporter inhibitors on cardiac autonomic function and mortality: no time to die
Authors: Lim Ven Gee , He Hejie , Lachlan Thomas , Ng Ghulam Andre , Kyrou Ioannis , Randeva Harpal S , Osman Faizel 
Published: December 2021

Abstract
Sodium-glucose co-transporter 2 (SGLT2) inhibitors have been shown to improve cardiovascular outcomes not only in patients with diabetes but also in those with heart failure, irrespective of diabetic status. However, the mechanisms underlying the cardioprotective effects of these newer anti-diabetic drugs remain to be fully elucidated. One exciting avenue that has been recently explored in both preclinical and clinical studies is the modulation of the cardiovascular autonomic nervous system. A reduction in sympathetic nervous system activity by SGLT2 inhibitors may potentially translate into a reduction in arrhythmic risk and sudden arrhythmic death, which may explain, at least partly, the cardioprotection shown in the cardiovascular outcome trials with different SGLT2 inhibitors. Although some of the data from the preclinical and clinical studies are promising, overall the findings can be contradictory. This highlights the need for more studies to address gaps in our knowledge of these novel drugs. The present review offers an in depth overview of the existing literature regarding the role of SGLT2 inhibitors in modulating cardiovascular autonomic function as one of the possible pathways of their cardioprotective effects.
Mycoplasmadecontamination inChlamydia trachomatisculture: a curative approach
Authors: Greer Madison , Elnaggar Jacob H , Taylor Christopher M , Shen Li 
Published: December 2021

AbstractMycoplasma contamination of cell culture represents a serious problem in research and decontamination from cell-propagated obligate intracellular bacteria has proven challenging. Here, we presented an optimized protocol to remove Mycoplasma from contaminated Chlamydia trachomatis culture. A stepwise procedure of Mycoplasma removal entails (i) incubation in nonionic detergent-containing solution and (ii) separation of viable chlamydial organisms by fluorescence-activated cell sorting (FACS), followed by subcloning using a focus-forming assay. We also adapted a polymerase chain reaction (PCR) assay using paired universal and Mycoplasma-specific primers, which are distinguishable from the C. trachomatis counterparts, in combination with Sanger sequencing to determine the presence of mycoplasmas’ 16S rRNA genes. These integrated approaches allow for full removal of Mycoplasma, as verified by the improved PCR assay, without compromising the capacity of viable C. trachomatis to adapt to new infection in epithelial cells. Some pitfalls during the Mycoplasma decontamination process are discussed.
A regularization by denoising (RED) scheme for 3-D FWI model updates in large-contrast media
Authors: Anagaw Amsalu , Sacchi Mauricio D 
Published: December 2021

SUMMARY
Full waveform inversion (FWI) endeavours to estimate high-resolution physical properties of subsurface structures. The technique minimizes the data misfit between observed and modelled seismograms. Despite its success, the application of FWI in areas with high-velocity contrasts remains a challenging problem. Often, quadratic regularization methods are chosen to stabilize inverse problems. Unfortunately, quadratic regularization does not preserve edges and sharp discontinuities adequately. Conversely, a regularization term that uses the l1 norm of the gradient of model parameters can preserve discontinuities. The latter leads to edge-preserving methods based on total variation regularization. This work adopts the framework named regularization by denoising (RED) to solve the FWI problem in high-contrast media. The RED technique only requires an image denoising engine, which, in our case, is a modified weighted total variation filter. One advantage of adopting the RED algorithm for solving FWI problems is its simplicity in the numerical implementation and selection of trade-off parameters. We have benchmarked our algorithm via the 2-D BP/EAGE model, a model with significant velocity contrasts and complex salt bodies. We have also tested the proposed regularization method with the 3-D SEG/EAGE overthrust P-wave velocity model. We also compare the proposed RED method and FWI with total variation regularization.
Models of convection and segregation in heterogeneous partially molten crustal roots with a VOF method – I: flow regimes
Authors: Louis–Napoléon Aurélie , Bonometti Thomas , Gerbault Muriel , Martin Roland , Vanderhaeghe Olivier 
Published: December 2021

SUMMARYWe investigate numerically some thermomechanical conditions for the development of crustal scale diapirism and convection in a heterogeneous continental crust independently from the action of regional tectonics. Here, we consider a hot crust, with unmolten and partially molten domains of specific temperature and strain-rate dependent power-law rheologies. We take advantage of the volume of fluid (VOF) method to capture the coalescence and separation of deformable inclusions in the partially molten domain. The inclusions, of several hundred metres in size, are more or less dense and viscous with respect to the ambient medium (they also behave with a power-law rheology). We restrict our study to a 20 Myr time scale, during which gravitational dynamics may dominate over lateral tectonics and lithospheric thermal re-equilibration. The motion of these inclusions during the development of gravitational instabilities displays distinct flow regimes that depend on two Rayleigh numbers denoted RaUM and RaPM, for the unmolten and partially molten rock properties, respectively. A ‘suspension’ regime occurs at high RaUM and high RaPM, in which most of the light compositional heterogeneities remain entrained in the convective cells. In contrast at low RaUM and high RaPM, a ‘layering’ regime is characterized by merging of the light inclusions as floating clusters below the rigid upper crustal lid. This regime occurs in association with a sharp viscosity gradient at upper-to-middle crust transitional depths. In these two regimes, the dense inclusions accumulate at the bottom of the partially molten zone. Finally at moderate RaPM, a ‘diapiric’ regime reflects the segregation of the heavy and the light inclusions, respectively downward and upward, without global convection. These numerical experiments lead to a first order evaluation of the physical parameters required for the segregation of deformable inclusions of variable densities and convection, in a partially molten crust, and provide insights on the conditions for the development of migmatite domes. Geological data indicate that these processes likely occur in a large number of settings from Archean to Phanerozoic times, and contribute to the differentiation of the continental crust.
A partial reduction of Drp1 improves cognitive behavior and enhances mitophagy, autophagy and dendritic spines in a transgenic Tau mouse model of Alzheimer disease
Authors: Kandimalla Ramesh , Manczak Maria , Pradeepkiran Jangampalli Adi , Morton Hallie , Reddy P Hemachandra 
Published: December 2021

AbstractThe purpose of our study is to understand the impact of a partial dynamin-related protein 1 (Drp1) on cognitive behavior, mitophagy, autophagy and mitochondrial and synaptic activities in transgenic Tau mice in Alzheimer’s disease (AD). Our laboratory reported increased levels of amyloid-beta (Aβ) and phosphorylated Tau (P-Tau) and reported that abnormal interactions between Aβ and Drp1, P-Tau and Drp1 induced increased mitochondrial fragmentation and reduced fusion and synaptic activities in AD. These abnormal interactions result in the proliferation of dysfunctional mitochondria in AD neurons. Recent research on mitochondria revealed that fission protein Drp1 is largely implicated in mitochondrial dynamics in AD. To determine the impact of reduced Drp1 in AD, we recently crossed transgenic Tau mice with Drp1 heterozygote knockout (Drp1+/−) mice and generated double mutant (P301LDrp1+/−) mice. In the current study, we assessed the cognitive behavior, mRNA and protein levels of mitophagy, autophagy, mitochondrial biogenesis, dynamics and synaptic genes, mitochondrial morphology and mitochondrial function and dendritic spines in Tau mice relative to double mutant mice. When compared with Tau mice, double mutant mice did better on the Morris Maze (reduced latency to find hidden platform, increased swimming speed and time spent on quadrant) and rotarod (stayed a longer period of time) tests. Both mRNA- and protein-level autophagy, mitophagy, mitochondrial biogenesis and synaptic proteins were increased in double mutant mice compared with Tau (P301L) mice. Dendritic spines were significantly increased; mitochondrial number was reduced and length was increased in double mutant mice. Based on these observations, we conclude that reduced Drp1 is beneficial in a symptomatic-transgenic Tau (P301L) mice.
Heavy fishery exploitation does not affect sizes at recruitment and maturity of squid Illex argentinus and Doryteuthis gahi, in the Southwest Atlantic
Authors: Arkhipkin A I , Winter A G , Nigmatullin C M 
Published: December 2021

Abstract
Commercial exploitation often impacts the life-history parameters of iteroparous and semelparous fishes, and prolonged fishing pressure may lead to fisheries-induced evolution. However, information is lacking on how fishing exploitation affects short-lived semelparous cephalopods. This study examines the impact of heavy commercial fishing on Illex argentinus and Doryteuthis gahi, two annual squid species around the Falkland Islands in the Southwest Atlantic. Changes in two life-history parameters; size at recruitment and size at maturity, were standardized for sea temperature and analysed in relation to relative biomass indices over 34 years for I. argentinus and 31 years for D. gahi. For both squid species, correlations of these life-history parameters were observed with biomass and temperature, but size at recruitment and size at maturity did not change significantly over the extended periods of their commercial exploitation. Sizes at recruitment and maturity of these short-lived squid appear to remain stable in absence of size selection in their respective fisheries. Both jigs and trawls capture the entire size ranges of squid recruited to the fishing grounds, thus avoiding direct fisheries-induced selection on their size-dependent life-history parameters. With only one cohort/generation at a time present during growth-phase fishery, both squid species studied seem to be more resilient to fisheries-induced changes in sizes at recruitment and maturity than short-lived semelparous fish and squid subjected to terminal fisheries. Instead, these size-dependent life-history traits of squid fished during their growth phase are mainly driven by short-term changes in population density and environment, including ambient temperature.
Extensively resistant Acinetobacter baumannii isolate RCH52 carries several resistance genes derived from an IncC plasmid
Authors: Ambrose Stephanie J. , Hamidian Mohammad , Hall Ruth M. 
Published: December 2021

Abstract

Objectives
To identify the origins of resistance in a sporadic extensively resistant Acinetobacter baumannii isolate.

Methods
The complete genome of RCH52 was determined by combining available Illumina short reads with MinION (Oxford Nanopore) long reads using Unicycler. Bioinformatic searches were used to identify features of interest.

Results
The complete genome of RCH52 revealed an unusual chromosomal region containing all of the antibiotic resistance genes, except tet39, which is in a plasmid. A 129 585 bp segment was bounded by inversely oriented copies of ISAba1 and included two groups of resistance genes separated by the large segment of the backbone of type 1 IncC plasmids that lies between the ARI-A and ARI-B resistance islands but does not include the replication region. The ISAba1-bounded segment was located in a novel integrative element that had integrated into the chromosomal thyA gene but provided a replacement thyA gene. Several resistance genes are derived from either the ARI-A or the ARI-B resistance islands found in IncC plasmids that have been brought together by an IS26-mediated deletion of the original plasmid. This non-replicating circular molecule (or translocatable unit) has been incorporated into a smaller ISAba1-bounded unit that includes oxa23 in Tn2008B via homologous recombination between sul2-CR2-floR segments found in both.

Conclusions
The plasmids shared by most Gram-negative pathogens, including the broad host range IncC plasmids, have not been detected in Acinetobacter species. However, it seems likely that they can conjugate into members of this genus and contribute pre-existing clusters of antibiotic resistance genes.