bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics and evolutionary analysis of plant CNGCs
Authors: Baloch Akram Ali , Kakar Kaleem U , Nawaz Zarqa , Mushtaq Muhammad , Abro Asma , Khan Samiullah , Latif Abdul 
Published: August 2022

Abstract
Comparative genomics and computational biology offer powerful research tools for studying evolutionary mechanisms of organisms, and the identification and characterization of conserved/distant genes and gene families. The plant CNGC gene family encodes evolutionary conserved ion channel proteins involved in important signaling pathways and biological functions. The fundamental ideas and standard procedures for genome-wide identification and evolutionary analysis of plant cyclic nucleotide-gated ion channels employing various software, tools, and online servers have been discussed. In particular, this developed method focused on practical procedures involving the comparative analysis of paralogs and orthologs of CNGC genes in different plant species at different levels including phylogenetic analysis, nomenclature and classification, gene structure, molecular protein evolution, and duplication events as mechanisms of gene family expansion and synteny.
CSF biomarkers in patients with epilepsy in Alzheimer’s disease: a nation-wide study
Authors: Banote Rakesh Kumar , Håkansson Samuel , Zetterberg Henrik , Zelano Johan 
Published: August 2022

Abstract
Alzheimer’s disease is the most common neurodegenerative dementia. A subset of Alzheimer’s disease patients develop epilepsy. The risk is higher in young-onset Alzheimer’s disease, but pathophysiological mechanisms remain elusive. The purpose of this study was to assess biomarkers reflecting neurodegeneration in Alzheimer’s disease patients with and without epilepsy. By cross-referencing the largest national laboratory database with Swedish National Patient Register, we could identify CSF biomarker results from 17901 Alzheimer’s disease patients, and compare levels of neurofilament light, glial fibrillary acidic protein, total tau, phosphorylated tau and amyloid beta 42 in patients with (n = 851) and without epilepsy. The concentrations of total tau and phosphorylated tau were higher in Alzheimer’s disease patients with epilepsy than Alzheimer’s disease patients without epilepsy and amyloid beta 42 levels were significantly lower in Alzheimer’s disease patients with epilepsy. No differences in the levels of neurofilament light and glial fibrillary acidic protein were observed. Our study suggests that epilepsy is more common in Alzheimer’s disease patients with more pronounced Alzheimer’s pathology, as determined by the CSF biomarkers. Further studies are needed to investigate the biomarker potential of these CSF markers as predictors of epilepsy course or as indicators of epileptogenesis in Alzheimer’s disease.
Effectiveness of Coronavirus Disease 2019 Vaccines Against Hospitalization and Death in Canada: A Multiprovincial, Test-Negative Design Study
Authors: Nasreen Sharifa , Febriani Yossi , Velásquez García Héctor Alexander , Zhang Geng , Tadrous Mina , Buchan Sarah A , Righolt Christiaan H , Mahmud Salaheddin M , Janjua Naveed Zafar , Krajden Mel , De Serres Gaston , Kwong Jeffrey C 
Published: August 2022

AbstractBackgroundA major goal of coronavirus disease 2019 (COVID-19) vaccination is to prevent severe outcomes (hospitalizations and deaths). We estimated the effectiveness of messenger RNA (mRNA) and ChAdOx1 COVID-19 vaccines against severe outcomes in 4 Canadian provinces between December 2020 and September 2021.MethodsWe conducted this multiprovincial, retrospective, test-negative study among community-dwelling adults aged ≥18 years in Ontario, Quebec, British Columbia, and Manitoba using linked provincial databases and a common study protocol. Multivariable logistic regression was used to estimate province-specific vaccine effectiveness against COVID-19 hospitalization and/or death. Estimates were pooled using random-effects models.ResultsWe included 2 508 296 tested participants, with 31 776 COVID-19 hospitalizations and 5842 deaths. Vaccine effectiveness was 83% after a first dose and 98% after a second dose against both hospitalization and death (separately). Against severe outcomes, effectiveness was 87% (95% confidence interval [CI], 71%–94%) ≥84 days after a first dose of mRNA vaccine, increasing to 98% (95% CI, 96%–99%) ≥112 days after a second dose. Vaccine effectiveness against severe outcomes for ChAdOx1 was 88% (95% CI, 75%–94%) ≥56 days after a first dose, increasing to 97% (95% CI, 91%–99%) ≥56 days after a second dose. Lower 1-dose effectiveness was observed for adults aged ≥80 years and those with comorbidities, but effectiveness became comparable after a second dose. Two doses of vaccines provided very high protection for both homologous and heterologous schedules and against Alpha, Gamma, and Delta variants.ConclusionsTwo doses of mRNA or ChAdOx1 vaccine provide excellent protection against severe outcomes.
Cytomegalovirus Immunoglobulin G (IgG) Titer and Coronary Artery Disease in People With Human Immunodeficiency Virus (HIV)
Authors: Schnittman Samuel R , Lu Michael T , Mayrhofer Thomas , Burdo Tricia H , Fitch Kathleen V , McCallum Sara , Fulda Evelynne S , Zanni Markella V , Foldyna Borek , Malvestutto Carlos , Fichtenbaum Carl J , Aberg Judith A , Bloomfield Gerald S , Overton Edgar T , Currier Judith , Tebas Pablo , Sha Beverly E , Ribaudo Heather J , Flynn Jacqueline M , Douglas Pamela S , Erlandson Kristine M , Grinspoon Steven K 
Published: August 2022

Abstract

Background
Cytomegalovirus (CMV) infection is thought to result in increased immune activation in people with human immunodeficiency virus (HIV, PWH). Although some data have linked asymptomatic CMV infection to cardiovascular disease among PWH, it remains unknown whether CMV is associated with increased or high-risk coronary plaque.

Methods
The Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) enrolled PWH aged 40–75 years on stable antiretroviral therapy (ART) with low-to-moderate atherosclerotic cardiovascular disease (ASCVD) risk. Among a subset of US REPRIEVE participants, coronary plaque was assessed by coronary computed tomography angiography. Here, we assessed the relationship between CMV immunoglobulin G (IgG) titer and (1) levels of immune activation, (2) inflammatory biomarkers, and (3) coronary plaque phenotypes at study entry.

Results
Of 672 participants, mean age was 51 years, 83% were men, median ASCVD risk score was 4.5%, and 66% had current CD4+ T-cell count ≥500 cells/mm3. Higher CMV IgG quartile group was associated with older age and lower current and nadir CD4+ T-cell counts. CMV IgG titer was associated with specific inflammatory biomarkers (sCD163, MCP-1, interleukin [IL]-6, hsCRP) in univariate analysis, but not after controlling for HIV-specific factors. In contrast, CMV IgG titer was not associated with coronary artery disease indexes, including presence of plaque, coronary artery calcium (CAC) score &gt;0, vulnerable plaque presence, or Leaman score &gt;5.

Conclusions
No meaningful association was seen between CMV IgG titer and coronary artery disease indexes among ART-treated PWH at study enrollment. Longitudinal assessments in REPRIEVE will determine the relationship of CMV IgG titer to plaque progression and cardiovascular events.

Clinical Trials Registration
NCT02344290.
Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity
Authors: Windler Miriam , Stuart Rhona , Deutzmann Joerg S , Mayali Xavier , Navid Ali , D'haeseleer Patrik , Marcu Oana E , Lipton Mary , Nicora Carrie , Spormann Alfred M 
Published: August 2022

Abstract
Algal-bacterial interactions provide clues to algal physiology, but mutualistic interactions are complicated by dynamic exchange. We characterized the response of Chlamydomonas reinhardtii to the presence of a putative alga-benefitting commensal bacterium (Arthrobacter strain ‘P2b’). Co-cultivation promoted chlorophyll content, biomass, average cell size, and number of dividing cells, relative to axenic cultures. Addition of bacterial spent medium (whole, size-fractionated and heat-treated) had similar effects, indicating P2b does not require algal interaction to promote growth. Nutrients and pH were excluded as putative effectors, collectively indicating a commensal interaction mediated by Arthrobacter-released small exometabolite(s). Proteogenomic comparison revealed similar response to co-cultivation and spent media, including differential cell cycle regulation, extensive downregulation of flagellar genes and histones, carbonic anhydrase and RubisCO downregulation, upregulation of some chlorophyll, amino acid and carbohydrate biosynthesis genes, and changes to redox and Fe homeostasis. Further, Arthrobacter protein expression indicated some highly expressed putative secondary metabolites. Together, these results revealed that low molecular weight bacterial metabolites can elicit major physiological changes in algal cell cycle regulation, perhaps through a more productive G1 phase, that lead to substantial increases in photosynthetically-produced biomass. This work illustrates that model commensal interactions can be used to shed light on algal response to stimulating bacteria.
Chromosome-level Genome Assembly of the High-altitude Leopard (Panthera pardus) Sheds Light on Its Environmental Adaptation
Authors: Zhou Chuang , Liu Yi , Zhang Rusong , Zheng Xiaofeng , Zhao Guangqing , Li Fengjun , Liu Wei , Yue Bisong , Yang Nan 
Published: August 2022

Abstract
The leopard (Panthera pardus) has the largest natural distribution from low- to high-altitude areas of any wild felid species, but recent studies have revealed that leopards have disappeared from large areas, probably owing to poaching, a decline of prey species, and habitat degradation. Here, we reported the chromosome-scale genome assembly of the high-altitude leopard (HL) based on nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) technology. Panthera genomes revealed similar repeat composition, and there was an appreciably conserved synteny between HL and the other two Panthera genomes. Divergence time analysis based on the whole genomes revealed that the HL and the low-altitude leopard differentiate from a common ancestor ∼2.2 Ma. Through comparative genomics analyses, we found molecular genetic signatures that may reflect high-altitude adaptation of the HL. Three HL-specific missense mutations were detected in two positively selected genes, that is, ITGA7 (Ala112Gly, Asp113Val, and Gln115Pro) and NOTCH2 (Ala2398Ser), which are likely to be associated with hypoxia adaptation. The chromosome-level genome of the HL provides valuable resources for the investigation of high-altitude adaptation and protection management of the vulnerable leopard.
The Role of the Gut Microbiome in Diet and Exercise Effects on Cognition: A Review of the Intervention Literature
Authors: Koblinsky Noah D , Power Krista A , Middleton Laura , Ferland Guylaine , Anderson Nicole D 
Published: August 2022

AbstractInterest in the gut–brain axis and its implications for neurodegenerative diseases, such as Alzheimer’s disease and related dementias, is growing. Microbial imbalances in the gastrointestinal tract, which are associated with impaired cognition, may represent a therapeutic target for lowering dementia risk. Multicomponent lifestyle interventions are a promising dementia risk reduction strategy and most often include diet and exercise, behaviors that are also known to modulate the gut microbiome. A better understanding of the role of the gut microbiome in diet and exercise effects on cognition may help to optimize these lifestyle interventions. The purpose of this review is to summarize findings from diet and exercise interventions that have investigated cognitive changes via effects on the microbiome. We aim to discuss the underlying mechanisms, highlight current gaps in the field, and provide new research directions. There is evidence mainly from rodent studies supporting the notion that microbiota changes mediate the effects of diet and exercise on cognition, with potential mechanisms including end-product metabolites and regulation of local and systemic inflammation. The field lacks whole diet and exercise interventions, especially those involving human participants. It is further limited by heterogeneous rodent models, outcome assessments, and the absence of proper mediation analyses. Trials including older adults with dementia risk factors, factorial designs of diet and exercise, and pre and post measures of microbiota, end-product metabolites, and inflammation would help to elucidate and potentially leverage the role of the microbiome in lowering dementia risk through lifestyle modification.
Sexual and Marital Satisfaction in Older Adulthood: Effects of Childhood and Adulthood Violence Exposure
Authors: Kong Jooyoung , Easton Scott D , Zhang Yan 
Published: August 2022

AbstractBackground and ObjectivesGuided by the life course perspective and traumagenic dynamics theory, the current study examines (a) the long-term effects of childhood sexual abuse (CSA) and other adverse childhood experiences (ACEs) on older adults’ sexual and marital outcomes, (b) the mediating role of intimate partner violence (IPV) victimization in the association between childhood adversities and sexual and marital satisfaction, and (c) whether gender moderates the mediational association.Research Design and MethodsWe examined 5,391 adults in their early 70s who participated in the 2010–2011 Wisconsin Longitudinal Study. A series of structural equation models was performed to examine the direct and indirect effect of CSA and other ACEs on sexual and marital outcomes in later life.ResultsCSA was directly associated with lower levels of sexual and marital satisfaction in late adulthood. Other ACEs were associated with currently not being married and greater numbers of marriages. Furthermore, other ACEs were significantly associated with low levels of marital satisfaction through IPV victimization. The moderated mediational analysis showed that the negative indirect effect of other ACEs on marital satisfaction via IPV victimization was stronger for women than men.Discussion and ImplicationsUsing a population-based sample, this is one of the first studies demonstrating that distal life events such as CSA and ACEs can undermine older adults’ sexual and marital health, and revictimization in adulthood may serve as a mechanism for the association. Timely intervention is needed to prevent persistent negative effects of childhood violence.
A re-examination of ellipticity corrections for seismic phases
Authors: Russell Stuart , Rudge John F , Irving Jessica C E , Cottaar Sanne 
Published: August 2022

SUMMARY
The Earth’s ellipticity of figure has an effect on the traveltimes of seismic waves over teleseismic distances. Tables of ellipticity corrections and coefficients have been used by seismologists for several decades; however, due to the increasing variety and complexity of seismic phases in use, current tables of ellipticity coefficients are now outmoded and incomplete. We present a Python package, EllipticiPy, for the calculation of ellipticity corrections, which removes the dependence on pre-calculated coefficients at discrete source depths and epicentral distances. EllipticiPy also facilitates the calculation of ellipticity corrections on other planetary bodies. When applied to both Earth and Mars, the magnitudes of ellipticity corrections are of the order of single seconds and are significant for some seismic studies on Earth but remain negligible on Mars due to other greater sources of uncertainty.
Influence of shear wave velocity heterogeneity on SH-wave reverberation imaging of the mantle transition zone
Authors: Liu Meichen , Ritsema Jeroen , Chaves Carlos A M 
Published: August 2022

SUMMARY
Long-period (T &gt; 10 s) shear wave reflections between the surface and reflecting boundaries below seismic stations are useful for studying phase transitions in the mantle transition zone (MTZ) but shear-velocity heterogeneity and finite-frequency effects complicate the interpretation of waveform stacks. We follow up on a recent study by Shearer & Buehler (hereafter SB19) of the top-side shear wave reflection Ssds as a probe for mapping the depths of the 410-km and 660-km discontinuities beneath the USArray. Like SB19, we observe that the recorded Ss410s-S and Ss660s-S traveltime differences are longer at stations in the western United States than in the central-eastern United States. The 410-km and 660-km discontinuities are about 40–50 km deeper beneath the western United States than the central-eastern United States if Ss410s-S and Ss660s-S traveltime differences are transformed to depth using a common-reflection point (CRP) mapping approach based on a 1-D seismic model (PREM in our case). However, the east-to-west deepening of the MTZ disappears in the CRP image if we account for 3-D shear wave velocity variations in the mantle according to global tomography. In addition, from spectral-element method synthetics, we find that ray theory overpredicts the traveltime delays of the reverberations. Undulations of the 410-km and 660-km discontinuities are underestimated when their wavelengths are smaller than the Fresnel zones of the wave reverberations in the MTZ. Therefore, modelling of layering in the upper mantle must be based on 3-D reference structures and accurate calculations of reverberation traveltimes.
An inverse data envelopment analysis model to consider ratio data and preferences of decision-makers
Authors: Mahla Deepak , Agarwal Shivi , Amin Gholam R , Mathur Trilok 
Published: August 2022

Abstract
Inverse data envelopment analysis (DEA) determines the optimal level of inputs and/or outputs of decision-making units (DMUs) to reach efficiency targets. This paper presents a new inverse DEA model for determining minimum inputs for working capital management. The proposed model is employed in the Indian textile industry to calculate working capital efficiency. Given the working capital efficiency, the decision maker’s preferences will be estimating the change in inputs when outputs increase. Furthermore, unlike the standard inverse DEA model, this article discusses the inverse DEA model when negative ratio data exist. The DEA model requires additional attention when ratio data are present; therefore, a novel inverse DEA ratio model is proposed. The input targets obtained from the proposed model are less than the standard inverse DEA model. Also, the proposed model is a closer estimate of the production probability set for ratio data.
Anti-cancer mechanisms of action of therapeutic alternating electric fields (tumor treating fields [TTFields])
Authors: Shams Shadi , Patel Chirag B 
Published: August 2022

ABSTRACT
Despite improved survival outcomes across many cancer types, the prognosis remains grim for certain solid organ cancers including glioblastoma and pancreatic cancer. Invariably in these cancers, the control achieved by time-limited interventions such as traditional surgical resection, radiation therapy, and chemotherapy is short-lived. A new form of anti-cancer therapy called therapeutic alternating electric fields (AEFs) or tumor treating fields (TTFields) has been shown, either by itself or in combination with chemotherapy, to have anti-cancer effects that translate to improved survival outcomes in patients. Although the pre-clinical and clinical data are promising, the mechanisms of TTFields are not fully elucidated. Many investigations are underway to better understand how and why TTFields is able to selectively kill cancer cells and impede their proliferation. The purpose of this review is to summarize and discuss the reported mechanisms of action of TTFields from pre-clinical studies (both in vitro and in vivo). An improved understanding of how TTFields works will guide strategies focused on the timing and combination of TTFields with other therapies, to further improve survival outcomes in patients with solid organ cancers.
Force-free magnetic flux ropes: String confinement of super-strong magnetic fields and flare energy release
Authors: Solov'ev A A 
Published: August 2022

ABSTRACT
A new class of force-free solutions for a horizontal magnetic filament with a circular cross-section is found, in which the magnetic field strength on the axis significantly (up to 2–3 orders of magnitude and more) exceeds the strength of the longitudinal external field that keeps the rope from lateral expansion. A weak transverse field leads to a small deviation from the force-free field structure and results in a density deficit and an increase in temperature on the rope axis. The possibility of a flare release of magnetic energy is shown when critical values ​​of the longitudinal electric current density in the filament are reached at which ‘anomalous resistance’ occurs, caused by the development of the current ion-sound plasma instability. It turns out to be much larger than the usual Coulomb resistance. The following values are determined: the scale of the current dissipation region, the electric field strength in it, which significantly exceeds the Dreicer value, and the possible energy of accelerated charged particles (up to hundreds of MeV). The critical density of the longitudinal current at which the plasma turbulence is excited does not depend on the presence of a super-strong field on the flux-rope axis, so that the current density depends only on the electron concentration, temperature, and anomalous conductivity. However, super-strong magnetic fields can manifest themselves in the fact that, in their presence, the excitation of plasma instabilities can occur at sufficiently high electron concentrations. This effect may explain the large number of accelerated particles sometimes observed in solar flares.
Propagating torsional Alfvén waves in thermally active solar plasma
Authors: Belov S A , Vasheghani Farahani S , Molevich N E 
Published: August 2022

ABSTRACT
The aim of this study is to shed light on the effects connected with thermal misbalance due to non-equal cooling and heating rates induced by density and temperature perturbations in solar active regions hosting either propagating torsional or shear Alfvén waves. A description for the non-linear forces connected with Alfvén waves in non-ideal conditions is provided, based on the second-order thin flux tube approximation. This provides insight into the effects of Alfvén-induced motions on the boundary of thin magnetic structures in thermally active plasmas. The equations describing the process of generating longitudinal velocity perturbations, together with density perturbations by non-linear torsional Alfvén waves, are obtained and solved analytically. It is shown that the phase shift (compared with the ideal case) and the amplitude of the induced longitudinal plasma motions against the period of the mother Alfvén wave are greater for shear Alfvén waves compared with torsional Alfvén waves, although following the same pattern. The difference in the influence of thermal misbalance on the induced velocity perturbations is governed by the plasma-β although its effect is stronger for shear waves. It is deduced that for a harmonic Alfvén driver the induced density perturbations are left uninfluenced by the thermal misbalance.
Fragmentation with discontinuous Galerkin schemes: non-linear fragmentation
Authors: Lombart Maxime , Hutchison Mark , Lee Yueh-Ning 
Published: August 2022

ABSTRACT
Small grains play an essential role in astrophysical processes such as chemistry, radiative transfer, and gas/dust dynamics. The population of small grains is mainly maintained by the fragmentation process due to colliding grains. An accurate treatment of dust fragmentation is required in numerical modelling. However, current algorithms for solving fragmentation equation suffer from an overdiffusion in the conditions of 3D simulations. To tackle this challenge, we developed a discontinuous Galerkin scheme to solve efficiently the non-linear fragmentation equation with a limited number of dust bins.