bluuebunny/crossref_metadata_2025 huggingface dataset:
Epistemic Reasons as Right-Kind Reasons
Authors: Schroeder Mark
Published: July 2021

Chapter 7 takes up the question of how we can determine whether some putative reasons for or against belief count as epistemic or not. It is argued that this is a special case of a much broader question as to how we can determine whether some putative reasons for or against any attitude count as bearing on the distinctive rationality of that kind of attitude, and that answers to the narrower question about belief should be informed by answers to the broader question about attitudes in general. The object-given/state-given theory is introduced as a prominent candidate to answer the general question, but shown to be inadequate. The alternative idea that the right-kind/wrong-kind distinction for each attitude derives from the nature of that attitude is defended and illustrated with representative cases. Finally, the implications of this account of the right-kind/wrong-kind distinction are drawn out for the case of belief by showing how different plausible theories of the nature of belief can result in different plausible answers to which of the reasons against belief identified in Chapter 6 are genuinely epistemic.
The Right of Access under EU Data Protection Law
Authors: Vrabec Helena U.
Published: July 2021

Chapter 5 focuses on Article 15 of the GDPR and explains the scope of the information that can be accessed under the right. The chapter then discusses the importance of the interface to submit data subject access requests. The core part of Chapter 5 is the analysis of the regulatory boundaries of the right of access and various avenues to limit the right, for instance, a conflict with the rights of another individual. Finally, the chapter illustrates how the right of access is applied in the data-driven economy by applying it to three different contexts: shared data, anonymised/pseudonymised data, and automated decision-making.
Resultant Luck and the Irrelevance Intuition
Authors: Lang Gerald
Published: July 2021

This chapter investigates the ‘Irrelevance Intuition’, which is the intuition that judgements of blameworthiness containing any element of resultant luck are irrelevant for judging agents. It deploys a number of claims against the Irrelevance Intuition. It holds that our interest in outcomes is fundamental, and these outcomes must in principle be relevant to the moral appraisal of agents who have acted wrongly (‘Relevance Claim’). It denies an agent a complaint against the fact her blameworthiness may exceed the blameworthiness of an identically motivated agent whose act caused less harm on the grounds that this agent had the option of not acting wrongly in the first place (‘Denial Claim’). And it holds that agents acting from descriptively identical mental states may differ in badness as a result of how their acts turn out on the grounds that their mental states differ in badness (‘Determination Claim’). The Determination Claim confirms that the main argument given for the Restricted Account is thoroughly externalist. The Restricted Account makes some allowance for acts prompted by ignorance or irrationality, and for acts that turn out in entirely unforeseeable ways.
Restraining Situational Luck
Authors: Lang Gerald
Published: July 2021

This chapter examines circumstantial luck, or the luck of being in circumstances where a moral response or course of action is called for. The anti-anti-luckist programme is maintained for circumstantial luck as well as resultant luck. The argument proceeds, first, through an examination of Good Cases, calling for praiseworthiness. The fact that a well-intentioned agent is not in a position to collect praise for performing a meritorious act does not generate any serious moral concern. We can still praise this inactive agent for her dispositions if we wish to, and morality does not insist, in any case, upon equal opportunities for collecting praise. These lessons are then transferred to Bad Cases, calling for blameworthiness. The chapter also engages in detail with Michael Zimmerman’s argument involving situational luck, which combines circumstantial luck with constitutive luck. Zimmerman’s radical argument suggests that one agent should be no more blameworthy than another agent if they are separated only by luck, whether of the resultant, circumstantial, or constitutive variety. It is suggested here that Zimmerman’s argument misfires, due to an inconsistency between two principles he relies upon: the ‘Control Principle’ and the ‘No-Difference Claim’.
Confessional Mobility of Secular Catholics
Authors: Ó hAnnracháin Tadhg
Published: July 2021

Chapter 3 analyzes how religion structured and inflected the migration and internal movement of Catholics. It explores the confessional dimension of the periodic exodus of large numbers of mercenary soldiers and the development of Catholic mercantile networks in exile. It also examines how famine and war resulted in displacement of large numbers of Irish Catholics, some of whom found refuge on the continent, but many of whom perished without record.
The Established Church
Authors: Ó hAnnracháin Tadhg
Published: July 2021

Chapter 4 provides an overview of the role played by migration in creating the Church of Ireland and its body of adherents. It discusses the manner in which secular Protestants derived great benefit from their religion and the manner in which they came to emphasize religious ‘reliability’ as a touchstone of loyalty, and the central role of the rebellion of 1641 in developing Irish Protestants’ understanding of their situation and role in Ireland. The chapter demonstrates the profoundly migratory character of Early Modern Irish Protestantism and the manner in which its leadership was dominated primarily by British-born bishops and then secondarily by New English migrants, to the almost complete exclusion of figures of native provenance. As a result, both the church and its community acquired a migrant stamp which contributed to its evangelical inefficacy in Ireland.
Path-Dependence
Authors: Levinthal Daniel A.
Published: July 2021

The intertemporal linkages that both constrain and enable an organization are central to its adaptive properties. The most narrow expression of path-dependence is the process of state-dependence—having a particular asset stock at one point in time impacts the distribution of asset stocks that can be reached at a subsequent period. Development, how an organizational form unfolds over time, can change those dynamics. A considerable literature has sprung up around the idea of “dynamic capabilities.” This broad idea is broken down into five distinct facets: accessibility of organizational states, robustness of organizations to changes in the state of nature, capacity to influence future states of “nature,” cost of accessing future sets of attributes, and capacity to value the set of organizational attributes. However, this discourse tends to treat “capabilities” as isolated attributes and not to view the organization as a complex adaptive system, a perspective developed here.
Auxin controls the division of root endodermal cells
Authors: Seo Deok Hyun , Jeong Haewon , Choi Yang Do , Jang Geupil
Published: July 2021

The root endodermis forms a selective barrier that prevents the free diffusion of solutes into the vasculature; to make this barrier, endodermal cells deposit hydrophobic compounds in their cell walls, forming the Casparian strip. Here, we showed that, in contrast to vascular and epidermal root cells, endodermal root cells do not divide alongside the root apical meristem in Arabidopsis thaliana. Auxin treatment induced division of endodermal cells in wild-type plants, but not in the auxin signaling mutant auxin resistant3-1. Endodermis-specific activation of auxin responses by expression of truncated AUXIN-RESPONSIVE FACTOR5 (ΔARF5) in root endodermal cells under the control of the ENDODERMIS7 promoter (EN7::ΔARF5) also induced endodermal cell division. We used an auxin transport inhibitor to cause accumulation of auxin in endodermal cells, which induced endodermal cell division. In addition, knockout of P-GLYCOPROTEIN1 (PGP1) and PGP19, which mediate centripetal auxin flow, promoted the division of endodermal cells. Together, these findings reveal a tight link between the endodermal auxin response and endodermal cell division, suggesting that auxin is a key regulator controlling the division of root endodermal cells, and that PGP1 and PGP19 are involved in regulating endodermal cell division.
The emerging role of GABA as a transport regulator and physiological signal
Authors: Xu Bo , Sai Na , Gilliham Matthew
Published: July 2021

While the proposal that γ-aminobutyric acid (GABA) acts a signal in plants is decades old, a signaling mode of action for plant GABA has been unveiled only relatively recently. Here, we review the recent research that demonstrates how GABA regulates anion transport through aluminum-activated malate transporters (ALMTs) and speculation that GABA also targets other proteins. The ALMT family of anion channels modulates multiple physiological processes in plants, with many members still to be characterized, opening up the possibility that GABA has broad regulatory roles in plants. We focus on the role of GABA in regulating pollen tube growth and stomatal pore aperture, and we speculate on its role in long-distance signaling and how it might be involved in cross talk with hormonal signals. We show that in barley (Hordeum vulgare), guard cell opening is regulated by GABA, as it is in Arabidopsis (Arabidopsis thaliana), to regulate water use efficiency, which impacts drought tolerance. We also discuss the links between glutamate and GABA in generating signals in plants, particularly related to pollen tube growth, wounding, and long-distance electrical signaling, and explore potential interactions of GABA signals with hormones, such as abscisic acid, jasmonic acid, and ethylene. We conclude by postulating that GABA encodes a signal that links plant primary metabolism to physiological status to fine tune plant responses to the environment.
Imaging plant cells and organs with light-sheet and super-resolution microscopy
Authors: Ovečka Miroslav , Sojka Jiří , Tichá Michaela , Komis George , Basheer Jasim , Marchetti Cintia , Šamajová Olga , Kuběnová Lenka , Šamaj Jozef
Published: July 2021

The documentation of plant growth and development requires integrative and scalable approaches to investigate and spatiotemporally resolve various dynamic processes at different levels of plant body organization. The present update deals with vigorous developments in mesoscopy, microscopy and nanoscopy methods that have been translated to imaging of plant subcellular compartments, cells, tissues and organs over the past 3 years with the aim to report recent applications and reasonable expectations from current light-sheet fluorescence microscopy (LSFM) and super-resolution microscopy (SRM) modalities. Moreover, the shortcomings and limitations of existing LSFM and SRM are discussed, particularly for their ability to accommodate plant samples and regarding their documentation potential considering spherical aberrations or temporal restrictions prohibiting the dynamic recording of fast cellular processes at the three dimensions. For a more comprehensive description, advances in living or fixed sample preparation methods are also included, supported by an overview of developments in labeling strategies successfully applied in plants. These strategies are practically documented by current applications employing model plant Arabidopsis thaliana (L.) Heynh., but also robust crop species such as Medicago sativa L. and Hordeum vulgare L. Over the past few years, the trend towards designing of integrative microscopic modalities has become apparent and it is expected that in the near future LSFM and SRM will be bridged to achieve broader multiscale plant imaging with a single platform.
Immunotherapy and cardiovascular diseases: novel avenues for immunotherapeutic approaches
Authors: Bonfiglio C A , Weber C , Atzler D , Lutgens E
Published: July 2021

As current therapies for cardiovascular disease (CVD), predominantly based on lipid lowering, still face an unacceptable residual risk, novel treatment strategies are being explored. Besides lipids, inflammatory processes play a major role in the pathogenesis of atherosclerosis, the underlying cause of the majority of CVD. The first clinical trials targeting the interleukin-1β-inflammasome axis have shown that targeting this pathway is successful in reducing cardiovascular events but did not decrease overall CVD mortality. Hence, novel and improved immunotherapeutics to treat CVD are being awaited.
ROS-responsive biomimetic nanoparticles for potential application in targeted anti-atherosclerosis
Authors: Tang Dan , Wang Yi , Wijaya Andy , Liu Boyan , Maruf Ali , Wang Jinxuan , Xu Jianxiong , Liao Xiaoling , Wu Wei , Wang Guixue
Published: July 2021

The development of nanomedicines provides new opportunities for the treatment of atherosclerosis (AS) due to their great advantages such as the improved drug solubility, enhanced bioavailability and reduced side effects. Despite these advantages, nanomedicines are still facing some challenges. The problems remain in the short circulation life, lack of specific targeting and poor drug release controllability. In order to overcome the shortages of conventional nanomedicines, the combination of biomimetic strategy with smart nanoagents has been proposed. In light with the high reactive oxygen species (ROS) level in AS microenvironment and the fact that macrophages play a critical role in the pathogenesis of AS, we fabricated ROS-responsive biomimetic nanoparticles (NPs), which camouflaged macrophage membrane (MM) on ROS-responsive NPs loaded with rapamycin (RNPs) for potential application in AS therapy. The resulting ROS-responsive biomimetic NPs (MM/RNPs) exhibited favorable hydrodynamic size with negative surface charge, retained the functional proteins from MM, and showed ROS-responsive drug release. Because of the biomimetic camouflaging on surface, MM/RNPs could effectively escape from macrophages uptake and target to inflammatory endothelial cells. Meanwhile, MM/RNPs could inhibit the proliferation of macrophages and smooth muscle cells in vitro. Furthermore, the MM-coated NPs were found to be nontoxic in both cytotoxicity assay and in vivo toxicity evaluation. Consequently, these results demonstrated that MM/RNPs could be a potential candidate of drug delivery system for safe and effective anti-AS applications.
Bbc3 Loss Enhances Survival and Protein Clearance in Neurons Exposed to the Organophosphate Pesticide Chlorpyrifos
Authors: Anderson Faith L , von Herrmann Katharine M , Young Alison L , Havrda Matthew C
Published: July 2021

Exposure to environmental toxicants can increase the risk of developing age-related neurodegenerative disorders. Exposure to the widely used organophosphate pesticide chlorpyrifos (CPF) is associated with increased risk of developing Alzheimer’s disease and Parkinson’s disease, but the cellular mechanisms underlying CPF toxicity in neurons are not completely understood. We evaluated CPF toxicity in mouse primary cortical neuronal cultures, using RNA-sequencing to identify cellular pathways modulated by CPF. CPF exposure altered the expression of genes associated with intrinsic apoptosis, significantly elevating expression of the pro-apoptotic mediator Bbc3/Puma. Bbc3 loss attenuated CPF driven neurotoxicity, induction of other intrinsic apoptosis regulatory genes including Trp53 and Pmaip1 (encoding the NOXA protein), and cleavage of apoptosis executors caspase 3 and poly (ADP-ribose) polymerase (PARP). CPF exposure was associated with enhanced expression of endoplasmic reticulum stress-related genes and proteins and the accumulation of high molecular weight protein species in primary neuronal cultures. No evidence of alterations in the ubiquitin-proteosome system were observed, however, autophagy-related proteins were upregulated in CPF-treated Bbc3−/− neuronal cultures compared with identically exposed WT cultures. Elevated autophagy-related protein expression in Bbc3−/− neuronal cultures was associated with a reduction in CPF-induced high molecular weight alpha-synuclein and tau immunoreactive protein aggregates. Studies indicate that Bbc3−/− neuronal cultures enhance the endoplasmic reticulum stress response and upregulate protein clearance mechanisms as a component of resistance to CPF-mediated toxicity.
A qualitative study of patient, caregiver, doctor and nurse views of factors influencing lumbar puncture uptake in Zambia
Authors: Elafros Melissa A , Belessiotis-Richards Clara , Birbeck Gretchen L , Bond Virginia , Sikazwe Izukanji , Kvalsund Michelle P
Published: July 2021

Background

Uptake of lumbar puncture (LP) remains low in regions with a high prevalence of central nervous system (CNS) infections like Zambia. Efforts to improve uptake are hindered by limited understanding of factors influencing LP uptake.

Methods

Semistructured qualitative interviews were conducted with patients with suspected CNS infection, caregivers, doctors and nurses at the University Teaching Hospitals in 2016. Questions focused on LP experiences, knowledge, the consent process and health system barriers to LP among patients with an LP indication. Interviews were transcribed, translated to English and analysed using a thematic approach.

Results

We recruited 24 adult patients, 36 caregivers of adult patients, 63 caregivers of paediatric patients, 20 doctors and 30 nurses (173 in total). LP barriers arose from both patients/caregivers and health providers and included community apprehension about LP, proxy (family) consensus consent practices, competing clinical demands, wariness of patient/caregiver responses, limitations in consumables and time to complete the LP. This could result in consent not being obtained correctly. LP enablers included patient/caregiver perceived LP utility, provider comfort with LP and in-person counselling.

Conclusions

LP uptake is a complex sociocultural process influenced by patient, healthcare and community-level factors. Interventions to improve uptake must address multiple barriers to be successful.
Paraphyly and low levels of genetic divergence in morphologically distinct taxa: revision of the Pseudoanthidium scapulare complex of carder bees (Apoidea: Megachilidae: Anthidiini)
Authors: Litman Jessica R , Fateryga Alexander V , Griswold Terry L , Aubert Matthieu , Proshchalykin Maxim Yu , Le Divelec Romain , Burrows Skyler , Praz Christophe J
Published: July 2021

The Palaearctic complex of anthidiine bees closely related to Pseudoanthidium scapulare has long been a source of unresolved taxonomic and systematic issues. Until now, the number of species in the complex and their geographical distributions were largely unclear, thus complicating the compilation of accurate species checklists and hindering conservation efforts. In order to address these issues, we use morphology and mitochondrial cytochrome c oxidase subunit I (COI) sequences, combined with a thorough examination of the relevant literature and type material, to delimit species within this complex, assign names to species and clarify geographical ranges. An unexpected result was that a certain number of morphologically distinct taxa exhibited low levels of genetic divergence at the COI locus, resulting in species paraphyly. A set of ultra-conserved elements (UCEs) was also sequenced in order to further investigate relationships among these taxa. One morphologically distinct species was also paraphyletic using UCE data, hinting at recent species divergences and genetic exchange at zones of contact between morphologically well-differentiated taxa. The results of our study reveal the presence of ten species in this complex, including a previously overlooked species for western continental Europe. A complete diagnosis of the males and females of these species is provided, as are maps detailing the geographic distributions of each. An illustrated identification key to the males and females of each species is presented. Two new species are described, Pseudoanthidium kaspareki sp. nov. and P. rozeni sp. nov. New synonymy is established for several species and Pseudoanthidium palestinicum and P. tropicum are raised to species level. The new combination, Icteranthidium floripetum comb. nov. is also established. Lectotypes are designated for the following species: Anthidium eversmanni, A. floripetum, A. frontale, A. karakalense, A. nanum and A. reptans. Previously unpublished lectotype designations are published here for A. sinuatum and A. tenellum.
Staged Treatment of Asymmetrical Age-related Changes in the Eyelid and Thyroid Eye Disease
Authors: Takahira Tokuei , Akita Shinsuke , Maei Haruka , Kubota Yoshitaka , Mitsukawa Nobuyuki
Published: July 2021

Blepharoplasty for thyroid eye disease (TED) has been indicated for the purpose of improving upper and lower eyelid retraction caused by exophthalmos. Both aponeurotic blepharoptosis and aging lower eyelid are common conditions that require plastic surgeries and could be complicated with other disease conditions, such as TED. This is the first report of planned and staged treatment of the contradictory pathophysiologies of aging changes of upper and lower eyelids associated with TED. A 59-year-old woman suffered complicated bilateral asymmetric aponeurosis blepharoptosis of the lower and upper eyelids, caused by both advanced aging and TED. To achieve aesthetic improvement, three-stage surgical treatments were planned, as follows: (1) Orbital decompression for exophthalmos; (2) Extraocular muscle surgery, if necessary; (3) Blepharoplasty for functional and aesthetic abnormalities due to loosening of the upper and lower eyelids. After medial and lateral orbital floors were opened bilaterally, the patient did not need extraocular surgery. As the final step, levator aponeurosis advancement procedure was performed in the upper eyelids for bilateral asymmetrical aponeurotic blepharoptosis, and transitional lower blepharoplasty using a skin-muscle flap technique via a sub-ciliary incision was performed in the lower eyelids for age-related loosening. The typical face displayed by Graves’ disease disappeared, and the symptoms associated with loosening of the upper and lower eyelids improved substantially. Improvement of exophthalmos by orbital decompression revealed the severity of the blepharoptosis and the aging change of lower eyelid. Step-by-step planning from decompression surgery to upper and lower blepharoplasty could lead to sufficient improvement in the facial appearance in TED.
Improving genetic diagnosis of Mendelian disease with RNA sequencing: a narrative review
Authors: Zhou Zhou , Sang Qing , Wang Lei
Published: July 2021

Targeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases; however, using DNA-based sequencing techniques, the current molecular diagnostic yield is at best 50%. In recent years, RNA sequencing has been shown to be able to provide a genetic diagnosis in patients whose conditions were previously unable to be identified by DNA analysis. RNA sequencing can reveal expression outliers, aberrant splicing events, allele-specific expression, and new pathogenic variants, and as such can complement and expand on the traditional genomic methods used to diagnose Mendelian diseases. Therefore, RNA sequencing is expected to become a routine method for genetic diagnosis in the future. This article reviews the applications and challenges of RNA sequencing in the genetic diagnosis of Mendelian diseases.
CRISPR/Cas9-mediated
pou4f3
knockout induces defects in the development of the zebrafish inner ear
Authors: Liu Jingwen , Duan Xuchu , Li Ming , Liu Dong , Bai Xiaohui
Published: July 2021

Objective:

The zebrafish is an excellent model for studying gene function in auditory system development.
Pou4f3
plays an important role in mouse hair cell formation. Here, we constructed a
pou4f3
-knockout
Tg(Brn3c:GFP)
zebrafish to provide an efficient fluorescence-visualized model for studying the molecular mechanisms of ear development.

Methods:

Cas9/single guide RNAs targeting exon 2 of
pou4f3
were designed and injected into one-cell stage zebrafish embryos (G0 generation). The G0 generation were crossed with
Tg(Brn3c:GFP)
zebrafish to obtain
pou4f3-
mutant
Tg(Brn3c:GFP)
zebrafish. The targeting efficiency was detected by polymerase chain reaction amplification and Sanger sequencing. Zebrafish hair cells were observed by laser scanning confocal microscopy
in vivo
. The morphology of the otoliths and semicircular canals were analyzed. All animal experiments were approved by the Animal Care and Use Committee of Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University (approval No. 2016-KY-040) on March 3, 2016.

Results:

The
pou4f3
-mutant
Tg(Brn3c:GFP)
zebrafish line was successfully established. Fluorescence observation suggested that hair cell development was delayed in
pou4f3
-knockout zebrafish. Knockout of
pou4f3
also induced defects in the otoliths and semicircular canals and impaired ear function in zebrafish.

Conclusion:

A CRISPR/Cas9-mediated
pou4f3
mutant
Tg(Brn3c:GFP)
zebrafish model was established for the first time to demonstrate the essential role of
pou4f3
in zebrafish ear development. Our study provides a highly efficient method for the establishment of a visualized model of gene knockout zebrafish and has the potential to allow high-throughput drug screening to explore therapeutics for related diseases.
Alpha Before Beta
Authors: Satapathy Swayamjeet , Sood Ashwani , Das Chandan Krushna , Kavanal Anwin Joseph , Mittal Bhagwant Rai
Published: July 2021

The utility of β-emitter 177Lu-DOTATATE in patients of neuroendocrine tumors (NETs) with widespread skeletal metastases is limited by its relatively modest response rates and a significant concern for hematotoxicity. In such situations, targeted α therapy with 225Ac-DOTATATE can be potentially beneficial. In this report, a 46-year-old man with rectal NET and extensive skeletal metastases was treated upfront with 6 cycles of 225Ac-DOTATATE at 8 weeks’ intervals. The patient showed excellent symptomatic, biochemical, and radiological response with no grade 3/4 adverse events. The first-line use of 225Ac-DOTATATE, therefore, presents a novel strategy for metastatic NETs with high skeletal disease burden.
Electric power processing using logic operation and error correction
Authors: Inagaki Shota , Mochiyama Shiu , Hikihara Takashi
Published: July 2021

In this study, electric power is processed using the logic operation method and the error correction algorithms to meet load demand. Electric power was treated as the physical flow through the distribution network, which was governed by circuit configuration and efficiency. The hardware required to digitize or packetize electric power, which is called power packet router, was developed in this research work for low power distribution. It provides an opportunity for functional electric power dispatching while disregarding the power flow in the circuit. This study proposes a new design for the network, which makes the logic operation of electric power possible and provides an algorithm to correct the inaccuracies caused by dissipation and noise. Phase shift of the power supply network is resulted by implementing the introduced design.
A brief review of vertebrate sex evolution with a pledge for integrative research: towards ‘sexomics’
Authors: Stöck Matthias , Kratochvíl Lukáš , Kuhl Heiner , Rovatsos Michail , Evans Ben J. , Suh Alexander , Valenzuela Nicole , Veyrunes Frédéric , Zhou Qi , Gamble Tony , Capel Blanche , Schartl Manfred , Guiguen Yann
Published: July 2021

Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue asexomicsintegrative research initiative across vertebrates. The vertebratesexomecomprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. Thesexomealso includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of thesexomesof many key vertebrate species.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
‘Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov., an endosymbiotic bacterium associated with nematode species of the genus Xiphinema (Nematoda, Longidoridae)
Authors: Palomares-Rius Juan E. , Gutiérrez-Gutiérrez Carlos , Mota Manuel , Bert Wim , Claeys Myriam , Yushin Vladimir V. , Suzina Natalia E. , Ariskina Elena V. , Evtushenko Lyudmila I. , Subbotin Sergei A. , Castillo Pablo
Published: July 2021

An intracellular bacterium, strain IAST, was observed to infect several species of the plant-parasitic nematode genus Xiphinema (Xiphinema astaregiense, Xiphinema incertum, Xiphinema madeirense, Xiphinema pachtaicum, Xiphinema parapachydermum and Xiphinema vallense). The bacterium could not be recovered on axenic medium. The 16S rRNA gene sequence of IAST was found to be new, being related to the family Burkholderiaceae, class Betaproteobacteria. Fungal endosymbionts

Mycoavidus cysteinexigens

B1-EBT (92.9 % sequence identity) and ‘Candidatus Glomeribacter gigasporarum’ BEG34 (89.8 % identity) are the closest taxa and form a separate phylogenetic clade inside Burkholderiaceae. Other genes (atpD, lepA and recA) also separated this species from its closest relatives using a multilocus sequence analysis approach. These genes were obtained using a partial genome of this bacterium. The localization of the bacterium (via light and fluorescence in situ hybridization microscopy) is in the X. pachtaicum females clustered around the developing oocytes, primarily found embedded inside the epithelial wall cells of the ovaries, from where they are dispersed in the intestine. Transmission electron microscopy (TEM) observations supported the presence of bacteria inside the nematode body, where they occupy ovaries and occur inside the intestinal epithelium. Ultrastructural analysis of the bacterium showed cells that appear as mostly irregular, slightly curved rods with rounded ends, 0.8–1.2 µm wide and 2.5–6.0 µm long, possessing a typical Gram-negative cell wall. The peptidoglycan layer is, however, evident only occasionally and not detectable by TEM in most cells. Another irregularly occurring shell surrounding the endosymbiont cells or the cell clusters was also revealed, probably originating from the host cell membrane. Flagella or spore-like cells do not occur and the nucleoid is diffusely distributed throughout the cell. This endosymbiont is transmitted vertically through nematode generations. These results support the proposal of IAST as a new species, although its obligate intracellular and obligate endosymbiont nature prevented isolation of a definitive type strain. Strain IAST is therefore proposed as representing ‘Candidatus Xiphinematincola pachtaicus’ gen. nov., sp. nov.
Description of Devosia faecipullorum sp. nov., harboring antibiotic- and toxic compound-resistant genes, isolated from poultry manure
Authors: Lin Shih-Yao , Tsai Chia-Fang , Hameed Asif , Tang Yu-Shan , Young Chiu-Chung
Published: July 2021

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696T, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696T were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696T associated with

Devosia chinhatensis

(97.9 % sequence identity),

Devosia riboflavina

(97.3 %) and

Devosia indica

(97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8–80.0 % (n=17) compared within the type strains of species of of the genus

Devosia

. CC-YST696T contained C16:0, C18:0, C18:1ω7c 11-methyl and C18:1ω6c/ C18:1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696T is proposed to represent a novel species of the genus

Devosia

, for which the name Devosia faecipullorum sp. nov. (type strain CC-YST696T=BCRC 81284T=JCM 34167T) is proposed.
Fermentation characteristics and inhibitory effect of brown rice
vinegar on adipocyte differentiation in 3T3-L1 cells
Authors: Sim Eun Ah , Oh Hyeon Hwa , Jeong Do Youn , Song Geun-Seoup , Kim Young-Soo
Published: July 2021

The brown rice vinegar was prepared by adding 10% of vinegar starter, and
incubated using the strain Acetobacter pasteurianus JBA172705.
The alcohol concentration of brown rice liquor was adjusted to 6%, and seed
vinegar was added to 10%. Then, it was cultured by shaking for 16 days
(30°C, 120 rpm). After fermentation, brown rice vinegar was extracted
with 70% ethanol to evaluate the anti-obesity effect using 3T3-L1 adipocyte
cells. The total acidity of brown rice vinegar increased to 6.43% after 16 days
of fermentation, and acetic acid increased 15 times and succinic acid 2.5 times
or more. The total phenolics and free amino acid contents decreased during the
acetic acid fermentation period, and were 48.53 mg GAE/mL and 18.79 mg% (w/v) at
the 16th day of fermentation. At a concentration of 100 μg/mL of brown
rice vineagar extract (BRV 16d), the lipid accumulation rate was 72.2%. The
leptin expression level was reduced by more than 50% according to the treatment
of brown rice vinegar extract. It was confirmed that the PPARγ and
SREBP-1c expression levels decreased at a concentration of 100 μg/mL. As
a result, brown rice vinegar is expected to be effective in anti-obesity by
suppressing the expression of transcription factors that induce obesity.
Vaccine Confidence and Hesitancy at the start of COVID-19 vaccine deployment in the UK: An embedded mixed-methods study
Authors: Roberts Chrissy h , Brindle Hannah , Rogers Nina T , Eggo Rosalind M , Enria Luisa , Lees Shelley
Published: July 2021

Introduction

Approval for the use of COVID-19 vaccines has been granted in a number of countries but there are concerns that vaccine uptake may be low amongst certain groups.

Methods

This study used a mixed methods approach based on online survey and an embedded quantitative/qualitative design to explore perceptions and attitudes that were associated with intention to either accept or refuse offers of vaccination in different demographic groups during the early stages of the UK’s mass COVID-19 vaccination programme (December 2020). Analysis used multivariate logistic regression, structural text modelling and anthropological assessments.

Results

Of 4,535 respondents, 85% (n=3,859) were willing to have a COVID-19 vaccine. The rapidity of vaccine development and uncertainties about safety were common reasons for COVID-19 vaccine hesitancy. There was no evidence for the widespread influence of mis-information, although broader vaccine hesitancy was associated with intentions to refuse COVID-19 vaccines (OR 20.60, 95% CI 14.20-30.30, p<0.001). Low levels of trust in the decision-making (OR 1.63, 95% CI 1.08, 2.48, p=0.021) and truthfulness (OR 8.76, 95% CI 4.15-19.90, p<0.001) of the UK government were independently associated with higher odds of refusing COVID-19 vaccines. Compared to political centrists, conservatives and liberals were respectively more (OR 2.05, 95%CI 1.51-2.80, p<0.001) and less (OR 0.30, 95% CI 0.22-0.41, p<0.001) likely to refuse offered vaccines. Those who were willing to be vaccinated cited both personal and public protection as reasons, with some alluding to having a sense of collective responsibility.

Conclusion

Dominant narratives of COVID-19 vaccine hesitancy are misconceived as primarily being driven by misinformation. Key indicators of UK vaccine acceptance include prior behaviours, transparency of the scientific process of vaccine development, mistrust in science and leadership and individual political views. Vaccine programmes should leverage the sense of altruism, citizenship and collective responsibility that motivated many participants to get vaccinated.
Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report
Authors: Brejová Broňa , Hodorová Viktória , Boršová Kristína , Čabanová Viktória , Szemes Tomáš , Mišík Matej , Klempa Boris , Nosek Jozef , Vinař Tomáš
Published: July 2021

We present an unofficial SARS-CoV-2 genomic surveillance report from Slovakia based on approximately 3500 samples sequenced between March 2020 and May 2021. Early samples show multiple independent imports of SARS-CoV-2 from other countries. In Fall 2020, three virus variants (B.1.160, B.1.1.170, B.1.258) dominated as the number of cases increased. In November 2020, B.1.1.7 (alpha) variant was introduced in Slovakia and quickly became the most prevalent variant in the country (> 75% of new cases by early February 2021 and > 95% in mid-March).
Racial Inequalities in Alcohol Use Disorder Diagnosis in a Sample of 700,000 Veterans
Authors: Vickers-Smith Rachel , Justice Amy C. , Becker William C. , Rentsch Christopher T. , Curtis Brenda , Fernander Anita , Hartwell Emily E. , Ighodaro Eseosa T. , Kember Rachel L. , Tate Janet , Kranzler Henry R.
Published: July 2021

Background

Studies show that Black and Hispanic Veterans have a higher prevalence of alcohol use disorder (AUD) than White Veterans. We examined whether the relationship between self-reported race/ethnicity and AUD diagnosis varies by self-reported alcohol consumption.

Methods

The sample included 700,013 Black, Hispanic, and White Veterans enrolled in the Million Veteran Program cohort. Alcohol consumption was defined as an individual’s maximum score on the Alcohol Use Disorders Identification Test–Consumption (AUDIT-C) questionnaire, a screen for hazardous or harmful drinking. The primary outcome, AUD, was defined by the presence of ICD-9/10 codes in the electronic health record. We used logistic regression with interactions to assess the association between race/ethnicity and AUD by maximum AUDIT-C score.

Results

Black and Hispanic Veterans were more likely to have an AUD diagnosis than White Veterans despite similar levels of alcohol consumption. The difference was greatest between Black and White men. At all but the lowest and highest levels of alcohol consumption, Black men had 24%-111% greater odds of an AUD diagnosis. The association between race/ethnicity and AUD diagnosis remained after adjustment for alcohol consumption, alcohol-related disorders, and other potential confounders.

Conclusions

The large discrepancy in AUD diagnosis across groups despite a similar distribution of alcohol consumption measures suggests that Veterans are differentially assigned an AUD diagnosis by race/ethnicity. Efforts are needed to examine the causes of the observed differences and to implement changes, such as structured diagnostic methods, to address a likely contributor to racial differences (i.e., bias) in AUD diagnosis.
Gender Based Differences in Risks and Comorbidities in Patients Hospitalized with Acute Exacerbation of COPD: A Retrospective Observational study in Eastern-Nepal
Authors: Baral Nischit , Karki Nabin R. , Parajuli Prem Raj , Bell Laura , Paudel Bidhan Raj , Paudel Anish C. , Adhikari Nirajan , Luitel Pankaj , Bhatta Narendra
Published: July 2021

Background

Acute Exacerbation of Chronic Obstructive Pulmonary Disease (AECOPD) share a complex relationship with gender, risk, and co-morbidities. There is paucity of data on the gender-based differences in the prevalence of risks and co-morbidities in AECOPD in Nepal.

Methods

We performed a retrospective cross-sectional study where data were collected from medical records of adult patients (age >40 years), hospitalized with clinical diagnosis of AECOPD in a tertiary level University hospital in eastern Nepal from April 15, 2014 to October 15, 2014 were included. Data analysis was performed by using SPSS software (Version 26.0, 2020; SPSS Inc., Chicago, IL).

Results

Of the 256 patients with the primary diagnosis of AECOPD, mean age was 69 years and 65.63% (n=168) of hospitalizations were female population. Compared to males, 64.32 % (n=137) of active smokers were females p= 0.299, 76.19% (n=32) of diabetics were females p= 0.155, 72.86% (n=51) of hypertensive were females, p= 0.143, 50% (n= 6) of underlying Atrial fibrillation were in females p= 0.350, 57.50% (n= 23) of anemics were females p= 0.278, 100% (n= 3) of asthmatics were females p= 0.553, 44.44% (n= 8) of Pulmonary tuberculosis were in females p= 0.070, and 78.76% (n= 89) of indoor air pollution exposure was in females p <0.001.

Conclusion

Females have higher association to indoor air pollution exposure compared to male and this association was found to be statistically significant. The higher incidence of AECOPD hospitalization in females can be explained by these findings. We need larger studies to validate these findings.
Sequencing SARS-CoV-2 from Antigen Tests
Authors: Nazario-Toole Ashley , Nguyen Holly M. , Xia Hui , Frankel Dianne N. , Kieffer John W. , Gibbons Thomas F.
Published: July 2021

Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW™ COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media.
Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity in uninfected and previously infected individuals
Authors: Lucas Carolina , Vogels Chantal B. F. , Yildirim Inci , Rothman Jessica E. , Lu Peiwen , Monteiro Valter , Gelhausen Jeff R. , Campbell Melissa , Silva Julio , Tabachikova Alexandra , Muenker M. Catherine , Breban Mallery I. , Fauver Joseph R. , Mohanty Subhasis , Huang Jiefang ,   Yale SARS-CoV-2 Genomic Surveillance Initiative, Pearson Claire , Muyombwe Anthony , Downing Randy , Razeq Jafar , Petrone Mary , Ott Isabel , Watkins Anne , Kalinich Chaney , Alpert Tara , Brito Anderson , Earnest Rebecca , Murphy Steven , Neal Caleb , Laszlo Eva , Altajar Ahmad , Tikhonova Irina , Castaldi Christopher , Mane Shrikant , Bilguvar Kaya , Kerantzas Nicholas , Ferguson David , Schulz Wade , Landry Marie , Peaper David , Shaw Albert C. , Ko Albert I. , Omer Saad B. , Grubaugh Nathan D. , Iwasaki Akiko
Published: July 2021

The emergence of SARS-CoV-2 variants with mutations in major neutralizing antibody-binding sites can affect humoral immunity induced by infection or vaccination1–6. We analysed the development of anti-SARS-CoV-2 antibody and T cell responses in previously infected (recovered) or uninfected (naive) individuals that received mRNA vaccines to SARS-CoV-2. While previously infected individuals sustained higher antibody titers than uninfected individuals post-vaccination, the latter reached comparable levels of neutralization responses to the ancestral strain than previously infected individuals 7 days after the second vaccine dose. T cell activation markers measured upon spike or nucleocapsid peptide in vitro stimulation showed a progressive increase after vaccination in the time-points analysed. Comprehensive analysis of plasma neutralization using 16 authentic isolates of distinct locally circulating SARS-CoV-2 variants revealed a range of reduction in the neutralization capacity associated with specific mutations in the spike gene: lineages with E484K and N501Y/T (e.g., B.1.351 and P.1) had the greatest reduction, followed by lineages with L452R (e.g., B.1.617.2) or with E484K (without N501Y/T). While both groups retained neutralization capacity against all variants, plasma from previously infected vaccinated individuals displayed overall better neutralization capacity when compared to plasma from uninfected individuals that also received two vaccine doses, pointing to vaccine boosters as a relevant future strategy to alleviate the impact of emerging variants on antibody neutralizing activity.
Noninvasive optical monitoring of cerebral blood flow and EEG Spectral responses after Severe Traumatic Brain Injury: A Case Report
Authors: Poon Chien-Sing , Rinehart Benjamin , Langri Dharminder S. , Rambo Timothy M. , Miller Aaron J. , Foreman Brandon , Sunar Ulas
Published: July 2021

Survivors of severe brain injury may require care in a neurointensive care unit (neuro-ICU), where the brain is vulnerable to secondary brain injury. Thus, there is a need for noninvasive, bedside, continuous cerebral blood flow monitoring approaches in the neuro-ICU. Our goal is to address this need through combined measurements of EEG and functional optical spectroscopy (EEG-Optical) instrumentation and analysis to provide a complementary fusion of data about brain activity and function. The present case demonstrates in a patient with traumatic brain injury, noninvasive cerebral blood flow transients can be recorded that correlate with gold-standard invasive measurements and with the frequency content changes in the EEG data during clinical care.