bluuebunny/crossref_metadata_2025 huggingface dataset:
The phylogeny of Salix revealed by whole genome re-sequencing suggests different sex-determination systems in major groups of the genus
Authors: Gulyaev Sergey , Cai Xin-Jie , Guo Fei-Yi , Kikuchi Satoshi , Applequist Wendy L , Zhang Zhi-Xiang , Hörandl Elvira , He Li
Published: January 2022

Background and Aims

The largest genus of Salicaceae sensu lato, Salix, has been shown to consist of two main clades: clade Salix, in which species have XY sex-determination systems (SDSs) on chromosome 7, and clade Vetrix including species with ZW SDSs on chromosome 15. Here, we test the utility of whole genome re-sequencing (WGR) for phylogenomic reconstructions of willows to infer changes between different SDSs.

Methods

We used more than 1 TB of WGR data from 70 Salix taxa to ascertain single nucleotide polymorphisms on the autosomes, the sex-linked regions (SLRs) and the chloroplast genomes, for phylogenetic and species tree analyses. To avoid bias, we chose reference genomes from both groups, Salix dunnii from clade Salix and S. purpurea from clade Vetrix.

Key Results

Two main largely congruent groups were recovered: the paraphyletic Salix grade and the Vetrix clade. The autosome dataset trees resolved four subclades (C1–C4) in Vetrix. C1 and C2 comprise species from the Hengduan Mountains and adjacent areas and from Eurasia, respectively. Section Longifoliae (C3) grouped within the Vetrix clade but fell into the Salix clade in trees based on the chloroplast dataset analysis. Salix triandra from Eurasia (C4) was revealed as sister to the remaining species of clade Vetrix. In Salix, the polyploid group C5 is paraphyletic to clade Vetrix and subclade C6 is consistent with Argus’s subgenus Protitea. Chloroplast datasets separated both Vetrix and Salix as monophyletic, and yielded C5 embedded within Salix. Using only diploid species, both the SLR and autosomal datasets yielded trees with Vetrix and Salix as well-supported clades.

Conclusion

WGR data are useful for phylogenomic analyses of willows. The different SDSs may contribute to the isolation of the two major groups, but the reproductive barrier between them needs to be studied.
Phylogeography of ancient and modern brown bears from eastern Eurasia
Authors: Molodtseva Anna S , Makunin Alexey I , Salomashkina Valentina V , Kichigin Ilya G , Vorobieva Nadezhda V , Vasiliev Sergey K , Shunkov Mikhail V , Tishkin Alexey A , Grushin Sergey P , Anijalg Peeter , Tammeleht Egle , Keis Marju , Boeskorov Gennady G , Mamaev Nikolai , Okhlopkov Innokenty M , Kryukov Alexey P , Lyapunova Elena A , Kholodova Marina V , Seryodkin Ivan V , Saarma Urmas , Trifonov Vladimir A , Graphodatsky Alexander S
Published: January 2022

The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5–40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.
Preferences, Confusion and Competition
Authors: Hefti Andreas , Liu Shuo , Schmutzler Armin
Published: January 2022

Existing literature has argued that firms benefit from confusing consumers of homogeneous goods. This paper shows that this insight generally breaks down with differentiated goods and heterogeneous preferences: with polarised taste distributions, firms fully educate consumers. In cases where firms nevertheless confuse consumers, the welfare consequences are worse than for homogeneous goods, as consumers choose dominated options. Similar insights are also obtained for political contests, in which candidates compete for voters with heterogeneous preferences: parties choose ambiguous platforms only when preferences are ‘indecisive’, featuring a concentration of indifferent voters.
Surveillance of RNase P, PMMoV, and CrAssphage in wastewater as indicators of human fecal concentration across urban sewer neighborhoods, Kentucky
Authors: Holm R H , Nagarkar M , Yeager R A , Talley D , Chaney A C , Rai J P , Mukherjee A , Rai S N , Bhatnagar A , Smith T
Published: January 2022

Wastewater surveillance has been widely used as a supplemental method to track the community infection levels of severe acute respiratory syndrome coronavirus 2. A gap exists in standardized reporting for fecal indicator concentrations, which can be used to calibrate the primary outcome concentrations from wastewater monitoring for use in epidemiological models. To address this, measurements of fecal indicator concentration among wastewater samples collected from sewers and treatment centers in four counties of Kentucky (N = 650) were examined. Results from the untransformed wastewater data over 4 months of sampling indicated that the fecal indicator concentration of human ribonuclease P (RNase P) ranged from 5.1 × 101 to 1.15 × 106 copies/ml, pepper mild mottle virus (PMMoV) ranged from 7.23 × 103 to 3.53 × 107 copies/ml, and cross-assembly phage (CrAssphage) ranged from 9.69 × 103 to 1.85 × 108 copies/ml. The results showed both regional and temporal variability. If fecal indicators are used as normalization factors, knowing the daily sewer system flow of the sample location may matter more than rainfall. RNase P, while it may be suitable as an internal amplification and sample adequacy control, has less utility than PMMoV and CrAssphage as a fecal indicator in wastewater samples when working at different sizes of catchment area. The choice of fecal indicator will impact the results of surveillance studies using this indicator to represent fecal load. Our results contribute broadly to an applicable standard normalization factor and assist in interpreting wastewater data in epidemiological modeling and monitoring.
How automation and skill gaps fail to explain wage suppression or wage inequality
Authors: Mishel Lawrence
Published: January 2022

Wage gaps between “skilled” and “unskilled” earners in the United States are conventionally attributed to U.S. workers’ “skill deficits,” or lack of skills necessary to deal with technological change, particularly automation. This paper argues instead that skills deficit/automation claims have always been a weak explanation for post-1979 trends. Since the mid-1990s all indications are that there is no basis for considering automation to be a significant factor in wage suppression or the growth of wage inequality. Rather, inequality growth has been an outgrowth of developments in the labor market rather than product markets. The key dynamic undercutting the typical worker’s wage growth has been the strengthening of employers’ power relative to their white-collar and blue-collar workers. The cause has not been monopoly firms exercising their power in product markets by charging higher prices to consumers. Monopolization has indeed contributed to wage suppression, but even this factor has largely run through the labor market, as monopoly firms squeezed supplier chain firms which in turn undercut their own workers’ wages while seeing a profit squeeze as well. The paper concludes that what is needed is a better balancing of power in the labor market rather than a perfecting of competition.
Macrophytes as habitat for fish
Authors: Christie Hartvig , Andersen Guri Sogn , Tveiten Lise Ann , Moy Frithjof Emil
Published: January 2022

As different macrophyte habitats house different distributions of invertebrates, we questioned if differences in the composition of fish in these habitats also could be identified. Additionally, we addressed the question if the fish communities could be affected a few years after sugar kelp beds had shifted to degraded turf habitats. Gill-nets of different mesh sizes were used to catch fish in the then four dominating subtidal macrophyte habitats; the kelp species Laminaria hyperborea and Saccharina latissima, the turf algae, and the seagrass Zostera marina. Each habitat was sampled in South Norway, day and night, and at two following months. Altogether, 31 species of fish and five species of larger crustaceans were caught. Both individuals and species numbers were dominated by wrasses and codfish. The wrasses were most active at daytime, while most codfish entered the habitats at night. Wrasses were mainly occurring in the seaweed habitats, while codfish dominated the seagrass samples. The kelps had highest numbers of individuals, while seagrasses showed highest species diversity. The turf habitats did not result in dramatic negative effects on the fish fauna. Fish can take advantage of other adjacent habitats, a benefit that could be reduced by expanding shifts from kelps to turfs.
Embodying Military Muscles and a Remasculinized West: Influencer Marketing, Fantasy, and “the Face of NATO”
Authors: Hedling Elsa , Edenborg Emil , Strand Sanna
Published: January 2022

In 2018, North Atlantic Treaty Organization (NATO) carried out Trident Juncture, its largest military exercise since the Cold War. The event was promoted on social media featuring Lasse Matberg as “the face of NATO.” Matberg is an Instagram influencer, model, and lieutenant in the Royal Norwegian Navy, with an impressive physique and Viking looks. He frequently appears on NATO’s social media accounts and lends his own platform to share activities such as working out with the Secretary-General. Drawing on the notion of “fantasmatic logics”, we study how visual narratives of influencer marketing can contribute to making war preparations appear normal, void of political significance and even desirable. The figure of Lasse Matberg is read in conjunction with international rearmament and increasing geopolitical antagonism bound up with ideas of “traditional masculinity” and “feminization.” We argue that the muscular yet ambiguously “soft” figure of Lasse Matberg projects a symbolic remasculinization of the West, operating through a fantasmatic logic that seemingly reconciles the contradiction between a West, which is imperial and militarily muscular on the one hand and caring, democratic, and progressive on the other. By shedding light on NATO's use of influencer marketing to promote a military exercise, this article contributes novel insights into the ways in which the figure of the NATO soldier and NATO military buildup are produced as appealing, allowing an ambivalent gendered geopolitical imaginary to emerge.
Depression and Physician-Aid-in-Dying
Authors: Tully Ian
Published: January 2022

In this paper, I address the question of whether it is ever permissible to grant a request for physician-aid-in-dying (PAD) from an individual suffering from treatment-resistant depression. I assume for the sake of argument that PAD is sometimes permissible. There are three requirements for PAD: suffering, prognosis, and competence. First, an individual must be suffering from an illness or injury which is sufficient to cause serious, ongoing hardship. Second, one must have exhausted effective treatment options, and one’s prospects for recovery must be poor. Third, the individual must be judged competent to request PAD. I argue that many cases of treatment-resistant depression meet the first two requirements. Thus, the key question concerns the third. I consider four features of depression that might compromise a person’s decision-making capacity. Ultimately, I conclude that PAD requests from depressed patients can be permissibly granted in some circumstances.
EU Consumer Law and the Boundaries of the Crowdfunding Regulation
Authors: Ebers Martin , Quarch Benedikt M
Published: January 2022

This chapter evaluates the interactions and the ‘boundaries’ between the Crowdfunding Regulation and European Consumer Law. These questions are particularly relevant, not only because some forms of crowdfunding fall outside of the scope of the Regulation, but also because EU Consumer Law may meaningfully complement the provisions of the Crowdfunding Regulation, protecting the ‘crowd’, in cases where the Regulation is applicable. The analysis shows that the Crowdfunding Regulation has not led to the harmonization of consumer crowdlending. Rather, there are still considerable gaps in the protection of consumers. Whereas the Crowdfunding Regulation protects consumers to a large extent when they act as investors in crowdfunding, it provides insufficient protection for consumers as project owners who conclude contracts with private investors.
The Regulatory Position and Obligations of Project Owners
Authors: van Poelgeest Jonneke , Louisse Marije
Published: January 2022

This chapter focuses on the position of project owners under the Crowdfunding Regulation. The Regulation requires Member States to ensure that project owners can pursue investment-based crowdfunding without any specific authorisation. This, however, does not mean that project owners have no regulatory obligations at all. The chapter starts with an introduction to the position of project owners, and the crowdfunding service providers’ obligations towards project owners, including the obligations to perform due diligence and credit risk assessment. It then assesses the obligations of project owners, including the (lack of an) authorisation requirement, the provision of information, and the cooperation with CSPs. Finally, the chapter discusses whether project owners require some form of protection, and whether that is a missing piece of the Crowdfunding Regulation.
Crowdfunding and Intellectual Property Protection
Authors: Cotropia Christopher A
Published: January 2022

This chapter assesses some intellectual property (IP) issues that are not directly covered by the Crowdfunding Regulation, but are of great practical relevance for project owners pursuing a crowdfunding campaign. When attempting to raise funds through crowdfunding, project owners provide information as to their plans, strategies, and business model. This often happens at a time when project owners are still in the start-up phase. In this delicate moment, IP rights can play a twofold rule. On the one hand, the crowd may be more inclined to invest in a project that is patented or patent-pending. From this point of view, IP rights can act as a sort of quality trustmark for crowdfunded projects. On the other hand, however, the disclosure of information at such an early stage entails the risk that the innovative aspects of the proposed business venture will be emulated by ‘copycats’, piggybacking on the project owner’s efforts. Far from being merely theoretical, this risk has already been reported in practice; therefore, it is useful to investigate the phenomenon in its complexity.
Reward-based Crowdfunding, the Digital Single Market, and EU Consumer Law
Authors: Amaxopoulou Margarita , Durovic Mateja
Published: January 2022

This chapter highlights the EU legal framework applicable to reward-based crowdfunding, and the consumer protection mechanisms enshrined therein. Reward-based crowdfunding campaigns help small and medium-sized enterprises (SMEs) or even solo start-ups not only with financial support from the ‘crowd’ but also with marketing tools, as well as useful insights and information to realise their dreams and sell their innovative products. While being excluded from the scope of the Crowdfunding Regulation, reward-based crowdfunding falls within the scope of application of EU Consumer Law. The EU consumer acquis is currently being reviewed and modernized, with a view to the creation of a Digital Single Market. The chapter assesses to what extent the current instruments of EU Consumer Law are adequate to deal with the rising phenomenon of reward-based crowdfunding, and how they could be modernised.
Victims of War
Authors: Clapham Andrew
Published: January 2022

This chapter covers the international humanitarian law dealing with the protection of victims of war (sometimes known as Geneva law). It explains who is protected under this regime and distinguishes international from non-international armed conflicts.. The regimes that cover prisoners of war and civilians are explained along with the problems associated with the law on occupation. The role of the International Committee of the Red Cross and its protective emblems is explained together with the scope of the crime of misuse of the emblem.
Railways as patient capital
Authors: Lewis Oliver , Offer Avner
Published: January 2022

Why are railways mostly in the public sector? Interest rates define a time limit for markets. Projects with longer break-evens cannot be funded by business alone. Corporate ‘franchise’ arrangements overcome the limit by means of revenue guarantees which transfer risks to government. Innovations originate bottom-up in private enterprise. Positive externalities create demand for universal provision but scaling up cannot be financed commercially. In the British railway manias of the 1830s, 1840s, and 1860s speculative fever overwhelmed prudence. Overinvestment left an excessive infrastructure legacy and wiped out windfall profits. In other countries railways required external support. Expanding access gave rise to stand-offs with investors which ended up in government regulation or takeover. The tramway boom of 1870–1914 followed this pattern, initially with horse power and then electricity. In the UK railway privatization of the 1990s, the free market delusion was confounded by the infrastructure requirement for long-term commitment.
Writing the Paris Commune in the Warsaw Ghetto
Authors: Sloin Andrew
Published: January 2022

This article examines the emergence and abrupt disappearance of discourses about the Paris Commune in the global Yiddish public sphere during the first half of the twentieth century. Drawing upon publications produced in transnational centres of Yiddish culture, it traces the rise of the Paris Commune as a historical trope through which Jewish authors sought to make sense of the class and anti-Jewish racial violence that erupted throughout the era of social revolution. As a narrative of class violence that exploded within the national body, the Commune also provided a political framework to critique dominant structures of power and privilege within Jewish society. Writing and re-writing the history of the Commune thus became a central mechanism to inculcate the politics of socialist internationalism among Yiddish readers. With the onset of the inter-war crisis and the rise of fascism, the Commune returned as a key trope through which to comprehend the existential threats to Jewish life and the politics of internationalism, globally, culminating in a remarkable retelling by Abraham Blum, written in the heart of the Warsaw Ghetto in 1941, which laid bare the political and class dynamics at the core of Nazi eliminationist violence.
Essential roles of SERKs in the ROOT MERISTEM GROWTH FACTOR-mediated signaling pathway
Authors: Ou Yang , Tao Bingqing , Wu Yujun , Cai Zeping , Li Huiqiang , Li Meizhen , He Kai , Gou Xiaoping , Li Jia
Published: January 2022

ROOT MERISTEM GROWTH FACTORs (RGFs), a group of peptide hormones, play key roles in root apical meristem development. In Arabidopsis (Arabidopsis thaliana), there are 11 members of RGFs, in which at least RGF1, RGF2, and RGF3 are expressed at the root tip and are involved in root stem cell niche maintenance. RGFs are perceived by five functionally redundant receptor-like protein kinases, RGF1 INSENSITIVE 1 (RGI1) to RGI5, to maintain the expression of two downstream APETALA 2 (AP2) transcription factor genes, PLETHORA 1 (PLT1) and PLT2, and to stabilize PLT2. RGI1 to RGI3 were also named RGF RECEPTOR 1 (RGFR1) to RGFR3, respectively. Although previous studies have suggested that BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) and its paralogs, SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASEs (SERKs), may act as coreceptors of RGIs, comprehensive genetic and biochemical analyses have not been well documented. Here, we report that single, double, and triple mutants of SERKs show various degrees of short root phenotypes and insensitivity to exogenously applied RGF1. The interaction between RGIs and BAK1 and their mutual phosphorylation are RGF1 dependent. We also found that RGF1-induced MAPK activation relies on both RGIs and SERKs. We demonstrate that RGIs play redundant roles in regulating root apical meristem development. Therefore, we genetically and biochemically substantiated that SERKs, as coreceptors, play essential roles in the RGF1-mediated signaling pathway.
Assembly of D1/D2 complexes of photosystem II: Binding of pigments and a network of auxiliary proteins
Authors: Knoppová Jana , Sobotka Roman , Yu Jianfeng , Bečková Martina , Pilný Jan , Trinugroho Joko P , Csefalvay Ladislav , Bína David , Nixon Peter J , Komenda Josef
Published: January 2022

Photosystem II (PSII) is the multi-subunit light-driven oxidoreductase that drives photosynthetic electron transport using electrons extracted from water. To investigate the initial steps of PSII assembly, we used strains of the cyanobacterium Synechocystis sp. PCC 6803 arrested at early stages of PSII biogenesis and expressing affinity-tagged PSII subunits to isolate PSII reaction center assembly (RCII) complexes and their precursor D1 and D2 modules (D1mod and D2mod). RCII preparations isolated using either a His-tagged D2 or a FLAG-tagged PsbI subunit contained the previously described RCIIa and RCII* complexes that differ with respect to the presence of the Ycf39 assembly factor and high light-inducible proteins (Hlips) and a larger complex consisting of RCIIa bound to monomeric PSI. All RCII complexes contained the PSII subunits D1, D2, PsbI, PsbE, and PsbF and the assembly factors rubredoxin A and Ycf48, but we also detected PsbN, Slr1470, and the Slr0575 proteins, which all have plant homologs. The RCII preparations also contained prohibitins/stomatins (Phbs) of unknown function and FtsH protease subunits. RCII complexes were active in light-induced primary charge separation and bound chlorophylls (Chls), pheophytins, beta-carotenes, and heme. The isolated D1mod consisted of D1/PsbI/Ycf48 with some Ycf39 and Phb3, while D2mod contained D2/cytochrome b559 with co-purifying PsbY, Phb1, Phb3, FtsH2/FtsH3, CyanoP, and Slr1470. As stably bound, Chl was detected in D1mod but not D2mod, formation of RCII appears to be important for stable binding of most of the Chls and both pheophytins. We suggest that Chl can be delivered to RCII from either monomeric Photosystem I or Ycf39/Hlips complexes.
New data on the mitochondrial genome of Nematocera (lower Diptera): features, structures and phylogenetic implications
Authors: Zhang Xiao , Yang Ding , Kang Zehui
Published: January 2022

Nematocera (lower Diptera) is a taxonomically diverse group with ~52 000 species in 40 families, including many important agricultural and sanitary pests. The number and composition of nematoceran infraorders have long been subject to debate. The use of mitochondrial genomes for resolving these questions shows considerable promise. Herein, we sequenced and annotated the complete or nearly complete mitochondrial genomes of eight nematoceran species from seven families, representing the first mitochondrial genomes of two infraorders and six families. They range in size from 14 447 to 16 255 bp and all contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and an AT-rich region. Like other nematocerans, the arrangement of genes of their mitochondrial genomes is identical to the presumed ancestral arrangement. A phylogenetic analysis was conducted by using mitochondrial genomes of 116 representatives from Diptera, Mecoptera and Siphonaptera. Our phylogenetic results support both new and traditional arrangements. The small, highly specialized family Deuterophlebiidae appears to be sister to all remaining Diptera, while Nymphomyiidae and Blephariceridae are nested within Culicomorpha and Psychodomorpha, respectively; hence, the recognition of ‘Blephariceromorpha’ as a valid monophyletic infraorder is discouraged. Anisopodidae is supported as the sister group of Brachycera.
Health Care at Home: The Backstory
Authors: Powell Suzanne K.
Published: January 2022

There is a growing trend to care for patients in their home: Families and patients want it, full hospitals demand it, and insurance companies will benefit from it. However, despite all the “positives,” there are real threats and dangers to this growth. A lot depends on upcoming choices health care workers make in the coming years.
Sphingobacterium faecale sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces
Authors: Chen Min , Li Ni , Zhang Xiao-Fei , Zhou Xing-Kui , Shi Rui , Su Yuan-Xiao , Liu Jian-Jin , Cao Yi , Mo Ming He , Ma Li
Published: January 2022

An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1T. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1T was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria–Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C15 : 0, summed feature 3 (C16 : 1
 ω6c and/or C16 : 1
 ω7c) and iso-C17 : 0 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1T was affiliated with the genus

Sphingobacterium

and had the highest sequence similarity to

Sphingobacterium tabacisoli

h337T (97.0 %) and Sphingobacterium paucimobilis HER1398T (95.6 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain C459-1T and

S. tabacisoli

h337T were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1T from other

Sphingobacterium

species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1T represents a novel species of the genus

Sphingobacterium

, for which the name Sphingobacterium faecale sp. nov. is proposed, with strain is C459-1T (CGMCC 1.18716T=KCTC 82381T) as the type strain.
Szabonella alba gen. nov., sp. nov., a motile alkaliphilic bacterium of the family Rhodobacteraceae isolated from a soda lake
Authors: Szuróczki Sára , Abbaszade Gorkhmaz , Bóka Károly , Schumann Peter , Neumann-Schaal Meina , Tóth Erika
Published: January 2022

A Gram-stain-negative, oxidase- and catalase-positive, rod-shaped, creamy white coloured bacterial strain, DMG-N-6T, was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain forms a distinct linage within the family

Rhodobacteraceae

. Its closest relatives are

Tabrizicola alkalilacus

DJCT (96.76% similarity) and

Tabrizicola piscis

K13M18T (96.76%), followed by

Tabrizicola sediminis

DRYC-M-16T (96.69 %),

Rhodobacter sediminicola

JA983T (96.62 %),

Tabrizicola aquatica

RCRI19T (96.47 %) and

Cereibacter johrii

JA192T (96.18 %). The novel bacterial strain favours an alkaline environment (pH 8.0-12.0) and grows optimally at 18–28°C in the presence of 2–4 % (w/v) NaCl. Cells of DMG-N-6T were motile by a single subpolar flagellum. Bacteriochlorophyll a was not detected. The predominant respiratory quinone was ubiquinone Q-10. The major cellular fatty acid was C18:1
ω7c. The polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, an unidentified phospholipid and five unidentified lipids. The assembled draft genome of strain DMG-N-6T had 52 contigs with a total length of 4 219 778 bp and a G+C content of 64.3 mol%. Overall genome-related indices (ANI <77.8 %, AAI <69.0 %, dDDH <19.6 %) with respect to close relatives were all significantly below the corresponding threshold to demarcate bacterial genus and species. Strain DMG-N-6T (=DSM 108208T=NCAIM B.02645T) is strongly different from its closest relatives and is suggested as the type strain of a novel species of a new genus in the family

Rhodobacteraceae

, for which the name Szabonella alba gen. nov., sp. nov. is proposed.
Escherichia marmotae - a human pathogen easily misidentified as Escherichia coli
Authors: Sivertsen Audun , Dyrhovden Ruben , Tellevik Marit Gjerde , Bruvold Torbjørn Sæle , Nybakken Eirik , Skutlaberg Dag Harald , Skarstein Ingerid , Kommedal Øyvind
Published: January 2022

We hereby present the first descriptions of human invasive infections caused byEscherchia marmotae, a recently described species that encompasses the former“Escherichiacryptic clade V”. We report four cases, one acute sepsis of unknown origin, one post-operative sepsis after cholecystectomy, one spondylodiscitis and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab during six months. Through genome sequencing of the causative strains combined with available genomes from elsewhere we demonstrateE. marmotaeto be a likely ubiquitous species containing genotypic virulence traits associated withEscherichiapathogenicity. The invasive isolates were scattered among isolates from a range of non-human sources, thus indicating inherent virulence in multiple phylogenetic lineages. Pan genome analyses indicate thatE. marmotaehas a large accessory genome and is likely to obtain ecologically advantageous traits like genes encoding antimicrobial resistance. Reliable identification might be possible by MALDI-ToF MS, but relevant spectra are missing in commercial databases.E. marmotaecan be identified through 16S rRNA sequencing.Escherichia marmotaecould represent a relatively common human pathogen and improved diagnostics will provide a better understanding of its clinical importance.
Investigation of air change rate and aerosol behavior during an outbreak of COVID-19 in a geriatric care facility
Authors: Ishigaki Yo , Yokogawa Shinji , Minamoto Yuki , Saito Akira , Kitamura Hiroko , Kawauchi Yuto
Published: January 2022

Background

Ventilation plays an important role in controlling aerosol transmission of coronavirus disease (COVID-19), and mass transmission of COVID- 19 has been reported in poorly ventilated areas.

Objective

A real-world mass infection outbreak which occurred in an elderly nursing home, in Miyagi Prefecture, Japan, was simulated experimentally and numerically to investigate the controlling factors and quantify the effectiveness of various natural ventilation settings by means of air change rate (ACR).

Methods

Using the CO2 tracer gas method, the ACR values at the time of the outbreak were estimated to be 2.0–6.2 h-1 in rooms in the facility. Furthermore, a low-cost intervention of opening windows improved the ventilation frequency by a factor of 1.48–5.74. This implies that advective fluid flows are the key in the spread of high CO2 concentration zones. A numerical simulation was performed to obtain spatio-temporal evolution on such high CO2 concentration zones under similar conditions to the present experiment.

Results

The results showed that ventilation was significantly dependent on the window opening conditions in all rooms (p-values ranging from 0.001 to 0.03 for all the rooms). In contrast, there was no significant dependence on the location of the sensor in any of the areas. Development of high CO2 concentration zones occurs in the first few minutes. Furthermore, the leading edge of such zones towards the common room yields a relatively high fluid velocity, suggesting that the large-scale advective flow dictates the spread of such high CO2 concentration zones.

Conclusions

The present results suggest that secondary infections could occur due to the aerosol advection driven by such large-scale flows, even when the building design adheres the ventilation guidelines. In elderly care facilities, open architectural spaces are recommended to realize quality of life and monitor residents. However, management is required to reduce the downwind infection risk from aerosols and ACR.
Acute upper airway disease in children with the omicron (B.1.1.529) variant of SARS-CoV-2: a report from the National COVID Cohort Collaborative (N3C)
Authors: Martin Blake , DeWitt Peter E. , Russell Seth , Sanchez-Pinto L. Nelson , Haendel Melissa A. , Moffitt Richard , Bennett Tellen D.
Published: January 2022

Background

Reports of SARS-CoV-2 causing laryngotracheobronchitis (commonly known as croup) have been limited to small case series. Early reports suggest the Omicron (B.1.1.529) strain of SARS-CoV-2 (the dominant circulating US strain since the week of 12/25/2021) replicates more efficiently in the conducting airways. This may increase the risk of a croup phenotype in children as they have smaller airway calibers.

Methods

Description of the incidence, change over time, and characteristics of children with SARS-CoV-2 and upper airway infection (UAI) diagnoses within the National COVID Cohort Collaborative (N3C) before and during the rise of the Omicron variant. We compare the demographics, comorbidities, and clinical outcomes of hospitalized SARS-CoV-2 positive children with and without UAI.

Results

SARS-CoV-2 positive UAI cases increased to the highest number per month (N = 170) in December 2021 as the Omicron variant became dominant. Of 15,806 hospitalized children with SARS-CoV-2, 1.5% (234/15,806) had an UAI diagnosis. Those with UAI were more likely to be male, younger, white, have asthma and develop severe disease as compared to those without UAI.

Conclusions

Pediatric acute UAI cases have increased during the Omicron variant surge with many developing severe disease. Improved understanding of this emerging clinical phenotype could aid in therapeutic decision-making and healthcare resource planning.
Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 - January 2022
Authors: Stefanelli Paola , Trentini Filippo , Petrone Daniele , Mammone Alessia , Ambrosio Luigina , Manica Mattia , Guzzetta Giorgio , d’Andrea Valeria , Marziano Valentina , Zardini Agnese , Grane Carla Molina , Ajelli Marco , Di Martino Angela , Riccardo Flavia , Bella Antonino , Schepisi Monica Sane , Maraglino Francesco , Poletti Piero , Palamara Anna Teresa , Brusaferro Silvio , Rezza Giovanni , Pezzotti Patrizio , Merler Stefano ,   the Genomic SARS-CoV-2 National Surveillance Working Group,   the Italian Integrated Surveillance of COVID-19 Study Group
Published: January 2022

The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Data from three genomic surveys conducted in Italy between December 2021 and January 2022 suggest that Omicron became dominant in less than one month (prevalence on January 3: 78.6%-83.8%) with a doubling time of 2.7–3.1 days. The mean net reproduction number rose from about 1.15 in absence of Omicron to a peak of 1.83 for symptomatic cases and 1.33 for hospitalized cases, while it remained stable for critical cases.
A Micronized Electrostatic Precipitator Respirator Effectively Removes Ambient SARS-CoV-2 Bioaerosols
Authors: Redmann Rachel K. , Beddingfield Brandon J. , Spencer Skye , Chirichella Nicole R. , Henley Julian L. , Hager Wes , Roy Chad J.
Published: January 2022

Rationale

Inhalation of ambient SARS-CoV-2-containing bioaerosols leads to infection and pandemic airborne transmission in susceptible populations. Filter-based respirators effectively reduce exposure but complicate normal respiration through breathing zone pressure differential and are therefore impractical for long-term use.

Objectives

We tested the comparative effectiveness of a prototyped micronized electrostatic precipitator (mEP) to a filter-based respirator (N95) in the removal of viral bioaerosols from a simulated inspired air stream.

Methods

Each respirator was tested within a 16-liter environmental chamber housed within a Class III biological safety cabinet within biosafety level 3 containment. SARS-CoV-2 containing bioaerosols were generated into the chamber, drawn by vacuum through each respirator, and physical particle removal and viral genomic RNA were measured distal to the breathing zone of each device.

Measurement and Main Results

The mEP respirator removed particles (96.5±0.4%) approximating efficiencies of the N95 (96.9±0.6%). The mEP respirator similarly decreased SARS-CoV-2 viral RNA (99.792%) when compared to N95 removal (99.942%) as a function of particle removal from the airstream distal to the breathing zone of each respirator.

Conclusions

The mEP respirator approximated performance of a filter-based N95 respirator for particle removal and viral RNA as a constituent of the SARS-CoV-2 bioaerosols generated for this evaluation. In practice, the mEP respirator would provide equivalent protection from ambient infectious bioaerosols as the N95 respirator without undue pressure drop to the wearer, thereby facilitating long-term use in an unobstructed breathing configuration.
Liver Echinococcosis Lesion Classification Tool by Deep Learning: development, deployment, and validations
Authors: Huang Liang , Xi Xiaohong , Chen Zhu , Zeng Yilan
Published: January 2022

The endemic of Echinococcosis imposed heavy disease burden in some areas. The sonography for Echinococcosis lesions was essential to disease diagnosis and managements. Especially the biological typing of lesions was key to disease treatments. We used deep-learning tools to help sonographer to classify the lesion types. The model achieved 85%(302/376) accuracy, in contrast to senior sonographer achieved 72%(61/85) accuracy. The accuracy of AI model was higher than senior sonographer (p-value=0.01), could be a feasible method to help sonographer in remote area.
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types
Authors: Ximerakis Methodios , Holton Kristina M. , Giadone Richard M. , Ozek Ceren , Saxena Monika , Santiago Samara , Adiconis Xian , Dionne Danielle , Nguyen Lan , Shah Kavya M. , Goldstein Jill M. , Gasperini Caterina , Lipnick Scott L. , Simmons Sean K. , Buchanan Sean M. , Wagers Amy J. , Regev Aviv , Levin Joshua Z. , Rubin Lee L.
Published: January 2022

Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors.
Encoding and decoding analysis of music perception using intracranial EEG
Authors: Bellier Ludovic , Llorens Anaïs , Marciano Déborah , Schalk Gerwin , Brunner Peter , Knight Robert T. , Pasley Brian N.
Published: January 2022

Music perception engages multiple brain regions, however the neural dynamics of this core human experience remains elusive. We applied predictive models to intracranial EEG data from 29 patients listening to a Pink Floyd song. We investigated the relationship between the song spectrogram and the elicited high-frequency activity (70-150Hz), a marker of local neural activity. Encoding models characterized the spectrotemporal receptive fields (STRFs) of each electrode and decoding models estimated the population-level song representation. Both methods confirmed a crucial role of the right superior temporal gyri (STG) in music perception. A component analysis on STRF coefficients highlighted overlapping neural populations tuned to specific musical elements (vocals, lead guitar, rhythm). An ablation analysis on decoding models revealed the presence of unique musical information concentrated in the right STG and more spatially distributed in the left hemisphere. Lastly, we provided the first song reconstruction decoded from human neural activity.
N Gene Target Failure (NGTF) for detection of Omicron: a way out for the ‘stealth’ too?
Authors: Harankhedkar Shivangi , Chatterjee Gaurav , Rajpal Sweta , Khan Afreen , Srivastava Tuhina , Mirgh Sumeet , Gokarn Anant , Punatar Sachin , Shetty Nitin , Joshi Amit , Nair Sudhir , Murthy Vedang , Tembhare Prashant , More Ashwini , Kamtalwar Sujeet , Chavan Preeti , Bhat Vivek , Patil Amar , Dhumal Sachin , Bhat Prashant , Subramanian Papagudi , Tripathi Rachana , Munipally Shesheer , Gujral Sumeet , Khattry Navin , Gupta Sudeep , Patkar Nikhil
Published: January 2022

S-gene target failure (SGTF) is neither specific nor accurate for identification of Omicron lineage of SARS-CoV-2. We observed N-gene target failure (NGTF) in 402 out of 412 SARS-CoV2 positive cases from December to mid-January 2022 using a commercially available assay. This phenomenon was not observed with more than 15,000 cases tested previously. We sequenced the genome of five samples with NGTF and compared these results with six cases where NGTF was not seen. We confirm that cases with NGTF were the Omicron lineage while cases with preserved N-gene amplification belonged to Delta lineage. We discovered that the ERS31-33 deletion (nucleotide 28362-28370del) overlaps with N gene probe used, explaining NGTF. As the ‘stealth’ Omicron variant also harbors ERS31-33 deletion, this approach will work for the detection of ‘stealth’ Omicron variant as well. We suggest that NGTF can be used as a low cost, rapid screening strategy for detection of Omicron.
Limit of Detection for Rapid Antigen Testing of the SARS-CoV-2 Omicron Variant
Authors: Stanley Sydney , Hamel Donald J. , Wolf Ian D. , Riedel Stefan , Dutta Sanjucta , Cheng Annie , Kirby James E. , Kanki Phyllis J.
Published: January 2022

There has been debate in the literature about the ability of antigen tests to detect the SARS-CoV-2 Omicron variant including indication on the US Food and Drug administration website that antigen tests may have lower sensitivity for the Omicron variant without provision of data or the potential scale of the issue (seehttps://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests-omicronvariantimpact, accessed 1/27/2022). Here we determined the limit of detection (LoD) for the Omicron variant compared with the WA1 strain used for LoD studies described in the Instructions for Use for all Emergency Use Authorization (EUA)-approved antigen tests. Using live virus (to avoid artifactual findings potentially obtained with gamma-irradiated or heat-killed virus) quantified by plaque forming units (PFU), we examined the analytical sensitivity of three antigen tests widely used in the United States: the Abbott Binax Now, the AccessBio CareStart, and LumiraDx antigen tests. We found that the 95% detection threshold (LoD) for antigen tests was at least as good for Omicron as for the WA1 strain. Furthermore, the relationship of genome copies to plaque forming units for Omicron and WA1 overlap. Therefore, the LoD equivalency also applies if the quantitative comparator is genome copies determined from live virus preparations. Taken together, our data support the continued ability of the antigen tests examined to detect the Omicron variant.
Continuing inequalities in COVID-19 mortality in England and Wales, and the changing importance of regional, over local, deprivation
Authors: Griffith Gareth J , Owen Gwilym , Manley David , Howe Laura D , Smith George Davey
Published: January 2022

Background

Observational studies have highlighted that where individuals live is far more important for risk of dying with COVID-19, than for dying of other causes. Deprivation is commonly proposed as explaining such differences. During the period of localised restrictions in late 2020, areas with higher restrictions tended to be more deprived. We explore how this impacted the relationship between deprivation and mortality and see whether local or regional deprivation matters more for inequalities in COVID-19 mortality.

Methods

We use publicly available population data on deaths due to COVID-19 and all-cause mortality between March 2020 and April 2021 to investigate the scale of spatial inequalities. We use a multiscale approach to simultaneously consider three spatial scales through which processes driving inequalities may act. We go on to explore whether deprivation explains such inequalities.

Results

Adjusting for population age structure and number of care homes, we find highest regional inequality in October 2020, with a COVID-19 mortality rate ratio of 5.86 (95% CI 3.31 to 19.00) for the median between-region comparison. We find spatial context is most important, and spatial inequalities higher, during periods of low mortality. Almost all unexplained spatial inequality in October 2020 is removed by adjusting for deprivation. During October 2020, one standard deviation increase in regional deprivation was associated with 2.45 times higher local mortality (95% CI, 1.75 to 3.48).

Conclusions

Spatial inequalities are greatest in periods of lowest overall mortality, implying that as mortality declines it does not do so equally. During the prolonged period of low restrictions and low mortality in summer 2020, spatial inequalities strongly increased. Contrary to previous months, we show that the strong spatial patterning during autumn 2020 is almost entirely explained by deprivation. As overall mortality declines, policymakers must be proactive in detecting areas where this is not happening, or risk worsening already strong health inequalities.

Key messages

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Spatial inequalities in local mortality are highest in periods of lower overall mortality.

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Spatial inequality in COVID-19 mortality peaked in October 2020, before decreasing strongly in November and over the winter period.

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Deprivation explains almost all inequality during October when inequality was at its highest.

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Regional deprivation was far more strongly associated with local mortality than local deprivation during September to November 2020.

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This is consistent with an overdispersed distribution of secondary infections governed by transmission heterogeneity structured by deprivation.