bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
Authors: Martin Darren P , Lytras Spyros , Lucaci Alexander G , Maier Wolfgang , Grüning Björn , Shank Stephen D , Weaver Steven , MacLean Oscar A , Orton Richard J , Lemey Philippe , Boni Maciej F , Tegally Houriiyah , Harkins Gordon , Scheepers Cathrine , Bhiman Jinal N , Everatt Josie , Amoako Daniel G , San James Emmanuel , Giandhari Jennifer , Sigal Alex ,   NGS-SA, Williamson Carolyn , Hsiao Nei-yuan , von Gottberg Anne , De Klerk Arne , Shafer Robert W , Robertson David L , Wilkinson Robert J , Sewell B Trevor , Lessells Richard , Nekrutenko Anton , Greaney Allison J. , Starr Tyler N. , Bloom Jesse D. , Murrell Ben , Wilkinson Eduan , Gupta Ravindra K , de Oliveira Tulio , Kosakovsky Pond Sergei L 
Published: January 2022

AbstractAmong the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.
Activation of the dorsal septum increases alcohol consumption in male C57BL/6J mice
Authors: Haun Harold L. , D’Ambrosio Shannon L. , Kash Thomas L. 
Published: January 2022

ABSTRACTBinge drinking is a common pattern of excessive alcohol consumption associated with Alcohol Use Disorder (AUD) and unraveling the neurocircuitry that promotes this type of drinking is critical to the development of novel therapeutic interventions. The septal region was once a focal point of alcohol research yet has seen limited study over the last decade in relation to binge drinking. Numerous studies point to involvement of the dorsal septum (dSep) in excessive drinking and withdrawal, but few studies have manipulated this region in the context of binge drinking behavior. The present experiments were primarily designed to determine the effect of chemogenetic manipulation of the dSep on binge-like alcohol drinking in male and female C57BL/6J mice. Mice received bilateral infusion of AAVs harboring hM4Di, hM3Dq, or mCherry into the dSep and subjects were challenged with systemic administration of clozapine-N-oxide (CNO; 3 mg/kg) and vehicle (saline; 0.9%) in the context of binge-like alcohol consumption, locomotor activity, and sucrose drinking. CNO-mediated activation (hM3Dq) of the dSep resulted in a significant increase in binge-like alcohol consumption, locomotor activity, and sucrose intake in male mice. DSep activation promoted sucrose drinking in female mice, but alcohol intake and locomotor activity were unaffected. Conversely, silencing (hM4Di) of the dSep modestly decreased locomotor activity in males and did not influence alcohol or sucrose intake in either sex. Lastly, CNO was without effect in mCherry-expressing control groups. These data support a role for the dSep in promoting excessive, binge-like drinking behavior in a sex-dependent fashion and suggests a broad role for the region in the modulation of locomotor activity as well as general appetitive behavior such as sucrose drinking.
RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
Authors: Lucaci Alexander G , Zehr Jordan D , Shank Stephen D , Bouvier Dave , Mei Han , Nekrutenko Anton , Martin Darren P , Kosakovsky Pond Sergei L 
Published: January 2022

AbstractAn important component of efforts to manage the ongoing COVID19 pandemic is the Rapid Assessment of how natural selection contributes to the emergence and proliferation of potentially dangerous SARS-CoV-2 lineages and CLades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations.AvailabilityRASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl. Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl.ContactDr. Sergei L Kosakovsky Pond (spond@temple.edu).Supplementary informationN/A
Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (the CLiP Mutant Library Background)
Authors: Zhang Ningning , Pazouki Leila , Nguyen Huong , Jacobshagen Sigrid , Xia Ming , Klebanovych Anastasiya , Czymmek Kirk J. , Zhang Ru 
Published: January 2022

AbstractThe unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more sensitive to heat than CC-1690. Furthermore, CC-5325 had an intact cell wall with comparable integrity to that in CC-1690, though appears to have reduced thickness. Finally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC160 did. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.
Population-specific association ofClockgene polymorphism with annual cycle timing in stonechats
Authors: Justen Hannah , Hasselmann Timo , Illera Juan Carlos , Delmore Kira , Serrano David , Flinks Heiner , Senzaki Masayuki , Kawamura Kazuhiro , Helm Barbara , Liedvogel Miriam 
Published: January 2022

AbstractTiming is essential for survival and reproduction of organisms across the tree of life. The core circadian clock geneClkhas been implicated in annual timing and shows highly conserved sequence homology across vertebrates except for one variable region of poly Glutamine repeats.Clkgenotype varies in some species with latitude, seasonal timing and migration. However, findings are inconsistent, difficult to disentangle from environmental responses, and biased towards high latitudes. Here we combine field data with a common-garden set up to study associations ofClkwith latitude, migration and annual-cycle timing within the stonechat species complex with trans-equatorial distribution range. Including 950 individuals from nine populations with diverse migratory strategies. Gene diversity was lowest in resident African and Canary Island populations and increased with latitude, independently of migration distance. Repeat length and annual-cycle timing was linked in a population-specific way. Specifically, equatorial African stonechats showed delayed timing with longer repeat length for all annual-cycle stages. Our data suggest that at low latitudes with constant photoperiod,Clkgenotype might orchestrate a range of consistent, individual chronotypes. In contrast, the influence ofClkon annual-cycle timing at higher latitudes might be mediated by its interactions with genes involved in (circadian) photoperiodic pathways.
On the Edge: Identifying priority areas for conservation of Fishing Cat, a threatened wetland felid, amidst rapidly altering freshwater landscapes
Authors: Adhya Tiasa , Bagaria Priyamvada , Dey Partha , Muñoz Vanessa Herranz , Weerawardana Ratnayaka Anya Avanthi , Thudugala Ashan , Aravind N.A. , Sanderson James G. 
Published: January 2022

AbstractFreshwater ecosystems have been most severely impacted in the Anthropocene with 27% of its species threatened with extinction. Fishing Cat is a globally threatened South and South-east Asian wetland felid that is also a highly rated Evolutionarily Distinct and Globally Endangered (EDGE) species, i.e., it is a global priority for conservation and research. Being an understudied species, knowledge gaps exist on its basic ecology, such as distribution and niche.To address this, ensemble species distribution modeling (ESDM) was used to clarify doubts on its potential distribution and niche. To provide a relatable current context, loss of suitable habitat to urbanization (2010-2020) was estimated by analyzing range-wide survey data with environmental and anthropogenic variables (night-time lights and land surface temperature as proxies for urbanization).Wetlands (18.36%) and elevation (17.15%) are the most important variables determining the ecological niche of Fishing Cat. It was predicted to be mainly restricted to low-elevation (<111 m) wetlands in river basins of South and South-east Asia. An estimated 23.74% suitable habitat was lost to urbanization.Incrementally building on the ESDM outputs, high priority movement corridors and landscape conservation units were identified.South Asia holds the core of the global Fishing Cat population with two very important regions - Ganges Brahmaputra Basin and Indus Basin - sharing transboundary areas with highly suitable habitat and many priority conservation units. The former is strategic to maintaining connectivity between South and South-east Asian Fishing Cat populations while isolation effects in the latter need investigation. Coastal wetlands of South-east Asia, though severely impacted, are crucial for the felid’s persistence.More than 90% of Fishing Cat’s potential range lies outside the protected area network. Here, the felid can be adopted as a flagship species to conserve rapidly degrading low- elevation wetlands within a socio-ecological framework by involving multiple stakeholders.
A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris
Authors: Ryu Taewoo , Herrera Marcela , Moore Billy , Izumiyama Michael , Kawai Erina , Laudet Vincent , Ravasi Timothy 
Published: January 2022

ABSTRACTBackgroundThe false clownfish Amphiprion ocellaris is a popular fish species and an emerging model organism for studying the ecology, evolution, adaptation, and developmental biology of reef fishes. Despite this, high-quality genomic resources for this species are scarce, hindering advanced genomic analyses. Leveraging the power of PacBio long-read sequencing and Hi-C chromosome conformation capture techniques, we constructed a high-quality chromosome-scale genome assembly for the clownfish A. ocellaris.ResultsThe initial genome assembly comprised of 1,551 contigs of 861.42 Mb, with an N50 of 863.85 kb. Hi-C scaffolding of the genome resulted in 24 chromosomes containing 856.61 Mb. The genome was annotated with 26,797 protein-coding genes and had 96.62 % completeness of conserved actinopterygian genes, making this genome the most complete and high quality among published anemonefish genomes. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further, comparative genomic analysis revealed 91 genome elements conserved only in A. ocellaris and its sister species Amphiprion percula, and not in other anemonefish species. These elements are close to genes that are involved in various nervous system functions and exhibited distinct expression patterns in brain tissue, potentially highlighting the genetic toolkits involved in lineage-specific divergence and behaviors of the clownfish branch.ConclusionsOverall, our study provides the highest quality A. ocellaris genome assembly and annotation to date, whilst also providing a valuable resource for understanding the ecology and evolution of reef fishes.
Exocyst stimulates each step of exocytic SNARE complex assembly and vesicle fusion
Authors: Lee Chanwoo , Lepore Dante , Munson Mary , Yoon Tae-Young 
Published: January 2022

AbstractThe exocyst is a large multisubunit tethering complex essential for targeting and fusion of secretory vesicles in eukaryotic cells. Although the assembled exocyst complex is proposed to tether vesicles to the plasma membrane and activate the SNARE proteins for membrane fusion, only little is known about the key biochemical steps that exocyst stimulates in the course of SNARE complex assembly, a critical question defining the essential molecular role of the exocyst complex. Here, we use a combination of single molecule and bulk fluorescence assays with purified octameric yeast exocyst complexes to examine the role of exocyst in a reconstituted SNARE assembly and fusion system. We show that the exocyst complex simulates multiple steps spanning from SNARE protein activation to ternary complex assembly, rather than affecting only a specific subset of steps. We also observed that the exocyst has important downstream roles in driving membrane fusion, up to full content mixing of vesicle lumens. Our results suggest that the exocyst complex provides extensive chaperoning functions for the entire process of SNARE complex assembly, presumably using its multi-faceted structure provided by the eight subunits.
Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant ofFusariumwilt into South America
Authors: Reyes-Herrera Paula H. , Torres-Bedoya Eliana , Lopez-Alvarez Diana , Burbano-David Diana , Carmona Sandra L. , Bebber Daniel P. , Studholme David J. , Betancourt Monica , Soto-Suarez Mauricio 
Published: January 2022

AbstractThe global banana industry is threatened by one of the most devastating diseases: Fusarium wilt (FWB). FWB is caused by the soil-borne fungusFusarium oxysporumf. sp.cubense(Foc), which almost annihilated the banana production in the late 1950s. A new strain ofFoc, known as tropical race 4 (TR4), attacks a wide range of banana varieties including Cavendish clones which are the source of 99% of banana exports. In 2019,FocTR4 was reported in Colombia, and more recently (2021) in Peru. In this study, we sequenced three fungal isolates identified asFocTR4 from La Guajira (Colombia) and compared them against 19 whole-genome sequences ofFocTR4 publicly available, including four genome sequences recently released from Peru. To understand the genetic relatedness of the ColombianFocTR4 isolates and those from Peru, we conducted a phylogenetic analysis based on a genome-wide set of single nucleotide polymorphisms (SNPs). Additionally, we compared the genomes of the 22 availableFocTR4 isolates looking for the presence-absence of gene polymorphisms and genomic regions. Our results reveal that (i) the Colombian and Peruvian isolates are genetically distant, which could be better explained by independent incursions of the pathogen to the continent, and (ii) there is a high correspondence between the genetic relatedness and geographic origin ofFocTR4. The profile of present/absent genes and the distribution of missing genomic regions showed a high correspondence to the clades recovered in the phylogenetic analysis, supporting the results obtained by SNP-based phylogeny.
Unconscious or conscious? The impacts of habit and social support receipt on older adults' continued participation in online health communities
Authors: Ma Dan , Zuo Meiyun 
Published: January 2022

PurposeOnline health communities (OHCs) can be complementary to healthcare systems to improve the health behaviors of older adults with chronic diseases. This study aims to examine the impacts of habit and social support receipt on older adults' continued participation in OHCs. Particularly, the authors discussed the influences of social support received in two ways: social support received by initiating threads (direct social support receipt) and social support received by being exposed to the threads initiated by others (indirect social support receipt).Design/methodology/approachBased on the dual-process model (i.e. conscious process and unconscious process), the authors developed the research model. Data from one of the biggest online diabetes communities in Europe were collected. Besides, we used the support vector machine algorithm for social support classification and used the Cox proportion hazards model for model validation.FindingsOlder adults' continued participation is influenced by habit and indirect informational support. Habit moderates the relationship between direct informational support receipt and older adults' continued participation. Furthermore, direct and indirect emotional support receipt are both not associated with older adults' continued participation, regardless of their habit strength.Originality/valueThis is the first study investigating older adults' continued participation in OHCs based on the dual-process model. The findings of this study reveal that older adults' continued participation is determined by both the habit and specific conscious evaluation of benefits based on the social support receipt.
Maximizing minimums: space-utilization in the small homes in the Mumbai metropolitan region
Authors: Chakraborty Shreyonti , Staub Alexandra , Bollo Christina 
Published: January 2022

PurposeMany people living in and around Mumbai face space scarcity within homes, an issue exacerbated for families with members having differing and conflicting spatial requirements. By investigating how families live in existing residential environments, planners and designers can enable families to cope better with space scarcity.Design/methodology/approachA case study approach is used to examine four small home settings in and around Mumbai, followed by a thematic analysis of the data collected.FindingsThis study contributes a framework for studying small homes in and around Mumbai wherein they are characterized by five categories of information: internal zoning pattern, expansion pattern, spatial specialization and stratification pattern, outdoor space appropriation pattern and household adjustment pattern. Analysis through this framework gives insight into how small home settings are used by residents.Originality/valueTo the best of the authors’ knowledge, this is the first study offering in-depth comparative analysis of small home typologies in India.
Effect of tasting and flavour on chocolate-evoked emotions by consumers
Authors: De Pelsmaeker Sara , Gellynck Xavier , Dewettinck Koen , Schouteten Joachim J. 
Published: January 2022

PurposeThere is a growing interest in measuring emotions evoked by food products to gain additional insights in how consumers perceive and choose food products. The aim of this study was to investigate if consumers' emotions are influenced by flavour, gender, consumption habits, actual tasting or consumer attitude towards a product. Chocolate was chosen as the product under study as its consumption is associated with evoking several emotions.Design/methodology/approachDuring a between-subjects experiment at a local food fair, consumers (n = 910) evaluated either the name “chocolate”, plain dark chocolate or raspberry flavoured dark chocolate. Participants rated the intensity of 24 emotions and answered the 24 statements of the Attitude to Chocolate Questionnaire.FindingsThe results showed that sensory characteristics have a significant influence on the emotional profiles whereas no difference was found between tasting and not tasting. Gender and prior liking had little to no influence. Finally, the results suggested that consumption frequency and attitudes towards chocolate did have an influence on the emotional profiles.Practical implicationsThe results show that producers should try to evoke positive emotions which could be emphasised through marketing. Gender differences for emotional profiling advocate that future research should not only analyse global results but also separately analyse by gender. Moreover, usage frequency and attitudes towards chocolate had an impact on the emotions meaning that future research should consider those when setting up research.Originality/valueThis study further contributes to the growing literature on emotions. It examines the added value of actual tasting chocolate while prior research focuses either just names or just sensory evaluation. Also, this paper further explores to which extent flavour, gender, consumption habits and attitude impact the emotional associations of chocolate.
Urban vibrancy, human capital and firm valuation in China
Authors: Jiang Danling , Shuying Liu , Li Feiyu , Zhu Hongquan 
Published: January 2022

PurposeThis paper intends to study how geographic heterogeneity in urban vibrancy, especially in human capital creation, helps explain persist firm valuation dispersion across cities in China.Design/methodology/approachThis paper studies geographic differences in firm valuations of 1,023 listed companies headquartered in 35 major cities in China from 2001 to 2018. The authors estimate panel regressions of local firm Tobin's q on city fixed effects or city endowed attributes in human capital creation after controlling industry-year fixed effects as well as a set of firm and city time variant attributes.FindingsThe results show persistent, significant city-to-city differences in Tobin's q, especially among large, mature or high labor-intensive firms. To explain such geographic differences in firm valuations, the authors identify several factors of the endowed city competitive advantages in creating human capital that play important roles in explaining the persistent geographic firm valuation premia.Originality/valueThis paper provides the first systematic analysis of urban vibrancy in human capital supply in explaining persistent geographic firm valuation dispersion in China. The evidence suggests that city endowed comparative advantages in supplying human capital have created long-lasting, and growing, shareholder wealth by attracting and retaining talents and human resources in local firms.