Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineering and Characterization of Avian Coronavirus Mutants Expressing Fluorescent Reporter Proteins from the Replicase Gene

Reverse genetics systems based on bacterial artificial chromosomes (BACs) are the most valuable systems in coronavirus research. Here, we describe the establishment of a reverse genetics system for the avian coronavirus strain Beaudette, the most intensively studied strain. ABSTRACT Infectious bronchitis virus (IBV) is an avian coronavirus that causes infectious bronchitis, an acute and highly contagious respiratory disease of chickens. IBV evolution under the pressure of comprehensive and widespread vaccination requires surveillance for vaccine resistance, as well as periodic vaccine updates. Reverse genetics systems are very valuable tools in virology, as they facilitate rapid genetic manipulation of viral genomes, thereby advancing basic and applied research. We report here the construction of an infectious clone of IBV strain Beaudette as a bacterial artificial chromosome (BAC). The engineered full-length IBV clone allowed the rescue of an infectious virus that was phenotypically indistinguishable from the parental virus. We used the infectious IBV clone and examined whether an enhanced green fluorescent protein (EGFP) can be produced by the replicase gene ORF1 and autocatalytically released from the replicase polyprotein through cleavage by the main coronavirus protease. We show that IBV tolerates insertion of the EGFP ORF at the 3′ end of the replicase gene, between the sequences encoding nsp13 and nsp16 (helicase, RNA exonuclease, RNA endonuclease, and RNA methyltransferase). We further show that EGFP is efficiently cleaved from the replicase polyprotein and can be localized in double-membrane vesicles along with viral RNA polymerase and double-stranded RNA, an intermediate of IBV genome replication. One of the engineered reporter EGFP viruses were genetically stable during passage in cultured cells. We demonstrate that the reporter EGFP viruses can be used to study virus replication in host cells and for antiviral drug discovery and development of diagnostic assays. IMPORTANCE Reverse genetics systems based on bacterial artificial chromosomes (BACs) are the most valuable systems in coronavirus research. Here, we describe the establishment of a reverse genetics system for the avian coronavirus strain Beaudette, the most intensively studied strain. We cloned a copy of the avian coronavirus genome into a BAC vector and recovered infectious virus in permissive cells. We used the new system to construct reporter viruses that produce enhanced green fluorescent protein (EGFP). The EGFP coding sequence was inserted into 11 known cleavage sites of the major coronavirus protease in the replicase gene ORF1. Avian coronavirus tolerated the insertion of the EGFP coding sequence at three sites. The engineered reporter viruses replicated with parental efficiency in cultured cells and were sufficiently genetically stable. The new system facilitates functional genomics of the avian coronavirus genome but can also be used for the development of novel vaccines and anticoronaviral drugs.
Human FcRn Is a Two-in-One Attachment-Uncoating Receptor for Echovirus 18

E18 is a member of enterovirus species B. As one of the most common enterovirus serotypes in nonpolio enterovirus detection, it easily infects children and causes various clinical symptoms. ABSTRACT Virus-receptor interactions determine viral host range and tissue tropism. CD55 and human neonatal Fc receptor (FcRn) were found to be the binding and uncoating receptors for some of the echovirus-related enterovirus species B serotypes in our previous study. Echovirus 18 (E18), as a member of enterovirus species B, is a significant causative agent of aseptic meningitis and viral encephalitis in children. However, it does not use CD55 as a critical host factor. We conducted CRISPR/Cas9 knockout screening to determine the receptors and entry mechanisms and identified FcRn working as a dual-function receptor for E18. Knockout of FCGRT and B2M, which encode the two subunits of FcRn, prevented infection by E18 and other echoviruses in the same physiological cluster. We then elucidated the underlying molecular mechanism of receptor recognition by E18 using cryogenic electron microscopy. The binding of the FCGRT subunit to the canyon region rotates the residues around the pocket, triggering the release of the pocket factor as observed for other enterovirus species B members. IMPORTANCE E18 is a member of enterovirus species B. As one of the most common enterovirus serotypes in nonpolio enterovirus detection, it easily infects children and causes various clinical symptoms. Aseptic meningitis and viral encephalitis are the most commonly reported syndromes associated with E18. No effective antiviral drugs or approved vaccines are available. Previous studies showed that CD55 and FcRn were the binding and uncoating receptors for some echoviruses. However, we found that CD55 is not the critical host factor for E18. Thus, we want to determine the receptors and elucidate the entry mechanism of E18. Our findings reveal that FcRn is a two-in-one attachment-uncoating receptor for E18.
A Numerical Tool for Dissolved Oxygen Simulation in the Western Mississippi Sound

ABSTRACT Bazgirkhoob, H. ; Linhoss, A. , and Armandei, M. , 2022. A numerical tool for dissolved oxygen simulation in the western Mississippi Sound. Journal of Coastal Research, 38(4), 699–711. Coconut Creek (Florida), ISSN 0749-0208. Dissolved oxygen is an indicator of aquatic health. Hydrodynamic–water quality models facilitate the understanding of flow dynamics and dissolved oxygen in estuarine systems. In this study, dissolved oxygen concentration, seasonality, and vertical stratification were studied in the western Mississippi Sound, Northern Gulf of Mexico. Visual Environmental Fluid Dynamic Code and the water quality model CE-QUAL-ICM were linked together to develop a three-dimensional hydrodynamic and water quality model of the western Mississippi Sound. The model was verified and validated for nutrients and chlorophyl a. Then, the modeled results for dissolved oxygen were compared to measured data. Mean observed dissolved oxygen ranged between 6.29 and 8.48 mg/L in the top and bottom layers at each site. The root mean squared error between measured and modeled dissolved oxygen ranged between 1.30 and 2.87 mg/L. Results indicate that the model was able to capture measured seasonal trends and vertical stratification. The model simulated more realistic results in shallower areas compared to deeper areas. Overall, the model simulated slightly higher dissolved oxygen than what was measured, although 27% of the stations showed no statistical difference between the modeled and measured dissolved oxygen. These results are useful for interpreting the value of this model for future ecological studies. The model can be used as a tool to provide better understanding of the dissolved oxygen dynamics due to multiple scenarios such as hurricanes and storms.
of Toad Urinary Bladder Epithelium Intercellular Electrical Coupling and Transepithelial Cellular and Shunt Conductances

The electrical resistances of the transcellular and paracellular pathways across the toad urinary bladder epithelium (a typical "tight" sodium- transporting epithelium) were determined by two independent sets of electro- physiological measurements: (a) the measurement of the total transepithelial resistance, the ratio of resistance of the apical to the basal cell membrane, and cable analysis of the voltage spread into the epithelium; (b) the measure- ment of the total transepithelial resistance and the ratio of resistances of both cell membranes before and after replacing all mucosal sodium with potassium (thus, increasing selectively the resistance of the apical membrane). The results obtained with both methods indicate the presence of a finite transepithelial shunt pathway, whose resistance is about 1.8 times the resistance of the trans- cellular pathway. Appropriate calculations show that the resistance of the shunt pathway is almost exclusively determined by the zonula occludens section of the limiting junctions. The mean resistance of the apical cell membrane is 1.7 times that of the basal cell membrane. The use of nonconducting materials on the mucosal side allowed us to demonstrate that apparently all epithelial cells are electrically coupled, with a mean space constant of 460 pum, and a voltage spread consistent with a thin sheet model.
Tourism graduate students’ employability skills: Results and implications of a Zimbabwean study

The study investigated perceptions of employability skills of Tourism and Hospitality Management (THM) graduates in the Zimbabwean sector. The participants included 15 THM university graduates and 15 tourism sector managers. The participants completed semi-structured interviews regarding the perceived employability skills required of THM graduates by the tourism industry. Following content analysis, three themes emerged from the data: (i) soft and hard employability skills; (ii) transferability of essential employability skills; and (iii) curriculum-based competencies. Study participants indicated that internship tasks provided limited training in practical skills. THM stakeholders reported a need for training aimed at improving the students’ employability skills with higher levels of collaboration between higher education and industry partners. The findings indicate the importance of developing practice-based skills through extended internship experiences to develop more skilled human resources for the tourism sector.
Predation promotes diversification in the mean and variance of antipredator traits

Predator species are separated along habitat gradients, with predation known to play an essential role in species' trait diversification. Because predator species differ dramatically in their hunting style and mode, a change in predator species will alter the mean and variance of prey's antipredator traits. Population trait variation has an impact on community ecology. It influences species' niche width and interactions in the food web. However, empirical studies on variance change by predation are scarce. In this study, we collected large numbers of the last instar Leucorrhinia pectoralis exuviae from lakes with predatory fish (fish lakes) and lakes with large invertebrate predators (dragonfly lakes) and compared their two antipredator traits (spines and body size). We found that individuals in dragonfly lakes grew shorter spines than individuals in fish lakes. Body size showed no significant difference between dragonfly‐lake individuals and fish‐lake individuals. Moreover, populations from dragonfly lakes showed a smaller variance of spine length than populations from fish lakes; while populations from dragonfly lakes had a larger variance in body size than populations from fish lakes. These results indicate that trait variance, as well as mean, is strongly modified by different predation regimes. Studying the mean and variance of traits can help to define the mode of selection forces (directional selection and stabilising selection) in nature. Moreover, dragonfly larvae might be ideal organisms for the study of phenotypic selection on quantitative traits in the wild.
Vulnerabilidade de mulheres vivendo com HIV/Aids

OBJETIVO: tracar o perfil de mulheres vivendo com o virus da imunodeficiencia humana/Aids em municipios do interior do Estado de Sao Paulo, buscando-se identificar caracteristicas relacionadas a vulnerabilidade individual, social e programatica e analisar as condicoes em que tiveram conhecimento de seu status sorologico. METODO: entre outubro de 2008 e dezembro de 2010, foi realizado estudo transversal, envolvendo 184 mulheres atendidas em servico especializado. Os dados foram obtidos por entrevista e exame ginecologico, com coleta de amostras para diagnostico etiologico de doencas sexualmente transmissiveis. RESULTADOS: predominaram mulheres brancas, entre 30 e 49 anos de idade, com companheiro, baixo nivel escolar, multiplos parceiros sexuais durante a vida e pratica de sexo inseguro. A prevalencia de doencas sexualmente transmissiveis foi de 87,0%. CONCLUSAO: o estudo sugere a necessidade de ofertar assistencia ginecologica em servicos especializados e realizacao de acoes multiprofissionais que reforcem a autonomia feminina na tomada de decisoes protetoras.
Ética na publicação de pesquisas sobre leishmaniose visceral humana em periódicos nacionais

OBJETIVO: Analisar os aspectos eticos dos artigos nacionais sobre leishmaniose visceral humana publicados apos a Resolucao CNS 196/1996 e analisar a politica de periodicos brasileiros sobre etica em pesquisa. METODOS: Estudo exploratorio de natureza bibliografica e documental. A selecao das publicacoes sobre pesquisas envolvendo seres humanos foi realizada na base SciELO Brasil a partir de 1996. Foram analisadas lacunas relacionadas as politicas editoriais dos periodicos medicos a partir de informacoes obtidas da secao "Instrucoes aos autores" de cada periodico. RESULTADOS: Observou-se que, enquanto no primeiro quadrienio (1997 a 2000) nenhum artigo mencionou o cumprimento dos aspectos eticos, no ano de 2009 do quadrienio (2009 a 2012), 75% cumpriram pelo menos uma das orientacoes eticas avaliadas. Seis em 11 periodicos indicaram que as informacoes sobre os aspectos eticos deveriam ser citadas no corpo do artigo. Tres periodicos fizeram exigencias quanto ao envio de carta ou documento assinado pelo(s) autor(es) informando o cumprimento dos aspectos; dois solicitaram copia do documento de obtencao do termo de consentimento livre e esclarecido; um explicitou a necessidade do envio de copia da autorizacao da aprovacao pelo comite de etica em pesquisa; e em quatro periodicos analisados nao foi identificada nenhuma exigencia sobre aspectos eticos. CONCLUSOES: Houve melhora em relacao a descricao do cumprimento dos aspectos eticos nos artigos. Sugere-se a padronizacao das orientacoes eticas relacionadas a pesquisa com seres humanos nos periodicos nacionais. Isso pode estimular o cumprimento dos pressupostos de documentos que regem a experimentacao humana.
BCI-FES With Multimodal Feedback for Motor Recovery Poststroke

An increasing number of research teams are investigating the efficacy of brain-computer interface (BCI)-mediated interventions for promoting motor recovery following stroke. A growing body of evidence suggests that of the various BCI designs, most effective are those that deliver functional electrical stimulation (FES) of upper extremity (UE) muscles contingent on movement intent. More specifically, BCI-FES interventions utilize algorithms that isolate motor signals—user-generated intent-to-move neural activity recorded from cerebral cortical motor areas—to drive electrical stimulation of individual muscles or muscle synergies. BCI-FES interventions aim to recover sensorimotor function of an impaired extremity by facilitating and/or inducing long-term motor learning-related neuroplastic changes in appropriate control circuitry. We developed a non-invasive, electroencephalogram (EEG)-based BCI-FES system that delivers closed-loop neural activity-triggered electrical stimulation of targeted distal muscles while providing the user with multimodal sensory feedback. This BCI-FES system consists of three components: (1) EEG acquisition and signal processing to extract real-time volitional and task-dependent neural command signals from cerebral cortical motor areas, (2) FES of muscles of the impaired hand contingent on the motor cortical neural command signals, and (3) multimodal sensory feedback associated with performance of the behavioral task, including visual information, linked activation of somatosensory afferents through intact sensorimotor circuits, and electro-tactile stimulation of the tongue. In this report, we describe device parameters and intervention protocols of our BCI-FES system which, combined with standard physical rehabilitation approaches, has proven efficacious in treating UE motor impairment in stroke survivors, regardless of level of impairment and chronicity.
Feeding Patterns of Three Widespread Carnivores—The Wolf, Snow Leopard, and Red Fox—in the Trans-Himalayan Landscape of India

The Trans-Himalayan landscape is an extreme cold desert with limited diversity and a low density of wild prey. The landscape has three widespread carnivores—the wolf Canis lupus chanco, snow leopard Panthera uncia, and red fox Vulpes vulpes—competing for similar prey. We studied predation patterns, dietary competition, and niche segregation of three sympatric carnivores in the Indian Trans-Himalayas. The Himalayan or wooly wolf is one of the oldest lineages and has adapted to extreme cold. We further studied the prey selection of the wolf in the high-altitude environment. We collected 1,600 carnivore scats (wolf = 542, snow leopard = 31, and red fox = 1,027), and additional data on 573 snow leopard scats from literature was used in the analyses. We found that livestock was a major contributor to the wolf (56.46%) and snow leopard diet (30.01%). The wolf consumed blue sheep (8.26%) and ibex (3.13%), whereas the snow leopard subsisted on blue sheep (30.79%) and ibex (17.15%), relatively more frequently. The red fox preyed upon small species like pika and marmots (18.85 %); however, livestock carrions (16.49%), fruits and seeds (15.05%), and human-derived material (11.89%) were also consumed frequently. The dietary niche of three carnivore species highly overlapped (Pianka's index = 0.503, simulated mean = 0.419, p = 0.15) due to livestock. The carnivores segregated their diet in prey items originating from the wild. We tested a relationship between carnivore diet variations and prey/predator functional traits using RLQ ordination. Predator morphology traits like body size, weight, and habitat preference significantly affected the prey selection (p < 0.05). The wolf and snow leopard avoided the competition through habitat selection, while the red fox coexisted by exploiting a broader niche. The wolf showed site-specific variation in prey preferences albeit no prey selection at the landscape level (G2 = 6.79, df = 12, p = 0.87). The wolf preferred wild prey over domestic species at the wild prey rich site. The carnivores in this pastoralist landscape have adapted to exploit livestock resources despite facing persecution. Therefore, managing livestock and simultaneously restoring wild prey is crucial for the conservation of the carnivore guild in the Trans-Himalayan ecosystem.
The “mid”-Cretaceous (Lower Cenomanian) Continental Vertebrates of Gara Samani, Algeria. Sedimentological Framework and Palaeodiversity

Excellent outcrops of the upper part of the “Continental Intercalaire” deposits occur in the Gara Samani area, southern Algeria. These strata are recognised herein as belonging to the Gara Samani Formation, which is composed of the Samani Vertebrate-rich Sand Member, the Samani Sandstone Member and the Méguidène Stratified Sand Member. The first two members are from a fluvial system and the last member corresponds to an aeolian (dune and interdune) system. They have preserved one of the most diverse continental vertebrate faunas of latest Albian–early Cenomanian age yet known from northern Africa. Most of the taxa identified there, cited for the first time for the “mid”-Cretaceous of Algeria, have not been analysed in detail so far; and many of them have never been figured. The faunal list of vertebrates from this locality was supplemented thanks to detailed analysis of new and relatively abundant finds. As a consequence, the Gara Samani vertebrate assemblage is recognised as composed of elasmobranchs (two Hybodontiformes, i.e., Tribodus sp. and Distobatidae indet.; and a Batoidea, Onchopristis numida), actinopterygians (Bawitius sp., Adrianaichthys sp., Obaichthys africanus, and Calamopleurus africanus), sarcopterygians (Mawsoniidae indet. and the Dipnoi, cf. Lavocatodus humei and Neoceratodus africanus), testudines (at least two Pelomedusoides, one of them being a representative of Araripemydidae), crocodyliforms (all remains being compatible with Neosuchia, represented at least by Elosuchus broinae), ornithocheirid pterosaurs, and non-avian dinosaurs (titanosauriform sauropods and at least two theropods, Spinosaurus aegyptiacus and Carcharodontosaurus saharicus). This fauna association displays close similarities to contemporaneous ones from North Africa, especially with that from the Kem Kem beds.
Microbial Genes of Agricultural Importance in Maize Rhizosphere Unveiled Through Shotgun Metagenomics

Genes possessed by microbes in the rhizosphere influence the metabolic activities that occur in this zone. Although the maize rhizosphere has been reported to be a hotspot of genes, these genes remain under-investigated. Hence, this study aimed at identifying putative microbial genes with plant beneficial functions in the underexplored maize rhizosphere microbiome using a shotgun metagenomics approach. Sampling was done at the flowering stage of the maize plants and both the rhizosphere and bulk soils were collected in triplicates. The metagenomes of the examined rhizosphere and bulk soils revealed genes involved in carbon fixation, nitrogen fixation, iron acquisition, heat and cold shock, phosphorus solubilization and utilization, sulfur cycling, and siderophore production. The beta diversity analysis showed significant variations (p < 0.05) in these genes across the examined rhizosphere and bulk soils which was further confirmed by the distinct separations between the samples as seen on the principal coordinate analysis (PCoA) plot. Contrarily, no significant difference was observed in diversity within the habitats (p = 0.99). The predominance of significant genes of agricultural importance such as the nifH, nifA, groES, and cspA in the rhizosphere metagenomes signifies that this region is endowed with beneficial organisms with potential for improving plant growth, mitigating stress, and reducing the effect of extreme temperatures, which can be optimized in developing biofertilizers. Therefore, the development of strategies that will help in cultivating these organisms, which are mostly unculturable, is encouraged. This would make them readily available for use as bio-inoculants and in other biotechnological applications.