bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antennal transcriptome sequencing and identification of candidate chemoreceptor proteins from an invasive pest, the American palm weevil, Rhynchophorus palmarum
Authors: Gonzalez Francisco , Johny Jibin , Walker William B. , Guan Qingtian , Mfarrej Sara , Jakše Jernej , Montagné Nicolas , Jacquin-Joly Emmanuelle , Alqarni Abdulaziz S. , Al-Saleh Mohammed Ali , Pain Arnab , Antony Binu 
Published: April 2021

AbstractFor decades, the American palm weevil (APW), Rhynchophorus palmarum, has been a threat to coconut and oil palm production in the Americas. It has recently spread towards North America, endangering ornamental palms, and the expanding date palm production. Its behavior presents several parallelisms with a closely related species, R. ferrugineus, the red palm weevil (RPW), which is the biggest threat to palms in Asia and Europe. For both species, semiochemicals have been used for management. However, their control is far from complete. We generated an adult antennal transcriptome from APW and annotated chemosensory related gene families to obtain a better understanding of these species' olfaction mechanism. We identified unigenes encoding 37 odorant-binding proteins (OBPs), ten chemosensory proteins (CSPs), four sensory neuron membrane proteins (SNMPs), seven gustatory receptors (GRs), 63 odorant receptors (ORs), and 28 ionotropic receptors (IRs). Noticeably, we find out the R. ferrugineus pheromone-binding protein and pheromone receptor orthologs from R. palmarum. Candidate genes identified and annotated in this study allow us to compare these palm weevils' chemosensory gene sets. Most importantly, this study provides the foundation for functional studies that could materialize as novel pest management strategies.
RETRACTED ARTICLE: GraphCovidNet: A graph neural network based model for detecting COVID-19 from CT scans and X-rays of chest
Authors: Saha Pritam , Mukherjee Debadyuti , Singh Pawan Kumar , Ahmadian Ali , Ferrara Massimiliano , Sarkar Ram 
Published: April 2021

AbstractCOVID-19, a viral infection originated from Wuhan, China has spread across the world and it has currently affected over 115 million people. Although vaccination process has already started, reaching sufficient availability will take time. Considering the impact of this widespread disease, many research attempts have been made by the computer scientists to screen the COVID-19 from Chest X-Rays (CXRs) or Computed Tomography (CT) scans. To this end, we have proposed GraphCovidNet, a Graph Isomorphic Network (GIN) based model which is used to detect COVID-19 from CT-scans and CXRs of the affected patients. Our proposed model only accepts input data in the form of graph as we follow a GIN based architecture. Initially, pre-processing is performed to convert an image data into an undirected graph to consider only the edges instead of the whole image. Our proposed GraphCovidNet model is evaluated on four standard datasets: SARS-COV-2 Ct-Scan dataset, COVID-CT dataset, combination of covid-chestxray-dataset, Chest X-Ray Images (Pneumonia) dataset and CMSC-678-ML-Project dataset. The model shows an impressive accuracy of 99% for all the datasets and its prediction capability becomes 100% accurate for the binary classification problem of detecting COVID-19 scans. Source code of this work can be found at GitHub-link.
Cyclin M2 (CNNM2) knockout mice show mild hypomagnesaemia and developmental defects
Authors: Franken Gijs A. C. , Seker Murat , Bos Caro , Siemons Laura A. H. , van der Eerden Bram C. J. , Christ Annabel , Hoenderop Joost G. J. , Bindels René J. M. , Müller Dominik , Breiderhoff Tilman , de Baaij Jeroen H. F. 
Published: April 2021

AbstractPatients with mutations in Cyclin M2 (CNNM2) suffer from hypomagnesaemia, seizures, and intellectual disability. Although the molecular function of CNNM2 is under debate, the protein is considered essential for renal Mg2+ reabsorption. Here, we used a Cnnm2 knock out mouse model, generated by CRISPR/Cas9 technology, to assess the role of CNNM2 in Mg2+ homeostasis. Breeding Cnnm2+/− mice resulted in a Mendelian distribution at embryonic day 18. Nevertheless, only four Cnnm2−/− pups were born alive. The Cnnm2−/− pups had a significantly lower serum Mg2+ concentration compared to wildtype littermates. Subsequently, adult Cnnm2+/− mice were fed with low, control, or high Mg2+ diets for two weeks. Adult Cnnm2+/− mice showed mild hypomagnesaemia compared to Cnnm2+/+ mice and increased serum Ca2+ levels, independent of dietary Mg2+ intake. Faecal analysis displayed increased Mg2+ and Ca2+ excretion in the Cnnm2+/− mice. Transcriptional profiling of Trpm6, Trpm7, and Slc41a1 in kidneys and colon did not reveal effects based on genotype. Microcomputed tomography analysis of the femurs demonstrated equal bone morphology and density. In conclusion, CNNM2 is vital for embryonic development and Mg2+ homeostasis. Our data suggest a previously undescribed role of CNNM2 in the intestine, which may contribute to the Mg2+ deficiency in mice and patients.
Cetacean distribution models based on visual and passive acoustic data
Authors: Frasier Kaitlin E. , Garrison Lance P. , Soldevilla Melissa S. , Wiggins Sean M. , Hildebrand John A. 
Published: April 2021

AbstractDistribution models are needed to understand spatiotemporal patterns in cetacean occurrence and to mitigate anthropogenic impacts. Shipboard line-transect visual surveys are the standard method for estimating abundance and describing the distributions of cetacean populations. Ship-board surveys provide high spatial resolution but lack temporal resolution and seasonal coverage. Stationary passive acoustic monitoring (PAM) employs acoustic sensors to sample point locations nearly continuously, providing high temporal resolution in local habitats across days, seasons and years. To evaluate whether cross-platform data synthesis can improve distribution predictions, models were developed for Cuvier’s beaked whales, sperm whales, and Risso’s dolphins in the oceanic Gulf of Mexico using two different methods: generalized additive models and neural networks. Neural networks were able to learn unspecified interactions between drivers. Models that incorporated PAM datasets out-performed models trained on visual data alone, and joint models performed best in two out of three cases. The modeling results suggest that, when taken together, multiple species distribution models using a variety of data types may support conservation and management of Gulf of Mexico cetacean populations by improving the understanding of temporal and spatial species distribution trends.
Interleukin-37 regulates innate immune signaling in human and mouse colonic organoids
Authors: Allaire Joannie M. , Poon Anita , Crowley Shauna M. , Han Xiao , Sharafian Zohreh , Moore Navjit , Stahl Martin , Bressler Brian , Lavoie Pascal M. , Jacobson Kevan , Li Xiaoxia , Vallance Bruce A. 
Published: April 2021

AbstractIntestinal epithelial cells (IEC) reside in close proximity to the gut microbiota and are hypo-responsive to bacterial products, likely to prevent maladaptive inflammatory responses. This is in part due to their strong expression of Single Ig IL-1 related receptor (SIGIRR), a negative regulator of interleukin (IL)-1 and toll-like receptor signaling. IL-37 is an anti-inflammatory cytokine that inhibits innate signaling in diverse cells by signaling through SIGIRR. Despite the strong expression of SIGIRR by IEC, few studies have examined whether IL-37 can suppress their innate immune signaling. We characterized innate immune responses of human and murine colonoids to bacteria (FliC, LPS) and host (IL-1β) products and the role of IL-37/SIGIRR in regulating these responses. We demonstrated that human colonoids responded only to FliC, but not to LPS or IL-1β. While colonoids derived from different donors displayed significant inter-individual variability in the magnitude of their innate responses to FliC stimulation, all colonoids released a variety of chemokines. Interestingly, IL-37 attenuated these responses through inhibition of p38 and NFκB signaling pathways. We determined that this suppression by IL-37 was SIGIRR dependent, in murine organoids. Along with species-specific differences in IEC innate responses, we show that IL-37 can promote IEC hypo-responsiveness by suppressing inflammatory signaling.
Spatiotemporal 7q11.23 protein network analysis implicates the role of DNA repair pathway during human brain development
Authors: Chen Liang , Wang Weidi , Cai Wenxiang , Song Weichen , Qian Wei , Lin Guan Ning 
Published: April 2021

AbstractRecurrent deletions and duplications of chromosome 7q11.23 copy number variants (CNVs) are associated with several psychiatric disorders. Although phenotypic abnormalities have been observed in patients, causal genes responsible for CNV-associated diagnoses and traits are still poorly understood. Furthermore, the targeted human brain regions, developmental stages, protein networks, and signaling pathways, influenced by this CNV remain unclear. Previous works showed GTF2I involved in Williams-Beuren syndrome, but pathways affected by GTF2I are indistinct. We first constructed dynamic spatiotemporal networks of 7q11.23 genes by combining data from the brain developmental transcriptome with physical interactions of 7q11.23 proteins. Topological changes were observed in protein–protein interaction (PPI) networks throughout different stages of brain development. Early and late fetal periods of development in the cortex, striatum, hippocampus, and amygdale were observed as the vital periods and regions for 7q11.23 CNV proteins. CNV proteins and their partners are significantly enriched in DNA repair pathway. As a driver gene, GTF2I interacted with PRKDC and BRCA1 to involve in DNA repair pathway. The physical interaction between GTF2I with PRKDC was confirmed experimentally by the liquid chromatography-tandem mass spectrometry (LC–MS/MS). We identified that early and late fetal periods are crucial for 7q11.23 genes to affect brain development. Our results implicate that 7q11.23 CNV genes converge on the DNA repair pathway to contribute to the pathogenesis of psychiatric diseases.
Activation of nuclear factor-kappa B by TNF promotes nucleus pulposus mineralization through inhibition of ANKH and ENPP1
Authors: Krzyzanowska Agata K. , Frawley Robert J. , Damle Sheela , Chen Tony , Otero Miguel , Cunningham Matthew E. 
Published: April 2021

AbstractSpontaneous mineralization of the nucleus pulposus (NP) has been observed in cases of intervertebral disc degeneration (IDD). Inflammatory cytokines have been implicated in mineralization of multiple tissues through their modulation of expression of factors that enable or inhibit mineralization, including TNAP, ANKH or ENPP1. This study examines the underlying factors leading to NP mineralization, focusing on the contribution of the inflammatory cytokine, TNF, to this pathologic event. We show that human and bovine primary NP cells express high levels of ANKH and ENPP1, and low or undetectable levels of TNAP. Bovine NPs transduced to express TNAP were capable of matrix mineralization, which was further enhanced by ANKH knockdown. TNF treatment or overexpression promoted a greater increase in mineralization of TNAP-expressing cells by downregulating the expression of ANKH and ENPP1 via NF-κB activation. The increased mineralization was accompanied by phenotypic changes that resemble chondrocyte hypertrophy, including increased RUNX2 and COL10A1 mRNA; mirroring the cellular alterations typical of samples from IDD patients. Disc organ explants injected with TNAP/TNF- or TNAP/shANKH-overexpressing cells showed increased mineral content inside the NP. Together, our results confirm interactions between TNF and downstream regulators of matrix mineralization in NP cells, providing evidence to suggest their participation in NP calcification during IDD.
Blastocyst cryopreservation and cryopreservation-warming transfer is an effective embryo transfer strategy for day 1 rescue intracytoplasmic sperm injection cycles
Authors: Li Ming , Li Qin , Wang Ying , Huang Jin , Liu Ping 
Published: April 2021

AbstractThis was a retrospective analysis of a total of 625 r-ICSI cycles using freeze-all-embryos and embryo transfers (ET) in subsequent cryopreservation-warming cycles to determine the effect of the ET method for day 1 rescue intracytoplasmic sperm injection cycles (r-ICSI). Two methods were used: in method 1, cleavage-stage embryos were frozen and were directly transferred in a subsequent cryopreservation-warming cycle (r-ICSI frozen cleavage), and 144 cleavage-stage ETs occurred. Similarly, in method 2, there were 188 blastocyst-stage ETs (r-ICSI frozen blast) performed. The live birth rate (LBR) for r-ICSI frozen blast was better than that for r-ICSI frozen cleavage in calculation of ET cycles (19.44% vs. 37.77%) and also remained better after the use of logistic regression analysis (OR = 2.721, 95% CI 1.604–4.616). Conservative cumulative LBR were compared between r-ICSI frozen cleavage and r-ICSI frozen blast with regard to oocyte retrieval cycles (17.39% vs. 15.30%). The same results were obtained for conservative cumulative LBR after logistic regression analysis (OR = 0.925, 95% CI 0.557–1.535). The results of this study confirmed that it was valuable to perform r-ICSI if using freeze-all-embryos. Further, r-ICSI embryos were cultured to blastocyst stage, cryopreserved, and used in subsequent cryopreservation-warming cycles, which was an effective embryo transfer strategy and obtained satisfactory results.
Joint improvements of radar/infrared stealth for exhaust system of unmanned aircraft based on sorting factor Pareto solution
Authors: Zhou Ze Yang , Huang Jun 
Published: April 2021

AbstractIn order to reduce the radar cross section (RCS) of the unmanned aircraft while suppressing its infrared signature, a comprehensive design method (CDM) based on sorting factor Pareto solution is presented. The physical optics and physical diffraction theory are used to evaluate the electromagnetic scattering characteristics of the aircraft, and the Monte Carlo and ray tracing method are used to evaluate the infrared radiation intensity of the exhaust system. CDM is used to evaluate and screen each individual in each offspring, and the design parameters and sub-models of the aircraft exhaust system are continuously improved. The results show that the exhaust port model, lower baffle and nozzle height are the main factors affecting the RCS indicators, nozzle stages, exhaust port model, lower baffle and outer width make the main contribution to infrared radiation suppression. The presented CDM is efficient and effective in enhancing the radar/infrared integrated stealth performance of the aircraft.
One-pot synthesis of zinc oxide nanoparticles via chemical precipitation for bromophenol blue adsorption and the antifungal activity against filamentous fungi
Authors: Akpomie Kovo G. , Ghosh Soumya , Gryzenhout Marieka , Conradie Jeanet 
Published: April 2021

AbstractIn this research, zinc oxide nanoparticles (ZnONPs) were prepared via a facile one-pot chemical precipitation approach and applied in the adsorption of bromophenol blue (BRB) and as antifungal agents against the filamentous fungi and plant pathogens; Alternaria alternata CGJM3078, Alternaria alternata CGJM3006 and Fusarium verticilliodes CGJM3823. The ZnONPs were characterized by the UV–Vis, FTIR, XRD, TGA, BET, SEM, TEM, and EDX techniques, which showed efficient synthesis. The characteristics ZnO UV–Vis absorption band was observed at 375 nm, while the XRD showed an average ZnONPs crystalline size of 47.2 nm. The SEM and TEM images showed an irregular shaped and aggregated porous structure of 65.3 nm average-sized ZnONPs. The TGA showed 22.9% weight loss at 800 °C indicating the high thermal stability of ZnONPs, while BET analysis revealed a surface area, pore volume and pore diameter of 9.259 m2/g, 0.03745 cm3/g and 9.87 nm respectively. The Freundlich, pseudo-second-order, and intra-particle diffusion models showed R2 > 0.9494 and SSE < 0.7412, thus, exhibited the best fit to the isotherm and kinetics models. Thermodynamics revealed feasible, endothermic, random, and spontaneous adsorption of BRB onto the synthesized ZnONPs. The antifungal assay conducted depicts strong antifungal activities against all three tested fungi. Noticeably, ZnONPs (0.002–5 mg/mL) showed maximum activities with the largest zone of inhibition against A. alternata CGJM 3006 from 25.09 to 36.28 mm. This was followed by the strain F. verticilliodes CGJM 3823 (range from 23.77 to 34.77 mm) > A. alternata CGJM3078 (range from 22.73 to 30.63 mm) in comparison to Bleach 5% (positive control). Additionally a model was proposed based on the possible underlying mechanisms for the antifungal effect. This research demonstrated the potent use of ZnONPs for the adsorption of BRB and as effective antifungal agents.
HIV clinical stages and lower extremity arterial disease among HIV infected outpatients in Burundi
Authors: Desormais Ileana , Harimenshi Deo , Niyongabo Théodore , Lacroix Philippe , Aboyans Victor , Preux Pierre Marie 
Published: April 2021

AbstractChronic disease of people living with human immunodeficiency virus (HIV) infection are now approaching those of the general population. Previous, in vitro studies shown that HIV causes arterial injuries resulting in inflammation and atherosclerosis but direct relationship between HIV infection clinical stages and lower extremity arterial disease (LEAD) remain controversial. No study assessed, with an accurate method, both the prevalence of LEAD and the influence of HIV severity on LEAD in HIV outpatients in Central Africa.
A cross-sectional study was conducted among 300 HIV-infected outpatients, aged ≥ 40 years in Bujumbura, Burundi. All patients underwent ankle-brachial index (ABI) measurement and LEAD was diagnosed by ABI ≤ 0.9. The prevalence of LEAD was 17.3% (CI 95% 13.2–22.1). The mean age was 49.6 ± 7.1 years. On multivariable analysis, factors associated with LEAD were hypertension (OR = 2.42; 95% CI 1.10–5.80), and stage IV HIV clinical infection (OR = 4.92, 95% CI 1.19–20.36). This is the first study performed on a large HIV population in Central Africa, reporting high LEAD prevalence. It underlines the influence of HIV infection on peripheral atherosclerosis at latest clinical stages and the need for LEAD screening in HIV-infected patients.
Behavioral responses of the European mink in the face of different threats: conspecific competitors, predators, and anthropic disturbances
Authors: Ortiz-Jiménez Lorena , Iglesias-Merchan Carlos , Barja Isabel 
Published: April 2021

AbstractPrey species assess the risk of threat using visual, olfactory, and acoustic cues from their habitat. Thus, they modify their behavior in order to avoid encounters with competitors, predators, and human disturbances that endanger their fitness. European mink (Mustela lutreola) is a critically endangered species that can be preyed upon by larger carnivores and displaced by dominant conspecifics to areas of lower quality, e.g., near to more anthropized localities which may be noisier. In this study, the behavioral responses of 24 European mink were evaluated by conducting an experiment in which the presence of a conspecific competitor was simulated with a visual cue (mirror) and the presence of predators (terrestrial and aerial) with odorous cues. Additionally, they were also exposed to potential sources of anthropic disturbance with acoustic cues (road traffic noise and human voices). Our results showed that European mink were hidden for longer periods of time due to the presence of conspecifics and being exposed to the fecal odors of a terrestrial predator such as dog, but especially when they were exposed to anthropic noises. In the presence of a conspecific, the females and the subadults were the ones who remained hidden for the longest time. As well, they were hidden for longer periods of time due to the presence of conspecifics but in combination with dog feces and anthropic sounds did not induce variations in the response, as both by themselves already triggered an increase in the time they spent hiding. The vigilance model showed the effects of the same factors as the hiding model, but with antagonistic effects in the case of vigilance time which decreased during anthropic noises exposition. Finally, we want to highlight that European mink showed an innate response favorable to all three types of threats, but attention should be focused on human disturbances—as they trigger the most extreme responses—which may affect the rate of survival of this threatened species.
Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
Authors: Parras-Moltó Marcos , Aguirre de Cárcer Daniel 
Published: April 2021

AbstractIn this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data (https://git.io/Jec5U).
Evidence of a hormonal reshuffle in the cecal metabolome fingerprint of a strain of rats resistant to decompression sickness
Authors: Vallee Nicolas , Dugrenot Emmanuel , Desruelle Anne-Virginie , Tardivel Catherine , Martin Jean-Charles , Guernec Anthony , Boussuges Alain , Rives Sarah , Risso Jean-Jacques , Guerrero François 
Published: April 2021

AbstractOn one side, decompression sickness (DCS) with neurological disorders lead to a reshuffle of the fecal metabolome from rat caecum. On the other side, there is high inter-individual variability in terms of occurrence of DCS. One could wonder whether the fecal metabolome could be linked to the DCS-susceptibility. We decided to study male and female rats selected for their resistance to decompression sickness, and we hypothesize a strong impregnation concerning the fecal metabolome. The aim is to verify whether the rats resistant to the accident have a fecal metabolomic signature different from the stem generations sensitive to DCS. 39 DCS-resistant animals (21 females and 18 males), aged 14 weeks, were compared to 18 age-matched standard Wistar rats (10 females and 8 males), i.e., the same as those we used for the founding stock. Conventional and ChemRICH approaches helped the metabolomic interpretation of the 226 chemical compounds analyzed in the cecal content. Statistical analysis shows a panel of 81 compounds whose expression had changed following the selection of rats based on their resistance to DCS. 63 compounds are sex related. 39 are in common. This study shows the spectral fingerprint of the fecal metabolome from the caecum of a strain of rats resistant to decompression sickness. This study also confirms a difference linked to sex in the metabolome of non-selected rats, which disappear with selective breeding. Results suggest hormonal and energetic reshuffle, including steroids sugars or antibiotic compounds, whether in the host or in the microbial community.