bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted disruption of pi–pi stacking in Malaysian banana lectin reduces mitogenicity while preserving antiviral activity
Authors: Covés-Datson Evelyn M. , King Steven R. , Legendre Maureen , Swanson Michael D. , Gupta Auroni , Claes Sandra , Meagher Jennifer L. , Boonen Arnaud , Zhang Lihong , Kalveram Birte , Raglow Zoe , Freiberg Alexander N. , Prichard Mark , Stuckey Jeanne A. , Schols Dominique , Markovitz David M. 
Published: January 2021

AbstractLectins, carbohydrate-binding proteins, have been regarded as potential antiviral agents, as some can bind glycans on viral surface glycoproteins and inactivate their functions. However, clinical development of lectins has been stalled by the mitogenicity of many of these proteins, which is the ability to stimulate deleterious proliferation, especially of immune cells. We previously demonstrated that the mitogenic and antiviral activities of a lectin (banana lectin, BanLec) can be separated via a single amino acid mutation, histidine to threonine at position 84 (H84T), within the third Greek key. The resulting lectin, H84T BanLec, is virtually non-mitogenic but retains antiviral activity. Decreased mitogenicity was associated with disruption of pi–pi stacking between two aromatic amino acids. To examine whether we could provide further proof-of-principle of the ability to separate these two distinct lectin functions, we identified another lectin, Malaysian banana lectin (Malay BanLec), with similar structural features as BanLec, including pi–pi stacking, but with only 63% amino acid identity, and showed that it is both mitogenic and potently antiviral. We then engineered an F84T mutation expected to disrupt pi–pi stacking, analogous to H84T. As predicted, F84T Malay BanLec (F84T) was less mitogenic than wild type. However, F84T maintained strong antiviral activity and inhibited replication of HIV, Ebola, and other viruses. The F84T mutation disrupted pi–pi stacking without disrupting the overall lectin structure. These findings show that pi–pi stacking in the third Greek key is a conserved mitogenic motif in these two jacalin-related lectins BanLec and Malay BanLec, and further highlight the potential to rationally engineer antiviral lectins for therapeutic purposes.
Longitudinal saliva omics responses to immune perturbation: a case study
Authors: Mias George I. , Singh Vikas Vikram , Rogers Lavida R. K. , Xue Shuyue , Zheng Minzhang , Domanskyi Sergii , Kanada Masamitsu , Piermarocchi Carlo , He Jin 
Published: January 2021

AbstractSaliva omics has immense potential for non-invasive diagnostics, including monitoring very young or elderly populations, or individuals in remote locations. In this study, multiple saliva omics from an individual were monitored over three periods (100 timepoints) involving: (1) hourly sampling over 24 h without intervention, (2) hourly sampling over 24 h including immune system activation using the standard 23-valent pneumococcal polysaccharide vaccine, (3) daily sampling for 33 days profiling the post-vaccination response. At each timepoint total saliva transcriptome and proteome, and small RNA from salivary extracellular vesicles were profiled, including mRNA, miRNA, piRNA and bacterial RNA. The two 24-h periods were used in a paired analysis to remove daily variation and reveal vaccination responses. Over 18,000 omics longitudinal series had statistically significant temporal trends compared to a healthy baseline. Various immune response and regulation pathways were activated following vaccination, including interferon and cytokine signaling, and MHC antigen presentation. Immune response timeframes were concordant with innate and adaptive immunity development, and coincided with vaccination and reported fever. Overall, mRNA results appeared more specific and sensitive (timewise) to vaccination compared to other omics. The results suggest saliva omics can be consistently assessed for non-invasive personalized monitoring and immune response diagnostics.
Preliminary indoor evidences of microplastic effects on freshwater benthic macroinvertebrates
Authors: Gallitelli Luca , Cera Alessandra , Cesarini Giulia , Pietrelli Loris , Scalici Massimiliano 
Published: January 2021

AbstractPlastics are to date considered one of the main detrimental drivers for the health of aquatic ecosystems, both in marine and inland waters. Regarding the latter habitat, it seems surprising how the plastic effects on benthic invertebrates are neglected since macroinvertebrates have a long tradition in the water quality assessment activities. In this context, we propose timely indoor observations on the exposure of caddisfly Odontocerum albicorne and mayfly Ephemera danica to various microplastic polymers (ABS, PET, PP, PS, PVDF). Three different experimental designs were performed on caddisflies and mayflies by exposing their larvae to natural and microplastic substrates. Our findings highlighted how microplastics affected both caddisflies in rebuilding its own case (after having removed the natural one) and mayflies burrowing. Particularly, all caddisflies rebuilt cases using the microplastic polymers provided instead of natural items only. Moreover, we provide the first evidence that mayflies burrow mainly in microplastic substrates rather than in natural ones. Our research highlights that macroinvertebrate larvae would use naturally occurring microplastics and this could be of particular concern in freshwaters with high contamination by plastics. Indeed, larvae appear to not necessarily perceive microplastics as a direct stressor. Further studies ought to be conducted to understand the chronic perturbation on larvae fitness and for example, on drift behaviour. Also, further investigations are needed to understand the potentialities of using plastics by benthic macroinvertebrates.
Sequential dual-drug delivery of BMP-2 and alendronate from hydroxyapatite-collagen scaffolds for enhanced bone regeneration
Authors: Lee Dongtak , Wufuer Maierdanjiang , Kim Insu , Choi Tae Hyun , Kim Byung Jun , Jung Hyo Gi , Jeon Byoungjun , Lee Gyudo , Jeon Ok Hee , Chang Hak , Yoon Dae Sung 
Published: January 2021

AbstractThe clinical use of bioactive molecules in bone regeneration has been known to have side effects, which result from uncontrolled and supraphysiological doses. In this study, we demonstrated the synergistic effect of two bioactive molecules, bone morphogenic protein-2 (BMP-2) and alendronate (ALN), by releasing them in a sequential manner. Collagen-hydroxyapatite composite scaffolds functionalized using BMP-2 are loaded with biodegradable microspheres where ALN is encapsulated. The results indicate an initial release of BMP-2 for a few days, followed by the sequential release of ALN after two weeks. The composite scaffolds significantly increase osteogenic activity owing to the synergistic effect of BMP-2 and ALN. Enhanced bone regeneration was identified at eight weeks post-implantation in the rat 8-mm critical-sized defect. Our findings suggest that the sequential delivery of BMP-2 and ALN from the scaffolds results in a synergistic effect on bone regeneration, which is unprecedented. Therefore, such a system exhibits potential for the application of cell-free tissue engineering.
Chronic stress and corticosterone exacerbate alcohol-induced tissue injury in the gut-liver-brain axis
Authors: Shukla Pradeep K. , Meena Avtar S. , Dalal Kesha , Canelas Cherie , Samak Geetha , Pierre Joseph F. , Rao RadhaKrishna 
Published: January 2021

AbstractAlcohol use disorders are associated with altered stress responses, but the impact of stress or stress hormones on alcohol-associated tissue injury remain unknown. We evaluated the effects of chronic restraint stress on alcohol-induced gut barrier dysfunction and liver damage in mice. To determine whether corticosterone is the stress hormone associated with the stress-induced effects, we evaluated the effect of chronic corticosterone treatment on alcoholic tissue injury at the Gut-Liver-Brain (GLB) axis. Chronic restraint stress synergized alcohol-induced epithelial tight junction disruption and mucosal barrier dysfunction in the mouse intestine. These effects of stress on the gut were reproduced by corticosterone treatment. Corticosterone synergized alcohol-induced expression of inflammatory cytokines and chemokines in the colonic mucosa, and it potentiated the alcohol-induced endotoxemia and systemic inflammation. Corticosterone also potentiated alcohol-induced liver damage and neuroinflammation. Metagenomic analyses of 16S RNA from fecal samples indicated that corticosterone modulates alcohol-induced changes in the diversity and abundance of gut microbiota. In Caco-2 cell monolayers, corticosterone dose-dependently potentiated ethanol and acetaldehyde-induced tight junction disruption and barrier dysfunction. These data indicate that chronic stress and corticosterone exacerbate alcohol-induced mucosal barrier dysfunction, endotoxemia, and systemic alcohol responses. Corticosterone-mediated promotion of alcohol-induced intestinal epithelial barrier dysfunction and modulation of gut microbiota may play a crucial role in the mechanism of stress-induced promotion of alcohol-associated tissue injury at the GLB axis.
Transfer of oral bacteria to the fetus during late gestation
Authors: Yu Kevin , Rodriguez Michelle , Paul Zubin , Gordon Elizabeth , Gu Tongjun , Rice Kelly , Triplett Eric W. , Keller-Wood Maureen , Wood Charles E. 
Published: January 2021

AbstractThe fetus develops in a privileged environment, as the placenta serves as both a gateway for nutrients and a barrier for pathogen transfer to the fetus. Regardless, recent evidence suggests the presence of bacterial DNA in both placenta and fetus, and we have reported that DNA and protein from small numbers of bacteria gain access to the fetus from the maternal bloodstream. Other routes of environmental bacterial transfer from the mother to fetus remain unknown, as well as the physiological relevance of their presence. In these experiments, we examine multiple routes by which bacterial cellular components can enter the fetus and the fetal response to influx of bacterial DNA and protein. We inoculated maternal sheep with genetically-labeled S. aureus (Staphylococcus aureus) using three routes: intravenously, orally, and intra-vaginally. The inoculum did not produce sepsis or fever in the ewes, therefore mimicking incidental exposure to bacteria during pregnancy. 3–5 days post inoculation, we assessed the presence of bacterial components in the fetal tissues and analyzed fetal brain tissue to identify any alterations in gene expression. Our results demonstrate that components of bacteria that were introduced into the maternal mouth were detected in the fetal brain and that they stimulated changes in gene expression. We conclude that an oral route of transmission is relevant for transfer of bacterial cellular components to the fetus.
CircRNA_103765 acts as a proinflammatory factor via sponging miR-30 family in Crohn’s disease
Authors: Ye Yulan , Zhang Liping , Hu Tong , Yin Juan , Xu Lijuan , Pang Zhi , Chen Weichang 
Published: January 2021

AbstractIncreasing evidence suggests that circular RNAs (circRNAs) play critical roles in various pathophysiological activities. However, the role of circRNAs in inflammatory bowel disease (IBD) remains unclear. Here we report the potential roles of hsa_circRNA_103765 in regulating cell apoptosis induced by TNF-α in Crohn’s disease (CD). We identify that CircRNA_103765 expression was significantly upregulated in peripheral blood mononuclear cells (PBMCs) of patients with active IBD. A positive correlation with TNF-α significantly enhanced circRNA_103765 expression in CD, which was significantly reversed by anti-TNF-α mAb (infliximab) treatment. In vitro experiments showed that TNF-α could induce the expression of circRNA_103765, which was cell apoptosis dependent, while silencing of circRNA_103765 could protect human intestinal epithelial cells (IECs) from TNF-α-induced apoptosis. In addition, circRNA_103765 acted as a molecular sponge to adsorb the miR-30 family and impair the negative regulation of Delta-like ligand 4 (DLL4). Collectively, CircRNA_103765 is a novel important regulator of the pathogenesis of IBD via sponging miR-30 family-mediated DLL4 expression changes. Blockade of circRNA_103765 could serve as a novel approach for the treatment of IBD patients.
A deep learning framework combined with word embedding to identify DNA replication origins
Authors: Wu Feng , Yang Runtao , Zhang Chengjin , Zhang Lina 
Published: January 2021

AbstractThe DNA replication influences the inheritance of genetic information in the DNA life cycle. As the distribution of replication origins (ORIs) is the major determinant to precisely regulate the replication process, the correct identification of ORIs is significant in giving an insightful understanding of DNA replication mechanisms and the regulatory mechanisms of genetic expressions. For eukaryotes in particular, multiple ORIs exist in each of their gene sequences to complete the replication in a reasonable period of time. To simplify the identification process of eukaryote’s ORIs, most of existing methods are developed by traditional machine learning algorithms, and target to the gene sequences with a fixed length. Consequently, the identification results are not satisfying, i.e. there is still great room for improvement. To break through the limitations in previous studies, this paper develops sequence segmentation methods, and employs the word embedding technique, ‘Word2vec’, to convert gene sequences into word vectors, thereby grasping the inner correlations of gene sequences with different lengths. Then, a deep learning framework to perform the ORI identification task is constructed by a convolutional neural network with an embedding layer. On the basis of the analysis of similarity reduction dimensionality diagram, Word2vec can effectively transform the inner relationship among words into numerical feature. For four species in this study, the best models are obtained with the overall accuracy of 0.975, 0.765, 0.885, 0.967, the Matthew’s correlation coefficient of 0.940, 0.530, 0.771, 0.934, and the AUC of 0.975, 0.800, 0.888, 0.981, which indicate that the proposed predictor has a stable ability and provide a high confidence coefficient to classify both of ORIs and non-ORIs. Compared with state-of-the-art methods, the proposed predictor can achieve ORI identification with significant improvement. It is therefore reasonable to anticipate that the proposed method will make a useful high throughput tool for genome analysis.
Renewable energy from biomass surplus resource: potential of power generation from rice straw in Vietnam
Authors: Cuong Tran Thien , Le Hoang Anh , Khai Nguyen Manh , Hung Pham Anh , Linh Le Thuy , Thanh Nguyen Viet , Tri Ngo Dang , Huan Nguyen Xuan 
Published: January 2021

AbstractBiomass, one of the renewable resources, is expected to play an important role in the world’s energy future. In Asia, rice straw is an abundant agricultural surplus because rice is one of the leading staple food crops in the region. Often, rice straw is burned directly in the field via uncontrolled combustion methods that emit large amounts of short-lived air pollutants, greenhouse gases, and other pollutants. In Vietnam, the energy and environment protection sectors are facing great challenges because of rapid urbanisation and industrialisation. A national strategic choice is to exploit renewable energy, including biomass-derived energy, to achieve energy security and CO2 emission reduction. This study investigates the potential of rice straw as an energy source for power plants at a local scale in Vietnam using data derived from satellite Sentinel-1 images. The results show that Vietnam can produce 2,565 MW from rice straw, for which 24 out of 63 provinces have a potential capacity higher than 30 MW, and the Kien Giang province has the highest capacity (245 MW). The study also analyses limitations and obstacles overcoming which can promote the biomass energy sector in the country.
AITRL, an evolutionarily conserved plant specific transcription repressor regulates ABA response in Arabidopsis
Authors: Ma Yanxing , Tian Hainan , Lin Rao , Wang Wei , Zhang Na , Hussain Saddam , Yang Wenting , Zhang Chen , Zhou Ganghua , Wang Tianya , Wang Shucai 
Published: January 2021

AbstractExpression of stress response genes can be regulated by abscisic acid (ABA) dependent and ABA independent pathways. Osmotic stresses promote ABA accumulation, therefore inducing the expression of stress response genes via ABA signaling. Whereas cold and heat stresses induce the expression of stress response genes via ABA independent pathway. ABA induced transcription repressors (AITRs) are a family of novel transcription factors that play a role in ABA signaling, and Drought response gene (DRG) has previously been shown to play a role in regulating plant response to drought and freezing stresses. We report here the identification of DRG as a novel transcription factor and a regulator of ABA response in Arabidopsis. We found that the expression of DRG was induced by ABA treatment. Homologs searching identified AITR5 as the most closely related Arabidopsis protein to DRG, and homologs of DRG, including the AITR-like (AITRL) proteins in bryophytes and gymnosperms, are specifically presented in embryophytes. Therefore we renamed DRG as AITRL. Protoplast transfection assays show that AITRL functioned as a transcription repressor. In seed germination and seedling greening assays, the aitrl mutants showed an increased sensitivity to ABA. By using qRT-PCR, we show that ABA responses of some ABA signaling component genes including some PYR1-likes (PYLs), PROTEIN PHOSPHATASE 2Cs (PP2Cs) and SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASES 2s (SnRK2s) were reduced in the aitrl mutants. Taken together, our results suggest that AITRLs are a family of novel transcription repressors evolutionally conserved in embryophytes, and AITRL regulates ABA response in Arabidopsis by affecting ABA response of some ABA signaling component genes.
Investigation of the selective color-changing mechanism of Dynastes tityus beetle (Coleoptera: Scarabaeidae)
Authors: Sun Jiyu , Wu Wei , Tian Limei , Li Wei , Zhang Fang , Wang Yueming 
Published: January 2021

AbstractNot only does the Dynastes tityus beetle display a reversible color change controlled by differences in humidity, but also, the elytron scale can change color from yellow-green to deep-brown in specified shapes. The results obtained by focused ion beam-scanning electron microscopy (FIB-SEM), show that the epicuticle (EPI) is a permeable layer, and the exocuticle (EXO) is a three-dimensional photonic crystal. To investigate the mechanism of the reversible color change, experiments were conducted to determine the water contact angle, surface chemical composition, and optical reflectance, and the reflective spectrum was simulated. The water on the surface began to permeate into the elytron via the surface elemental composition and channels in the EPI. A structural unit (SU) in the EXO allows local color changes in varied shapes. The reflectance of both yellow-green and deep-brown elytra increases as the incidence angle increases from 0° to 60°. The microstructure and changes in the refractive index are the main factors that influence the process of reversible color change. According to the simulation, the lower reflectance causing the color change to deep-brown results from water infiltration, which increases light absorption. Meanwhile, the waxy layer has no effect on the reflection of light. This study lays the foundation to manufacture engineered photonic materials that undergo controllable changes in iridescent color.
Evaluation for pharmacokinetic exposure of cytotoxic anticancer drugs in elderly patients receiving (R-)CHOP therapy
Authors: Nakagawa Junichi , Takahata Takenori , Hyodo Rui , Chen Yu , Hasui Kengo , Sasaki Kota , Saito Kensuke , Ueno Kayo , Hosoi Kazuhiro , Terui Kazufumi , Sato Atsushi , Niioka Takenori 
Published: January 2021

Abstract(R-)miniCHOP therapy, which delivers approximately half-doses of the (R-)CHOP regimen, has shown efficacy and safety in patients who are more than 80 years old. This study aimed to compare the area under the plasma concentration–time curves (AUCs) of vincristine (VCR), doxorubicin (DXR), and cyclophosphamide (CPA) between (R-)CHOP and (R-)miniCHOP regimens. The AUCs were compared between patients aged 65–79 years receiving (R-)CHOP therapy and those aged 80 years and older receiving (R-)miniCHOP therapy. Age was not an independent variable for predicting the dose-adjusted AUCs (AUC/Ds) of cytotoxic anticancer drugs. The median AUCs of DXR and CPA were significantly smaller in the (R-)miniCHOP group than in the (R-)CHOP group (168.7 vs. 257.9 ng h/mL,P = 0.003, and 219.9 vs. 301.7 µg h/mL,P = 0.020, respectively). The median AUCs of VCR showed the same trend but the difference was not significant (24.83 vs. 34.85 ng h/mL,P = 0.135). It is possible that the AUCs of VCR, DXR, and CPA in patients aged 80 years and older receiving (R-)miniCHOP therapy may be lower than those in patients 65–79 years old receiving (R-)CHOP therapy.
Pseudogymnoascus destructans growth in wood, soil and guano substrates
Authors: Urbina Jenny , Chestnut Tara , Allen Jennifer M. , Levi Taal 
Published: January 2021

AbstractUnderstanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose syndrome (WNS) in many bat species and can persist in, and transmit from, the environment. We experimentally evaluated Pd growth on common substrates to better understand mechanisms of pathogen persistence, transmission and viability. We inoculated autoclaved guano, fresh guano, soil, and wood with live Pd fungus and evaluated (1) whether Pd grows or persists on each (2) if spores of the fungus remain viable 4 months after inoculation on each substrate, and (3) whether detection and quantitation of Pd on swabs is sensitive to the choice to two commonly used DNA extraction kits. After inoculating each substrate with 460,000 Pd spores, we collected ~ 0.20 g of guano and soil, and swabs from wood every 16 days for 64 days to quantify pathogen load through time using real-time qPCR. We detected Pd on all substrates over the course of the experiment. We observed a tenfold increase in pathogen loads on autoclaved guano and persistence but not growth in fresh guano. Pathogen loads increased marginally on wood but declined ~ 60-fold in soil. After four months, apparently viable spores were harvested from all substrates but germination did not occur from fresh guano. We additionally found that detection and quantitation of Pd from swabs of wood surfaces is sensitive to the DNA extraction method. The commonly used PrepMan Ultra Reagent protocol yielded substantially less DNA than did the QIAGEN DNeasy Blood and Tissue Kit. Notably the PrepMan Ultra Reagent failed to detect Pd in many wood swabs that were detected by QIAGEN and were subsequently found to contain substantial live conidia. Our results indicate that Pd can persist or even grow on common environmental substrates with results dependent on whether microbial competitors have been eliminated. Although we observed clear rapid declines in Pd on soil, viable spores were harvested four months after inoculation. These results suggest that environmental substrates and guano can in general serve as infectious environmental reservoirs due to long-term persistence, and even growth, of live Pd. This should inform management interventions to sanitize or modify structures to reduce transmission risk as well early detection rapid response (EDRR) planning.