bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombinant HA-based vaccine outperforms split and subunit vaccines in elicitation of influenza-specific CD4 T cells and CD4 T cell-dependent antibody responses in humans
Authors: Richards K. A. , Moritzky S. , Shannon I. , Fitzgerald T. , Yang H. , Branche A. , Topham D. J. , Treanor J. J. , Nayak J. , Sant Andrea J. 
Published: August 2020

AbstractAlthough traditional egg-based inactivated influenza vaccines can protect against infection, there have been significant efforts to develop improved formats to overcome disadvantages of this platform. Here, we have assessed human CD4 T cell responses to a traditional egg-based influenza vaccine with recently available cell-derived vaccines and recombinant baculovirus-derived vaccines. Adults were administered either egg-derived Fluzone®, mammalian cell-derived Flucelvax® or recombinant HA (Flublok®). CD4 T cell responses to each HA protein were assessed by cytokine EliSpot and intracellular staining assays. The specificity and magnitude of antibody responses were quantified by ELISA and HAI assays. By all criteria, Flublok vaccine exhibited superior performance in eliciting both CD4 T cell responses and HA-specific antibody responses, whether measured by mean response magnitude or percent of responders. Although the mechanism(s) underlying this advantage is not yet clear, it is likely that both qualitative and quantitative features of the vaccines impact the response.
Nanoscale mechanisms in age-related hip-fractures
Authors: Ma Shaocheng , Goh En Lin , Tay Tabitha , Wiles Crispin C. , Boughton Oliver , Churchwell John H. , Wu Yong , Karunaratne Angelo , Bhattacharya Rajarshi , Terrill Nick , Cobb Justin P. , Hansen Ulrich , Abel Richard L. 
Published: August 2020

AbstractNanoscale mineralized collagen fibrils may be important determinants of whole-bone mechanical properties and contribute to the risk of age-related fractures. In a cross-sectional study nano- and tissue-level mechanics were compared across trabecular sections from the proximal femora of three groups (n = 10 each): ageing non-fractured donors (Controls); untreated fracture patients (Fx-Untreated); bisphosphonate-treated fracture patients (Fx-BisTreated). Collagen fibril, mineral and tissue mechanics were measured using synchrotron X-Ray diffraction of bone sections under load. Mechanical data were compared across groups, and tissue-level data were regressed against nano. Compared to controls fracture patients exhibited significantly lower critical tissue strain, max strain and normalized strength, with lower peak fibril and mineral strain. Bisphosphonate-treated exhibited the lowest properties. In all three groups, peak mineral strain coincided with maximum tissue strength (i.e. ultimate stress), whilst peak fibril strain occurred afterwards (i.e. higher tissue strain). Tissue strain and strength were positively and strongly correlated with peak fibril and mineral strains. Age-related fractures were associated with lower peak fibril and mineral strain irrespective of treatment. Indicating earlier mineral disengagement and the subsequent onset of fibril sliding is one of the key mechanisms leading to fracture. Treatments for fragility should target collagen-mineral interactions to restore nano-scale strain to that of healthy bone.
Adipose-derived mesenchymal stem cells promote the malignant phenotype of cervical cancer
Authors: Castro-Oropeza Rosario , Vazquez-Santillan Karla , Díaz-Gastelum Claudia , Melendez-Zajgla Jorge , Zampedri Cecilia , Ferat-Osorio Eduardo , Rodríguez-González Arturo , Arriaga-Pizano Lourdes , Maldonado Vilma 
Published: August 2020

AbstractEpidemiological studies indicate that obesity negatively affects the progression and treatment of cervical-uterine cancer. Recent evidence shows that a subpopulation of adipose-derived stem cells can alter cancer properties. In the present project, we described for the first time the impact of adipose-derived stem cells over the malignant behavior of cervical cancer cells. The transcriptome of cancer cells cultured in the presence of stem cells was analyzed using RNA-seq. Changes in gene expression were validated using digital-PCR. Bioinformatics tools were used to identify the main transduction pathways disrupted in cancer cells due to the presence of stem cells. In vitro and in vivo assays were conducted to validate cellular and molecular processes altered in cervical cancer cells owing to stem cells. Our results show that the expression of 95 RNAs was altered in cancer cells as a result of adipose-derived stem cells. Experimental assays indicate that stem cells provoke an increment in migration, invasion, angiogenesis, and tumorigenesis of cancer cells; however, no alterations were found in proliferation. Bioinformatics and experimental analyses demonstrated that the NF-kappa B signaling pathway is enriched in cancer cells due to the influence of adipose-derived stem cells. Interestingly, the tumor cells shift their epithelial to a mesenchymal morphology, which was reflected by the increased expression of specific mesenchymal markers. In addition, stem cells also promote a stemness phenotype in the cervical cancer cells. In conclusion, our results suggest that adipose-derived stem cells induce cervical cancer cells to acquire malignant features where NF-kappa B plays a key role.
Newly identified Gon4l/Udu-interacting proteins implicate novel functions
Authors: Tsai Su-Mei , Chu Kuo-Chang , Jiang Yun-Jin 
Published: August 2020

AbstractMutations of the Gon4l/udu gene in different organisms give rise to diverse phenotypes. Although the effects of Gon4l/Udu in transcriptional regulation have been demonstrated, they cannot solely explain the observed characteristics among species. To further understand the function of Gon4l/Udu, we used yeast two-hybrid (Y2H) screening to identify interacting proteins in zebrafish and mouse systems, confirmed the interactions by co-immunoprecipitation assay, and found four novel Gon4l-interacting proteins: BRCA1 associated protein-1 (Bap1), DNA methyltransferase 1 (Dnmt1), Tho complex 1 (Thoc1, also known as Tho1 or HPR1), and Cryptochrome circadian regulator 3a (Cry3a). Furthermore, all known Gon4l/Udu-interacting proteins—as found in this study, in previous reports, and in online resources—were investigated by Phenotype Enrichment Analysis. The most enriched phenotypes identified include increased embryonic tissue cell apoptosis, embryonic lethality, increased T cell derived lymphoma incidence, decreased cell proliferation, chromosome instability, and abnormal dopamine level, characteristics that largely resemble those observed in reported Gon4l/udu mutant animals. Similar to the expression pattern of udu, those of bap1, dnmt1, thoc1, and cry3a are also found in the brain region and other tissues. Thus, these findings indicate novel mechanisms of Gon4l/Udu in regulating CpG methylation, histone expression/modification, DNA repair/genomic stability, and RNA binding/processing/export.
Novel research on nanocellulose production by a marine Bacillus velezensis strain SMR: a comparative study
Authors: Abouelkheir Samia S. , Kamara Marwa S. , Atia Salma M. , Amer Sara A. , Youssef Marina I. , Abdelkawy Rana S. , Khattab Sherine N. , Sabry Soraya A. 
Published: August 2020

AbstractBacterial nanocellulose (BNC) is a nanofibrillar polymer that possesses unique characteristics such as high chemical purity, mechanical strength, flexibility, and absorbency. In addition, different bacterial strains can form nanocellulose (NC) in multiple shapes and sizes. This study describes the first report of a marine Bacillus strain that is able to synthesize NC. The strain identified as B. velezensis SMR based on 16S rDNA sequencing, produced highly structured NC, as confirmed by X-ray diffraction (XRD) and Scanning Electron Microscopic Analysis (SEM). In Hestrin-Schramm (HS) medium, B. velezensis SMR produced twice the quantity of BNC in comparison to the reference strain, G. xylinus ATCC 10245. The ability of B. velezensis SMR to produce NC using different industrial waste materials as growth media was tested. Growth in Ulva seaweed extract supported a 2.5-fold increase of NC production by B. velezensis SMR and a threefold increase in NC production by G. xylinus ATCC 10245. As proof of principle for the usability of NC from B. velezensis SMR, we successfully fabricated a BNC-based polyvinyl alcohol hydrogel (BNC-PVA) system, a promising material used in different fields of application such as medicine, food, and agriculture.
Cold damage from wax deposition in a shallow, low-temperature, and high-wax reservoir in Changchunling Oilfield
Authors: Xie Jun , Hu Xiao , Liang Hui-zhen , Wang Meng-qi , Guo Fa-jun , Zhang Shu-juan , Cai Wu-chao , Wang Rui 
Published: August 2020

AbstractWax deposition is an important factor that influences oil production for high-wax crude oilfield. There are few studies on the formation damage by wax deposition, especially cold damage to the shallow low-temperature reservoir. With laboratory tests conducted on reservoir oil and cores of Changchunling Oilfield, this study aims to experimentally investigate the influence of temperature variations on characteristics of oil–water percolation and cold damage mechanisms, as well as the relative permeability of high-wax reservoirs. Experimental results show that seepage flow of high-wax crude is significantly sensitive to temperature-wax deposition evidently increases, whereas the cold damage such as the pore-throat radius and relative permeability sharply decrease with the decline in formation temperature. The research results can be applied to enhance oil recovery of high-viscosity or high-wax oilfields.
Assessing haemorrhage-critical values of cerebral blood flow by modelling biomechanical stresses on capillaries in the immature brain
Authors: Sidorenko Irina , Turova Varvara , Botkin Nikolai , Kovtanyuk Andrey , Eckardt Laura , Alves-Pinto Ana , Felderhoff-Müser Ursula , Rieger-Fackeldey Esther , Lampe Renée 
Published: August 2020

AbstractThe development of intraventricular haemorrhages (IVH) in preterm newborns is triggered by a disruption of the vessels responsible for cerebral microcirculation. Analysis of the stresses exerted on vessel walls enables the identification of the critical values of cerebral blood flow (CBF) associated with the development of IVH in preterm infants. The purpose of the present study is the estimation of these critical CBF values using the biomechanical stresses obtained by the finite element modelling of immature brain capillaries. The properties of the endothelial cells and basement membranes employed were selected on the basis of published nanoindentation measurements using atomic force microscopes. The forces acting on individual capillaries were derived with a mathematical model that accounts for the peculiarities of microvascularity in the immature brain. Calculations were based on clinical measurements obtained from 254 preterm infants with the gestational age ranging from 23 to 30 weeks, with and without diagnosis of IVH. No distinction between the affected and control groups with the gestational age of 23 to 26 weeks was possible. For infants with the gestational age of 27 to 30 weeks, the CBF value of 17.03 ml/100 g/min was determined as the critical upper value, above which the likelihood of IVH increases.
Ik2/TBK1 and Hook/Dynein, an adaptor complex for early endosome transport, are genetic modifiers of FTD-associated mutant CHMP2B toxicity in Drosophila
Authors: Lu Yubing , West Ryan J. H. , Pons Marine , Sweeney Sean T. , Gao Fen-Biao 
Published: August 2020

AbstractMutations in CHMP2B, encoding a protein in the endosomal sorting complexes required for transport (ESCRT) machinery, causes frontotemporal dementia linked to chromosome 3 (FTD3). FTD, the second most common form of pre-senile dementia, can also be caused by genetic mutations in other genes, including TANK-binding kinase 1 (TBK1). How FTD-causing disease genes interact is largely unknown. We found that partial loss function of Ik2, the fly homologue of TBK1 also known as I-kappaB kinase ε (IKKε), enhanced the toxicity of mutant CHMP2B in the fly eye and that Ik2 overexpression suppressed the effect of mutant CHMP2B in neurons. Partial loss of function of Spn-F, a downstream phosphorylation target of Ik2, greatly enhanced the mutant CHMP2B phenotype. An interactome analysis to understand cellular processes regulated by Spn-F identified a network of interacting proteins including Spn-F, Ik2, dynein light chain, and Hook, an adaptor protein in early endosome transport. Partial loss of function of dynein light chain or Hook also enhanced mutant CHMP2B toxicity. These findings identify several evolutionarily conserved genes, including ik2/TBK1, cut up (encoding dynein light chain) and hook, as genetic modifiers of FTD3-associated mutant CHMP2B toxicity and implicate early endosome transport as a potential contributing pathway in FTD.
The human papillomavirus E6 protein targets apoptosis-inducing factor (AIF) for degradation
Authors: Shimada Masaru , Yamashita Akio , Saito Manami , Ichino Motohide , Kinjo Takao , Mizuki Nobuhisa , Klinman Dennis M. , Okuda Kenji 
Published: August 2020

AbstractOncoprotein E6 of high-risk human papillomavirus (HPV) plays a critical role in inducing cell immortalization and malignancy. E6 downregulates caspase-dependent pathway through the degradation of p53. However, the effect of HPV E6 on other pathways is still under investigation. In the present study, we found that HPV E6 directly binds to all three forms (precursor, mature, and apoptotic) of apoptosis-inducing factor (AIF) and co-localizes with apoptotic AIF. This binding induced MG132-sensitive reduction of AIF expression in the presence of E6 derived from HPV16 (16E6), a cancer-causing type of HPV. Conversely, E6 derived from a non-cancer-causing type of HPV, HPV6 (6E6), did not reduce the levels of AIF despite its interaction with AIF. Flow cytometric analysis revealed that 16E6, but not 6E6, suppressed apoptotic AIF-induced chromatin degradation (an indicator of caspase-independent apoptosis) and staurosporine (STS, a protein kinase inhibitor)-induced apoptosis. AIF knockdown reduced STS-induced apoptosis in both of 16E6-expressing and 6E6-expressing cells; however, the reduction in 16E6-expressing cells was lower than that in 6E6-expressing cells. These findings indicate that 16E6, but not 6E6, blocks AIF-mediated apoptosis, and that AIF may represent a novel therapeutic target for HPV-induced cervical cancer.
Intraoperative high-resolution esophageal manometry during peroral endoscopic myotomy
Authors: Barret Maximilien , Guillaumot Marie-Anne , Leandri Chloé , Leblanc Sarah , Coriat Romain , Belle Arthur , Chaussade Stanislas 
Published: August 2020

AbstractPeroral endoscopic myotomy is an accepted treatment of achalasia. Some of the treatment failures can be attributable to an insufficient length of the myotomy on the gastric side, because of a more technically challenging submucosal dissection. We assessed the feasibility and the impact of an intraoperative esophageal manometry during the peroral endoscopic myotomy procedure. A high-resolution manometry catheter was introduced through the nostril before the endoscope, and left in place during the peroral endoscopic myotomy procedure. The lower esophageal sphincter pressure was recorded throughout the peroral endoscopic myotomy. The myotomy was extended on the gastric side until the lower esophageal sphincter pressure dropped below 10 mmHg. We included 10 patients (mean age = 55 years old, 3 men) treated by peroral endoscopic myotomy for type I (3/10), type II (3/10), type III achalasia (3/10) or esophagogastric junction outflow obstruction (1/10). Manometric recording was possible in all patients. The median (IQR) lower esophageal sphincter resting pressure was 23 (17–37) mmHg before myotomy, 15 (13–19) mmHg at the end of the tunnel, and 7 (6–11) mmHg at the end of the myotomy. In 4 patients out of 10, the myotomy was extended on the base of the intraoperative manometry findings. High-resolution esophageal manometry is feasible during the peroral endoscopic myotomy procedure, and leads to increase the length of the gastric myotomy in 4 out of 10 patients. However, the cumbersome nature of intraoperative high-resolution manometry during peroral endoscopic myotomy and the high frequency of gastro-esophageal reflux disease after extended gastric myotomy suggest to limit this technique to selected patients refractory to a first myotomy.
On the instability of the giant direct magnetocaloric effect in CoMn0.915Fe0.085Ge at. % metamagnetic compounds
Authors: Bruno N. M. , Yuce S. 
Published: August 2020

AbstractThe giant magnetocaloric effect was quantified in CoMn1-xFexGe (x = 0.085–0.12) nom. at. % polycrystals across the high temperature hexagonal (P63/mmc) to low temperature orthorhombic (Pnma) phase transition via differential scanning calorimetry (DSC) and multiple (thermo) magnetization measurements. It was found that increasing Fe content led to the decrease of both the martensitic transformation temperature and entropy change ($$\Delta S$$

Δ
S

) at the point of the phase transition. Moreover, first-time magnetocaloric measurements resulted in irreproducible entropy change versus temperature diagrams, which was attributed to the release of internal pressure in bulk samples that disintegrated into powder upon transformation. CoMn1-xFexGe demonstrated larger magnetic field-induced entropy changes and giant magnetocaloric effect (MCE) compared to other CoMnGe alloys doped with Si, Sn, Ti, and Ga. However, the observed brittleness and apparent change in volume at the magnetic transition was posited to influence the material’s potential for regenerative applications.
Downscaling global ocean climate models improves estimates of exposure regimes in coastal environments
Authors: Fagundes Matheus , Litvin S. Y. , Micheli F. , De Leo G. , Boch C. A. , Barry J. P. , Omidvar S. , Woodson C. B. 
Published: August 2020

AbstractClimate change is expected to warm, deoxygenate, and acidify ocean waters. Global climate models (GCMs) predict future conditions at large spatial scales, and these predictions are then often used to parameterize laboratory experiments designed to assess biological and ecological responses to future change. However, nearshore ecosystems are affected by a range of physical processes such as tides, local winds, and surface and internal waves, causing local variability in conditions that often exceeds global climate models. Predictions of future climatic conditions at local scales, the most relevant to ecological responses, are largely lacking. To fill this critical gap, we developed a 2D implementation of the Regional Ocean Modeling System (ROMS) to downscale global climate predictions across all Representative Concentration Pathway (RCP) scenarios to smaller spatial scales, in this case the scale of a temperate reef in the northeastern Pacific. To assess the potential biological impacts of local climate variability, we then used the results from different climate scenarios to estimate how climate change may affect the survival, growth, and fertilization of a representative marine benthic invertebrate, the red abalone Haliotis rufescens, to a highly varying multi-stressor environment. We found that high frequency variability in temperature, dissolved oxygen (DO), and pH increases as pCO2 increases in the atmosphere. Extreme temperature and pH conditions are generally not expected until RCP 4.5 or greater, while frequent exposure to low DO is already occurring. In the nearshore environment simulation, strong RCP scenarios can affect red abalone growth as well as reduce fertilization during extreme conditions when compared to global scale simulations.
Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus
Authors: Yuan Hao , Zhang Xue , Zhao Lina , Chang Huihui , Yang Chao , Qiu Zhongying , Huang Yuan 
Published: August 2020

AbstractAcrididae are diverse in size, body shape, behavior, ecology and life history; widely distributed; easy to collect; and important to agriculture. They represent promising model candidates for functional genomics, but their extremely large genomes have hindered this research; establishing a reference transcriptome for a species is the primary means of obtaining genetic information. Here, two Acrididae species, Gomphocerus licenti and Mongolotettix japonicus, were selected for full-length (FL) PacBio transcriptome sequencing. For G. licenti and M. japonicus, respectively, 590,112 and 566,165 circular consensus sequences (CCS) were generated, which identified 458,131 and 428,979 full-length nonchimeric (FLNC) reads. After isoform-level clustering, next-generation sequencing (NGS) short sequences were used for error correction, and remove redundant sequences with CD-HIT, 17,970 and 16,766 unigenes were generated for G. licenti and M. japonicus. In addition, we obtained 17,495 and 16,373 coding sequences, 1,082 and 813 transcription factors, 11,840 and 10,814 simple sequence repeats, and 905 and 706 long noncoding RNAs by analyzing the transcriptomes of G. licenti and M. japonicus, respectively, and 15,803 and 14,846 unigenes were annotated in eight functional databases. This is the first study to sequence FL transcriptomes of G. licenti and M. japonicus, providing valuable genetic resources for further functional genomics research.
Dynamics of the ACE2–SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms
Authors: Ali Amanat , Vijayan Ranjit 
Published: August 2020

AbstractThe coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major public health concern. A handful of static structures now provide molecular insights into how SARS-CoV-2 and SARS-CoV interact with its host target, which is the angiotensin converting enzyme 2 (ACE2). Molecular recognition, binding and function are dynamic processes. To evaluate this, multiple 500 ns or 1 μs all-atom molecular dynamics simulations were performed to better understand the structural stability and interfacial interactions between the receptor binding domain of the spike (S) protein of SARS-CoV-2 and SARS-CoV bound to ACE2. Several contacts were observed to form, break and reform in the interface during the simulations. Our results indicate that SARS-CoV-2 and SARS-CoV utilizes unique strategies to achieve stable binding to ACE2. Several differences were observed between the residues of SARS-CoV-2 and SARS-CoV that consistently interacted with ACE2. Notably, a stable salt bridge between Lys417 of SARS-CoV-2 S protein and Asp30 of ACE2 as well as three stable hydrogen bonds between Tyr449, Gln493 and Gln498 of SARS-CoV-2 and Asp38, Glu35 and Lys353 of ACE2 were observed, which were absent in the ACE2–SARS-CoV interface. Some previously reported residues, which were suggested to enhance the binding affinity of SARS-CoV-2, were not observed to form stable interactions in these simulations. Molecular mechanics-generalized Born surface area based free energy of binding was observed to be higher for SARS-CoV-2 in all simulations. Stable binding to the host receptor is crucial for virus entry. Therefore, special consideration should be given to these stable interactions while designing potential drugs and treatment modalities to target or disrupt this interface.