bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytotoxic T-lymphocyte elicited vaccine against SARS-CoV-2 employing immunoinformatics framework
Authors: Kumar Neeraj , Admane Nikita , Kumari Anchala , Sood Damini , Grover Sonam , Prajapati Vijay Kumar , Chandra Ramesh , Grover Abhinav 
Published: April 2021

AbstractDevelopment of effective counteragents against the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, requires clear insights and information for understanding the immune responses associated with it. This global pandemic has pushed the healthcare system and restricted the movement of people and succumbing of the available therapeutics utterly warrants the development of a potential vaccine to contest the deadly situation. In the present study, highly efficacious, immunodominant cytotoxic T-lymphocyte (CTL) epitopes were predicted by advanced immunoinformatics assays using the spike glycoprotein of SARS-CoV2, generating a robust and specific immune response with convincing immunological parameters (Antigenicity, TAP affinity, MHC binder) engendering an efficient viral vaccine. The molecular docking studies show strong binding of the CTL construct with MHC-1 and host membrane specific TLR2 receptors. The molecular dynamics simulation in an explicit system confirmed the stable and robust binding of CTL epitope with TLR2. Steep magnitude RMSD variation and compelling residual fluctuations existed in terminal residues and various loops of the β linker segments of TLR2-epitope (residues 105-156 and 239-254) to about 0.4 nm. The reduced Rgvalue (3.3 nm) and stagnant SASA analysis (275 nm/S2/N after 8 ns and 5 ns) for protein surface and its orientation in the exposed and buried regions suggests more compactness due to the strong binding interaction of the epitope. The CTL vaccine candidate establishes a high capability to elicit the critical immune regulators, like T-cells and memory cells as proven by the in silico immunization assays and can be further corroborated through in vitro and in vivo assays.
A virtual reality interface for the immersive manipulation of live microscopic systems
Authors: Ferretti Stefano , Bianchi Silvio , Frangipane Giacomo , Di Leonardo Roberto 
Published: April 2021

AbstractFor more than three centuries we have been watching and studying microscopic phenomena behind a microscope. We discovered that cells live in a physical environment whose predominant factors are no longer those of our scale and for which we lack a direct experience and consequently a deep intuition. Here we demonstrate a new instrument which, by integrating holographic and virtual reality technologies, allows the user to be completely immersed in a dynamic virtual world which is a simultaneous replica of a real system under the microscope. We use holographic microscopy for fast 3D imaging and real-time rendering on a virtual reality headset. At the same time, hand tracking data is used to dynamically generate holographic optical traps that can be used as virtual projections of the user hands to interactively grab and manipulate ensembles of microparticles or living motile cells.
A strain of Phoma species improves drought tolerance of Pinus tabulaeformis
Authors: Zhou Xiu Ren , Dai Lei , Xu Gui Fang , Wang Hong Sheng 
Published: April 2021

AbstractGlobal warming has led to frequent droughts, posing challenges for afforestation in arid and semiarid regions. In search of labor-saving and money-saving methods to improve the survival and growth rates of trees in these regions, we isolated and identified fungal endophytes that can potentially enhance the drought-resistance abilities of seedlings. We isolated 93 endophytic strains from the roots of Pinus tabulaeformis trees grown on an arid cliff. Three isolates increased the drought resistance of the tree seedlings. Using morphological, molecular, and physiological-biochemical methods, we identified three isolates as different clones of a strain of Phoma spp. and studied the strain’s effect on stress resistance-related substances in the seedlings. The results showed that the strain improved drought tolerance and increased the seedlings’ proline levels and antioxidant enzyme activities. The strain also secreted abundant extracellular abscisic acid, which likely triggered the seedlings’ protective mechanisms. This endophytic strain may provide a cheaper labor-saving, sustainable alternative to traditional methods of enhancing drought resistance.
Different Zn loading in Urea–Formaldehyde influences the N controlled release by structure modification
Authors: Giroto Amanda S. , do Valle Stella F. , Guimarães Gelton G. F. , Jablonowski Nicolai D. , Ribeiro Caue , Mattoso Luiz Henrique C. 
Published: April 2021

AbstractNitrogen fertilization has been a critical factor for high crop productivity, where urea is currently the most used N source due to its high concentration and affordability. Nevertheless, urea fast solubilization leads to frequent losses and lower agronomic efficiency. The modification of urea structure by condensation with formaldehyde has been proposed to improve nutrient uptake by plants and to reduce environmental losses. Herein we show that the co-formulation with Zn strongly modifies the N release (in lab conditions) and, more important, the Zn source—ZnSO4 or ZnO—has a critical role. Urea–formaldehyde (UF) served as a matrix for the zinc sources, and chemical characterizations revealed that Zn particles influenced the length of the polymeric chain formation. Release tests in an aqueous medium showed that the UF matrix favors ZnO release and, on the other hand, delays ZnSO4 delivery. Soil incubation with the fertilizer composites proved the slow-release of N from UF, is ideal for optimizing nutritional efficiency. Our results indicated that the ZnO-UF system has beneficial effects for both nutrients, i.e., reduces N volatilization and increases Zn release.
Reduction of dopant ions and enhancement of magnetic properties by UV irradiation in Ce-doped TiO2
Authors: Wu Tai-Sing , Syu Leng-You , Lin Bi-Hsuan , Weng Shih-Chang , Jeng Horng-Tay , Huang Yu-Shan , Soo Yun-Liang 
Published: April 2021

AbstractWe report the experimental observation of and theoretical explanation for the reduction of dopant ions and enhancement of magnetic properties in Ce-doped TiO2 diluted magnetic semiconductors from UV-light irradiation. Substantial increase in Ce3+ concentration and creation of oxygen vacancy defects in the sample due to UV-light irradiation was observed by X-ray and optical methods. Magnetic measurements demonstrate a combination of paramagnetism and ferromagnetism up to room temperatures in all samples. The magnetization of both paramagnetic and ferromagnetic components was observed to be dramatically enhanced in the irradiated sample. First-principle theoretical calculations show that valence holes created by UV irradiation can substantially lower the formation energy of oxygen vacancies. While the electron spin densities for defect states near oxygen vacancies in pure TiO2 are in antiferromagnetic orientation, they are in ferromagnetic orientations in Ce-doped TiO2. Therefore, the ferromagnetically-oriented spin densities near oxygen vacancies created by UV irradiation are the most probable cause for the experimentally observed enhancement of magnetism in the irradiated Ce-doped TiO2.
Discovery of uncompetitive inhibitors of SapM that compromise intracellular survival of Mycobacterium tuberculosis
Authors: Fernández-Soto Paulina , Casulli Joshua , Solano-Castro Danilo , Rodríguez-Fernández Pablo , Jowitt Thomas A. , Travis Mark A. , Cavet Jennifer S. , Tabernero Lydia 
Published: April 2021

AbstractSapM is a secreted virulence factor from Mycobacterium tuberculosis critical for pathogen survival and persistence inside the host. Its full potential as a target for tuberculosis treatment has not yet been exploited because of the lack of potent inhibitors available. By screening over 1500 small molecules, we have identified new potent and selective inhibitors of SapM with an uncompetitive mechanism of inhibition. The best inhibitors share a trihydroxy-benzene moiety essential for activity. Importantly, the inhibitors significantly reduce mycobacterial burden in infected human macrophages at 1 µM, and they are selective with respect to other mycobacterial and human phosphatases. The best inhibitor also reduces intracellular burden of Francisella tularensis, which secretes the virulence factor AcpA, a homologue of SapM, with the same mechanism of catalysis and inhibition. Our findings demonstrate that inhibition of SapM with small molecule inhibitors is efficient in reducing intracellular mycobacterial survival in host macrophages and confirm SapM as a potential therapeutic target. These initial compounds have favourable physico-chemical properties and provide a basis for exploration towards the development of new tuberculosis treatments. The efficacy of a SapM inhibitor in reducing Francisella tularensis intracellular burden suggests the potential for developing broad-spectrum antivirulence agents to treat microbial infections.
Past climate variations recorded in needle-like aragonites correlate with organic carbon burial efficiency as revealed by lake sediments in Croatia
Authors: Razum Ivan , Bajo Petra , Brunović Dea , Ilijanić Nikolina , Hasan Ozren , Röhl Ursula , Miko Martina Šparica , Miko Slobodan 
Published: April 2021

AbstractThe drivers of organic carbon (OC) burial efficiency are still poorly understood despite their key role in reliable projections of future climate trends. Here, we provide insights on this issue by presenting a paleoclimate time series of sediments, including the OC contents, from Lake Veliko jezero, Croatia. The Sr/Ca ratios of the bulk sediment are mainly derived from the strontium (Sr) and calcium (Ca) concentrations of needle-like aragonite in Core M1-A and used as paleotemperature and paleohydrology indicators. Four major and six minor cold and dry events were detected in the interval from 8.3 to 2.6 calibrated kilo anno before present (cal ka BP). The combined assessment of Sr/Ca ratios, OC content, carbon/nitrogen (C/N) ratios, stable carbon isotope (δ13C) ratios, and modeled geochemical proxies for paleoredox conditions and aeolian input revealed that cold and dry climate states promoted anoxic conditions in the lake, thereby enhancing organic matter preservation and increasing the OC burial efficiency. Our study shows that the projected future increase in temperature might play an important role in the OC burial efficiency of meromictic lakes.
Magnetoelastic interactions and magnetic damping in Co2Fe0.4Mn0.6Si and Co2FeGa0.5Ge0.5 Heusler alloys thin films for spintronic applications
Authors: Chumak O. M. , Pacewicz A. , Lynnyk A. , Salski B. , Yamamoto T. , Seki T. , Domagala J. Z. , Głowiński H. , Takanashi K. , Baczewski L. T. , Szymczak H. , Nabiałek A. 
Published: April 2021

AbstractCo2Fe0.4Mn0.6Si (CFMS) and Co2FeGa0.5Ge0.5 (CFGG) Heusler alloys are among the most promising thin film materials for spintronic devices due to a high spin polarization, low magnetic damping and giant/tunneling magnetoresistance ratios. Despite numerous investigations of Heusler alloys magnetic properties performed up to now, magnetoelastic effects in these materials remain not fully understood; due to quite rare studies of correlations between magnetoelastic and other magnetic properties, such as magnetic dissipation or magnetic anisotropy. In this research we have investigated epitaxial CFMS and CFGG Heusler alloys thin films of thickness in the range of 15–50 nm. We have determined the magnetoelastic tensor components and magnetic damping parameters as a function of the magnetic layer thickness. Magnetic damping measurements revealed the existence of non-Gilbert dissipation related contributions, including two-magnon scattering and spin pumping phenomena. Magnetoelastic constant B11 values and the effective magnetic damping parameter αeff values were found to be in the range of − 6 to 30 × 106 erg/cm3 and between 1 and 12 × 10–3, respectively. The values of saturation magnetostriction λS for CFMS Heusler alloy thin films were also obtained using the strain modulated ferromagnetic resonance technique. The correlation between αeff and B11, depending on magnetic layer thickness was determined based on the performed investigations of the above mentioned magnetic properties.
Structural transformation and phase change properties of Se substituted GeTe
Authors: Shekhawat Roopali , Pamuluri Haritha , Erkkara Madhavan Vinod , Ramesh K. 
Published: April 2021

AbstractGeTe1−xSex (0 ≤ x ≤ 1.0) alloys have been prepared both in bulk and thin film forms to study the effect of selenium (Se) substitution for tellurium (Te) on the phase change properties. It is observed that with increasing Se substitution in GeTe, the structure transforms from rhombohdral structure to orthorhombic structure. Rietveld Refinement analysis support the phase transformation and show that the short and long bond lengths in crystalline GeTe decrease with increasing Se substitution but the rate of reduction of shorter bond length is more than the longer bond length. The GeTe1−xSex thin films undergo amorphous to crystalline phase change when annealed at high temperatures. The transition temperature shows an increasing trend with the Se substitution. The contrast in electrical resistivity between the amorphous and crystalline states is 104 for GeTe, and with the Se substitution, the contrast increases considerably to 106 for GeTe0.5Se0.5. Devices fabricated with thin films show that the threshold current decreases with the Se substitution indicating a reduction in the power required for WRITE operation. The present study shows that the crystalline structure, resistance, bandgap, transition temperature and threshold voltage of GeTe can be effectively controlled and tuned by the substitution of Te by Se, which is conducive for phase change memory applications.
Effect of selection bias on two sample summary data based Mendelian randomization
Authors: Wang Kai , Han Shizhong 
Published: April 2021

AbstractMendelian randomization (MR) is becoming more and more popular for inferring causal relationship between an exposure and a trait. Typically, instrument SNPs are selected from an exposure GWAS based on their summary statistics and the same summary statistics on the selected SNPs are used for subsequent analyses. However, this practice suffers from selection bias and can invalidate MR methods, as showcased via two popular methods: the summary data-based MR (SMR) method and the two-sample MR Steiger method. The SMR method is conservative while the MR Steiger method can be either conservative or liberal. A simple and yet more powerful alternative to SMR is proposed.
New cladotherian mammal from southern Chile and the evolution of mesungulatid meridiolestidans at the dusk of the Mesozoic era
Authors: Martinelli Agustín G. , Soto-Acuña Sergio , Goin Francisco J. , Kaluza Jonatan , Bostelmann J. Enrique , Fonseca Pedro H. M. , Reguero Marcelo A. , Leppe Marcelo , Vargas Alexander O. 
Published: April 2021

AbstractIn the last decades, several discoveries have uncovered the complexity of mammalian evolution during the Mesozoic Era, including important Gondwanan lineages: the australosphenidans, gondwanatherians, and meridiolestidans (Dryolestoidea). Most often, their presence and diversity is documented by isolated teeth and jaws. Here, we describe a new meridiolestidan mammal,Orretherium tzengen. et sp. nov., from the Late Cretaceous of southern Chile, based on a partial jaw with five cheek teethin locisand an isolated upper premolar. Phylogenetic analysis placesOrretheriumas the earliest divergence within Mesungulatidae, before other forms such as the Late CretaceousMesungulatumandColoniatherium, and the early PaleocenePeligrotherium. Thein locotooth sequence (last two premolars and three molars) is the first recovered for a Cretaceous taxon in this family and suggests that reconstructed tooth sequences for other Mesozoic mesungulatids may include more than one species. Tooth eruption and replacement show that molar eruption in mesungulatids is heterochronically delayed with regard to basal dryolestoids, with therian-like simultaneous eruption of the last premolar and last molar. Meridiolestidans seem endemic to Patagonia, but given their diversity and abundance, and the similarity of vertebrate faunas in other regions of Gondwana, they may yet be discovered in other continents.
A lower maximum bite force is a risk factor for developing cardiovascular disease: the Suita study
Authors: Hashimoto Sakae , Kosaka Takayuki , Nakai Michikazu , Kida Momoyo , Fushida Shuri , Kokubo Yoshihiro , Watanabe Makoto , Higashiyama Aya , Ikebe Kazunori , Ono Takahiro , Miyamoto Yoshihiro 
Published: April 2021

AbstractDecreases in masticatory function are believed to be related to the development of cardiovascular disease (CVD) through inappropriate nutritional intake. This study focused on maximum bite force (MBF), which is an objective, quantitative index of masticatory function, and its association with the development of CVD (stroke and coronary heart disease) was investigated. The subjects were 1547 participants of the Suita study with no history of CVD who underwent medical and dental health examinations between June 2008 and June 2013. In addition to undergoing a basic physical examination at baseline, their MBF was measured. They subsequently underwent follow-up surveys for the development of CVD (mean follow-up, 3.5 years). The association between baseline MBF and the development of CVD was investigated by multivariate adjustment using a Cox proportional hazards model. CVD developed in 32 subjects during follow-up. The trend test showed a significant association between baseline MBF and CVD in a model that combined men and women. When analysed by sex, the trend test found a significant association between baseline MBF and CVD in women. Low MBF, which is an objective and quantitative index of masticatory function, may be a risk factor for the development of CVD.
The beneficial role of Asian-based RecurIndex test in the prognostic prediction in Chinese male breast cancer patients
Authors: Zhang Shuo , Liu Beichen , Zhou Mengli , Wang Jintian , Liu Jinzhao , Wang Li , Yang Chao , Liu Yueping , Niu Shuyao , Du Furong , Du Xiaohua , Wang Ning , Tang Jiyu , Song Chao , Liu Yunjiang 
Published: April 2021

AbstractRecurIndex, a multigene profiling assay, can predict the risk of local recurrence and distant metastasis in female breast cancer (FBC), but its role in male breast cancer (MBC) remains unclear. In this study, the clinicopathological data of 43 consecutive MBC patients undergoing surgeries between 2009 and 2018 were retrospectively analysed. Their paraffin-embedded tissue sections were examined by RecurIndex test which comprised 2 models: recurrence index for local recurrence (RI-LR) and recurrence index for distant recurrence (RI-DR). Of 43 patients, there were 26 low-risk and 17 high-risk patients assessed by RI-LR, while 17 low-risk and 26 high-risk patients by RI-DR. For RI-LR, tumor N stage showed statistically significant (P < 0.001) between low- and high-risk patients; for RI-DR, differences were pronounced in tumor grade (P = 0.033), T stage (P = 0.043) and N stage (P = 0.003). In terms of clinical outcomes, the overall survival (OS) of low- and high-risk patients stratified by RI-LR showed no statistically significant differences (P = 0.460), while high-risk patients identified by RI-DR had a significantly worse distant recurrence-free survival (DRFS) (P = 0.035), progression-free survival (PFS) (P = 0.019) and OS (P = 0.044) than low-risk patients. Overall, RI-DR can effectively predict the DRFS, PFS and OS of MBC patients and identify those at low risk of recurrence, which may serve as a potential prognostic tool for MBC.
Nicotinamide mononucleotide production by fructophilic lactic acid bacteria
Authors: Sugiyama Kazane , Iijima Kana , Yoshino Miyako , Dohra Hideo , Tokimoto Yuji , Nishikawa Koji , Idogaki Hideaki , Yoshida Nobuyuki 
Published: April 2021

AbstractNicotinamide mononucleotide (NMN), an intermediate in nicotinamide adenine dinucleotide biosynthesis, is recently attracting much attention for its pharmacological and anti-aging efficacies. However, current commercial products containing NMN are very high-priced because efficient and facile methods for industrial NMN production are limited. In this study, aiming for its nutraceutical application, we attempted to screen lactic acid bacteria for intracellular and/or extracellular NMN production. Using a bioassay system with an auxotrophic yeast that requires nicotinamide riboside (NR; dephosphorylated NMN), three candidates were obtained from a library of 174 strains of facultative anaerobic lactic acid bacteria. All three candidates belonged to the genus Fructobacillus and produced NR in the culture media (0.8–1.5 mg/l). Lactic acid bacteria of the genus Fructobacillus are known to use d-fructose as an electron acceptor in anaerobic lactic acid fermentation; addition of d-fructose to the medium caused intracellular accumulation of NMN and NR, but no extracellular production of these compounds was observed. Draft genome sequencing for one of the candidates suggested that nicotinamide phosphoribosyltransferase, which exists commonly in mammals but is less reported in microorganisms, is a key enzyme for NMN and NR production in the fructophilic bacteria.
Identification of loss-of-function RyR2 mutations associated with idiopathic ventricular fibrillation and sudden death
Authors: Zhong Xiaowei , Guo Wenting , Wei Jinhong , Tang Yijun , Liu Yingjie , Zhang Joe Z. , Tan Vern Hsen , Zhang Lin , Wang Ruiwu , Jones Peter P. , Napolitano Carlo , Priori Silvia G. , Chen S.R. Wayne 
Published: April 2021

Abstract
Mutations in cardiac ryanodine receptor (RyR2) are linked to catecholaminergic polymorphic ventricular tachycardia (CPVT). Most CPVT RyR2 mutations characterized are gain-of-function (GOF), indicating enhanced RyR2 function as a major cause of CPVT. Loss-of-function (LOF) RyR2 mutations have also been identified and are linked to a distinct entity of cardiac arrhythmia termed RyR2 Ca2+ release deficiency syndrome (CRDS). Exercise stress testing (EST) is routinely used to diagnose CPVT, but it is ineffective for CRDS. There is currently no effective diagnostic tool for CRDS in humans. An alternative strategy to assess the risk for CRDS is to directly determine the functional impact of the associated RyR2 mutations. To this end, we have functionally screened 18 RyR2 mutations that are associated with idiopathic ventricular fibrillation (IVF) or sudden death. We found two additional RyR2 LOF mutations E4146K and G4935R. The E4146K mutation markedly suppressed caffeine activation of RyR2 and abolished store overload induced Ca2+ release (SOICR) in human embryonic kidney 293 (HEK293) cells. E4146K also severely reduced cytosolic Ca2+ activation and abolished luminal Ca2+ activation of single RyR2 channels. The G4935R mutation completely abolished caffeine activation of and [3H]ryanodine binding to RyR2. Co-expression studies showed that the G4935R mutation exerted dominant negative impact on the RyR2 wildtype (WT) channel. Interestingly, the RyR2-G4935R mutant carrier had a negative EST, and the E4146K carrier had a family history of sudden death during sleep, which are different from phenotypes of typical CPVT. Thus, our data further support the link between RyR2 LOF and a new entity of cardiac arrhythmias distinct from CPVT.