Pyrazolidines are very important compounds that widely exist in many natural products. Herein, we have employed high-level DFT calculations to systematically investigate the underlying mechanism of Cu(OTf)2 catalyzed [3+2] cycloaddition reactions that synthesis CF3substituted pyrazolidines. About eight possible initial configurations of the [3+2] reaction is considered and all relevant reactants, transition states and products are optimized. Based on these structures, IRC paths and the wavefunction analysis, we concluded that the Cu(OTf)2 catalyzed [3+2] cycloaddition follow a concerted asynchronous mechanism. The CN bond forms immediately after the formation of the CC bond. Among all eight reaction paths, the energy barrier for the [3+2] reaction that lead to the CF3substituted synpyrazolidine is the lowest one, ca. 3.2 kcal/mol, which might result in the diastereoselectivity that observed in experiment. We have also investigated the reaction processes that without Cu(OTf)2 molecule. The computational results indicate that the energy barriers that form the diastereoisomers are much closer and also larger than the Cu(OTf)2 catalyzed one. Therefore, Cu(OTf)2 catalyst plays an important role for the diastereoselectivity of the [3+2] cycloaddition reaction. Our present work not only gives the detail mechanism of the Cu(OTf)2 catalyzed [3+2] cycloaddition, but can also be helpful for the future designation of Cu(OTf)2 based cycloaddition processes.
Pathogen persistence in host communities is influenced by a hierarchy of heterogeneities from individual host to landscape-level attributes, but isolating the relative contributions of these heterogeneities is challenging. We developed theory to partition the influence of host species, habitat patches, and landscape connectivity on pathogen persistence within host-pathogen metacommunities. We used the framework to quantify the contributions of host species composition and habitat patch identity on the persistence of an amphibian pathogen across the landscape. By sampling over 11,000 hosts of six amphibian species, we found that a single host species could maintain the pathogen in 91% of the metacommunities we observed. Moreover, this dominant maintenance species contributed, on average, twice as much to landscape-level pathogen persistence compared to the most influential source patch in a metacommunity. Our analysis demonstrates substantial inequality in how species and patches contribute to pathogen persistence, with important implications for targeted disease management.
Clinical use of pancreatic beta islets for regenerative medicine applications requires mass production of functional cells. Current technologies are insufficient for large-scale production in a cost-efficient manner. Here, we evaluate advantages of a porous cellulose scaffold and demonstrate scale-up to a wicking-matrix bioreactor as a platform for culture of human endocrine cells. Scaffold modifications were evaluated in a multi-well platform to find the optimum surface condition for pancreatic cell expansion followed by bioreactor culture to confirm suitability. Preceding scale-up, cell morphology, viability and proliferation of primary pancreatic cells were evaluated. Two optimal surface modifications were chosen and evaluated further for insulin secretion, cell morphology and viable cell density for human induced pluripotent stem cell-derived pancreatic cells at different stages of differentiation. Scale-up was accomplished with uncoated, amine-modified cellulose in a miniature bioreactor, and insulin secretion and cell metabolic profiles were determined for 13 days. We achieved 10-fold cell expansion in the bioreactor along with a significant increase in insulin secretion compared with cultures on tissue-culture plastic. Our findings define a new method for expansion of pancreatic cells on wicking-matrix cellulose platform to advance cell therapy biomanufacturing for diabetes.
Calcium carbonate (CaCO3) is an inorganic compound which is widely used in industry, chemistry, construction, ocean acidification and biomineralization due to its rich constituent on earth and excellent performance, in which calcium carbonate hydrates are important systems. In Z.Y. Zou et al’s work (Science, 2019, 363, 396–400), they found a novel calcium carbonate hemihydrate phase, but the structure stability, optical and mechanical properties has not been studied. In this work, the stability, electronic, optical, and mechanical properties of novel calcium carbonate hydrates were investigated by using the first-principles calculations within density functional theory (DFT). CaCO3·xH2O (x=1/2, 1 and 6) are determined dynamically stable phases by phonon spectrum, but the Gibbs energy of reaction of CaCO3·1/2H2O is higher than other calcium carbonate hydrates. That’s why the CaCO3·1/2H2O is hard to synthesize in the experiments. In addition, the optical and mechanical properties of CaCO3·xH2O (x=1/2, 1 and 6) are expounded in detail. It shows that the CaCO3·1/2H2O has the largest bulk modulus, shear modulus, Young’s modulus with the values 60.51, 36.56 and 91.28 GPa with respect to other two calcium carbonate hydrates investigated in this paper. This work will provide guidance for experiments and its applications, such as biomineralization, geology, and industrial processes.
On the example of forty ion pairs, the study demonstrates how the core-level binding energy values can be calculated and used to plot theoretical spectra at a low computational cost using density functional theory methods. Three approaches for obtaining the binding energy values are based on delta Kohn–Sham (ΔKS) calculations, 1s Kohn–Sham orbital energies, and atomic charges. The ΔKS results show a good agreement between the available experimental X-ray photoelectron data. 1s Kohn–Sham orbital energies and atomic charges also correlate with the ΔKS results.
The Irtysh River is the main water resource of eastern Kazakhstan and its upper basin is severely affected by spring floods each year, primarily as a result of snowmelt. Knowledge of the large scale processes that influence the timing of these snow-induced floods is currently lacking, but critical for the management of water resources in the area. In this study, we evaluated the variability in winter-spring snow cover in five major sub-basins of the Upper Irtysh basin between 2000 and 2017 as a possible explanatory factor of spring flood events, assessing the time of peak snow cover depletion rate and snow cover disappearance from the MODIS MOD10A2 dataset. We found that on average, peak snow cover retreat occurs between 22 March and 14 April depending on the basin, with large inter-annual variations but no clear trend over the observation period. In contrast, the annual peak snow cover depletion rate displays a weak increasing trend over the study period and exceeded 5900 km2 day-1 in 2017. The timing of snow disappearance in spring shows significant correlations of up to 0.82 for the largest basin with winter indices of the Arctic Oscillation over the region. The primary driver is the impact of the large scale pressure anomalies upon the mean spring (MAM) air temperatures and resultant timing of snow cover disappearance, particularly at elevations 500-2000 m above sea level. This suggests a lagged effect of this atmospheric circulation pattern in spring snow cover retreat. The winter Arctic Oscillation index could therefore be incorporated into long-term runoff forecasts for the Irtysh. Our approach is easily transferable to other similar catchments, and could support flood management strategies in Kazakhstan and other countries.
Manually collected snow data are often considered as ground truth for many applications such as climatological or hydrological studies. However, there are many sources of uncertainty that are not quantified in detail. For the determination of water equivalent of snow cover (SWE), different snow core samplers and scales are used, but they are all based on the same measurement principle. We conducted two field campaigns with 9 samplers commonly used in observational measurements and research in Europe and northern America to better quantify uncertainties when measuring depth, density and SWE with core samplers. During the first campaign, as a first approach to distinguish snow variability measured at the plot and at the point scale, repeated measurements were taken along two 20 m long snow pits. The results revealed a much higher variability of SWE at the plot scale (resulting from both natural variability and instrumental bias) compared to repeated measurements at the same spot (resulting mostly from error induced by observers or very small scale variability of snow depth). The exceptionally homogeneous snowpack found in the second campaign permitted to almost neglect the natural variability of the snowpack properties and focus on the separation between instrumental bias and error induced by observers. Under such measurement conditions, the uncertainty in bulk snow density estimation is about 5% for an individual instrument and is close to 10% among different instruments. Results confirmed that instrumental bias exceeded both the natural variability and the error induced by observers, even in the case when observers were not familiar with a given snow core sampler.
The onset of acute illness may be accompanied by a profound sense of disorientation for patients. Addressing this vulnerability is a key part of a physician’s purview, yet well-intended efforts to do so may be impeded by myriad competing tasks in clinical practice. Resolving this dilemma goes beyond appealing to altruism, as its limitless demands may lead to physician burnout, disillusionment, and a narrowed focus on the biomedical aspects of care in the interest of self-preservation. The authors propose an ethic of hospitality that may better guide physicians in attending to the comprehensive needs of patients that have entered “the kingdom of the sick”. Using philosophical methods, the authors explore what compels people to present to emergent medical attention and why altruism may not offer physicians a sustainable way to address the vulnerabilities that occur in such situations. They then present the concept of hospitality from a Derridean perspective and use it to interpret a narrative case of an on-call paediatrician caring for an infant with bronchiolitis to demonstrate how this approach may be practically implemented in the acute care hospital context. Hospitality allows physicians to acknowledge that clinical presentations that are routine in their world may be disorienting and frightening to patients experiencing them acutely. Further, it recognizes that the vulnerability that accompanies acute illness may be compounded by the unfamiliarity of the hospital environment in which patients have sought support. While it is unlikely that anything physicians do will make the hospital a place where patients and caregivers will desire to be, hospitality may focus their efforts upon making it less unwelcoming. Specifically, it offers an orientation that supports patients in navigating the disorienting and unfamiliar terrains of acute illness, the hospital setting in which help is sought, and engagement with the health care system writ large.
We investigate the ability of mechanical and electronic density functional theory (DFT)-based embedding approaches to describe the solvent effects on nuclear magnetic resonance (NMR) shielding constants of the ⁹⁵Mo nucleus in the molybdate ion in aqueous solution. From the description obtained from calculations with two- and four-component relativistic Hamiltonians, we find that for such systems spin-orbit coupling effects are clearly important for absolute shielding values, but for relative quantities a scalar relativistic treatment provides a sufficient estimation of the solvent effects. We find that the electronic contributions to the solvent effects are relatively modest yet decisive to provide a more accurate magnetic response of the system, when compared to reference supermolecular calculations. We analyze the errors in the embedding calculations by statistical methods as well as through a real-space representation of NMR shielding densities, which are shown to provide a clear picture of the physical processes at play.
Local correlation methods rely on the assumption that electronic correlation is nearsighted. In this work, we develop a method to alleviate this assumption. The first step is to approximately decompose the electron correlation to the nearsighted and farsighted components based on the wavelength decomposition of electron correlation by Langreth and Perdew. The nearsighted component is then calculated using the recently developed embedded cluster density approximation (ECDA) which is a local correlation method formulated in the context of density functional theory. The farsighted component is calculated based on the system’s Kohn-Sham orbitals. The accuracy of this new method depends on the quality of the decomposition. We examined the method’s accuracy by patching the random phase approximation (RPA) correlation energy in a H₂₄ chain in which the electron correlation is highly nonlocal. This new method predicts bond stretching energies, RPA correlation potential, and Kohn-Sham eigenvalues in good agreement with the benchmarks. Our results demonstrate the importance of including the farsighted part of electron correlation for studying systems having nonlocal correlations.
In this work, geometries, stabilities and electronic properties of carbon monoxide (CO) molecule as an adsorbent on simple carbon nanotube (CNT) and N, B, S-doped carbon nanotubes (NCNT, BCNT and SCNT) with parallel and perpendicular configurations are fully considered using ONIOM, natural bond orbital (NBO), and quantum theory of atom in molecule (QTAIM) calculations. The adsorption energies (Ead) demonstrate that CO molecule could be adsorbed on the surface of the simple carbon nanotube with parallel configuration (CNT-p) and N-doped carbon nanotube with perpendicular configuration (NCNT-d) in exothermic process. QTAIM calculations are showed the close-shell (non-covalent) interactions between CO molecule and CNT or N, B, S-doped CNTs. Also, the energy gap (Eg) values between the highest occupied molecular orbital and the lowest unoccupied molecular orbital are calculated. In accordance to the results of energy gap, simple and N-doped carbon nanotubes could be used as CO-sensors.
Plant-soil feedback is commonly pointed out as driver of plant community dynamics and species co-existence. However, experimental evidence for soil legacy effects of conditioning plant communities on responding plant communities under natural conditions is lacking. We conditioned 192 grassland plots with plant communities with different ratios of grasses and forbs and fast and slow-growing plants. Soil microbial legacies were most evident for soil fungi. Soil abiotic parameters did not change in response to conditioning. The soil legacies affected the composition of the succeeding vegetation. Plant communities of a specific functional type caused negative feedbacks on succeeding plants when they belonged to the same functional type. Richness, relative species cover and belowground biomass of the responding vegetation were all influenced by the growth rate of the conditioning community. We conclude that plant-soil feedbacks play an important role in vegetation assembly of natural communities.
Academic journal publication is the currency of University faculty. It can go without saying that publications play an important role in securing an academic appointment and research grants, achieving promotion within the University, and more importantly, advancing knowledge, which is to me the primary purpose of any academic pursuit. Despite its importance, academics seem to receive little or no formal training in how to prepare a manuscript for publication or how to respond to reviewer criticism1. Quite often, such skills are acquired through mentorship during graduate training. Unfortunately, it is often the case that graduate students do not produce enough manuscripts during their training to develop expertise in how to translate completed research or scholarship into a published report. As an editor, I often see manuscripts that are diminished by how they are written, which often causes confusion in the reviewer, resulting in a recommendation for rejection. I do not profess to be an expert on writing for an academic audience. I have no idea exactly how I learned to get my work published (I assume it was through practice and good mentorship), nor do I have any idea if I am skilled at it – I am left to assume my level of expertise from my successes and failures. However, from reading several manuscripts each day, I have picked up on some common errors and have developed an appreciation for what editors and reviewers expect in a published manuscript. In what follows, I present a bit of what I have learned in my, albeit it short, time as an editor.2
The rare ginsenosides are recognized as the functionalized molecules after oral administration of Panax ginseng and its products. The sources of rare ginsenosides are extremely limited because of low ginsenoside contents in wild plants, hindering their application in functional foods and drugs. We developed an effective combinatorial biotechnology approach including tissue culture, immobilization, and hydrolyzation methods. Rh2 and nine other rare ginsenosides were produced by MeJA-induced culture of adventitious roots in a 10 L bioreactor associated with enzymatic hydrolysis using six β-glycosidases and their combination with yields ranging from 5.54-32.66 mg L-1. The yield of Rh2 was furthermore increased 7% by using immobilized BglPm and Bgp1 in optimized pH and temperature condition, with the highest yield reaching 51.17 mg L-1 (17.06% of PPD-type ginsenosides mixture). Our combinatorial biotechnology method provides a highly efficient approach to acquiring diverse rare ginsenosides, replacing direct extraction from Panax plants, and can also be used to supplement yeast cell factories.
Rationale, aims and objectives The article looks at how, during consultations, pregnant women identified as presenting an increased risk of giving birth to a child with an impairment, and practitioners in the field of prenatal diagnosis, decide whether or not to accept the risk of a miscarriage and proceed with a diagnostic examination. Methods We conducted 63 observations of consultations in France and 22 in England. Participants were women for whom an elevated risk of abnormality had been identified and the practitioners involved in their care. Our analytical approach consisted in suspending the normative concepts of non-directiveness and autonomy, and in drawing on Goffman’s (1974) notion of “frame” to take account of the experiential and structural aspects that the protagonists bring into the (inter)actions. Results We identified four frames: medico-scientific expertise, medical authority, religious authority and compassion. Observation of the ways in which the frames intertwine during consultations revealed configurations that facilitate or hinder the fluidity of the interactions and the decision-making process. The medico-scientific expertise frame, imposed by the guidelines, heavily dominated our observations, but frequently caused distress and misunderstanding. Temporary or sustained use of the compassion and/or medical authority frames could help to repair the discussion and create the conditions that enable women/couples to reach a decision. Variations in configuration highlighted the differences between practitioners in the two countries. Conclusions Combining frames allows protagonists to exert reflective abilities and to maintain/restore interactions. The frame analysis promotes a vision of autonomy that is sociological, relational and processual rather than philosophical. The frames are anchored in different structural conditions in England and France.
The presence of long abandoned, hexagonal omega (ω) phase in steel samples is recently gaining momentum on account of accurate transmission electron microscopy (TEM) measurements. The formation and stabilization of this metastable phase down to room temperature is attributed to the combined effect of factors such as accelerated cooling, special atomic constraints at twin boundaries, and the enrichment of solute elements such as Al, Mn, Si, C, and Cr in the nanometer sized regimes. Here, we present a density functional theory (DFT) study of the effect of the above alloying elements in ω-Fe and confirm the predictions using high resolution TEM observations of the structure of an experimental steel at high magnifications. It is found that the FM and ++- spin states are the most stable for a primitive cell of ω-Fe. The density of states calculations show that the d band occupancy of ω-Fe is changing in presence of the alloying elements, and this in turn will affect the cohesive energy. Further, the dynamical stability analysis from phonon band structure reveals that only ω-Fe with substitutional C exhibits thermodynamic stability. This is in line with experimental indications that the stabilization of ω-phase in ferritic/martensitic steels occurs due to the presence of special symmetry constraints at grain boundaries
Motivated by the particularly short metal-metal distance that has been predicted for the D3h [BeH3Be]+ cation, comparable to those anticipated for triple bonds, we investigate the nature of the bonding interactions in the D3h [MH3M]+ cations (M = Be, Mg). CCSD(T)/cc pVQZ calculations are used to determine optimized geometries for all of the various species, including those ‘capped’ by He or Ne atoms (as proxies for an inert gas matrix). The primary tools that are then used to investigate the nature of the chemical bonding are spin-coupled generalized valence bond calculations and the analysis of localized natural orbitals and of domain-averaged Fermi holes. The various results for all of the systems considered indicate the presence of highly polar three-centre two-electron M−H−M bonding character instead of any significant direct metal-metal bonding.
Site-specific integration has emerged as a promising strategy for precise Chinese hamster ovary (CHO) cell line engineering and predictable cell line development. CRISPR/Cas9 with homology-directed repair (HDR) pathway enables precise integration of transgenes into target genomic sites. However, inherent recalcitrance to HDR-mediated targeted integration (TI) of transgenes results in low targeting efficiency, thus requires selection process to acquire targeted integrant in CHO cells. Here we explored several parameters that influence the targeting efficiency using the promoter-trap based single or double knock-in (KI) monitoring system. A simple change in the donor template design by adding sgRNA recognition sequences strongly increased KI efficiency by 2.9–36 fold depending on integration sites and culture mode, compared with conventional circular donor plasmids. Furthermore, sequential and simultaneous KI strategies enabled the generation of double KI populations about 1–4% without the need of additional enrichment processes. This simple optimized strategy not only allowed efficient CRISPR/Cas9-mediated TI in CHO cells but also paved the way for the applicability of multiplexed KIs in one experimental step without the requirement of sequential and independent CHO cell line development procedures.