Synthesis, Structure and Magnetic Properties of NiFe3O5

A new CaFe3O5-type phase NiFe3O5 (orthorhombic Cmcm symmetry, cell parameters a = 2.89126(7), b = 9.71988(21) and c = 12.52694(27) Å) has been synthesised under pressures of 12-13 GPa at 1200 °C. NiFe3O5 has an inverse cation site distribution and reveals an interesting evolution from M2+(Fe3+ )2Fe2+O5 to Fe2+(M2+ 0.5Fe3+ 0.5)2Fe3+O5 distributions over three distinct cation sites as M2+ cation size decreases from Ca to Ni. Magnetic susceptibility measurements show successive transitions at 275, ~150, and ~20 K and neutron diffraction data reveal a series of at least three spin-ordered phases with evolving propagation vectors k = [0 0 0] [0 ky 0]  [½ ½ 0] on cooling. The rich variety of magnetically ordered phases in NiFe3O5 likely results from frustration of Goodenough-Kanamori exchange interactions between the three spin sublattices, and further interesting magnetic materials are expected to be accessible within the CaFe3O5-type family.

Is the Mandibular Condyle Involved in Medication-Related Osteonecrosis of the Jaw? Audit of a Single Tertiary Referral Center and Literature Review

Background: Medication-related osteonecrosis of the jaw (MRONJ) may manifest as exposed mandible bone. Recent reviews of the incidence of MRONJ report primarily as exposed cortical bone of the mandibular body, ramus, and symphysis with no reports of condylar involvement. Objective: The aim of this study is to analyze the topographical incidence of MRONJ, comorbidities, demographics data, and clinical characteristics of patients diagnosed with MRONJ between 2014 and 2019 in the Maxillo-Facial Surgery Department University of Campania “Luigi Vanvitelli”, and compare these results with published reports. Methods: Data on 179 patients were collected for the study, including gender, age, underlying malignancy, medical history, and specific lesion location-identifying premaxilla and posterior sectors area involvement for the maxilla and symphysis, body, ramus, and condyle area for the mandible. A literature review was performed in order to compare our results with similar or higher sample sizes and find if any condylar involvement was ever reported. The research was carried out on PubMed database identifying articles from January 2003 to November 2020, where MRONJ site distribution was discussed, and data were examined to scan for condylar localization reports. Results: 30 patients had maxillary MRONJ, 136 patients had mandibular MRONJ, and 13 patients had lesions located in both maxilla and mandible. None of the patients reported condylar involvement, neither as a single site nor as an additional localization. Literature review results were coherent to our findings showing no mention of condylar MRONJ. Conclusion: Results do not show reports of condylar involvement in MRONJ. Although the pathophysiology of the disease has not been fully elucidated, two possible explanations were developed: the first one based on the condyle embryogenetic origin; the second one based on the bisphosphonate and anti-resorptive medications effects on the different vascular patterns of the mandible areas.

Evolution of Charge-Lattice Dynamics across the Kuramoto Synchronization Phase Diagram of Quantum Tunneling Polarons in Cuprate Superconductors

Because of its sensitivity to the instantaneous structure factor, S(Q,t = 0), Extended X-ray Absorption Fine Structure (EXAFS) is a powerful tool for probing the dynamic structure of condensed matter systems in which the charge and lattice dynamics are coupled. When applied to hole-doped cuprate superconductors, EXAFS has revealed the presence of internal quantum tunneling polarons (IQTPs). An IQTP arises in EXAFS as a two-site distribution for certain Cu–O pairs, which is also duplicated in inelastic scattering but not observed in standard diffraction measurements. The Cu–Sr pair distribution has been found to be highly anharmonic and strongly correlated to both the IQTPs and to superconductivity, as, for example, in YSr2Cu2.75Mo0.25O7.54(Tc=84 K). In order to describe such nontrivial, anharmonic charge-lattice dynamics, we have proposed a model Hamiltonian for a prototype six-atom cluster, in which two Cu-apical-O IQTPs are charge-transfer bridged through Cu atoms by an O atom in the CuO2 plane and are anharmonically coupled via a Sr atom. By applying an exact diagonalization procedure to this cluster, we have verified that our model indeed produces an intricate interplay between charge and lattice dynamics. Then, by using the Kuramoto model for the synchronization of coupled quantum oscillators, we have found a first-order phase transition for the IQTPs into a synchronized, phase-locked phase. Most importantly, we have shown that this transition results specifically from the anharmonicity. Finally, we have provided a phase diagram showing the onset of the phase-locking of IQTPs as a function of the charge-lattice and anharmonic couplings in our model. We have found that the charge, initially confined to the apical oxygens, is partially pumped into the CuO2 plane in the synchronized phase, which suggests a possible connection between the synchronized dynamic structure and high-temperature superconductivity (HTSC) in doped cuprates.

Domain Organization of Lentiviral and Betaretroviral Surface Envelope Glycoproteins Modeled with AlphaFold

The surface envelope glycoproteins of non-primate lentiviruses and betaretroviruses share sequence similarity with the inner proximal domain β-sandwich of the human immunodeficiency virus type 1 (HIV-1) gp120 glycoprotein that faces the transmembrane glycoprotein as well as patterns of cysteine and glycosylation site distribution that points to a similar two-domain organization in at least some lentiviruses. Here, high reliability models of the surface glycoproteins obtained with the AlphaFold algorithm are presented for the gp135 glycoprotein of the small ruminant caprine arthritis-encephalitis (CAEV) and visna lentiviruses and the betaretroviruses jaagsiekte sheep retrovirus (JSRV), mouse mammary tumor virus (MMTV) and consensus human endogenous retrovirus type K (HERV-K). The models confirm and extend the inner domain structural conservation in these viruses and identify two outer domains with a putative receptor binding site in the CAEV and visna virus gp135. The location of that site is consistent with patterns of sequence conservation and glycosylation site distribution in gp135. In contrast, a single domain is modeled for the JSRV, MMTV and HERV-K betaretrovirus envelope proteins that is highly conserved structurally in the proximal region and structurally diverse in apical regions likely to interact with cell receptors. The models presented here identify sites in small ruminant lentivirus and betaretrovirus envelope glycoproteins likely to be critical for virus entry and virus neutralization by antibodies and will facilitate their functional and structural characterization. Importance Structural information on the surface envelope proteins of lentiviruses and related betaretroviruses is critical to understand mechanisms of virus-host interactions. However, experimental determination of these structures has been challenging and only the structure of the human immunodeficiency virus type 1 gp120 has been determined. The advent of the AlphaFold artificial intelligence method for structure prediction allows high-quality modeling of the structures of small ruminant lentiviral and betaretroviral surface envelope proteins. The models are consistent with much of previously described experimental data, show regions likely to interact with receptors and identify domains that may be involved in mechanisms of antibody neutralization resistance in the small ruminant lentiviruses. The models will allow more precise design of mutants to further determine mechanisms of viral entry and immune evasion in this group of viruses and constructs for structure of these surface envelope proteins.

Optimization for Cost-Effectively Monitoring Ecological Effects of Water Diversion on the Urban Drinking Water Sources in a Large Eutrophic Lake

Due to the inputs of allochthonous pollutants and biological species from imported water, ecological effects of water diversion on urban drinking sources require long-term monitoring. Since spatial distributions of biological and environmental elements are always susceptible to water diversion, the monitoring specifications in water-receiving regions are always different from conventional ecological monitoring, especially in monitoring parameter selection and site distribution. To construct the method for selecting sensitive monitoring parameters and optimizing sites distribution in lakes, the large river-to-lake water diversion project, Water Diversion from Yangtze River to Lake Taihu in China, was taken as an example. The physicochemical properties and phytoplankton communities in the water-receiving Gonghu Bay and the referenced lake center were investigated and compared between the water diversion and non-diversion days in different seasons from 2013 to 2014. The comparative and collinearity analyses for selecting sensitive physicochemical parameters to water diversion, and the multidimensional scaling analysis based on the matrices of biological and sensitive physicochemical data, were integrated to optimize the monitoring in the water-receiving lake regions. Seven physicochemical parameters, including water temperature, pH, dissolved oxygen, total nitrogen, total phosphorus, chlorophyll a, and active silicate, were demonstrated to be sensitive to seasonal water diversion activities and selected for optimizing the site distribution and daily water quality monitoring. The nonmetric multidimensional scaling analysis results based on the data matrices of sensitive physicochemical parameters and phytoplankton communities were consistent for sites distribution optimization. For cost-effective monitoring, the sites distribution scheme could choose the optimizing results based on the Euclidean distance from 3.0 to 4.0 and the Bray-Curtis similarity from 40 to 60%. This scheme divided the Gonghu Bay into three water regions: the inflow river inlet, bay center, and bay mouth adjacent to the open water region. In each of the three regions, one representative site could be selected. If focusing on more details of each region, the standards with the Euclidean distance lower than 2.0 and the Bray-Curtis similarity higher than 60% should be considered. This optimization method provided an available way to fulfill the cost-effective long-term monitoring of urban drinking water sources influenced by water diversion projects.

Spatial Patterns of a Lethal White Syndrome Outbreak in Pseudodiploria strigosa

We analyzed the spatial distribution patterns of a white syndrome (WS) outbreak affecting Pseudodiploria strigosa colonies in the northern Mexican Caribbean during 2018–2019. The purpose of the study was to describe the outbreak progression in a single species and determine if this WS incidence is related to the nearest diseased neighbor distance. Two separated sites with different P. strigosa colonial densities (Bocana: 0.08 col/m2; Picudas: 0.2 col/m2) were selected in similar habitats of the same reef complex. P. strigosa colonies within the survey sites were mapped, and their status was recorded (healthy, diseased, or dead) in sequential surveys until colonies died or the study terminated (306 days). Spatial distribution modes were assessed using Ripley’s K function. The spatial colony distribution was random in one site (Bocana) and clustered in the other (Picudas). However, the WS disease incidence per survey was randomly distributed in both sites throughout the observation period of the outbreak, suggesting that WS transmission at small spatial scales was independent of the colony distribution pattern and from the nearest diseased colonies. Survival probability since WS onset in surveyed colonies was different: 0% at Bocana and 14% at Picudas by April 2019. But, eventually, all diseased colonies died in both sites. WS outbreak timing was different at the two sites: Initial prevalence 8% at the Bocana site vs. 44% at Picudas site. Distribution of time to disease onset shown multimodality, with modes varying from 17 to 184 days and wide main modes amplitude suggest a highly variable resistance to the WS. Disease incidence was not abated during winter surveys. Differences between sites in the WS disease outbreak distribution and progression suggest that colony condition, environmental quality, and perhaps several transmission events played an essential role in the complex outbreak dynamics at the local spatial scale of our study.

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture

Background Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming. Methods and results Here we developed a platform for Ribo-Seq library construction and data analysis to enable rapid quality assessment of Ribo-Seq libraries with the help of a small-scale sequencer. Our data show that several qualitative features of a Ribo-Seq library, such as read length distribution, P-site distribution, reading frame and triplet periodicity, can be effectively evaluated using only the data generated by a benchtop sequencer with a very limited number of reads. Conclusion Our pipeline enables rapid evaluation of Ribo-Seq libraries, opening up possibilities for optimization of Ribo-Seq library construction from difficult samples, and leading to better decision making prior to more costly deep sequencing.

Domain Organization of Lentiviral and Betaretroviral Surface Envelope Glycoproteins Modeled with AlphaFold

The surface envelope glycoproteins of non-primate lentiviruses and betaretroviruses share sequence similarity with the inner proximal domain β-sandwich of the human immunodeficiency virus type 1 (HIV-1) gp120 glycoprotein that faces the transmembrane glycoprotein as well as patterns of cysteine and glycosylation site distribution that points to a similar two-domain organization in at least some lentiviruses. Here, high reliability models of the surface glycoproteins obtained with the AlphaFold algorithm are presented for the gp135 glycoprotein of the small ruminant caprine arthritis-encephalitis (CAEV) and visna lentiviruses and the betaretroviruses jaagsiekte sheep retrovirus (JSRV), mouse mammary tumor virus (MMTV) and consensus human endogenous retrovirus type K (HERV-K). The models confirm and extend the inner domain structural conservation in these viruses and identify two outer domains with a putative receptor binding site in the CAEV and visna virus gp135. The location of that site is consistent with patterns of sequence conservation and glycosylation site distribution in gp135. In contrast, a single domain is modeled for the JSRV, MMTV and HERV-K betaretrovirus envelope proteins that is highly conserved structurally in the proximal region and structurally diverse in apical regions likely to interact with cell receptors. The models presented here identify sites in small ruminant lentivirus and betaretrovirus envelope glycoproteins likely to be critical for virus entry and virus neutralization by antibodies and will facilitate their functional and structural characterization.

Insights into the Crystal Chemistry of the Serandite–Schizolite–Pectolite Series

ABSTRACT The compositional series {Na} [[M1+M2](Ca2XMn2–2X)Si3O8(OH)] includes the minerals serandite (X = 0), schizolite (X = 0.5), and pectolite (X = 1). Six crystals are structurally and chemically characterized in detail (four from Ilímaussaq, Greenland; two from Mont Saint-Hilaire, Québec, Canada): one serandite, one pectolite, and four schizolite crystals. Those originating from Greenland show up to 0.05 apfu LREE3+ (La + Ce + Pr + Nd + Eu + Gd). For each, all H atoms were located, and final R1 factors were below 4.4% (<R1> = 2.35%). The results are compared with previously published crystal structure data from an additional 16 samples, originating from worldwide (mostly) igneous environments. Across the series, for all investigated samples, Ca and Mn order preferentially at the octahedral M1 and M2 sites, respectively, following the exchange M2Ca + M1Mn ↔ M1Ca + M2Mn. Site-occupancies closely adhere to a two-site distribution coefficient, calculated here to be K = 20.0(5), for ideal mixing where activity coefficients approach unity. For the above order-disorder exchange, ΔHex is calculated to be –1.77 kcal. With knowledge of K, site assignment and species determination may be accurately made solely with compositional data, where 0 ≤ ΣCa < 0.55 apfu, serandite; 0.55 ≤ ΣCa < 1.45 apfu, schizolite; and 1.45 ≤ ΣCa ≤ 2 apfu, pectolite, with the dominant-constituent rule mandating M1Ca < M1Mn (M2Ca < M2Mn), serandite; M1Ca > M1Mn (M2Ca < M2Mn), schizolite; and M1Ca > M1Mn (M2Ca > M2Mn), pectolite. Polyhedral distortion and structural strain at the M1 and M2 sites, calculated using the equations of Robinson et al. (1971) and solutions to Kirchhoff network equations, respectively, show a predictable, cooperative variation across the entire compositional series; however, prominent discontinuities in distortion and strain behavior are observed for the schizolite composition.