Mixed-effect modeling of codon usage

textLogistic mixed effects models are used to determine whether optimal codons associate with two specific properties of the expressed protein: solvent accessibility, aggregation propensity, or evolutionary conservation. Both random components and fixed structures in the models are decided by following certain selection procedures. More models are also developed by considering different factor combinations using the same selection procedure. The results show that evolutionary conservation is the most important factor for predicting for the optimal codon usage for most amino acids; aggregation propensity is also an important factor, and solvent accessibility is the least important factor for most amino acids.The results of this analysis are consistent with the previous literature, provide more straightforward way to study the research question and also more information for the insight relationships.Statistic

Optimization of Millet Axial Flow Threshing and Separation Device Based on Discrete Element Method

The difficulties of threshing and separation of millet have not been solved yet which has restricted the development of the millet industry because of the special biological structure and lack of professional agricultural machinery. In order to improve the quality of millet harvest and meet the market demand for millet, in this paper, according to the branching structure of millet, the millet earhead model was established by Discrete Element Method. Using virtual models of millet and device, the simulation tests were carried out whose results have shown that the threshing effect of the rasp-bar threshing element is better than that of the teeth threshing element. Then the rotor structure was optimized into a combined type of the rasp-bar and the teeth. A three-factor five-level quadratic orthogonal rotation combination test was carried out whose results have shown that the combined rotor can meet the requirements of millet harvest

Roles of Social Capital in the Association Between Internalized Homophobia and Condomless Sex Among Men Who Have Sex With Men in Southwest China: A Four-Way Decomposition

Objectives: This study examined whether social capital (SC) mediated the association between internalized homophobia (IH) and condomless sex among men who have sex with men (MSM), with the interaction of SC and IH considered.Methods: A cross-sectional study was conducted between November 2018 and April 2019 in Sichuan Province, China. A total of 540 participants were recruited to investigate their IH, SC, and condomless sex. A four-way decomposition of causal mediation analysis was used to test SC’s roles in the association between IH and condomless sex.Results: Condomless sex was prevalent (46.7%) among the participants, which was significantly associated with IH [odds ratio (OR) = 1.70] and SC (OR = 0.55). A direct effect [excess risk ratio (RR = 0.32)] and an indirect effect (excess RR = 0.16) of SC were found to be significant in the association between IH and condomless sex. Heterogeneities in effects were observed when taking the SC’s domains (e.g., individual and family-based SC) as mediators. SC’s effects were significant only in the homosexual subgroup.Conclusion: IH-based intervention with consideration of SC can be tailored to MSM to decrease condomless sex and curb the spread of HIV, especially for the homosexual subgroup

Ground-State Tuning of Metal-Insulator Transition by Compositional Variations in BaIr\u3csub\u3e1−\u3cem\u3ex\u3c/em\u3e\u3c/sub\u3eRu\u3csub\u3e\u3cem\u3ex\u3c/em\u3e\u3c/sub\u3eO\u3csub\u3e3\u3c/sub\u3e (0 ≤ \u3cem\u3ex\u3c/em\u3e ≤ 1)

Hexagonal BaIrO3 is a magnetic insulator driven by the spin-orbit interaction (SOI), whereas BaRuO3 is an enhanced paramagnetic metal. Our investigation of structural, magnetic, transport, and thermal properties reveals that substitution of Ru4+ (4d4) ions for Ir4+ (5d5) ions in BaIrO3 reduces the magnitudes of the SOI and a monoclinic structural distortion and rebalances the competition between the SOI and the lattice degrees of freedom to render an evolution from a magnetic insulting state to a robust metallic state. The central findings of this paper are as follows: (1) light Ru doping (0 \u3c x ≤ 0.15) prompts simultaneous, precipitous drops in both the magnetic ordering temperature TN and the electrical resistivity, and (2) heavier Ru doping (0.41 ≤ x ≤ 0.9) induces a robust metallic state without any long-range magnetic order. All results suggest a critical role of the lattice degrees of freedom in determining the ground state in the heavy transition-metal oxides

Simultaneous Metal-Insulator and Antiferromagnetic Transitions in Orthorhombic Perovskite Iridate Sr\u3csub\u3e0.94\u3c/sub\u3eIr\u3csub\u3e0.78\u3c/sub\u3eO\u3csub\u3e2.68\u3c/sub\u3e Single Crystals

The orthorhombic perovskite SrIrO3 is a semimetal, an intriguing exception in iridates where the strong spin-orbit interaction coupled with electron correlations tends to impose an insulating state. We report results of our investigation of bulk single-crystal Sr0.94Ir0.78O2.68 or Ir-deficient, orthorhombic perovskite SrIrO3. It retains the same crystal structure as stoichiometric SrIrO3 but exhibits a sharp, simultaneous antiferromagnetic (AFM) and metal-insulator (MI) transition occurring in the basal-plane resistivity at 185 K. Above it, the basal-plane resistivity features an extended regime of almost linear temperature dependence up to 800 K but the strong electronic anisotropy renders an insulating behavior in the out-of-plane resistivity. The Hall resistivity undergoes an abrupt sign change and grows below 40 K, which along with the Sommerfeld constant of 20mJ/molK2 suggests a multiband effect. All results including our first-principles calculations underscore a delicacy of the paramagnetic, metallic state in SrIrO3 that is in close proximity to an AFM insulating state. The contrasting ground states in isostructural Sr0.94Ir0.78O2.68 and SrIrO3 illustrate a critical role of lattice distortions and Ir deficiency in rebalancing the ground state in the iridates. Finally, the concurrent AFM and MI transitions reveal a direct correlation between the magnetic transition and formation of an activation gap in the iridate, which is conspicuously absent in Sr2IrO4

Analysis of clinical characteristics of 617 patients with benign airway stenosis

IntroductionBenign airway stenosis (BAS), namely airway narrowing caused by a variety of benign lesions, can lead to varying degrees of breathing difficulties and even death due to asphyxia. This study aimed to elucidate the clinical characteristics of BAS, including etiology, treatment and pathology, by analyzing the clinical data of BAS patients.MethodsA retrospective analysis was conducted using the clinical data of 617 BAS cases from January 2017 to December 2022. The pathological characteristics of the tissues were assessed by hematoxylin–eosin (H&E) and Masson’s staining. Besides, protein expression levels were determined by immunohistochemistry (IHC).ResultsA total of 617 patients were included (333 females [53.97%] and 284 males [46.03%]), with an average age of 48.93 ± 18.30 (range 14–87). Tuberculosis (n = 306, 49.59%) and trauma (n = 179, 29.02%) were the two leading etiologies of BAS, followed by airway foreign bodies (FB, n = 74, 11.99%), external compression (n = 25, 4.05%) and other etiologies (n = 33, 5.35%). Among 306 tuberculous tracheobronchial stenosis (TBTS) cases, most were females (n = 215, 70.26%), and TBTS mainly occurred in the left main bronchus (n = 97, 31.70%), followed by the right middle bronchus (n = 70 cases, 22.88%). The majority of TBTS patients (n = 259, 84.64%) were treated by interventional therapy. The condition of 179 BAS patients was ascribed to trauma, such as tracheal intubation (n = 92, 51.40%), tracheotomy (n = 69, 38.56%), injury (n = 15, 8.38%) and surgery (n = 3, 1.68%), which mostly took place in the trachea (n = 173, 96.65%). TAS patients mainly received interventional therapy (n = 168, 93.85%) and stent implantation (n = 47, 26.26%). The granulation tissues of BAS primarily featured inflammation, proliferation and fibrosis. IHC indicated the up-regulated expressions of transforming growth factor-β1 (TGF-β1), α-smooth muscle actin (α-SMA), collagen type I protein (COL-I) and vimentin, and the down-regulated expression of E-cadherin, which indicated fibrosis and epithelial-mesenchymal transition (EMT).ConclusionTuberculosis was the main etiology, and trauma was the secondary etiology. The granulation tissues of BAS were characterized by inflammation, fibrosis and probably EMT. Comprehensive interventional therapy is an effective method of treating BAS

Lattice-Tuned Magnetism of Ru\u3csup\u3e4+\u3c/sup\u3e(4\u3cem\u3ed\u3c/em\u3e\u3csup\u3e4\u3c/sup\u3e) Ions in Single Crystals of the Layered Honeycomb Ruthenates Li\u3csub\u3e2\u3c/sub\u3eRuO\u3csub\u3e3\u3c/sub\u3e and Na\u3csub\u3e2\u3c/sub\u3eRuO\u3csub\u3e3\u3c/sub\u3e

We synthesize and study single crystals of the layered honeycomb lattice Mott insulators Na2RuO3 and Li2RuO3 with magnetic Ru4+(4d4) ions. The newly found Na2RuO3 features a nearly ideal honeycomb lattice and orders antiferromagnetically at 30 K. Single crystals of Li2RuO3 adopt a honeycomb lattice with either C2/m or more distorted P21/m below 300 K, depending on detailed synthesis conditions. We find that Li2RuO3 in both structures hosts a well-defined magnetic state, in contrast to the singlet ground state found in polycrystalline Li2RuO3. A phase diagram generated based on our results uncovers a new, direct correlation between the magnetic ground state and basal-plane distortions in the honeycomb ruthenates

Decoupling of the Antiferromagnetic and Insulating States in Tb-Doped Sr\u3csub\u3e2\u3c/sub\u3eIrO\u3csub\u3e4\u3c/sub\u3e

Sr2IrO4 is a spin-orbit-coupled insulator with an antiferromagnetic (AFM) transition at TN=240K. We report results of a comprehensive study of single-crystal Sr2Ir1−xTbxO4(0≤x≤0.03). This study found that a mere 3% (x=0.03) of tetravalent Tb4+(4f7) substituting for Ir4+ (rather than Sr2+) completely suppresses the long-range collinear AFM transition but retains the insulating state, leading to a phase diagram featuring a decoupling of the magnetic interactions and charge gap. The insulating state at x=0.03 is characterized by an unusually large specific heat at low temperatures and an incommensurate magnetic state having magnetic peaks at (0.95,0,0) and (0,0.95,0) in the neutron diffraction, suggesting a spiral or spin-density-wave order. It is apparent that Tb doping effectively changes the relative strength of the spin-orbit interaction (SOI) and the tetragonal crystal electric field and enhances the Hund\u27s rule coupling that competes with the SOI, and destabilizes the AFM state. However, the disappearance of the AFM is accompanied by no metallic state chiefly because an energy level mismatch for the Ir and Tb sites weakens charge carrier hopping and causes a persistent insulating state. This work highlights an unconventional correlation between the AFM and insulating states in which the magnetic transition plays no critical role in the formation of the charge gap in the iridate

Coexisting Charge and Magnetic Orders in the Dimer-Chain Iridate Ba\u3csub\u3e5\u3c/sub\u3eAlIr\u3csub\u3e2\u3c/sub\u3eO\u3csub\u3e11\u3c/sub\u3e

We have synthesized and studied single-crystal Ba5AlIr2O11 that features dimer chains of two inequivalent octahedra occupied by tetravalent Ir4+(5d5) and pentavalent Ir5+(5d4) ions, respectively. Ba5AlIr2O11 is a Mott insulator that undergoes a subtle structural phase transition near TS=210K and a magnetic transition at TM=4.5K; the latter transition is surprisingly resistant to applied magnetic fields μoH≤12T but more sensitive to modest applied pressure (dTM/dp≈+0.61K/GPa). All results indicate that the phase transition at TS signals an enhanced charge order that induces electrical dipoles and strong dielectric response near TS. It is clear that the strong covalency and spin-orbit interaction (SOI) suppress double exchange in Ir dimers and stabilize a novel magnetic state that is neither S=3/2 nor J=1/2, but rather lies in an “intermediate” regime between these two states. The novel behavior of Ba5AlIr2O11 therefore provides unique insights into the physics of SOI along with strong covalency in competition with double-exchange interactions of comparable strength

Ether phospholipids metabolism is a latent vulnerability for pancreatic cancer resistance

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