Transport Studies Research Articles

Localized Phonon Transport Study of GaN/SiO2 Core/shell Nanowires under Thermal-Stress Coupling.

In order to comprehensively explore the intricate mechanisms of thermo-mechanical interactions, this study employs the molecular dynamics method to investigate the influence of heat flux density, shell thickness and length, as well as stress on the radial interface phonon transport in GaN/SiO2 core/shell nanowire. Additionally, the surface eigenmode decomposition method is employed to analyze the interface phonon dispersion curves. The investigation reveals that with increasing heat flux density, internal thermal stresses intensify, leading to a complex distribution of thermal stresses within the system. Under the influence of thermal stress, the nonlinear acoustic properties interact with phonon scattering, resulting in the pronounced localization of interface phonons. Compressive stress causes an upshift in low-frequency phonons, while tensile stress induces a downward shift in the high-frequency optical branches at the interface. The localized phonon vibrations at the SiO2/GaN interface under nonuniform stress are identified as the primary cause for the abundant presence of nondispersive phonon modes at the radial interface. By elucidating the subtle interplay between lattice vibrations and stress fields, this study offers a novel and profound understanding of thermo-mechanical coupling effects, thereby providing innovative theoretical foundations for the design and performance management of thermoelectric devices.

Bose-Einstein condensation of non-ground-state caesium atoms

Bose-Einstein condensates of ultracold atoms serve as low-entropy sources for a multitude of quantum-science applications, ranging from quantum simulation and quantum many-body physics to proof-of-principle experiments in quantum metrology and quantum computing. For stability reasons, in the majority of cases the energetically lowest-lying atomic spin state is used. Here, we report the Bose-Einstein condensation of caesium atoms in the Zeeman-excited mf = 2 state, realizing a non-ground-state Bose-Einstein condensate with tunable interactions and tunable loss. We identify two regions of magnetic field in which the two-body relaxation rate is low enough that condensation is possible. We characterize the phase transition and quantify the loss processes, finding unusually high three-body losses in one of the two regions. Our results open up new possibilities for the mixing of quantum-degenerate gases, for polaron and impurity physics, and in particular for the study of impurity transport in strongly correlated one-dimensional quantum wires.

Modelling the dynamic gas/particle partitioning process of semi-volatile organic compounds emitted from point sources: Quantitative analysis and impact assessment

The deleterious impact of pollution point sources on the surrounding environment and human has long been a focal point of environmental research. When considering the local atmospheric dispersion of semi-volatile organic compounds (SVOCs) around the emission sites, it is essential to account the dynamic process for the gas/particle (G/P) partitioning, which involves the transition from an initial state to a steady state. In this study, we have developed a model that enables the prediction of the dynamic process for G/P partitioning of SVOCs, particularly considering the influence from emission. It is important to note that the dynamic processes of the concentrations of SVOCs in particle phase (CP) and in gas phase (CG) differ significantly. These differences arise due to the influence of two critical factors: particulate proportion of SVOCs in the emissions (ϕ0) and octanol-air partitioning coefficient (KOA). The validity of our model was assessed by comparing its predictions of the extremum value of the G/P partitioning quotient (KP) with the results obtained from the steady-state model. Remarkably, the characteristic time (tC), used to evaluate the timescale required for SVOCs to reach steady state, demonstrated different variations with KOA for CP and CG. Additionally, the values of tC were quite different for CP and CG, which were markedly influenced by ϕ0. For some SVOCs with high KOA values, it took approximately 35 h to reach steady state. Furthermore, it was found that the time to achieve 95 % of steady state (t95 ≈ 3tC) could reach approximately 105 h. This duration is sufficient for chemicals to disperse from their emission site to the surrounding areas. Therefore, it is crucial to consider the dynamic process of G/P partitioning in local atmospheric transport studies. Moreover, the influence of ϕ0 should be incorporated into future investigations examining the dynamic process of G/P partitioning.

Investigating SARS-CoV-2 virion material trafficking in syrian hamster neocortecal neurons

Introduction. Taking into account the experience on the new coronavirus infection COVID-19 pandemic, the relevance of studies assessing the cellular processes of SARS-CoV-2 virus assembly and transport to justify the choice of pharmacological action points has now markedly increased. The study was aimed at analyzing morphologically assessed events of SARS-CoV-2 life cycle in neocortical neurons using electron microscopy based on its traced wide prevalence in vivo and ability to penetrate the blood-brain barrier accounts. Materials and methods. Patient-derived SARS-CoV-2 virus was obtained and accumulated in Vero(B) cell culture. An electron microscopy study (EMR) of the viral particle transport was carried out in male Syrian hamsters. Animals were inoculated intranasally with 26 μl of virus culture in an amount of 4 × 104 TCID50/ml. Animals were euthanized on day 3, 7, and 28 post-infection. The extracted brain was prepared for EMR according to methods previously described in the literature. The results were recorded using an FEI Tecnai G2 Spitit BioTWIN electron microscope. Results. Using EMR, the morphological equivalents of virus transport variants in neocortical neurons were traced dynamically during infectious process in Syrian hamsters. After synthesis, viral membrane proteins are included in transport vesicles in the endoplasmic reticulum (ER) terminal tubules and enter the intermediate compartment (IC), a collection of smooth-walled membrane vesicles between the endoplasmic reticulum (ER) and the Golgi apparatus (AG). In the first 3 days post-infection, viral copies are included in the Ag in PC membrane-formed transport vesicles. Due to the large size, viral particles are restricted to the expanded ends of the mobile AG tanks. Morphologically, destruction of AG membranes was revealed on day 7 post-infection, which indicates an interaction between PC vesicles and preserved AG membrane elements or the implementation of their independent transport function to deliver SARS-CoV-2 virus to the cell periphery and further into the intercellular space. In the neuronal processes, the transport of mature SARS-CoV-2 viral particles associated with cytoskeletal elements was observed, which was not detected in other loci of virus persistence. Conclusion. Based on data obtained, it is possible to hypothesize about a cumulative importance for progression and persistence of SARS-CoV-2 infection in cortical neurons. Early signs of neuron infection are represented by characteristic changes in the nuclei, ER hypertrophy and formation of “viral factories” based on the ER, PC and AG. The formation of viral biomass occurs inside neurons; virion exit from target cells is more accompanied by cell death rather than if a virus becomes incorporated in the lysosomal-endosomal system.

Autonomous inland navigation: a literature review and extracontractual liability issues

Pilot tests for (semi-)autonomous transport via inland waterways are already taking place in Belgium and other European countries. However, the full commercial implementation of autonomous inland shipping might be hampered by liability issues. The allocation of liability, especially extracontractual liability, is an important concern for shipowners who want to invest in autonomous barges, and for other ecosystem actors. For this reason, a balanced risk distribution framework could boost the investment decision. A legal analysis of the current laws and regulations is necessary to evaluate whether they can be applied to new autonomous systems. The research approach consists of two steps. First, an in-depth literature review is carried out to determine whether extracontractual liability research has already been conducted and to highlight the gaps in autonomous inland waterways transport studies. Once it is proved that the vast majority of the research focuses on technology, it can be affirmed that there is a need to inquire about extracontractual liability. In the second part, thus, the two international Conventions on liability limitation and collision in inland navigation are examined.

Delivery of Vitamins through the Intraoral Cavity with Toothpaste Using Penetration Enhancers

Dental health is rarely deemed a significant factor for a healthy life despite its considerable impact on the human body. Many presume that regular dental check-ups and daily toothbrushing are sufficient to prevent oral health diseases. However, consuming certain nutrients is also required to attain a healthy oral cavity. Nutrients necessary for preserving dental health, namely calcium, phosphorus, fluorine, and various vitamins, contribute to the development, maintenance, and repair of oral tissues. Nevertheless, it can be challenging to be conscious of taking such nutrients on a daily basis. In this study, aiming to abolish such inconveniences, vitamins essential for dental health were combined in a toothpaste formulation with penetration enhancers (PEs) to achieve intraoral delivery of the vitamins while toothbrushing. Multiple tests were performed to evaluate the characteristics of the intraoral vitamin-delivery toothpaste (IOVT), such as abrasiveness and antibacterial strength tests. The same tests were also conducted on three different commercial toothpaste to draw comparisons with the IOVT. Additionally, to verify the IOVT’s penetration capability, a mass transport study, and a transepithelial electric resistance (TEER) value test were conducted using nightcrawlers’ skin. The data collected demonstrated congruency between multiple characteristics of the IOVT and those of the commercial toothpaste. Our key finding was that the greater TEER values demonstrated the high plausibility of effective intraoral delivery of vitamins, assisted by PEs, as components of the IOVT.

Identification of iodotyrosines as novel substrates for the thyroid hormone transporter MCT8.

Background Monocarboxylate transporter 8 (MCT8) is the most specific thyroid hormone transporter identified to date, deficiency of which has been associated with severe intellectual and motor disability and abnormal serum thyroid function tests. However, it is currently unknown if MCT8, like other thyroid hormone transporters, also accepts additional substrates, and if disruption of their transport may contribute to the observed phenotype. Methods In this study, we aimed to identify such substrates by applying LC-MS-based metabolome analysis in lysates of control and MCT8-overexpressing Xenopus oocytes. A subset of identified candidate substrates was validated by direct transport studies in transiently transfected COS-1 cells and human fibroblasts which endogenously express MCT8. Moreover, transport characteristics were determined, including transport saturation and cis-inhibition potency of thyroid hormone transport. Results Metabolome analysis identified 21 m/z ratios, corresponding to 87 candidate metabolites, with a 2.0-times differential abundance in MCT8-injected oocytes compared to controls. These metabolites included 3,5-diiodotyrosine (DIT) and several amino acids, including glutamate and glutamine. In accordance, MCT8-expressing COS-1 cells had 2.2-times lower intracellular accumulation of [125I]-DIT compared to control cells. This effect was largely blocked in the presence of T3 (IC50: 2.5±1.5 µM) or T4 (IC50: 5.8±1.3 µM). Conversely, increasing concentrations of DIT enhanced the accumulation of T3 and T4. The MCT8-specific inhibitor silychristin increased the intracellular accumulation of DIT in human fibroblasts. COS-1 cells expressing MCT8 also exhibited a 50%-reduction in intracellular accumulation of [125I]-3-monoiodotyrosine (MIT). In contrast, COS-1 cells expressing MCT8 did not alter the intracellular accumulation of [3H]-glutamate or [3H]-glutamine in. However, studies in human fibroblasts showed a 1.5-1.9-times higher glutamate uptake in control fibroblasts compared to fibroblasts derived from patients with MCT8 deficiency, which was not affected in the presence of silychristin. Conclusions Taken together, our results suggest that the iodotyrosines DIT and MIT can be exported by MCT8. MIT and DIT interfere with MCT8-mediated transport of thyroid hormone in vitro, and vice versa. Future studies should elucidate if MCT8, being highly expressed in thyroidal follicular cells, also transports iodotyrosines in vivo.

Molecular dynamics simulations of heat transport using machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution potentials

Molecular dynamics (MD) simulations play an important role in understanding and engineering heat transport properties of complex materials. An essential requirement for reliably predicting heat transport properties is the use of accurate and efficient interatomic potentials. Recently, machine-learned potentials (MLPs) have shown great promise in providing the required accuracy for a broad range of materials. In this mini-review and tutorial, we delve into the fundamentals of heat transport, explore pertinent MD simulation methods, and survey the applications of MLPs in MD simulations of heat transport. Furthermore, we provide a step-by-step tutorial on developing MLPs for highly efficient and predictive heat transport simulations, utilizing the neuroevolution potentials as implemented in the GPUMD package. Our aim with this mini-review and tutorial is to empower researchers with valuable insights into cutting-edge methodologies that can significantly enhance the accuracy and efficiency of MD simulations for heat transport studies.

Characterization of herpetrione amorphous nanoparticles stabilized by hydroxypropylmethyl cellulose and its absorption mechanism in vitro

Herpetrione(HPE) is an effective compound that has been used in the treatment of liver diseases. To improve its dissolution and absorption, herpetrione nanosuspensions was prepared. Nanosuspensions were proved to achieve intact absorption in vivo. However, the transport mechanisms are not fully understood, especially lack of direct evidence of translocation of particulates. In this study, an environment-responsive dye, P4, was loaded into herpetrione amorphous nanoparticles (HPE-ANPs) to elucidate the absorption and transport mechanism of the nanoparticles. And the amount of HPE and nanoparticles in the samples were quantified using HPLC/LC-MS/MS and IVIS with the model of Caco-2 and Caco-2/HT29-MTX. Results demonstrated that HPE is mainly taken up by passive diffusion in the form of free drugs, while HPE-ANPs are internalized by an energy dependent active transport pathway or intracellular endocytosis. It is speculated that HPE-ANPs may change the original entry pathway of drug molecules. Furthermore, the presence of mucus layer and the use of HPMC E15 may contribute to drug absorption to some extent. Transcellular transport study indicates that HPE-ANPs has a poor absorption. In conclusion, the differences in the absorption behavior trends of HPE-ANPs are caused by the difference in particle properties and the form of existence of the drug.

Water transport in PEMFC with metal foam flow fields: Visualization based on AI image recognition

Water transport is an essential process in proton exchange membrane fuel cells (PEMFC). For the novel metal foam flow fields, water transport is difficult to be visualized and still remains inadequately understood. In this work, for the first time, the two-phase flows in the metal foam flow fields of a transparent PEMFC was visualized by using an artificial intelligence (AI) image recognition method. In order to distinguish water from the metal foam ligaments, a scoring system was developed, which effectively solved the problem of inconsistent reflectance of liquid water between the ligament and the gas diffusion layer. According to the state of liquid water, the scoring system categorized the local images into three labels of waterless state, wet state, and slug state for AI image recognition network training. The trained AI image recognition model was then used to visualize the liquid water state in the metal foam flow fields under different operating conditions of relative humidity (RH), temperature, and inlet flow rate. Results show that, since the porous structure of the metal foam provides flexible transport paths, the PEMFC can operate effectively in a wide range of wet states. Even a 25% difference in the wet-state percentage between different operating conditions yields an almost consistent voltage. The increased slugs in the flow fields are the primary reason for the performance degradation of the PEMFC. At a high current density of 2 A/cm2, the voltage is as low as 0.03 V when the slug state occupies 35% of the flow fields (100% RH, 60 °C, 1.0 SLPM cathode inlet flow rate), and as high as 0.56 V when the slug state is absent in the flow fields (100% RH, 60 °C, 2.0 SLPM cathode inlet flow rate). The present work provides a novel approach for the studies of water transport in PEMFC.

Numerical Study of Water Transport and Operating Strategy for Fuel Cells with Segmented Water Management Flow Fields

Numerical Study of Water Transport and Operating Strategy for Fuel Cells with Segmented Water Management Flow Fields

Exploring travel behavior among women with disabilities in Jakarta

Although interest in the travel patterns and behavior of women is increasing in the field of transportation studies, there is a notable lack of discourse surrounding the travel behavior of women with disabilities. In fact, the current prevalence of disabilities among women exceeds that of men. Conversely, women with disabilities experience elevated levels of risk in transportation as a result of various circumstances, including budgetary constraints, safety and security concerns, and discriminatory practices. Conversations about the travel behavior exhibited by women with disabilities might contribute to developing appropriate transportation strategies and enhancing the productivity and mobility of women with disabilities. This study explored the behaviors of women with disabilities in DKI Jakarta, Indonesia. This was accomplished by examining the travel diaries of 12 participants for one week, followed by interviews. The findings indicate certain resemblances in travel behavior between women with disabilities and women in the general population. However, disparities are shown regarding trip chaining frequency, transportation modes utilized, and companionship during travels. This study also emphasizes the significance of advancing assistive technology in transportation to address the travel needs and barriers of women with disabilities. The aim is to enhance their independence, particularly while fulfilling significant domestic responsibilities and facilitating their engagement in the workforce.

Revolutionizing energy flow: Unleashing the influence of MHD in the presence of free convective heat transfer with radiation

This study investigates the complex interplay between radiation and magneto-flow on a porous, perpendicular plate immersed in a viscoelastic Maxwell fluid. The significance lies in understanding how the Lorentz force shapes dynamics and energy transfer in such systems, which is crucial for various industrial applications. Utilizing a comprehensive model that accounts for heat generation and absorption, we transform partial differential equations into ordinary ones through flow similarity analysis, providing valuable insights into the system's behavior. Employing the bvp4c solver in MATLAB, we evaluate velocity and energy profiles in Maxwell fluid flow. Graphical representations allow for a thorough examination of the influence of thermophysical parameters. Our findings reveal an intensified velocity profile attributed to prolonged material relaxation times.Furthermore, temperature profiles progressively increase with higher radiation and porous parameters. These results hold significant implications for industrial applications, particularly in Maxwell fluids' heat transport studies. Insights from this research can inform the design and optimization of systems such as ovens, boilers, cross-flow heat exchangers, and solar panels, enhancing efficiency and performance. Overall, this study contributes novel insights that advance understanding beyond previous efforts in the literature, paving the way for further exploration in this field. The primary finding of this study indicates that as the Rayleigh number increases, the velocity profile experiences an increase, whereas the temperature profile shows a decrease.

Transcriptomic and western blot characterisation of the human CLEFF4 clone, a new rapid cell line replacement for the Caco2 model

The CLEFF4 sub clone from stock late passage Caco2 cells has a unique property of being able to develop polarised cell monolayers with high P-gp expression and tight junctions much quicker than the original cell line. Instead of being useful for transport studies 21–24 days after initiating culture, the CLEFF4 cell line matures in 5–6 days with tight junctions surpassing that of 3 week old Caco2 cells in that time frame [1].This has enabled the CLEFF4 cell line to provide measures of apparent permeability for potential drug candidates, so important for pre-clinical drug development, 4 times faster than the original cell line. RNA samples were collected and analysed at days 4 and 7 of culture over a 3 year period and had full RNA transcriptome analysed by the ranaseq.eu open bioinformatics platform. Protein was also collected from day 4 to day 22 of culture. Differential expression data from the FASTQ files have shown significant differences in expression in multiple genes involved with drug efflux, tight junctions, phase 2 metabolism and growth factors, which have been confirmed from protein determination that may hold the key to understanding accelerated human cell maturation. These gene expression results may be significant for other tissues beyond the gastrointestinal tract, and potentially for accelerated cell growth for the new field of laboratory grown tissues for organ replacement. The data also confirms the different genetic expression in CLEFF4 cells compared to Caco2 and the stable nature of the different expression over many years.

Comparative Analysis of the Physiological and Transport Functions of Various Sources of Renal Proximal Tubule Cells Under Static and Fluidic Conditions in PhysioMimix{trade mark, serif} T12 Platform.

In vitro models that can faithfully replicate critical aspects of kidney tubule function such as directional drug transport are in high demand in pharmacology and toxicology. Accordingly, development and validation of new models is underway. The objective of this study was to characterize physiological and transport functions of various sources of human renal proximal tubule epithelial cells (RPTECs). We tested TERT1-immortalized RPTEC, including OAT1-, OCT2- or OAT3-overexpressing variants, and primary RPTECs. Cells were cultured on transwell membranes in static (24-well transwells) and fluidic (transwells in PhysioMimix{trade mark, serif} T12 organ-on-chip with 2 mL/s flow) conditions. Barrier formation, transport, and gene expression were evaluated. We show that two commercially available primary RPTECs were not suitable for studies of directional transport on transwells because they formed a substandard barrier even though they exhibited higher expression of transporters, especially under flow. TERT1-parent, -OAT1 and -OAT3 cells formed robust barriers, but were unaffected by flow. TERT1-OAT1 cells exhibited inhibitable para-aminohippurate transport, it was enhanced by flow. However, efficient tenofovir secretion and perfluorooctanoic acid reabsorption by TERT1-OAT1 cells were not modulated by flow. Gene expression showed that TERT1 and TERT1-OAT1 cells were most correlated with human kidney than other cell lines, but that flow did not have noticeable effects. Overall, our data show that addition of flow to in vitro studies of the renal proximal tubule may afford benefits in some aspects of modeling kidney function, but that careful consideration of the impact such adaptations would have on the cost and throughput of the experiments is needed. Significance Statement The topic of reproducibility and robustness of the complex microphysiological systems is looming large in the field of biomedical research; therefore, the uptake of these new models by the end-users is slow. This study systematically compared various RPTEC sources and experimental conditions, aiming to identify the level of model complexity needed for testing renal tubule transport. We demonstrate that while tissue chips may afford some benefits, their throughput and complexity need careful consideration in each context of use.

Transport of Non-Steroidal Anti-Inflammatory Drugs across an Oral Mucosa Epithelium In Vitro Model.

Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most prescribed drugs to treat pain or fever. However, oral administration of NSAIDs is frequently associated with adverse effects due to their inhibitory effect on the constitutively expressed cyclooxygenase enzyme 1 (COX-1) in, for instance, the gastrointestinal tract. A systemic delivery, such as a buccal delivery, of NSAIDs would be beneficial and additionally has the advantage of a non-invasive administration route, especially favourable for children or the elderly. To investigate the transport of NSAIDs across the buccal mucosa and determine their potential for buccal therapeutic usage, celecoxib, diclofenac, ibuprofen and piroxicam were tested using an established oral mucosa Transwell® model based on human cell line TR146. Carboxyfluorescein and diazepam were applied as internal paracellular and transcellular marker molecule, respectively. Calculated permeability coefficients revealed a transport ranking of ibuprofen > piroxicam > diclofenac > celecoxib. Transporter protein inhibitor verapamil increased the permeability for ibuprofen, piroxicam and celecoxib, whereas probenecid increased the permeability for all tested NSAIDs. Furthermore, influence of local inflammation of the buccal mucosa on the transport of NSAIDs was mimicked by treating cells with a cytokine mixture of TNF-α, IL-1ß and IFN-γ followed by transport studies with ibuprofen (+ probenecid). Cellular response to pro-inflammatory stimuli was confirmed by upregulation of cytokine targets at the mRNA level, increased secreted cytokine levels and a significant decrease in the paracellular barrier. Permeability of ibuprofen was increased across cell layers treated with cytokines, while addition of probenecid increased permeability of ibuprofen in controls, but not across cell layers treated with cytokines. In summary, the suitability of the in vitro oral mucosa model to measure NSAID transport rankings was demonstrated, and the involvement of transporter proteins was confirmed; an inflammation model was established, and increased NSAID transport upon inflammation was measured.

Current-induced spin polarization in chiral tellurium: A first-principles quantum transport study

Current-induced spin polarization in chiral tellurium: A first-principles quantum transport study

Treatment of tibial bone defects caused by infection: a retrospective comparative study of bone transport using a combined technique of unilateral external fixation over an intramedullary nail versus circular external fixation over an intramedullary nail

BackgroundThe purpose of the study was to assess and compare the clinical efficacy of bone transport with either circular or unilateral external fixators over an intramedullary nail in the treatment of tibial bone defects caused by infection.MethodsBetween May 2010 and January 2019, clinical and radiographic data were collected and analyzed for patients with bone defects caused by infection. Thirteen patients underwent bone transport using a unilateral external fixator over an intramedullary nail (Group A), while 12 patients were treated with a circular external fixator over an intramedullary nail (Group B). The bone and functional outcomes of both groups were assessed and compared using the Association for the Study and Application of the Method of the Ilizarov criteria, and postoperative complications were evaluated according to the Paley classification.ResultsA total of 25 patients were successfully treated with bone transport using external fixators over an intramedullary nail, with a mean follow-up time of 31.63 ± 5.88 months. There were no significant statistical differences in age, gender, previous surgery per patient, duration of infection, defect size, and follow-up time between Group A and Group B (P > 0.05). However, statistically significant differences were observed in operation time (187.13 ± 21.88 min vs. 255.76 ± 36.42 min, P = 0.002), intraoperative blood loss (39.26 ± 7.33 mL vs. 53.74 ± 10.69 mL, P < 0.001), external fixation time (2.02 ± 0.31 month vs. 2.57 ± 0.38 month, P = 0.045), external fixation index (0.27 ± 0.08 month/cm vs. 0.44 ± 0.09 month/cm, P = 0.042), and bone union time (8.37 ± 2.30 month vs. 9.07 ± 3.12, P = 0.032) between Group A and Group B. The excellent and good rate of bone and functional results were higher in Group A compared to Group B (76.9% vs. 75% and 84.6% vs. 58.3%). Statistically significant differences were observed in functional results (excellent/good/fair/poor, 5/6/2/0 vs. 2/5/4/1, P = 0.013) and complication per patient (0.38 vs. 1.16, P = 0.012) between Group A and Group B.ConclusionsBone transport using a combined technique of external fixators over an intramedullary nail proved to be an effective method in treating tibial bone defects caused by infection. In comparison to circular external fixators, bone transport utilizing a unilateral external fixator over an intramedullary nail resulted in less external fixation time, fewer complications, and better functional outcomes.

Study of nonlinear gas transport in double-porous and double-permeable coal rocks based on the increasing fractal construction method

Study of nonlinear gas transport in double-porous and double-permeable coal rocks based on the increasing fractal construction method

Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F.

Glutamate transporters play key roles in nervous physiology by modulating excitatory neurotransmitter levels, when malfunctioning, involving in a wide range of neurological and physiological disorders. However, integral transmembrane proteins including the glutamate transporters remain notoriously difficult to study, due to their localization within the cell membrane. Here we present the structural bioinformatics studies of glutamate transporters and their water-soluble variants generated through QTY-code, a protein design strategy based on systematic amino acid substitutions. These include 2 structures determined by X-ray crystallography, cryo-EM, and 6 predicted by AlphaFold2, and their predicted water-soluble QTY variants. In the native structures of glutamate transporters, transmembrane helices contain hydrophobic amino acids such as leucine (L), isoleucine (I), and phenylalanine (F). To design water-soluble variants, these hydrophobic amino acids are systematically replaced by hydrophilic amino acids, namely glutamine (Q), threonine (T) and tyrosine (Y). The QTY variants exhibited water-solubility, with four having identical isoelectric focusing points (pI) and the other four having very similar pI. We present the superposed structures of the native glutamate transporters and their water-soluble QTY variants. The superposed structures displayed remarkable similarity with RMSD 0.528Å-2.456Å, despite significant protein transmembrane sequence differences (41.1%->53.8%). Additionally, we examined the differences of hydrophobicity patches between the native glutamate transporters and their QTY variants. Upon closer inspection, we discovered multiple natural variations of L->Q, I->T, F->Y and Q->L, T->I, Y->F in these transporters. Some of these natural variations were benign and the remaining were reported in specific neurological disorders. We further investigated the characteristics of hydrophobic to hydrophilic substitutions in glutamate transporters, utilizing variant analysis and evolutionary profiling. Our structural bioinformatics studies not only provided insight into the differences between the hydrophobic helices and hydrophilic helices in the glutamate transporters, but they are also expected to stimulate further study of other water-soluble transmembrane proteins.