De novo design of drug-binding proteins with predictable binding energy and specificity.

The de novo design of small molecule-binding proteins has seen exciting recent progress; however, high-affinity binding and tunable specificity typically require laborious screening and optimization after computational design. We developed a computational procedure to design a protein that recognizes a common pharmacophore in a series of poly(ADP-ribose) polymerase-1 inhibitors. One of three designed proteins bound different inhibitors with affinities ranging from <5 nM to low micromolar. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free energy calculations performed directly on the designed models were in excellent agreement with the experimentally measured affinities. We conclude that de novo design of high-affinity small molecule-binding proteins with tuned interaction energies is feasible entirely from computation.

De novo-designed transmembrane proteins bind and regulate a cytokine receptor.

Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has the potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking the binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom-designed topologies.

Exciton dynamics of an aggregation-induced delayed fluorescence emitter in non-doped OLEDs and its application as host for high-efficiency red phosphorescent OLEDs.

Aggregation-induced delayed fluorescence (AIDF) materials have great potential in non-doped OLEDs due to their high photoluminescence (PL) quantum efficiency in film, high exciton utilization in the aggregated state and negligible efficiency roll-off at high luminance. However, their efficient mechanism in OLEDs is not yet well understood. Here, the exciton dynamics are used to investigate the electroluminescence (EL) mechanism of an AIDF emitter (4-(10H-phenoxazin-10-yl)phenyl)-(9-phenyl-9H-carbazol-3-yl)methanone (CP-BP-PXZ) in detail. It can be seen that the high efficiency and negligible efficiency roll-off in non-doped OLEDs based on CP-BP-PXZ as the emitter are ascribed to the effective reverse intersystem crossing (RISC) from high level triplet T2 to singlet S1 in the aggregated state. Furthermore, CP-BP-PXZ also exhibits excellent properties as a phosphor host due to its good AIDF properties. Thus, high-efficiency red phosphorescent OLEDs with low roll-off efficiency are successfully fabricated based on CP-BP-PXZ as the host. The maximum external quantum efficiency (EQEmax) reaches 23% and is maintained at 21% at a luminance of 1000 cd m-2.

Understanding the degradation mechanism of TTA-based blue fluorescent OLEDs by exciton dynamics and transient electroluminescence measurements.

The lifetime of blue organic light-emitting diodes (OLEDs) has always been a big challenge in practical applications. Blue OLEDs based on triplet-triplet annihilation (TTA) up-conversion materials have potential to achieve long lifetimes due to fusing two triplet excitons to one radiative singlet exciton, but there is a lack of an in-depth understanding of exciton dynamics on degradation mechanisms. In this work, we established a numerical model of exciton dynamics to study the impact factors in the stability of doped blue OLEDs based on TTA up-conversion hosts. By performing transient electroluminescence experiments, the intrinsic parameters related to the TTA up-conversion process of aging devices were determined. By combining the change of excess charge density in the emitting layer (EML) with aging time, it is concluded that the TTA materials are damaged by the excess electrons in the EML during ageing, which is the main degradation mechanism of OLEDs. This work provides a theoretical basis for preparing long-lifetime blue fluorescent OLEDs.

Analysis on coupling dynamic effect of human errors in aviation safety.

Human factors have increasingly been the leading cause of aircraft accidents. In most cases, human factors are not working alone, instead they are coupled with complex environment, mechanical factors, physiological and psychological factors of pilots, and organizational management, all of which form a complex aviation safety system. It is vital to investigate the coupling impact of human errors to avoid the occurrence of aviation accidents. In view that the Human Factors Analysis and Classification System (HFACS) provides a hierarchical classification principle of human errors in aviation accidents, and the System Dynamics (SD) approach is helpful to describe the risk evolution process, this paper establishes a hybrid HFACS-SD model by employing the HFACS and the SD approach to reveal the aviation human factors risk evolution mechanism, in which the HFACS is first used to capture the causal factors of human errors risk, and a coupling SD model is then built to describe the evolution of aviation human factors risk supported by historical data. The eigenvalue elasticity analysis is taken to identify critical loops and parameters that have a substantial impact on the system structural behavior, and the influence of parameters and loops is assessed. Simulation results show that the evolution trend of the accident rate can be replicated by the proposed HFACS-SD model, and the structural dominance analysis can efficiently identify critical loops and parameters. Simulation results further show that, with the recommended safety enhancement measures, the stability of the aviation system is increased, and thus lowering the overall accident rate.

A grooved conduit combined with decellularized tissues for peripheral nerve regeneration.

Peripheral nerve injury (PNI) is a common and severe clinical disease worldwide, which leads to a poor prognosis because of the complicated treatments and high morbidity. Autologous nerve grafting as the gold standard still cannot meet the needs of clinical nerve transplantation because of its low availability and limited size. The development of artificial nerve conduits was led to a novel direction for PNI treatment, while most of the currently developed artificial nerve conduits was lack biochemical cues to promote nerve regeneration. In this study, we designed a novel composite neural conduit by inserting decellularized the rat sciatic nerve or kidney in a poly (lactic-co-glycolic acid) (PLGA) grooved conduit. The nerve regeneration effect of all samples was analyzed using rat sciatic nerve defect model, where decellularized tissues and grooved PLGA conduit alone were used as controls. The degree of nerve regeneration was evaluated using the motor function, gastrocnemius recovery, and morphological and histological assessments suggested that the combination of a grooved conduit with decellularized tissues significantly promoted nerve regeneration compared with decellularized tissues and PLGA conduit alone. It is worth to note that the grooved conduits containing decellularized nerves have a promotive effect similar to that of autologous nerve grafting, suggesting that it could be an artificial nerve conduit used for clinical practice in the future.

The landscape of tolerated genetic variation in humans and primates.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

CIGAF-a database and interactive platform for insect-associated trichomycete fungi.

Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.

The landscape of tolerated genetic variation in humans and primates.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary: Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

EMBER multidimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains.

In neurodegenerative diseases, proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. However, there is a need to rapidly identify amyloid conformations in situ. Here, we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid-binding dyes to identify six distinct different conformational strains in vitro, as well as amyloid-ß (Aß) deposits in different transgenic mouse models. Our EMBER (excitation multiplexed bright emission recording) imaging method rapidly identifies conformational differences in Aß and tau deposits from Down syndrome, sporadic and familial Alzheimer's disease human brain slices. EMBER has in situ identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick's disease. In future studies, EMBER should enable high-throughput measurements of the fidelity of strain transmission in cellular and animal neurodegenerative diseases models, time course of amyloid strain propagation, and identification of pathogenic versus benign strains.

Evaluation of Facial Trauma Scars After Treating by Refining Plastic Surgery Techniques: A Follow-Up Study.

BACKGROUND: Although early debridement and refining plastic surgery techniques have been shown to be effective in the treatment of facial scars after trauma, their postoperative outcomes have not been quantitatively evaluated by the relevant Scar Cosmesis Assessment and Rating (SCAR) Scale. This study was designed to provide a fair assessment of the appearance and local symptoms of scars after treatment by refining plastic surgery techniques and to share the operational skills of surgical repairs. PATIENTS AND METHODS: Patients who received refining plastic surgery techniques were followed up, and facial scars were taken as high-definition photos, which were presented to 6 professional observers, 6 lay observers, and patients themselves to score the facial scars, including: scar spread, erythema, dyspigmentation, track marks or suture marks, hypertrophy/atrophy, itch and pain according to the SCAR. RESULTS: There were 56 patients who met the inclusion criteria and 25 agreed to participate in the study. No hypertrophic scar was found, and all patients were satisfied with the scar control effect. The scores showed that the treatment was achieved good results in scar spread (pro group: 0.85±0.55, lay group: 0.96±0.68, patients: 0.92±0.64), erythema (pro group: 0.34±0.26, lay group: 0.45±0.37, patients: 0.32±0.48), hypertrophy/atrophy (pro group: 0.21±0.27, lay group: 0.21±0.31, patients: 0.32±0.48), and there was no significant difference in the scores of the 3 observation groups ( P >0.05). However, it is difficult to eliminate dyspigmentation (pro group: 0.29±0.26, lay group: 0.30±0.30, patients: 0.40±0.50), track marks or suture marks (pro group: 0.45±0.33, lay group: 0.59±0.30, patients: 0.36±0.49). Two (8%) patients complained of itch and 1 (4%) patient complained of both itch and pain in the past 24 hours. CONCLUSIONS: The appearance of facial scars is satisfactory, the local symptoms are mild, and the evaluation among different aesthetics is affirmative after receiving refining plastic surgery techniques, which is just in line with the purpose of seeking beauty for the patients, and meanwhile can provide a good foundation for the comprehensive treatment of late scars, so that the treatment plan should be promoted.

EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains.

In neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. However, there is a need to rapidly identify amyloid conformations in situ . Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strains in vitro , as well as Aß deposits in different transgenic mouse models. Our EMBER (excitation multiplexed bright emission recording) imaging method rapidly identifies conformational differences in Aß and tau deposits from Down syndrome, sporadic and familial Alzheimer's disease human brain slices. EMBER has in situ identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick's disease. In future studies, EMBER should enable high-throughput measurements of the fidelity of strain transmission in cellular and animal neurodegenerative diseases models, time course of amyloid strain propagation, and identification of pathogenic versus benign strains. Significance: In neurodegenerative diseases proteins fold into amyloid structures with distinct conformations (strains) that are characteristic of different diseases. There is a need to rapidly identify these amyloid conformations in situ . Here we use machine learning on the full information available in fluorescent excitation/emission spectra of amyloid binding dyes to identify six distinct different conformational strains in vitro , as well as Aß deposits in different transgenic mouse models. Our imaging method rapidly identifies conformational differences in Aß and tau deposits from Down syndrome, sporadic and familial Alzheimer's disease human brain slices. We also identified distinct conformational strains of tau inclusions in astrocytes, oligodendrocytes, and neurons from Pick's disease. These findings will facilitate the identification of pathogenic protein aggregates to guide research and treatment of protein misfolding diseases.

Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology.

Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.

Increasing the operating lifetime of green phosphorescent organic light emitting diodes by reducing charge accumulation at the interface.

The stability and degradation mechanism of phosphorescent organic light emitting diodes (OLEDs) has been an unresolved problem in the past decades. Here, we found that electron accumulation at the interface between the electron blocking layer and the emitting layer is one of the reasons for device degradation. By inserting a thin layer with a shallower LUMO level than that of the electron transporting layer between the emitting layer and the electron transporting layer, we successfully reduced the density of electrons at the interface and greatly improved the lifetime of the resulting green phosphorescent OLEDs. The half decay lifetime LT50 at the initial luminance of 1000 cd m-2 reached as high as 399 h, which is 1.7 times longer than that of the compared device without a thin layer.

De novo design of drug-binding proteins with predictable binding energy and specificity.

The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low µM, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles.

A UHPLC-QTOF-MS/MS method with a superimposed multiple product ion strategy and esterase inhibitor improved sensitivity for the determination of xylocarpin H in rat plasma.

Xylocarpin H is a natural limonoid that has the potential to be a viable therapeutic candidate whether used alone or in combination with other medications. However, the pharmacokinetic properties of xylocarpin H are still not well understood and require further investigation. Sensitive analysis of xylocarpin H using liquid chromatography tandem triple-quadrupole mass spectrometry is challenging due to its structural feature. In the present research, a sensitive UHPLC-QTOF-MS/MS method was developed and validated to determine xylocarpin H in rat plasma. After simple methanol protein precipitation pretreatment with 50 mM esterase inhibitor bis(4-nitrophenyl)-phosphate (BNPP), xylocarpin H and Schisandrin (internal standard) were separated on a Synergi 4 u fusion-RP C18 column (50 mm × 3.0 mm, 4 µm) using isocratic elution with a mobile phase consisting of formic acid (0.1%) and acetonitrile, which were detected only within 3 min. The QTOF-MS/MS detection, which is a high-resolution mode, can accurately quantify analytes (ppm<5). The peak area of xylocarpin H was determined by adding the single peak areas of m/z 483.2013, m/z 465.1930 and m/z 345.1333 as the superimposed multiple product ions (SMPI) mode for data processing with optimized the high-resolution extraction widths of fragment ions at ± 0.05 Da. The S/N of the SMPI mode was found to be approximately two to seven times greater than the independent product ion mode. The linearity, precision, accuracy, and stability were completely validated for the method. Finally, the validated method was employed for the pharmacokinetic study of xylocarpin H in rats. The study indicated that the optimized high-resolution extraction widths of fragment ions and SMPI mode for data processing significantly improve the quantitative sensitivity of QTOF-MS/MS. In addition, esterase inhibitor BNPP was added in the process of sample treatment to inhibit the degradation of xylocarpin H in rat blood, which further improved the sensitivity of the quantitative method.

Xylomexicanins K-N: limonoids from the leaves and twigs of Xylocarpus granatum.

Six new compounds, xylomexicanins K-N (1-4), granasteroid (5) and 5-methoxy-2-pentylbenzofuran-7-ol (6), along with nine known compounds were isolated from the leaves and twigs of Xylocarpus granatum. Among them, 1 was a biogenetic precursor of 1,8,9-phragmalin limonoid, and 4 represent the first example of degraded A-ring limonoid. The structures of them were elucidated on the basis of one- and two-dimensional NMR spectroscopic data (including 1H, 13C-NMR, DEPT, 1H-1H COSY, HSQC, HMBC, and NOESY) and confirmed by high-resolution mass spectrometry.[Formula: see text].

Effects of short-term Huatou Chan training on health.

Previous studies have shown that perennial Chan training leads to improvements in brain functioning. However, few studies have investigated the effects of short-term Huatou Chan training. The current study explored the effects of a three-day Huatou Chan training on physical and emotional health, as well as brain state. Seventy healthy subjects were recruited and divided into two groups: the Huatou Chan group and the Control group. The Huatou Chan group received a 3-day Huatou Chan training, while the Control group waited for three days. Both groups completed a 6 min Brain State Index recording, the SCL-90, the brief profile of mood state, the meaning in life questionnaire, and the Index of Well-being, prior to and after the training or waiting period. Results showed that short-term Huatou Chan training had significant benefits on some aspects such as physical and emotional health (obsessive-compulsive, depression, hostility, and psychoticism), negative emotions (tension-anxiety, depression-dejection, anger-hostility, fatigue-inertia, and confusion-bewilderment), well-being, and attitude towards life. In addition, short-term Chan training can significantly improve brain state, as shown by the index of depression, anxiety, alerting and intelligence. This is the first study to provide direct evidence for the benefits of short-term intensive Huatou Chan training on physical and mental health.

Pt/(InGa)2O3/n-Si Heterojunction-Based Solar-Blind Ultraviolet Photovoltaic Detectors with an Ideal Absorption Cutoff Edge of 280 nm.

Ga2O3 is a popular material for research on solar-blind ultraviolet detectors. However, its absorption cutoff edge is 253 nm, which is not an ideal cutoff edge of 280 nm. In this work, by adjusting the ratio of In/Ga elements in the films, a high-quality (In0.11Ga0.89)2O3 film with an absorption cutoff edge of 280 nm was obtained, which owns a uniform surface and preferred orientation. On this basis, a solar-blind ultraviolet photovoltaic detector was constructed based on the Pt/(In0.11Ga0.89)2O3/n-Si heterojunction. When the device is exposed to 254 nm UV light, its open-circuit voltage (VOC) can reach 354 mV. Under 0 V bias, the device has a responsivity of 0.48 mA/W with a rise time of 0.47 s and a decay time of 0.37 s; under -7 V bias, the device achieves a responsivity of 16.96 mA/W with a rise time of 0.17 s and a decay time of 0.33 s. The spectral response characteristics of the device show that it has a selective response to solar-blind ultraviolet light (cutoff wavelength is 280 nm) with a rejection ratio (R254 nm/R310 nm), which is greater by more than two orders of magnitude. This work provides a good reference for adjusting the band gap of Ga2O3-based films and broadening their application fields.

Efficacy of Large Groove Texture on Rat Sciatic Nerve Regeneration In Vivo Using Polyacrylonitrile Nerve Conduits.

Physical guidance cues play an important role in enhancing the efficiency of nerve conduits for peripheral nerve injury repair. However, very few in vivo investigations have been performed to evaluate the repair efficiency of nerve conduits with micro-grooved inner textures. In this study, polyacrylonitrile nerve conduits were prepared using dry-jet wet spinning, and micro-grooved textures were incorporated on the inner surface. The nerve conduits were applied to treat 10 mm sciatic nerve gaps in Sprague-Dawley (SD) rats. Sixteen weeks following implantation, nerve function was evaluated based on heat sensory tests, electrophysiological assessments and gastrocnemius muscle mass measurements. The thermal latency reaction and gastrocnemii weight of SD rats treated with grooved nerve conduits were almost 25% faster and 60% heavier than those of SD rats treated with smooth nerve conduits. The histological and immunohistochemical stain analyses showed the repair capacity of inner grooved conduits was found to be similar to that of autografts. These results suggest that grooved nerve conduits with groove width larger than 300 µm significantly improve peripheral nerve regeneration by introducing physical guidance cues. The obtained results can support the design of nerve conduits and lead to the improvement of nerve tissue engineering strategies.