Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.

Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology.

A genome-scale resource for in vivo tag-based protein function exploration in C. elegans.

Understanding the in vivo dynamics of protein localization and their physical interactions is important for many problems in biology. To enable systematic protein function interrogation in a multicellular context, we built a genome-scale transgenic platform for in vivo expression of fluorescent- and affinity-tagged proteins in Caenorhabditis elegans under endogenous cis regulatory control. The platform combines computer-assisted transgene design, massively parallel DNA engineering, and next-generation sequencing to generate a resource of 14,637 genomic DNA transgenes, which covers 73% of the proteome. The multipurpose tag used allows any protein of interest to be localized in vivo or affinity purified using standard tag-based assays. We illustrate the utility of the resource by systematic chromatin immunopurification and automated 4D imaging, which produced detailed DNA binding and cell/tissue distribution maps for key transcription factor proteins.

Van der Waals Magnetic Electrode Transfer for Two-Dimensional Spintronic Devices.

Two-dimensional (2D) materials are promising candidates for spintronic applications. Maintaining their atomically smooth interfaces during integration of ferromagnetic (FM) electrodes is crucial since conventional metal deposition tends to induce defects at the interfaces. Meanwhile, the difficulties in picking up FM metals with strong adhesion and in achieving conductance match between FM electrodes and spin transport channels make it challenging to fabricate high-quality 2D spintronic devices using metal transfer techniques. Here, we report a solvent-free magnetic electrode transfer technique that employs a graphene layer to assist in the transfer of FM metals. It also serves as part of the FM electrode after transfer for optimizing spin injection, which enables the realization of spin valves with excellent performance based on various 2D materials. In addition to two-terminal devices, we demonstrate that the technique is applicable for four-terminal spin valves with nonlocal geometry. Our results provide a promising future of realizing 2D spintronic applications using the developed magnetic electrode transfer technique.

Modifying electronic and optical properties of violet phosphorus through variable fluorine coverage.

We present a comprehensive investigation of the electronic properties of fluorinated monolayer violet phosphorus using first-principles calculations. Our results reveal a strong dependence of the electronic properties on the different fluorine coverages of fluorination. As the fluorine coverage increases, monolayer violet phosphorus undergoes a significant transition from a wide direct bandgap semiconductor to a narrow indirect bandgap semiconductor. Moreover, both semi-fluorinated and fully fluorinated monolayer violet phosphorus exhibit advantageous semiconducting characteristics, with a tunable bandgap of 0.50 ~ 1.04 eV under biaxial strain ranging from -6% to 6%. Notably, the fully fluorinated monolayer violet phosphorus demonstrates a higher coefficient of light absorption within the visible range. Therefore, our findings highlight the tunability of monolayer violet phosphorus properties through the absorption of various fluorine coverages, providing valuable insights for the design and development of novel semiconductor devices based on this material.

Quantum nonlinear effect in a dissipatively coupled optomechanical system.

A full-quantum approach is used to study the quantum nonlinear properties of a compound Michelson-Sagnac interferometer optomechanical system. By deriving the effective Hamiltonian, we find that the reduced system exhibits a Kerr nonlinear term with a complex coefficient, entirely induced by the dissipative and dispersive couplings. Unexpectedly, the nonlinearities resulting from the dissipative coupling possess non-Hermitian Hamiltonian-like properties preserving the quantum nature of the dispersive coupling beyond the traditional system dissipation. This protective mechanism allows the system to exhibit strong quantum nonlinear effects when the detuning (the compound cavity detuning Δc and the auxiliary cavity detuning Δe) and the tunneling coupling strength (J) of two cavities satisfy the relation J2 = ΔcΔe. Moreover, the additive effects of dispersive and dissipative couplings can produce strong anti-bunching effects, which exist in both strong and weak coupling conditions. Our work may provide a new way to study and produce strong quantum nonlinear effects in dissipatively coupled optomechanical systems.

Dermatology residents' perspectives on virtual dermatopathology education.

BACKGROUND: Dermatopathology education accounts for 30% of U.S. dermatology residency training. The COVID-19 pandemic expedited the implementation of virtual dermatopathology in place of traditional microscopy for resident education. This study examined U.S. dermatology residents' perceptions of virtual dermatopathology, as research in this area is lacking. METHODS: An anonymous, confidential, institutional review board-approved survey was electronically distributed to U.S. dermatology residents consisting of 16 questions comparing attitudes towards virtual and traditional dermatopathology education. Responses were n = 59. Statistical analysis was performed using SAS software. RESULTS: Participants believe virtual imaging is superior to conventional microscopy in schedule flexibility (96.6% vs. 1.7%, p < 0.0001), lecture convenience (94.8% vs. 0.0%, p < 0.0001), personal review (96.6% vs. 0.0%, p < 0.0001), cost-effectiveness (64.4% vs. 6.8%, p < 0.0001), and board exam preparation (52.5% vs. 16.9%, p = 0.0005). Conventional microscopy was favored for image quality (50.8% vs. 25.4%, p = 0.0127) and overall utility (50.8% vs. 27.1%, p = 0.0195). CONCLUSIONS: Our study supports virtual dermatopathology utilization as a valuable tool in dermatology residency training. Also it is shown that conventional microscopy training continues to play a key role. Further studies should examine whether, if ever, virtual dermatopathology could gradually replace conventional microscopy with the advent of newer and more powerful digital and scanning technology.

Noncanonical amino acid mutagenesis in response to recoding signal-enhanced quadruplet codons.

While amber suppression is the most common approach to introduce noncanonical amino acids into proteins in live cells, quadruplet codon decoding has potential to enable a greatly expanded genetic code with up to 256 new codons for protein biosynthesis. Since triplet codons are the predominant form of genetic code in nature, quadruplet codon decoding often displays limited efficiency. In this work, we exploited a new approach to significantly improve quadruplet UAGN and AGGN (N = A, U, G, C) codon decoding efficiency by using recoding signals imbedded in mRNA. With representative recoding signals, the expression level of mutant proteins containing UAGN and AGGN codons reached 48% and 98% of that of the wild-type protein, respectively. Furthermore, this strategy mitigates a common concern of reading-through endogenous stop codons with amber suppression-based system. Since synthetic recoding signals are rarely found near the endogenous UAGN and AGGN sequences, a low level of undesirable suppression is expected. Our strategy will greatly enhance the utility of noncanonical amino acid mutagenesis in live-cell studies.

Electroacupuncture and Growth Hormone for Pain Management Post-Quadriceps Ligament Reconstruction: A Prospective Study.

Objective: This study aimed to investigate the efficacy of electroacupuncture (EA) combined with growth hormone in alleviating pain and enhancing knee function following quadriceps ligament reconstruction. Methods: A prospective study was conducted, and a total of 90 patients exhibiting quadriceps atrophy after anterior cruciate ligament reconstruction were recruited between July 2020 and July 2022 from Shenzhen Pingle Orthopedic Hospital. They were randomly assigned to either the control group or the observation group , with 45 patients in each. The control group received routine rehabilitation training along with growth hormone treatment, while the observation group received routine rehabilitation training in addition to EA and growth hormone treatment. The study assessed the visual analogue score (VAS) for postoperative pain, knee function, and clinical outcomes in both groups. Results: The total effective rate in the observation group was significantly higher compared to the control group, with a statistically significant difference (P < .05). Initially, there were no significant differences between the two groups in peri-thigh atrophy index, VAS score, Lysholm score, knee swelling, knee stability, and range of motion (ROM) score (P > .05). However, after 3 and 6 months of treatment, significant reductions were observed in peri-thigh atrophy index, VAS score, knee swelling, and ROM score in the observation group compared to the control group (P < .05). Moreover, Lysholm score and knee stability significantly increased in the observation group (P < .05), with changes significantly higher than those in the control group (P < .05). Conclusions: EA combined with growth hormone treatment significantly improves postoperative pain and knee joint function in patients undergoing quadriceps ligament reconstruction. This combination therapy holds promise for enhancing rehabilitation outcomes in this patient population.

Preventing secondary screw perforation following proximal humerus fracture after locking plate fixation: a new clinical prognostic risk stratification model.

INTRODUCTION: After locking plate (LP) fixation, secondary screw perforation (SSP) is the most common complication in proximal humerus fracture (PHF). SSP is the main cause of glenoid destruction and always leads to reoperation. This study aimed to identify independent risk parameters for SSP and establish an individualized risk prognostic model to facilitate its clinical management. METHODS: We retrospectively reviewed the medical information of patients with PHF who underwent open reduction and internal LP fixation at one medical center (n = 289) between June 2013 and June 2021. Uni- and multivariate regression analyses identified the independent risk factors. A novel nomogram was formulated based on the final independent risk factors for predicting the risk of SSP. We performed internal validation through concordance indices (C-index) and calibration curves. To implement the clinical use of the model, we performed decision curve analyses (DCA) and risk stratification according to the optimal cutoff value. RESULTS: A total of 232 patients who met the inclusion criteria were enrolled. The incidence of SSP was 21.98% at the last follow-up. We found that fracture type (odds ratio [OR], 3.111; 95% confidence interval [CI], 1.223-7.914; P = 0.017), postoperative neck-shaft angle (OR, 4.270; 95% CI 1.622-11.239; P = 0.003), the absence of calcar screws (OR, 3.962; 95% CI 1.753-8.955; P = 0.003), and non-medial metaphyseal support (OR,7.066; 95% CI 2.747-18.174; P = 0.000) were independent predictors of SSP. Based on these variables, we developed a nomogram that showed good discrimination (C-index = 0.815). The predicted values of the new model were in good agreement with the actual values demonstrated by the calibration curve. Furthermore, the model's DCA and risk stratification (cutoff = 140 points) showed significantly higher clinical benefits. CONCLUSIONS: We developed and validated a visual and personalized nomogram that could predict the individual risk of SSP and provide a decision basis for surgeons to create the most optional management plan. However, future prospective and externally validated design studies are warranted to verify our model's efficacy.

Highly Selective N2 Electroreduction to NH3 Using a Boron-Vacancy-Rich Diatomic NbB Catalyst.

The ambient electrochemical N2 reduction reaction (NRR) is a future approach for the artificial NH3 synthesis to overcome the problems of high-energy consumption and environmental pollution by Haber-Bosch technology. However, the challenge of N2 activation on a catalyst surface and the competitive hydrogen evolution reaction make the current NRR unsatisfied. Herein, this work demonstrates that NbB2 nanoflakes (NFs) exhibit excellent selectivity and durability in NRR, which produces NH3 with a production rate of 30.5 µg h-1 mgcat -1 and a super-high Faraday efficiency (FE) of 40.2%. The high-selective NH3 production is attributed to the large amount of active B vacancies on the surface of NbB2 NFs. Density functional theory calculations suggest that the multiple atomic adsorption of N2 on both unsaturated Nb and B atoms results in a significantly stretched N2 molecule. The weakened NN triple bonds are easier to be broken for a biased NH3 production. The diatomic catalysis is a future approach for NRR as it shows a special N2 adsorption mode that can be well engineered.

Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis.

Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.

Optomechanical noise suppression with the optimal squeezing process.

Quantum squeezing-assisted noise suppression is a promising field with wide applications. However, the limit of noise suppression induced by squeezing is still unknown. This paper discusses this issue by studying weak signal detection in an optomechanical system. By solving the system dynamics in the frequency domain, we analyze the output spectrum of the optical signal. The results show that the intensity of the noise depends on many factors, including the degree or direction of squeezing and the choice of the detection scheme. To measure the effectiveness of squeezing and to obtain the optimal squeezing value for a given set of parameters, we define an optimization factor. With the help of this definition, we find the optimal noise suppression scheme, which can only be achieved when the detection direction exactly matches the squeezing direction. The latter is not easy to adjust as it is susceptible to changes in dynamic evolution and sensitive to parameters. In addition, we find that the additional noise reaches a minimum when the cavity (mechanical) dissipation κ(γ) satisfies the relation κ = Nγ, which can be understood as the restrictive relationship between the two dissipation channels induced by the uncertainty relation. Furthermore, by taking into account the noise source of our system, we can realize high-level noise suppression without reducing the input signal, which means that the signal-to-noise ratio can be further improved.

Sensing of triglyceride concentration in blood solution using photoacoustic microscopy.

The level of triglyceride (TG) in blood is essential to human health, and hypertriglyceridemia (TG level > 150 mg/dL) would lead to cardiovascular disease and acute pancreatitis that threaten human life. Routine methods for measuring the TG level in blood depend on a lipid panel blood test, which is invasive and not convenient. Here, we use photoacoustic (PA) microscopy to test the PA amplitude of blood solutions (based on hemoglobin powder as well as flowing sheep blood) with different TG concentrations. Interestingly, we observe that the PA amplitude increases with increasing TG concentration in blood solutions, which is attributed to the increase of the Grüneisen coefficient. The preliminary in vitro study shows that the PA methodology is able to detect the TG level down to 450 mg/dL. This finding provides an opportunity for using photoacoustics to noninvasively diagnose hypertriglyceridemia.

Rhodamine-based fluorescent sensors for the rapid and selective off-on detection of salicylic acid and their use in plant cell imaging.

Salicylic acid (SA) is a key hormone that regulates plant growth and immunity, and understanding the physiologic processes induced by SA enables the development of highly pathogen-resistant crops. Here, we report the synthesis of three new SA-sensors (R1-R3) from hydroxyphenol derivatives of a rhodamine-acylhydrazone scaffold and their characterization by NMR and HRMS. Spectroscopic analyses revealed that structural variations in R1-R3 resulted in sensors with different sensitivities for SA. Sensor R2 (with the 3-hydroxyphenyl modification) outperformed R1 (2-hydroxyphenyl) and R3 (4-hydroxyphenyl). The SA-detection limit of R2 is 0.9 µM with an ultra-fast response time (<60 s). In addition, their plant imaging indicated that designed sensor R2 is useful for the further study of SA biology and the discovery and development of new inducers of plant immunity.

The repair and regeneration mechanism of platelet-rich fibrin-promoting tissue after alveolar bone defect through the notch pathway.

This work investigated the effects of platelet-rich fibrin (PRF) combined with bone mesenchymal stem cells (BMSCs) on the repair of alveolar bone defect (ABD) and the related mechanism of the Notch1/Wnt3a signaling pathway. 28 healthy male New Zealand white rabbits were selected to prepare the BMSCs and PRF. Rabbits were rolled into a combination group (implanted with PRF + BMSCs for treatment), a PRF group (treated with PRF) a BMSC group (BMSCs for treatment), and a control group (Ctrl group, no material implantation), with 7 rabbits in each. The Notch1, Wnt3a, bone morphogenetic protein 9 (BMP9), and p-JNK in rabbits in various groups were compared. It was found that Notch1 and Wnt3a in the combination group were sharply higher than those in the PRF and BMSC groups at postoperative 5 and 10 weeks, exhibiting great differences (P<0.05). The osteocalcin (OCN) and alkaline phosphatase (ALP) in the combination group were higher based on those in the PRF group, BMSC group, and Ctrl group (all P<0.05). Meanwhile, BMP9 and P-JNK proteins in the combination group were much higher than those in the PRF, BMSC, and Ctrl groups, presenting obvious differences (P<0.05). The results revealed that PRF + BMSCs could more effectively downregulate the Notch1 and Wnt3a and activate the Notch1/Wnt3a signaling pathway, thus promoting the osteogenesis of ABD and improving the repair effect.

Proximity-enhanced protein crosslinking through an alkene-tetrazine reaction.

The inverse electron demand Diels-Alder (iEDDA) reaction between a tetrazine and a strained alkene has been widely explored as useful bioorthogonal chemistry for selective labeling of biomolecules. In this work, we exploit the slow reaction between a non-conjugated terminal alkene and a tetrazine, and apply this reaction to achieving a proximity-enhanced protein crosslinking. In one protein subunit, a terminal alkene-containing amino acid was site-specifically incorporated in response to an amber nonsense codon. In another protein subunit, a tetrazine moiety was introduced through the attachment to a cysteine residue. Fast protein crosslinking was achieved due to a large increase in effective molarity of the two reactants that were brought to close proximity by the two interacting protein subunits. Such a proximity-enhanced protein crosslinking is useful for the study of protein-protein interactions.

Loss of POGZ alters neural differentiation of human embryonic stem cells.

POGZ is a pogo transposable element derived protein with multiple zinc finger domains. Many de novo loss-of-function (LoF) variants of the POGZ gene are associated with autism and other neurodevelopmental disorders. However, the role of POGZ in human cortical development remains poorly understood. Here we generated multiple POGZ LoF lines in H9 human embryonic stem cells (hESCs) using CRISPR/CAS9 genome editing. These lines were then differentiated into neural structures, similar to those found in early to mid-fetal human brain, a critical developmental stage for studying disease mechanisms of neurodevelopmental disorders. We found that the loss of POGZ reduced neural stem cell proliferation in excitatory cortex-patterned neural rosettes, structures analogous to the cortical ventricular zone in human fetal brain. As a result, fewer intermediate progenitor cells and early born neurons were generated. In addition, neuronal migration from the apical center to the basal surface of neural rosettes was perturbed due to the loss of POGZ. Furthermore, cortical-like excitatory neurons derived from multiple POGZ homozygous knockout lines exhibited a more simplified dendritic architecture compared to wild type lines. Our findings demonstrate how POGZ regulates early neurodevelopment in the context of human cells, and provide further understanding of the cellular pathogenesis of neurodevelopmental disorders associated with POGZ variants.

Sclareol attenuates liver fibrosis through SENP1-mediated VEGFR2 SUMOylation and inhibition of downstream STAT3 signaling.

Liver fibrosis is a key global health care burden. Sclareol, isolated from Salvia sclarea, possesses various biological activities. Its effect on liver fibrosis remains unknown. This study was proposed to evaluate the antifibrotic activity of sclareol (SCL) and explore its underlying mechanisms. Stimulated hepatic stellate cells served as an in vitro liver fibrosis model. The expression of fibrotic markers was assessed by western blot and real-time PCR. Two classical animal models, bile duct-ligated rats and carbon tetrachloride-treated mice, were utilized for the in vivo experiments. The liver function and fibrosis degree were determined by serum biochemical and histopathological analyses. VEGFR2 SUMOylation was analyzed using coimmunoprecipitation assay. Our results indicated that SCL treatment restricted the profibrotic propensity of activated HSCs. In fibrotic rodents, SCL administration alleviated hepatic injury and reduced collagen accumulation. Mechanistic studies indicated that SCL downregulated the protein level of SENP1 and enhanced VEGFR2 SUMOylation in LX-2 cells, which affected its intracellular trafficking. Blockade of the interaction between VEGFR2 and STAT3 was observed, resulting in the suppression of downstream STAT3 phosphorylation. Our findings demonstrated that SCL has therapeutic efficacy against liver fibrosis through mediating VEGFR2 SUMOylation, suggesting that SCL may be a potential candidate compound for its treatment.

Structural Characterization and Immunobiological Activity of Polysaccharides from Astragalus Oyster Mushroom.

When added to mushroom growing substrates, edible and medicinal herbs affect the mushrooms' nutritional and medicinal value. In this study, polysaccharides (P0OP-I and P15OP-I) were extracted and purified from oyster mushrooms grown on substrates supplemented with 0% and 15% Astragalus roots (P0 and P15), respectively, and their chemical structure and immunobiological activities were compared. P15OP-I and P0OP-I were extracted using ultrasound-assisted hot water and deproteinized with the Sevage method, depigmented with 30% H2O2, desalted with dialysis, and purified using DEAE-52 cellulose and Sephadex G-100 dextran column chromatography. The molecular weight of P0OP-I and P15OP-I was 21,706.96 and 20,172.65 Da, respectively. Both were composed of monosaccharides D-mannose, galacturonic acid, D-glucose, D-galactose, and L-arabinose but in different molar ratios, and both were connected by a pyranoside linkage. P15OP-I consisted of higher contents of mannose, glucose, galactose and arabinose and lower content of galacturonic acid as compared to P0OP-I. Both P0OP-I and P15OP-I induced NO and TNF-α production but did not show cytotoxic effect or induce ROS generation in RAW264.7 cells. P15OP-I showed a stronger ability to promote NO and TNF-α production relative to P0OP-I. In vitro experiments showed that the immunomodulatory activity of P0OP-I and P15OP-I in RAW264.7 macrophages were mediated by the JNK/MAPK, Erk/MAPK, and NF-κB signaling pathways. The results would be helpful for elucidation of the health promoting mechanism of Astragalus oyster mushrooms as a source of neutraceuticals.

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network.

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.