A two-task predictor for discovering phase separation proteins and their undergoing mechanism.

Liquid-liquid phase separation (LLPS) is one of the mechanisms mediating the compartmentalization of macromolecules (proteins and nucleic acids) in cells, forming biomolecular condensates or membraneless organelles. Consequently, the systematic identification of potential LLPS proteins is crucial for understanding the phase separation process and its biological mechanisms. A two-task predictor, Opt_PredLLPS, was developed to discover potential phase separation proteins and further evaluate their mechanism. The first task model of Opt_PredLLPS combines a convolutional neural network (CNN) and bidirectional long short-term memory (BiLSTM) through a fully connected layer, where the CNN utilizes evolutionary information features as input, and BiLSTM utilizes multimodal features as input. If a protein is predicted to be an LLPS protein, it is input into the second task model to predict whether this protein needs to interact with its partners to undergo LLPS. The second task model employs the XGBoost classification algorithm and 37 physicochemical properties following a three-step feature selection. The effectiveness of the model was validated on multiple benchmark datasets, and in silico saturation mutagenesis was used to identify regions that play a key role in phase separation. These findings may assist future research on the LLPS mechanism and the discovery of potential phase separation proteins.

PredLLPS_PSSM: a novel predictor for liquid-liquid protein separation identification based on evolutionary information and a deep neural network.

The formation of biomolecular condensates by liquid-liquid phase separation (LLPS) has become a universal mechanism for spatiotemporal coordination of biological activities in cells and has been widely observed to directly regulate the key cellular processes involved in cancer cell pathology. However, the complexity of protein sequences and the diversity of conformations are inherently disordered, which poses great challenges for LLPS protein calculations and experimental research. Herein, we proposed a novel predictor named PredLLPS_PSSM for LLPS protein identification based only on sequence evolution information. Because finding real and reliable samples is the cornerstone of building predictors, we collected anew and collated the LLPS proteins from the latest versions of three databases. By comparing the performance of the position-specific score matrix (PSSM) and word embedding, PredLLPS_PSSM combined PSSM-based information and two deep learning frameworks. Independent tests using three existing independent test datasets and two newly constructed independent test datasets demonstrated the superiority of PredLLPS_PSSM compared with state-of-the-art methods. Furthermore, we tested PredLLPS_PSSM on nine experimentally identified LLPS proteins from three insects that were not included in any of the databases. In addition, the powerful Shapley Additive exPlanation algorithm and heatmap were applied to find the most critical amino acids relevant to LLPS.

Study of composite Al2O3-Ce:Y3Mg1.8Al1.4Si1.8O12 ceramic phosphors.

The nominal composition of Al2O3-Ce:Y3Mg1.8Al1.4Si1.8O12 (A-Ce:YMASG) ceramic phosphors was fabricated by the vacuum sintering technique. The introduction of Al2O3 as a second phase partially enters the crystal lattice, which was confirmed by the composition changing of the samples through x-ray diffraction measurement. An impurity phase of Y4MgSi3O13 was observed in Ce:YMASG and disappeared with the introduction of Al2O3 at the concentration of 10 wt. %. When the content of Al2O3 increased to 30 and 50 wt. %, the second phase of Al2O3 was measured with actual weight ratios of 7.72 and 20.55 wt. %, respectively. The third phase of MgAl2O4 was found with the further addition of Al2O3at 70 wt. %; the weight ratios of Ce:YMASG, Al2O3, and MgAl2O4 were 68.756, 18.457, and 12.787 wt. %, respectively. The luminescent characters of the samples were measured by the photoluminescence spectra and electroluminescent spectra. With the increase of Al2O3 from 0 to 30 wt. %, the emission wavelength of Ce3+ plummeted from 610 to 552 nm, and the luminous efficacy of the samples increased from 35 to 65 lm/W.

Thermo-optical properties of terbium-aluminum garnet ceramics doped with silicon and titanium.

The Verdet constant and thermo-optical characteristics of a Si-doped and Ti-doped terbium aluminum garnet ceramics have been investigated. It is shown that the Verdet constant of the samples is ∼40% higher than that of TGG ceramics at 1064 nm. The best samples of Si:TAG have magneto-optical figures of merit more than 1.5 times greater than those of TGG ceramics. Si:TAG is better than TGG ceramics as a medium for high-power Faraday isolators.

Composite phase ceramic phosphor of Al2O3-Ce:YAG for high efficiency light emitting.

We present our achievement which is a ceramic plate phosphorable to produce white light when directly combined with commercially available blue light emitting diodes. The ceramic phase structure is that the Al2O3 particle is uniformly distributed in the Ce:YAG matrix. The Al2O3-Ce:YAG ceramic phosphor has a better luminous efficacy than the transparent Ce:YAG ceramic phosphor under the same test condition. The Al2O3 particle plays an important role in promoting the luminous efficacy. The Al2O3 particle changes the propagation of the light in ceramic, and it reduces the total internal reflection. That is why the composite phase ceramic phosphor improves extraction efficiency of light.

High-power Faraday isolators based on TAG ceramics.

The Faraday isolator based on a new magneto-optical medium--TAG (terbium aluminum garnet) ceramics was implemented and investigated experimentally. The magneto-optical element was temperature-stabilized using water cooling. The device provides a stable isolation ratio of 38 dB at 300 W laser power. Estimates show high performance of the device at a kilowatt laser power.

Improving characteristics of Faraday isolators based on TAG ceramics by cerium doping.

A Faraday isolator (FI) based on a new magneto-optical medium-Ce:TAG ceramics-has been fabricated and studied in experiments. Compensation of thermally induced depolarization in the FI increases the isolation ratio from 31 to 39 dB at the laser power of 300 W. Estimates predict stable operation of the device with kilowatt laser power.

Unveiling the destabilization of sp3 and sp2 bonds in transition metal-modified borohydrides to improve reversible dehydrogenation and rehydrogenation.

Borohydrides offer promise as potential carriers for hydrogen storage due to their high hydrogen concentration. However, the strong chemical bonding within borohydrides poses challenges for efficient hydrogen release during usage and restricts the re-hydrogenation process when attempting to regenerate the material. These high thermodynamic and kinetic barriers present obstacles in achieving reversible de-hydrogenation and re-hydrogenation of borohydrides, impeding their practical application in hydrogen storage systems. Employing density functional theory calculations, we conduct a comprehensive investigation into the influence of transition metals on both the BH4 cluster, a fundamental building block of borohydrides, and pure boron, which is formed as the end product following hydrogen release. Our research reveals correlations among the d-band center, work function, and surface energy of 3d and 4d transition metals. These correlations are directly linked to the weakening of bonding within the BH4 cluster when adsorbed on catalyst surfaces. On the other hand, we also explore how various intrinsic properties of transition metals influence the formation of boron vacancies and the hydrogen bonding process. By establishing a comprehensive correlation between the weakening of sp3 hybridization in the BH4 cluster and the sp2 hybridization in boron, we facilitate the identification and screening of optimal candidates capable of achieving reversible de-hydrogenation and re-hydrogenation in borohydrides.

SPREAD: An ensemble predictor based on DNA autoencoder framework for discriminating promoters in Pseudomonas aeruginosa.

Regulatory elements in DNA sequences, such as promoters, enhancers, terminators and so on, are essential for gene expression in physiological and pathological processes. A promoter is the specific DNA sequence that is located upstream of the coding gene and acts as the "switch" for gene transcriptional regulation. Lots of promoter predictors have been developed for different bacterial species, but only a few are designed for Pseudomonas aeruginosa, a widespread Gram-negative conditional pathogen in nature. In this work, an ensemble model named SPREAD is proposed for the recognition of promoters in Pseudomonas aeruginosa. In SPREAD, the DNA sequence autoencoder model LSTM is employed to extract potential sequence information, and the mean output probability value of CNN and RF is applied as the final prediction. Compared with G4PromFinder, the only state-of-the-art classifier for promoters in Pseudomonas aeruginosa, SPREAD improves the prediction performance significantly, with an accuracy of 0.98, recall of 0.98, precision of 0.98, specificity of 0.97 and F1-score of 0.98.

BaAl2O4:Eu2+-Al2O3 ceramics for wide range optical temperature sensing.

In this paper, BaAl2O4:Eu2+-Al2O3 ceramics were successfully prepared by spark plasma sintering (SPS). The optical properties of the multiphase ceramics doped with different concentrations of alumina were studied. Under excitation with 365 nm ultraviolet light, the luminescent color of the samples can be adjusted by changing the sintering temperature and the contents of alumina addition. The temperature dependent fluorescence spectra in the temperature range of 4 K-434 K were measured, and the temperature dependent fluorescence intensity ratio (FIR) was calculated. The FIR monotonically increased with the increase of temperature, indicating that the material could be used for temperature sensing. The absolute sensitivity Sa of the temperature sensing fluorescent material is larger than 0.005 K-1 at 334 K-434 K, and the relative sensitivity Sr is larger than 0.75% K-1 at 304 K-434 K. The results show that the BaAl2O4:Eu2+-Al2O3 ceramic is a promising non-contact temperature sensing material.

Selective phase synthesis of a high luminescence Gd2O3:Eu nanocrystal phosphor through direct solution combustion.

A Gd(2)O(3):Eu nanocrystal phosphor has been directly synthesized by a mild solution combustion method with a single step approach while avoiding further thermal annealing. The as-combusted Gd(2)O(3):Eu powders have been characterized by x-ray diffraction, infrared spectroscopy, transmission electron microscopy and photoluminescence spectra. The ratio of citric acid to metal nitrate (C/M) has a critical impact on the phase composition and crystallization of as-combusted Gd(2)O(3):Eu. An optimal C/M ratio of 0.7 gave highly crystalline powders with a single cubic phase, and a high luminescence intensity comparable with that of a commercial Y(2)O(3):Eu phosphor, even without further thermal annealing. This direct solution combustion method can be used to prepare a variety of high quality oxide nanocrystals.

Precise determination of anomalous scattering factors of Ge by using X-ray resonant scattering.

Variations of peak position of the rocking curve in the Bragg case are measured from a Ge thin crystal near the K-absorption edge. The variations are caused by a phase change of the real part of the atomic scattering factor. Based on the measurement, the values of the real part are determined with an accuracy of better than 1%. The values are the most reliable ones among those reported values so far as they are directly determined from the normal atomic scattering factors.

Anomalous scattering factor determined by semicircle fitting near the K-absorption edge of Ge.

It is shown that the locus of the f' + if'' plot in the complex plane, f' being determined from measured f'' by using the dispersion relation, looks like a semicircle very near the absorption edge of Ge. The semicircular locus is derived from a quantum theory of X-ray resonant scattering when there is a sharp isolated peak in f'' just above the K-absorption edge. Using the semicircular behavior, an approach is proposed to determine the anomalous scattering factors in a crystal by fitting known calculated values based on an isolated-atom model to a semicircular focus. The determined anomalous scattering factors f' show excellent agreement with the measured values just below the absorption edge. In addition, the phase determination of a crystal structure factor has been considered by using the semicircular behavior.

Antidiabetic effect of Pycnogenol French maritime pine bark extract in patients with diabetes type II.

A double-blind, placebo-controlled, randomized, multi-center study was performed with 77 diabetes type II patients to investigate anti-diabetic effects of the French maritime pine bark extract, Pynogenol. Supplementation with 100 mg Pycnogenol for 12 weeks, during which a standard anti-diabetic treatment was continued, significantly lowered plasma glucose levels as compared to placebo. HbA1(c) was also lowered; however, the difference as compared to placebo was statistically significant only for the first month. In the Pycnogenol-group endothelin-1 was significantly decreased, while 6-ketoprostaglandin F(1a) in plasma was elevated compared to placebo. Nitric oxide levels in plasma increased during treatment in both groups, but, differences did not reach statistical significance. Pycnogenol was well-tolerated with ECG, electrolytes, creatinine and blood urea nitrogen remaining unchanged in both groups. Mild and transient unwanted effects were reported for both groups without significant differences. Supplementation of Pycnogenol to conventional diabetes treatment lowers glucose levels and improves endothelial function.

Pycnogenol, French maritime pine bark extract, improves endothelial function of hypertensive patients.

A placebo-controlled, double-blind, parallel group study was performed with 58 patients to investigate effects of French maritime pine bark extract, Pycnogenol, on patients with hypertension. Supplementation of the patients with 100 mg Pycnogenol over a period of 12 weeks helped to reduce the dose of the calcium antagonist nifedipine in a statistically significant manner. The intake of Pycnogenol decreased endothelin-1 concentrations significantly compared to placebo while concentrations of 6-keto prostaglandin F1a in plasma were significantly higher compared to placebo. Values for nitric oxide (NO) in plasma increased in both groups, but the differences were not significant. Angiotensin II concentrations in plasma were lowered in the placebo group to a larger extent than in the Pycnogenol group. Heart rate, electrolytes and blood urea nitrogen were not changed during treatment in both groups of patients. Unwanted effects observed in both groups were of mild and transient nature, such as gastrointestinal problems, vertigo, headache and nausea. Differences in rate of side effects were not statistically significant between the two groups. Study results support a supplementation with Pycnogenol for mildly hypertensive patients.

Extinction effect and Borrmann effect of resonant dynamical scattering in the Bragg case.

In the Bragg case, X-ray beams suffer from anomalous absorption due to extinction effects without photo-absorption and are localized in the surface when X-ray total reflection occurs around an exact Bragg angle from a perfect crystal. On the other hand, the Borrmann effect due to anomalous transmission occurs in a thin perfect crystal with photo-absorption under a proper condition. There is a clear distinction between the extinction effect and the Borrmann effect. It is found that it is possible to separate the Borrmann effect from the extinction effect when the real part of the atomic scattering factor is zero. The calculated rocking curves agree well with the measured ones around the Ge K-absorption edge of the Ge 844 reflection.

The anticancer effect of cytotoxin 1 from Naja atra Cantor venom is mediated by a lysosomal cell death pathway involving lysosomal membrane permeabilization and cathepsin B release.

The cytotoxin family of cobra venom proteins, also called cardiotoxins, can activate both necrotic and apoptotic cell death pathways in cancer cells. Cytotoxin 1 (CTX1)from Naja atra Cantor venom is a 60 amino acid, 6698 Da protein with as yet untested anticancer efficacy and cell selectivity. We tested the toxicity of CTX1 on a number of cancer cell lines (MCF-7, P388, K562, and H22) and on one normal human cell line (16HBE). The rank order of cytotoxicity was MCF-7 > P388 ≈ K562 >H22 ≈ 16HBE, indicating that the effect of CTX1 on certain cancer cell types was relatively selective.Treatment with CTX1 greatly prolonged the survival of P388 ascites tumors bearing KM mice compared to cyclophosphamide treatment. Cell viability, apoptosis, and lysosomal permeability assays all demonstrated that CTX1 induced dose- and time-dependent cell death, with most cells exhibiting the morphological and biochemical features of late apoptosis and necrosis. Mitochondrial membrane potential was lost in CTX1-treated P388 cells. In addition, CTX1 induced an increase in both lysosomal membrane permeability and cathepsin B protease activity. These analyses reveal that CTX1 possesses significant and selective anticancer activity, likely by inducing programmed cell death through mitochondrial and/or lysosomal pathways.

Change of lattice distortion images in X-ray topography with resonant scattering in the Laue case.

Plane-wave topographs of X-rays for the GaAs 200 reflection were recorded using synchrotron radiation near the K-absorption edges of Ga and As. The topographic contrasts caused by lattice defects were changed by tuning the X-ray energy to four typical resonant scattering conditions. A sharp image of a lattice defect was observed when the Borrmann effect disappeared. When the Borrmann effect was conspicuous, an image of lattice distortion around a dislocation was observed, and its contrast was reversed by changing the phase factor of the resonant scattering. The lattice distortion image and its contrast reversal are discussed based on the resonant scattering dynamical theory by introducing the edge-dislocation model. The results show that topographs using resonant scattering should be a new characteristic method in synchrotron topography.