IAnimal: a cross-species omics knowledgebase for animals.

With the exponential growth of multi-omics data, its integration and utilization have brought unprecedented opportunities for the interpretation of gene regulation mechanisms and the comprehensive analyses of biological systems. IAnimal (https://ianimal.pro/), a cross-species, multi-omics knowledgebase, was developed to improve the utilization of massive public data and simplify the integration of multi-omics information to mine the genetic mechanisms of objective traits. Currently, IAnimal provides 61 191 individual omics data of genome (WGS), transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq) and genome annotation information for 21 species, such as mice, pigs, cattle, chickens, and macaques. The scale of its total clean data has reached 846.46 TB. To better understand the biological significance of omics information, a deep learning model for IAnimal was built based on BioBERT and AutoNER to mine 'gene' and 'trait' entities from 2 794 237 abstracts, which has practical significance for comprehending how each omics layer regulates genes to affect traits. By means of user-friendly web interfaces, flexible data application programming interfaces, and abundant functional modules, IAnimal enables users to easily query, mine, and visualize characteristics in various omics, and to infer how genes play biological roles under the influence of various omics layers.

Enhanced Photoelectric Properties of CsPbBr3 by SiO2 and TiO2 Bilayer Heterostructures.

CsPbBr3/SiO2 heterostructures were synthesized by the hydrolysis reaction of a mixture of CsPbBr3 nanocrystals (NCs) and (3-aminopropyl)triethoxysilane (APTS) in air. Compared with CsPbBr3 NCs, the CsPbBr3/SiO2 heterostructures exhibit stronger photoluminescence (PL) intensity, longer lifetime of PL (∼40.5 ns), and higher PL-quantum yield (PLQY, ∼86%). The carrier dynamics of CsPbBr3/SiO2 was detected by the transient absorption (TA) spectrum. The experimental results show that SiO2 passivates the surface traps of CsPbBr3 NCs and enhances the PL intensity. However, photoelectrochemical impedance spectra (PEIS) demonstrate that the impedance of CsPbBr3/SiO2 is higher than that of CsPbBr3 NCs, which reduces carrier transport and extraction. Because the application of CsPbBr3/SiO2 in optoelectronics is limited, CsPbBr3/SiO2/TiO2 heterostructures were synthesized by the further reaction of tetrabutyl titanate (TBT). The TiO2 coating can reduce the impedance of the CsPbBr3/SiO2. Importantly, ∼68% of the PL intensity of CsPbBr3/SiO2 is retained. Compared with CsPbBr3/SiO2 and CsPbBr3 NCs, the CsPbBr3/SiO2/TiO2 demonstrates faster carrier transport (κct = 2.4 × 109 s-1) and higher photocurrent density (J = 76 nA cm-2). In addition, CsPbBr3/SiO2/TiO2 shows good stability under (ultraviolet) UV irradiation, along with water stability and thermal stability. Therefore, the double protection approach can enhance the stability of CsPbBr3 NCs and tune the optoelectronic properties of CsPbBr3 NCs.

Dynamic range enhancement of self-referenced spectral interferometry with extended time excursion method by the cascaded Kerr lens process.

Self-referenced spectral interferometry with extended time excursion (SRSI-ETE) is a powerful method for single-shot characterization of the temporal contrast of a high peak power laser, which has high temporal resolution but a low dynamic range. Here, a temporal contrast reduction method is proposed that uses the cascaded Kerr lens process in two thin glass plates. Combined with the SRSI-ETE method, the measurement dynamic range of the method is increased about two orders of magnitude while having a 20 fs temporal resolution and a 40 ps time window in single shot.

Evaluation of different air distribution systems in a commercial airliner cabin in terms of comfort and COVID-19 infection risk.

The air distribution system in an airliner plays a key role in maintaining a comfortable and healthy environment in the aircraft cabin. To evaluate the performance of a novel displacement ventilation (DV) system and a traditional mixing ventilation (MV) system in an airliner cabin, this study conducted experiments and simulations in a seven-row cabin mockup. This investigation used ultrasonic anemometers and T-thermocouples to measure the air velocity, temperature and distribution of 1 µm and 5 µm particles. Simulation verifications were performed for these operating conditions, and additional scenarios with different occurrence source locations were also simulated. This study combined the Wells-Riley equation with a real case based on a COVID-19 outbreak among passengers on a long-distance bus to obtain the COVID-19 quanta value. Through an evaluation of the airflow organization, thermal comfort, and risk of COVID-19 infection, the two ventilation systems were compared. This investigation found that polydisperse particles should be used to calculate the risk of infection in airliner cabins. In addition, at the beginning of the pandemic, the infection risk with DV was lower than that with MV. In the middle and late stages of the epidemic, the infection risk with MV can be reduced when passengers wear masks, leading to an infection risk approximately equal to that of DV.

Corrigendum to "Evaluation of different air distribution systems in a commercial airliner cabin in terms of comfort and COVID-19 infection risk" Build. Environ., Volume 208, January 2022, 108590.

[This corrects the article DOI: 10.1016/j.buildenv.2021.108590.].

Multistep pulse compressor for 10s to 100s PW lasers.

High-energy tens (10s) to hundreds (100s) petawatt (PW) lasers are key tools for exploring frontier fundamental researches such as strong-field quantum electrodynamics (QED), and the generation of positron-electron pair from vacuum. Recently, pulse compressor became the main obstacle on achieving higher peak power due to the limitation of damage threshold and size of diffraction gratings. Here, we propose a feasible multistep pulse compressor (MPC) to increase the maximum bearable input and output pulse energies through modifying their spatiotemporal properties. Typically, the new MPC including a prism pair for pre-compression, a four-grating compressor (FGC) for main compression, and a spatiotemporal focusing based self-compressor for post-compression. The prism pair can induce spatial dispersion to smooth and enlarge the laser beam, which increase the maximum input and output pulse energies. As a result, as high as 100 PW laser with single beam or more than 150 PW through combining two beams can be obtained by using MPC and current available optics. This new optical design will simplify the compressor, improve the stability, and save expensive gratings/optics simultaneously. Theoretically, the output pulse energy can be increased by about 4 times using the MPC method in comparison to a typical FGC. Together with the multi-beam tiled-aperture combining method, the proposed tiled-grating based tiled-aperture method, larger gratings, or negative chirp pulse based self-compression method, several 100s PW laser beam is expected to be obtained by using this MPC method in the future, which will further extend the ultra-intense laser physics research fields.

Properties of the generation and propagation of spatiotemporal optical vortices.

Spatiotemporal optical vortex (STOV) light is a new type of vortex light with transverse orbital angular momentum (OAM) which is different from conventional spatial vortex light. Understanding the properties of STOV are meaningful before STOV are applied. We present a theoretical study on the generation and propagation of spatiotemporal vortices step by step based on diffraction theory. The properties of the output pulses with different topological charges generated using 4 f pulse shaper in both the near-field and the far-field are analyzed. Using spiral phase mask, the intensity profiles of the output pulses immediately after the 4 f pulse shaper are of multi-lobe structures. With energies circulating around the phase singularity in the space-time plane, energy coupling occurs between the spatial and temporal domains in the wave packets during propagation, then the intensity profiles evolve into multi-hole shapes, and the holes tend to be merged for higher order STOV. The conservation of OAM in the space-time domain is shown clearly. The profiles of the output pulses in the near-field form donut rectangle shapes using π-step mask, and in the far-field, they split into a multi-lobe structure. The rules of the generation and evolution of STOV are revealed. The results demonstrate the physical properties of the STOV and the generation and propagation processes directly and clearly. It provides a guidance on the application of STOV.

Associations of indoor carbon dioxide concentrations, air temperature, and humidity with perceived air quality and sick building syndrome symptoms in Chinese homes.

The indoor environment influences occupants' health. From March 1, 2018, to February 28, 2019, we continuously monitored indoor temperature (T), relative humidity (RH), and CO2 concentration in bedrooms via an online system in 165 residences that covered all five climate zones of China. Meanwhile, we asked one specific occupant in each home to complete questionnaires about perceived air quality and sick building syndrome (SBS) symptoms at the end of each month. Higher CO2 concentration was significantly associated with a higher percentage of perceived stuffy odor and skin SBS symptoms. Higher relative humidity was associated with higher percentage of perceived moldy odor and humid air, while lower RH was associated with a higher percentage of perceived dry air. Occupants who lived in residences with high RH were less likely to have mucosal and skin SBS symptoms (adjusted odds ratio (AOR): 0.73-0.78). However, the benefit of high humidity for perceived dry air and skin dryness symptoms is weaker if there is a high CO2 concentration level.

Cross-polarized wave-generation-based single-shot fourth-order autocorrelator.

A single-shot fourth-order autocorrelator based on cross-polarized wave generation (XPW) is proposed for the temporal contrast measurement, where the XPW process has the advantages of higher energy conversion efficiency, more compact setup, and less sensitivity to misalignment in comparison to the self-diffraction process. The measurement dynamic of 1012 is obtained with only 6 mJ input laser pulse, where the input beam for XPW is focused by a cylindrical lens and XPW signal with the energy of 400 µJ and time duration of 27.2 fs is obtained. Furthermore, beta-barium borate crystal with the thickness of 6 mm and cutting angle of 56° is used for the sum-frequency generation process to benefit the correlation efficiency. The compact setup could help explore the temporal contrast property of the high-power laser pulse.

Multicolor concentric annular ultrafast vector beams.

Novel multicolor concentric annular ultrafast vector beams (MUCAU-VB) are firstly generated simply by using cascaded four-wave mixing (CFWM) in a glass plate pumped by two intense vector femtosecond pulses. A proof-of-principle experiment shows that up to 10 frequency up-conversion concentric annular radially polarized sidebands are obtained simultaneously based on CFWM process, where the spectra range of the first 7 order sidebands extending from 545 nm to 725 nm. The results prove the polarization transfer property from the pump beam to the signal beams even in the CFWM, a third-order optical parametric process. The pulse duration of the first order sideband is measured to be 74 fs which is according with those of two input beams. These novel MUCAU-VB, which are manipulated in temporal, spectral, spatial domain and polarization state simultaneously, are expected to apply in wide fields, such as manipulating particles and multicolor pump-probe experiments.

In-house beam-splitting pulse compressor for high-energy petawatt lasers.

One of the most significant bottlenecks in achieving kilojoule-level high-energy petawatt (PW) to hundreds-petawatt (100PW) lasers is the requirement of as large as meter-sized gratings so as to avoid the laser-induced damage in the compressor. High-quality meter-sized gratings have so far been difficult to manufacture. This paper proposes a new in-house (intra-) beam-splitting compressor based on the property that the damage threshold of gratings depends on the pulse duration. The proposed scheme will simultaneously improve the stability, save on expensive gratings, and simplify compressor size because the split beams share the first two parallel gratings. Furthermore, as the transmitted wavefront of a glass plate can be better and more precisely controlled than the diffraction wavefront of a large grating, we propose glass plates with designed transmitted wavefront to compensate for the wavefront distortion introduced by the second and third gratings, and other in-house optics, such as the beam splitter. This simple and economical method can compensate for the space-time distortion in the compressor, and thus improve focal intensity, which otherwise cannot be compensated by a deformable mirror outside the compressor. Together with a multi-beam tiled-aperture combining scheme, the proposed novel compressor provides a new scheme for achieving high-energy PW-100PW lasers or even exawatt lasers with relatively small gratings in the future.

Exogenous pancreatic kininogenase protects against renal fibrosis in rat model of unilateral ureteral obstruction.

Tissue kallikrein has protective function against various types of injury. In this study, we investigated whether exogenous pancreatic kininogenase (PK) conferred renoprotection in a rat model of unilateral ureteral obstruction (UUO) and H2O2-treated HK-2 cells in vitro. SD rats were subjected to UUO surgery, then PK (7.2 U/g per day, ip) was administered for 7 or 14 days. After the treatment, rats were euthanized; the obstructed kidneys were harvested for further examination. We found that PK administration significantly attenuated interstitial inflammation and fibrosis, and downregulated the expression of proinflammatory (MCP-1, TLR-2, and OPN) and profibrotic (TGF-ß1 and CTGF) cytokines in obstructed kidney. UUO-induced oxidative stress, closely associated with excessive apoptotic cell death and autophagy via PI3K/AKT/FoxO1a signaling, which were abolished by PK administration. We further showed that PK administration increased the expression of bradykinin receptors 1 and 2 (B1R and B2R) mRNA and the production of NO and cAMP in kidney tissues. Coadministration with either B1R antagonist (des-Arg9-[Leu8]-bradykinin) or B2R antagonist (icatibant) abrogated the renoprotective effects of PK, and reduced the levels of NO and cAMP in obstructed kidney. In H2O2-treated HK-2 cells, addition of PK (6 pg/mL) significantly decreased ROS production, regulated the expression of oxidant and antioxidant enzymes, suppressed the expression of TGF-ß1 and MCP-1, and inhibited cell apoptosis. Our data demonstrate that PK treatment protects against the progression of renal fibrosis in obstructed kidneys.

Generation of high-energy clean multicolored ultrashort pulses and their application in single-shot temporal contrast measurement.

We demonstrate the generation of 100-µJ-level multicolored femtosecond pulses based on a single-stage cascaded four-wave mixing (CFWM) process in a thin glass plate by using cylinder lenses. The generated high-energy CFWM signals can shift the central wavelength and have well-enhanced temporal contrast because of the third-order nonlinear process. They are innovatively used as clean sampling pulses of a cross-correlator for single-shot temporal contrast measurement. With a simple homemade setup, the proof-of-principle experimental results demonstrate the single-shot cross-correlator with dynamic range of 1010, temporal resolution of about 160 fs and temporal window of 50 ps. To the best of our knowledge, this is the first demonstration in which both the dynamic range and the temporal resolution of a single-shot temporal contrast measurement are comparable to those of a commercial delay-scanning cross-correlator.

Temporal contrast reduction techniques for high dynamic-range temporal contrast measurement.

A single-shot characterization of the temporal contrast of a petawatt laser pulse with a high dynamic-range, is important not only for improving conditions of the petawatt laser facility itself, but also for various high-intensity laser physics experiments, which is still a difficult problem. In this study, a new idea for improving the dynamic-range of a single-shot temporal contrast measurement using novel temporal contrast reduction techniques is proposed. The proof-of-principle experiments applying single stage of pulse stretching, anti-saturated absorption, or optical Kerr effect successfully reduce the temporal contrast by approximately one order of magnitude. Combining with the SRSI-ETE method, its dynamic-range characterization capability is improved by approximately one order of magnitude to approximately 109. It is expected that a higher dynamic-range temporal contrast can be characterized by using cascaded temporal contrast reduction processes. The proposed techniques can also be used in the delay-scanning temporal contrast measurement to improve its dynamic range.

High-performance seed pulses at 910 nm for 100 pw laser facilities by using single-stage nondegenerate four-wave mixing.

As the first step in a 100 petawatt (PW) laser facility, seed pulses with high performance are important to guarantee the quality of the output laser pulse. Here we propose a novel method based on a single-stage four-wave mixing process for the generation of seed pulses with a smooth and broadband spectrum, high energy, and high temporal contrast (TC). As high as 250 µJ pulses at approximately 910 nm central wavelength with a high TC and broader than 200 nm bandwidth are obtained in a piece of transparent medium directly after a commercial Ti:sapphire amplifier. The angular dispersion of the generated seed pulse is linear to the wavelength, which can be compensated well by using angular dispersive optics, such as a prism. The extremely simple process and setup make the output seed pulses stable and reliable for 100 PW laser facilities.

Air change rates in urban Chinese bedrooms.

The ventilation modalities in most Chinese residences are infiltration and opening windows. We measured infiltration rates and air change rates at night, with no attempt to change occupants' behaviors, of urban residences in five climate zones of China during four seasons. Using the CO2 decay method, we found the median infiltration rate for 294 residences to be 0.34 h-1 . Using occupant-generated CO2 as tracer gas, we determined air change rates over the course of 1 year in 46 bedrooms at night from mass balance considerations. In 54% of the measurements, windows were closed, so ventilation was only by infiltration. Windows were mainly closed when the outdoor temperature was below 15°C and above 26°C. The median infiltration rates did not differ appreciably among seasons and climate zones and were always less than 0.45 h-1 .

Application of dispersive liquid-liquid microextraction for the preconcentration of eight parabens in real samples and their determination by high-performance liquid chromatography.

A simple and sensitive method for the simultaneous determination of eight parabens in human plasma and urine samples was developed. The samples were preconcentrated using dispersive liquid-liquid microextraction based on the solidification of floating organic drops and determined by high-performance liquid chromatography with ultraviolet detection. The influence of variables affecting the extraction efficiency was investigated and optimized using Placket-Burman design and Box-Behnken design. The optimized values were: 58 µL of 1-decanol (as extraction solvent), 0.65 mL methanol (as disperser solvent), 1.5% w/v NaCl in 5.0 mL of sample solution, pH 10.6, and 4.0 min centrifugation at 4000 rpm. The extract was injected into the high-performance liquid chromatography system for analysis. Under the optimum conditions, the linear ranges for eight parabens in plasma and urine were 1.0-1000 ng/mL, with correlation coefficients above 0.994. The limit of detection was 0.2-0.4 and 0.1-0.4 ng/mL for plasma and urine samples, respectively. Relative recoveries were between 80.3 and 110.7%, while relative standard deviations were less than 5.4%. Finally, the method was applied to analyze the parabens in 98 patients of primary breast cancer. Results showed that parabens existed widely, at least one paraben detected in 96.9% (95/98) of plasma samples and 98.0% (96/98) of urine samples.

Compact transient-grating self-referenced spectral interferometry for sub-nanojoule femtosecond pulse characterization.

The self-referenced spectral interferometry (SRSI) technique, which is usually used for microjoule-level femtosecond pulse characterization, is improved to characterize weak femtosecond pulses with nanojoule based on the transient-grating effect. Both femtosecond pulses from an amplifier with 3 nJ per pulse at 1 kHz repetition rates and femtosecond pulses from an oscillator with less than 0.5 nJ per pulse at 84 MHz repetition rates are successfully characterized. Furthermore, through a special design, the optical setup of the device is even smaller than a palm, which will make it simple and convenient during the application. These improvements extend the application of the SRSI technique to the characterization of femtosecond pulses in a broad range. Not only pulses from an amplifier but also pulses from an oscillator or weak pulses used in ultrafast spectroscopy can be monitored with this SRSI method right now.

Correlation between HER-2/neu(erbB-2) expression level and therapeutic effect of combination treatment with HERCEPTIN and chemotherapeutic agents in gastric cancer cell lines.

INTRODUCTION: Although advanced gastric cancer has many limitations and response rate is marginal in chemotherapy. Overexpression of human epidermal growth factor receptor 2(HER-2/neu) gene and its protein are associated with increased cell division and a high rate of tumor growth and have been reported in several malignancies. Especially, approximately 30% of breast cancer patients have overexpression of HER-2/neu protein and the overexpression metastasize faster, induces resistance of the chemotherapy and down-regulate function of estrogen receptor. Recombinant humanized anti-HER2 antibody (Herceptin) inhibits proliferation of HER-2/neu overexpressing tumor cells and the use of that in combination in metastatic breast cancer have increased cytotoxicity of chemotherapeutic agents. METHODS: We evaluated the expression of HER-2/neu protein in gastric cell lines by FACS and then comparing the cytotoxicity in chemotherapeutics (doxorubicin, cisplatin, paclitaxel, 5-FU) alone and in combination with Herceptin according to the expression of HER-2/neu protein by MTT assay. RESULTS: 1. NCI-N87 (88%) gastric cancer cell line and SK-BR-3 (89%) breast cancer cell line with strong positivity of HER-2/neu expression. YBC-2 (55%) and YBC-3 (48%) gastric cancer cell line with intermediated, weak positivity respectively. Negative control U-87 MG (6%) brain cancer cell line were showed low expression of HER-2/neu. 2. Cell growth was dose-dependently inhibited in HER-2/neu positive, control cell line SK-BR-3 by Herceptin treatment but not observed in HER-2/neu negative control cell line U-87 MG. Effective growth inhibition was not observed in gastric cancer cell lines with single treatment of Herceptin, all cell lines observed the dose-dependent growth inhibition to chemotherapeutic agents (doxorubicin, cisplatin, paclitaxel and 5-FU). 3. Combination of Herceptin with doxorubicin observed synergistic effects in all cancer cell lines except YBC-3, combination of Herceptin with cisplatin observed NCI-N87 and SK-BR-3 and combination of Herceptin with paclitaxel observed synergistic effects in YBC-2. Combination of Herceptin with 5-FU observed antagonistic effects in all cancer cell lines. CONCLUSIONS: According to HER-2/neu expression level, effect of anti-cancer agents was observed differently in combination of Herceptin with chemotherapeutic agents. This suggests that HER-2/neu expression level can be applied standard of combination drug selection in combination of Herceptin With chemotherapeutic agents in gastric cancer.

The Genetic Characteristics of FT-MIRS-Predicted Milk Fatty Acids in Chinese Holstein Cows.

Fourier Transform Mid-Infrared Spectroscopy (FT-MIRS) can be used for quantitative detection of milk components. Here, milk samples of 458 Chinese Holstein cows from 11 provinces in China were collected and we established a total of 22 quantitative prediction models in milk fatty acids by FT-MIRS. The coefficient of determination of the validation set ranged from 0.59 (C18:0) to 0.76 (C4:0). The models were adopted to predict the milk fatty acids from 2138 cows and a new high-throughput computing software HiBLUP was employed to construct a multi-trait model to estimate and analyze genetic parameters in dairy cows. Finally, genome-wide association analysis was performed and seven novel SNPs significantly associated with fatty acid content were selected, investigated, and verified with the FarmCPU method, which stands for "Fixed and random model Circulating Probability Unification". The findings of this study lay a foundation and offer technical support for the study of fatty acid trait breeding and the screening and grouping of characteristic dairy cows in China with rich, high-quality fatty acids. It is hoped that in the future, the method established in this study will be able to screen milk sources rich in high-quality fatty acids.