HGD: an integrated homologous gene database across multiple species.

Homology is fundamental to infer genes' evolutionary processes and relationships with shared ancestry. Existing homolog gene resources vary in terms of inferring methods, homologous relationship and identifiers, posing inevitable difficulties for choosing and mapping homology results from one to another. Here, we present HGD (Homologous Gene Database, https://ngdc.cncb.ac.cn/hgd), a comprehensive homologs resource integrating multi-species, multi-resources and multi-omics, as a complement to existing resources providing public and one-stop data service. Currently, HGD houses a total of 112 383 644 homologous pairs for 37 species, including 19 animals, 16 plants and 2 microorganisms. Meanwhile, HGD integrates various annotations from public resources, including 16 909 homologs with traits, 276 670 homologs with variants, 398 573 homologs with expression and 536 852 homologs with gene ontology (GO) annotations. HGD provides a wide range of omics gene function annotations to help users gain a deeper understanding of gene function.

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome.

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops, and is a valuable resource to secure food diversity and combat drought stresses under the global warming scenario. However, due to the absence of extant diploid progenitors, the polyploidy genome of broomcorn millet remains poorly understood. Here, we report the chromosome-scale genome assembly of broomcorn millet. We divided the broomcorn millet genome into two subgenomes using the genome sequence of Panicum hallii, a diploid relative of broomcorn millet. Our analyses revealed that the two subgenomes diverged at ~4.8 million years ago (Mya), while the allotetraploidization of broomcorn millet may have occurred about ~0.48 Mya, suggesting that broomcorn millet is a relatively recent allotetraploid. Comparative analyses showed that subgenome B was larger than subgenome A in size, which was caused by the biased accumulation of long terminal repeat retrotransposons in the progenitor of subgenome B before polyploidization. Notably, the accumulation of biased mutations in the transposable element-rich subgenome B led to more gene losses. Although no significant dominance of either subgenome was observed in the expression profiles of broomcorn millet, we found the minimally expressed genes in P. hallii tended to be lost during diploidization of broomcorn millet. These results suggest that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels.

Application of CMV-IVIg as prophylaxis against cytomegalovirus reactivation in allogeneic hematopoietic stem cell transplantation patients.

Cytomegalovirus (CMV) reactivation remains one of the major and life-threatening complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Yet, there is still a lack of safe and effective ways to prevent CMV reactivation in allo-HSCT patients. Here, we retrospectively analyzed a cohort of patients who underwent HSCT at our transplant center between 2018 and 2022 to evaluate the efficacy of prophylactic CMV-specific intravenous immunoglobulin (CMV-IVIg) against CMV reactivation. After Propensity Score Matching, the CMV reactivation rate was significantly decreased in the CMV-IVIg group (HR, 2.952; 95% CI,1.492-5.841; P = .002) compared with the control group. Additionally, the time duration of CMV reactivation (P = .001) and bacterial infection rate (P = .013) were significantly lower in the CMV-IVIg group. Moreover, prophylactic CMV-IVIg was more effective in CMV seropositive patients who received ATG as part of GVHD prevention (HR, 8.225; 95% CI,1.809-37.39; P = .006). In conclusion, CMV-IVIg is considered an effective and safe way to prevent CMV reactivation in HSCT recipients, which may be related to the acceleration of immune reconstitution in the early stage after transplantation.

Astragaloside IV inhibits idiopathic pulmonary fibrosis through activation of autophagy by miR-21-mediated PTEN/PI3K/AKT/mTOR pathway.

As the main active ingredient of Astragalus, Astragaloside IV (AS-IV) can ameliorate pulmonary fibrosis. In this experiment, we studied how AS-IV reduces idiopathic pulmonary fibrosis (IPF). Bleomycin (BLM) or TGF-ß1 was treated in mice or alveolar epithelial cells to mimic IPF in vivo as well as in vitro. ASV-IV alleviated levels of inflammatory cytokines and fibrosis markers in IPF model. Through detection of autophagy-related genes, ASV-IV was observed to induce autophagy in IPF. Besides, ASV-IV inhibited miR-21 expression in IPF models, and overexpression of miR-21 could reverse the protective potential of ASV-IV on IPF. PTEN was targeted by miR-21 and was up-regulated by ASV-IV in IPF models. In addition, levels of inflammatory cytokines and fibrosis markers, autophagy, as well as the PI3K/AKT/mTOR pathway regulated by ASV-IV could be neutralized after treatment with autophagy inhibitors, miR-21 mimics, or si-PTEN. Our study demonstrates that ASV-IV inhibits IPF through activation of autophagy by miR-21-mediated PTEN/PI3K/AKT/mTOR pathway, suggesting that ASV-IV could be acted to be a promising therapeutic method for IPF.

Increasing 1,4-Diaminobutane Production in Escherichia coli by Optimization of Cofactor PLP and NADPH Synthesis.

1,4-diaminobutane is widely used in the industrial production of polymers, pharmaceuticals, agrochemicals and surfactants. Owing to economic and environmental concerns, there has been a growing interest in using microbes to produce 1,4-diaminobutane. However, there is lack of research on the influence of cofactors pyridoxal phosphate (PLP) and NADPH on the synthesis of 1,4-diaminobutane. PLP serves as a cofactor of ornithine decarboxylase in the synthesis of 1,4-diaminobutane. Additionally, the synthesis of 1 mol 1,4-diaminobutane requires 2 mol NADPH, thus necessitating consideration of NADPH balance in the efficient synthesis of 1,4-diaminobutane by Escherichia coli. The aim of this study was to enhance the synthesis efficiency of 1,4-diaminobutane through increasing production of PLP and NADPH. By optimizing the expression of the genes associated with synthesis of PLP and NADPH in E. coli, cellular PLP and NADPH levels increased, and the yield of 1,4-diaminobutane also increased accordingly. Ultimately, using glucose as the primary carbon source, the yield of 1,4-diaminobutane in the recombinant strain NAP19 reached 272 mg/L·DCW, by increased 79% compared with its chassis strain.

Multi-aperture imaging with Fermat spiral sub-aperture arrangement.

Multi-aperture optical telescopes have been extensively studied owing to their high resolution, low cost, and light weight. The next generation of optical telescopes is predicted to be equipped with dozens or even hundreds of segmented lenses; therefore, it is necessary to optimize the arrangement of the lens array. This paper proposes a new structure called the Fermat spiral array (FSA) to replace the conventional hexagonal or ring array for the sub-aperture arrangement of a multi-aperture imaging system. The point spread function (PSF) and modulation transfer function (MTF) of the imaging system are compared in detail at single and multiple incident wavelengths. The FSA can effectively weaken the sidelobe intensity of the PSF, which is 12.8 dB lower on average than conventional ones with a single incident wavelength in the simulation and 4.45 dB lower in the experiment. A new MTF evaluation function is proposed to describe the mean level of MTF at mid-frequencies. The FSA can improve the MTF of the imaging system and weaken the ringing effect in the images. The imaging simulation indicates that FSA has superior imaging quality compared to conventional arrays, with a higher peak signal-to-noise ratio (PSNR) and structural similarity (SSIM). The imaging experiments also achieve a higher SSIM with the FSA, which agrees well with the simulation results. The proposed FSA multi-aperture will help improve the imaging performance of next-generation optical telescopes.

Detection of fluid motion direction based on the rotational Doppler effect of grafted perfect vortex beam.

Vortex beams have attracted much attention due to their unique rotational Doppler effect. With the in-depth study of vortex beams, many new vortex beams have been proposed gradually, while the detection of fluid motion is of great significance for the study of ocean turbulence. Based on the rotational Doppler effect of the grafted perfect vortex beam, we propose a non-embedded optical method for real-time detection of the magnitude and direction of fluid velocity and establish a two-dimensional fluid model for simulation verification. It is proved that the grafted perfect vortex beam can detect the magnitude and direction of the fluid velocity at the same time, which may provide a new way and theoretical support for the detection of fluid motion direction.

The Application and Efficacy of Second Allogeneic Hematopoietic Stem Cell Transplantation in Acute Leukemia.

BACKGROUND: We retrospectively analyzed the application and clinical efficacy of second allogeneic hematopoietic stem cell transplantation (allo-HSCT) in acute leukemia patients who relapsed or had primary graft failure (PGF) after first transplantation. METHODS: From 2007 to 2021, eight patients with acute leukemia who received second allo-HSCT in our hospital were collected, including 6 relapsed patients and 2 patients with PGF after the first HSCT. RESULTS: All the patients received complete donor implantation after second transplantation. The median time of neutrophils and platelet implantation were 12 days (10 days - 13 days) and 23 days (12 days - 123 days). Two cases (25.0%) developed grade II aGVHD, and 4 cases (50.0%) developed cGVHD. Leukemia-free survival (LFS) and overall survival (OS) at 1 year both were 71.4% and at 3 years both were 28.6%. After a median follow-up of 1,556 days (range, 257 - 5,252 days), 3 of the patients (37.5%) survived and 5 (62.5%) died. One patient with NR before second transplantation, treated with a conditioning regime of CLAG-M bridging BuCy, has survived for more than 5 years (61 months). Relapse was the main death reason. CONCLUSIONS: Second allo-HSCT is an effective means to treat acute leukemia patients with relapsed and PGF after first transplantation.

Long-term running exercise alleviates cognitive dysfunction in APP/PSEN1 transgenic mice via enhancing brain lysosomal function.

Amyloid-ß peptide (Aß) aggregation is the hallmark of Alzheimer's disease (AD). The imbalance between the production and clearance of Aß results in the accumulation and aggregation of Aß in the brain. Thus far, few drugs are available for AD treatment, but exercise has been recognized for its cognition-enhancing properties in AD patients. The underlying mechanisms remain unclear. Our recent study showed that long-term running exercise could activate the lysosomal function in the brains of mice. In this study, we investigated whether exercise could reduce Aß accumulation by activating lysosomal function in APP/PSEN1 transgenic mice. Started at the age of 5 months, the mice were trained with a running wheel at the speed of 18 r/min, 40 min/d, 6 d/week for 5 months, and were killed at the end of the 10th month, then brain tissue was collected for biochemical analyses. The cognitive ability was assessed in the 9th month. We showed that long-term exercise significantly mitigated cognitive dysfunction in AD mice, accompanied by the enhanced lysosomal function and the clearance of Aß in the brain. Exercise significantly promoted the nuclear translocation of transcription factor EB (TFEB), and increased the interaction between nuclear TFEB with AMPK-mediated acetyl-CoA synthetase 2, thus enhancing transcription of the genes associated with the biogenesis of lysosomes. Exercise also raised the levels of mature cathepsin D and cathepsin L, suggesting that more Aß peptides could be degraded in the activated lysosomes. This study demonstrates that exercise may improve the cognitive dysfunction of AD by enhancing lysosomal function.

Influence of watertight optical window with plain glass on receiving field for underwater wireless optical communication.

Underwater wireless optical communication (UWOC) has attracted much attention recently due to its superiority of high transmission speed. In many UWOC applications, to establish communication links easier, the receiver has quite a wide field. However, the performance of the receiving field is affected by watertight encapsulation in practice, especially when the optical window is produced with plain glass. To study such an influence, in this paper, we first establish a theoretical model based on the Monte Carlo method. Then, we analyze the influence with different structure parameters of watertight encapsulation. The simulation results show that to reduce such an impact, the optical window should be thinner, the detector photosurface and optical window surface should be larger, and the space between the detector and optical window should be smaller. In the ideal situation, the largest workable receiving field is about 96° for UWOC. In other situations, the workable receiving field would be smaller. The simulation method and results presented in this paper are pragmatic and useful to UWOC receiver design.

Experimental demonstration of a transmitter with a 50° divergence angle, 50 Mbps rate, and 476 mW optical power for underwater wireless optical communication based on an engineered diffuser.

In practical application of underwater wireless optical communication (UWOC), the transmitter should have a larger divergence angle to make it easier to establish a communication link, besides high modulated rate and high optical power. Laser diodes (LD) are suitable to design such transmitter, thanks to their simpler structure and much faster switching speed. However, it is difficult to implement for widespread use in ocean engineering because of its quite small divergence angle. For this, we present a simple way to enlarge the divergence angle for an LD transmitter based on an engineered diffuser in this paper. First, we design a blue LD transmitter that has 476 mW output power, 50 Mbps rate, and 50° divergence angle. Then, using such transmitter, we establish a UWOC system in a large experimental tank with 13.3 m communication distance and about 0.26m-1 attenuation coefficient of water. The results show that if the deviation of the transmitting direction is up to ±25∘, the communication system is workable. Emission light from the transmitter could cover a 42.5% solid angle of the hemisphere space. The combination performances of speed, angular coverage, and optical power are suitable for ocean engineering. Also, it implies that a light field could be designed by using a suitable engineered diffuser for UWOC. The method presented in this paper is simple and pragmatic, which is useful to reduce the difficulty in establishing communication links and is easy to popularize.

Influence of a watertight optical window with plain glass on the light distribution of an LED transmitter for underwater wireless optical communications.

Underwater wireless optical communication (UWOC) has attracted much attention recently, thanks to its high transmission speed. In many UWOC applications, the transmitter is based on light emitting diodes (LEDs). This is because it has up to a 120° divergence angle, which is helpful with establishing the communication link more easily. However, the light field of such a transmitter is affected by watertight encapsulation in practice. In this paper, we establish a theoretical model based on the Monte Carlo method to study this influence when the watertight optical window is based on plain glass. The results show that both the divergence angle and transmittance become smaller because of the optical window. In order to reduce this influence, the illumination surface, distance from the light source to the optical window, and thickness of the optical window should be smaller, while the optical window surface should be larger. In the ideal situation, the largest divergence angle is 94.4°, which is defined with full width at half-maximum (FWHM). The maximum transmittance is related to the optical materials of the window, while it is 93.54% for quartz glass. When light is modulated with on-off keying (OOK) format, if the signal-to-noise ratio (SNR) is larger than 40 at 0° radiation angle, the UWOC system could work when the angle is up to ±48.7∘. While the SNR reduces, the workable angle range decreases. The simulation model presented in this paper is convenient to analyze the influence of a watertight optical window with plain glass. The simulation results presented in this paper are useful to the UWOC transmitter design.

High-resolution dynamic imaging system based on a 2D optical phased array.

We propose an imaging system with scanning feedback of an optical phased array (OPA) for moving targets with unknown speed. The system combines OPA scanning velocimetry capability with OPA-based ghost imaging to enable trajectory tracking of targets moving within the field-of-view of the system while accomplishing image reconstruction. The proposed system can perform image reconstruction for millimeter-scale moving targets placed up to 20 m away from the camera. The system can be applied in areas such as autonomous driving and high-resolution imaging.

LncRNA Miat knockdown alleviates endothelial cell injury through regulation of miR-214-3p/Caspase-1 signalling during atherogenesis.

Atherosclerosis is a common problem in healthy people around the world. Long noncoding RNAs (lncRNAs) play important roles in atherosclerosis. Myocardial infarction-associated transcript (Miat) is a cardiovascular disease-associated lncRNA. Its role and mechanism in atherosclerosis is still not fully clarified. Our study aims to explore the role and mechanism of lncRNA Miat in atherosclerosis. The atherosclerosis models were established both in vitro and in vivo. Real-time PCR was used to measure the expression of lncRNA Miat, miR-214, Caspase-1 and IL-1ß. Western blot was performed to detect the protein expression of Caspase-1. CCK-8 assay, Tunel staining, and flow cytometry analysis were conducted to detect proliferation and apoptosis of human aortic endothelial cells (HAECs), respectively. Oil red O staining and HE staining were used to evaluated the histological changes of the aorta. The results found that lncRNA Miat was upregulated in ox-LDL-induced atherosclerosis model in vitro. The inhibition of lncRNA Miat protects against ox-LDL-induced HAEC injury, presented as increased cell viability and decreased apoptosis. LncRNA Miat and miR-214 has binding site, and CASP1, which encodes Caspase-1, is a target of miR-214. The downregulation of lncRNA Miat increased the expression of miR-214-3p and decreased the expression of Caspase-1, as well as its downstream molecule IL-1ß in HAECs. However, the inhibition of miR-214-3p attenuated the effect of lncRNA Miat downregulation on HAECs. Furthermore, the downregulation of lncRNA Miat alleviated atherosclerosis in ApoE-deficient mice. Correspondingly, the expression of miR-214-3p was upregulated and Caspase-1 was downregulated after knockdown of lncRNA Miat. In conclusion, downregulation of lncRNA Miat exerts a protective effect against atherosclerosis through the regulation miR-214-3p/Caspase-1 signalling pathway. Therefore, the inhibition of lncRNA Miat expression may be an effective strategy in the treatment of atherosclerosis.

4-O-galloylalbiflorin inhibits the activity of CYP3A, 2C9, and 2D in human liver microsomes.

The effect of 4-O-galloylalbiflorin on the activity of cytochrome P450 enzymes (CYP450s) is an important factor that may induce drug-drug interaction.The effect of 4-O-galloylalbiflorin on the activity of CYP450s was evaluated in the presence of 0, 2.5, 5, 10, 25, 50, and 100 µM 4-O-galloylalbiflorin in pooled human liver microsomes. The inhibition model and corresponding parameters were assessed b fitting with Lineweaver-Burk plots. The time-dependent study was performed with the incubation time of 0, 5, 10, 15, and 30 min.4-O-galloylalbiflorin significantly inhibited the activity of CYP3A, 2C9, and 2 D in a concentration-dependent manner with the IC50 values of 8.2, 13, and 11 µM, respectively. The inhibition of CYP3A was found to be non-competitive and time-dependent with the Ki value of 4.0 µM and the KI/Kinact value of 2.2/0.030 (µM·min). The inhibition of CYP2C9 and 2 D was not affected by the incubation time but was found to be competitive with the Ki values of 6.7 and 6.6 µM, respectively.The inhibitory effect of 4-O-galloylalbiflorin on the activity of CYP3A, 2C9, and 2 D implying the potential drug-drug interaction between 4-O-galloylalbiflorin and the drugs metabolized by these CYP450s.

Efficient algorithm for tracking the single target applied to optical-phased-array LiDAR.

A centroid dynamic programming track-before-detect algorithm is proposed, which is applied for tracking the moving target with an unknown speed. Using the inertialess scanning based on an optical phased array, the experimental tracking system is established, and the obtained maximum signal-to-noise ratio is 9.97 dB. Targets of different motion states can be accurately tracked with this algorithm. In addition, we innovated the original track-before-detect algorithm by adding the variable step, so that the target with large accelerations can be tracked accurately. The accuracy of our proposed algorithm is verified numerically and experimentally, which shows that our algorithm can be used to track the target trajectory effectively, and the error in extracting the target velocity is below 2%.

Beam-quality improvement with a bio-inspired sunflower array for coherent beam combining.

The beam quality of coherent beam combing (CBC) is significantly affected by the beam array schemes, which are regular hexagon arrays in most research. Here, we propose a bio-inspired Fermat spiral array (FSA) for large-array CBC, for the first time to our knowledge. The far-field distribution and beam quality of CBC with various designed FSAs was investigated numerically and experimentally; the simulated and experimental results agreed with each other. The power in the bucket (PIB) increased with the central space density of the FSA, accompanying by the weakening of the far-field sidelobes. In addition, for the FSA with constant space density, the PIB increased, and sidelobes weakened with the increase of the array filling factor. The FSA could effectively improve the PIB and weaken the sidelobe of the CBC far field by the aperiodic and nonuniform space density arrangement, compared to the regular arrays. These results provide a new approach for the beam arrangement of large-array CBC.

A novel intensive conditioning regimen for allogeneic hematopoietic stem cell transplantation in the treatment of relapsed/refractory acute myeloid leukemia.

We conducted a prospective study to evaluate the efficacy and safety of cladribine, cytarabine, mitoxantrone, and granulocyte colony-stimulating factor (CLAG-M) regimen combined with busulfan and cyclophosphamide (BuCy) as new intensive conditioning before allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the treatment of relapsed/refractory acute myeloid leukemia (AML). 24 patients were enrolled. The median follow-up was 15.2 months (range 1.9-67.0 months). Except for one patient who died before graft infusion, the evaluable 23 patients (96%) achieved complete remission (CR). The two-year overall survival (OS) rate and leukemia-free survival (LFS) rate were 61.4% and 59.4%, respectively. The non-relapse mortality (NRM) was 9.1%. Univariate analysis revealed that the myeloid blast phase of chronic myelomonocytic leukemia (CMML), an EVI1 mutated, blood blasts ≥20% at transplant, and extramedullary disease were risk factors for LFS.

Nimodipine attenuates dibutyl phthalate-induced learning and memory impairment in kun ming mice: An in vivo study based on bioinformatics analysis.

Dibutyl phthalate (DBP), a typical representative of phthalate esters (PAEs), is used as a plasticizer in various industrial applications and has been reported to be responsible for neurobehavioral changes. Despite mounting evidence showing that nimodipine (Nim) palys a neuropharmacological and psychopharmacological role in neurons, the attenuating effects of Nim on learning and memory impairment induced by DBP exposure remain unknown. Based on bioinformatics analysis we found that the biological processes affected by both DBP and Nim may involve the calcium signaling pathway, the MAPK signaling pathway and the apoptosis pathway. The results of an in vivo study confirmed that DBP affects the levels of Ca2+ -related proteins, up-regulates phosphorylated -ERK1/2 expression and results in hippocampal neuronal damage and apoptosis, whereas Nim as a Ca2+ antagonist, has a certain neuroprotective role to avoid these adverse effects. Our data suggest that Nim could be used to attenuate the learning and memory impairment in DBP-exposed mice, to down-regulate intracellular Ca2+ levels, subordinate the ERK1/2 pathway and attenuate apoptosis in hippocampal tissue.

GSA-Human: Genome Sequence Archive for Human.

The Genome Sequence Archive for Human (GSA-Human) is a data repository specialized for human genetic related data derived from biomedical researches, and also supports the data collection and management of National Key Research and Development Projects. GSA-Human has a data security management strategy according to the national regulations of human genetic resources. It provides two different models of data access: Open-access and Controlled-access. Open-access data are universally and freely accessible for global researchers, while Controlled-access ensures that data are accessed only by authorized users with the permission of the Data Access Committee (DAC). Till July 2021, GSA-Human has housed more than 5.27 PB of data from 750 datasets.