Terahertz dynamic multichannel holograms generated by spin-multiplexing reflective metasurface.

In recent years, metasurfaces have attracted considerable interest for their unprecedented capabilities to manipulate intensity, phase, and polarization of an electromagnetic wave. Although metasurface-based wavefront modulation has achieved numerous successful results, implementation of multifunctional devices in a single metasurface still meet significant challenges. Here, a novel multilayer structure is designed using properties of vanadium dioxide (VO2). Propagation phase and geometric phase are introduced in this structure to achieve multichannel holographic imaging in terahertz band. When the temperature is above 68°C, VO2 becomes a metal and it plays a role in wavefront modulation for terahertz wave. The left-handed channel realizes a hologram letter L and the right-handed channel realizes a hologram letter R. When the temperature is below 68°C, VO2 changes to an insulator, and electromagnetic wave is controlled by gold structures embedded inside a VO2 film. In this case, hologram number 2 is realized in the left-handed channel and hologram number 6 appears in the right-handed channel. Our structure has advantages of low crosstalk, multiple channels, and large bandwidth. This novel design paves a new road for multichannel imaging and information encryption.

Smoking may increase the usage of antidepressant: evidence from genomic perspective analysis.

This study uses the two-sample Mendelian randomization (TSMR) method to explore the causal relationships between smoking initiation (SMKI), never smoking (NSMK), past tobacco smoking (PTSMK), and the usage of antidepressants (ATD). Single-nucleotide polymorphisms (SNPs) with genome-wide significance (P < 5E-08) related to SMKI, NSMK, and PTSMK were selected from the genome-wide association study (GWAS) database as instrumental variables (IVs). The main method, inverse variance weighted (IVW), was utilized to investigate the causal relationship. The results demonstrated a positive causal relationship between SMKI and ATD use, where SMKI leads to an increase in ATD use. Conversely, NSMK and PTSMK showed a negative causal relationship with ATD use, meaning that NSMK and PTSMK lead to a reduction in ATD use. Additionally, sensitivity analysis showed that the results of this study were robust and reliable. Using the TSMR method and from a genetic perspective, this study found that SMKI leads to an increase in ATD use, while NSMK and PTSMK reduce ATD use.

Exploring adverse events of Vilazodone: evidence from the FAERS database.

OBJECTIVE: This study aims to conduct an exhaustive evaluation of Vilazodone's safety in clinical application and to unearth the potential adverse event (AE) risks associated with its utilization based on FDA Adverse Event Reporting System (FAERS) database. METHODS: This research employed data spanning from the first quarter of 2011 to the third quarter of 2023 from the FAERS database. Various signal detection methodologies, including the Reporting Odds Ratio (ROR), Proportional Reporting Ratio (PRR), Bayesian Confidence Propagation Neural Network (BCPNN), and Empirical Bayesian Geometric Mean (EBGM), were utilized to ascertain the correlation between Vilazodone and specific AEs. RESULTS: The study compiled a total of 17,439,268 reports of drug AEs, out of which 5,375 were related to Vilazodone. Through signal mining, 125 Preferred Terms (PTs) encompassing 27 System Organ Classes (SOCs) were identified. The findings indicated a higher prevalence among females and patients within the 45 to 65 age bracket. The principal categories of AEs included Psychiatric disorders, Nervous system disorders, and Gastrointestinal disorders, with prevalent incidents of Diarrhoea, Nausea, and Insomnia. Moreover, the study identified robust signals of novel potential AEs, notably in areas such as sleep disturbances (Sleep paralysis, Hypnagogic hallucination, Rapid eye movements sleep abnormal, Sleep terror, Terminal insomnia, Tachyphrenia), sexual dysfunctions (Female orgasmic disorder, Orgasm abnormal, Disturbance in sexual arousal, Spontaneous penile erection, Anorgasmia, Sexual dysfunction, Ejaculation delayed), and other symptoms and injuries (Electric shock sensation, Violence-related symptom, Gun shot wound). CONCLUSION: Although Vilazodone presents a positive prospect in the management of MDD, the discovery of AEs linked to its use, particularly the newly identified potential risks such as sleep and sexual dysfunctions, necessitates heightened vigilance among clinicians.

Residual network improves the prediction accuracy of genomic selection.

Genetic improvement of complex traits in animal and plant breeding depends on the efficient and accurate estimation of breeding values. Deep learning methods have been shown to be not superior over traditional genomic selection (GS) methods, partially due to the degradation problem (i.e. with the increase of the model depth, the performance of the deeper model deteriorates). Since the deep learning method residual network (ResNet) is designed to solve gradient degradation, we examined its performance and factors related to its prediction accuracy in GS. Here we compared the prediction accuracy of conventional genomic best linear unbiased prediction, Bayesian methods (BayesA, BayesB, BayesC, and Bayesian Lasso), and two deep learning methods, convolutional neural network and ResNet, on three datasets (wheat, simulated and real pig data). ResNet outperformed other methods in both Pearson's correlation coefficient (PCC) and mean squared error (MSE) on the wheat and simulated data. For the pig backfat depth trait, ResNet still had the lowest MSE, whereas Bayesian Lasso had the highest PCC. We further clustered the pig data into four groups and, on one separated group, ResNet had the highest prediction accuracy (both PCC and MSE). Transfer learning was adopted and capable of enhancing the performance of both convolutional neural network and ResNet. Taken together, our findings indicate that ResNet could improve GS prediction accuracy, affected potentially by factors such as the genetic architecture of complex traits, data volume, and heterogeneity.

Efficacy comparison of repeated low-level red-light therapy and orthokeratology lenses for myopia control.

PURPOSE: This study aimed to compare and analyze the efficacy of repeated low-level red-light therapy and orthokeratology lenses for myopia control in children. METHODS: Exactly 138 participants were enrolled in this retrospective study. Comprehensive eye examinations were performed prior to treatment. The repeated low-level red-light therapy and orthokeratology lenses groups comprised 67 and 71 patients, respectively. The age range was between 6 and 14 years, with myopia of ≤-0.50 D and astigmatism of ≤2.50 D after cycloplegia. Follow-up data were collected during the initial visit and the treatment period. Changes in axial length over a 2-year period and associated factors were analyzed. RESULTS: Over the 2-year period, the repeated low-level red-light therapy group exhibited significantly less axial length growth compared with the orthokeratology lenses group (0.17 ± 0.40 vs. 0.50 ± 0.27 mm, p<0.001). In the first year, the axial length growth in the repeated low-level red-light therapy group was significantly less than that in the orthokeratology lenses group (0.03 ± 0.22 vs. 0.28 ± 0.18 mm, p<0.001), with no significant difference observed in the second year (0.14 ± 0.29 vs. 0.21 ± 0.14 mm, p=0.06). The repeated low-level red-light therapy group showed a 55% reduction in axial length after 1 month and a 42% reduction after 1 year, compared with 4% and 3% reductions in the orthokeratology lenses group, respectively. Linear mixed-effects model analysis indicated that the annual axial length change rate in the repeated low-level red-light therapy group was 0.10 mm (95% confidence interval [CI], 0.07 to 0.14), compared with 0.25 mm in the orthokeratology lenses group (95% CI, 0.24 to 0.27), with an average difference of 0.15 mm (95% CI, -0.17 to -0.12, p<0.001). CONCLUSIONS: Repeated low-level red-light therapy demonstrated slightly superior efficacy in controlling myopia progression in children compared with orthokeratology lenses.

Stress hyperglycemia ratio and its influence on mortality in elderly patients with severe community-acquired pneumonia: a retrospective study.

BACKGROUND: Community-acquired pneumonia (CAP) is a significant health issue among the elderly, with severe cases (SCAP) having high mortality rates. This study assesses the predictive significance of the stress hyperglycemia ratio (SHR) in elderly SCAP patients and its impact on outcomes in both diabetic and non-diabetic patients. METHODS AND MATERIALS: This retrospective study included 406 SCAP patients aged 65 or older from the Second People's Hospital of Lianyungang (January 2020 to December 2023). Data collected included demographics, medical history, vital signs, and lab results. SHR was calculated from initial blood glucose and estimated average glucose (HbA1c). Statistical analyses, including Cox regression and Kaplan-Meier analysis, evaluated SHR's impact on mortality. Mediation models explored the effects of neutrophil-lymphocyte ratio (NLR) and SHR. RESULTS: The 28-day mortality rate was 21.67%. Deceased patients had higher age, Charlson Comorbidity Index, procalcitonin, NLR, glucose, and SHR levels compared to survivors (P < 0.05). Both SHR and NLR significantly increased mortality risk, particularly in non-diabetic patients. Combining NLR and SHR improved ROC AUC to 0.898, with 89.80% sensitivity and 81.10% specificity. Kaplan-Meier analysis showed higher cumulative survival for SHR < 1.14, regardless of diabetes status (P < 0.05). NLR mediated 13.02% of the SHR-survival relationship, while SHR mediated 14.06% of the NLR-survival relationship. CONCLUSION: Elevated SHR is a significant mortality risk factor in elderly SCAP patients, independent of diabetes status. Stringent glucose control and careful monitoring of SHR may improve outcomes in elderly patients with acute respiratory conditions.

Triangular pulley traction facilitates endoscopic full-thickness resection of exogenous gastric tumor in the fornix of the stomach.

A 65-year-old woman was diagnosed with an exogenous submucosal tumor located in the fornix of the stomach, on the basis of the endoscopic ultrasound and enhanced CT findings. She refused surgery and referred for EFTR. It is difficult to perform EFTR at the gastric fornix and suture the large surgical defect. Therefore, we created technique of triangular pulley traction combined with pre-closure.

Gut metagenome-derived image augmentation and deep learning improve prediction accuracy of metabolic disease classification.

In recent years, statistics and machine learning methods have been widely used to analyze the relationship between human gut microbial metagenome and metabolic diseases, which is of great significance for the functional annotation and development of microbial communities. In this study, we proposed a new and scalable framework for image enhancement and deep learning of gut metagenome, which could be used in the classification of human metabolic diseases. Each data sample in three representative human gut metagenome datasets was transformed into image and enhanced, and put into the machine learning models of logistic regression (LR), support vector machine (SVM), Bayesian network (BN) and random forest (RF), and the deep learning models of multilayer perceptron (MLP) and convolutional neural network (CNN). The accuracy performance of the overall evaluation model for disease prediction was verified by accuracy (A), accuracy (P), recall (R), F1 score (F1), area under ROC curve (AUC) and 10 fold cross-validation. The results showed that the overall performance of MLP model was better than that of CNN, LR, SVM, BN, RF and PopPhy-CNN, and the performance of MLP and CNN models was further improved after data enhancement (random rotation and adding salt-and-pepper noise). The accuracy of MLP model in disease prediction was further improved by 4%-11%, F1 by 1%-6% and AUC by 5%-10%. The above results showed that human gut metagenome image enhancement and deep learning could accurately extract microbial characteristics and effectively predict the host disease phenotype. The source code and datasets used in this study can be publicly accessed in https://github.com/HuaXWu/GM_ML_Classification.git.

Dual-Mode Undistorted Visual Fluorescent Sensing Strategy through Manipulating the Coffee-Ring Effect on Microfluidic Paper-Based Chip.

To overcome the insufficient sensitivity due to distortion of the fluorescent images by mobile devices, we first developed a novel dual-mode strategy for undistorted visual fluorescent sensing on µPAD by technically manipulating the coffee-ring effect of the fluid sample. Based on the manipulating coffee-ring effect, we divided the horizontal direction of the resulting fluorescence image into 600 pixels and obtained more accurate quantitative information to avoid image distortion. The bovine serum albumin-stabilized gold nanoclusters-copper ion complex was used as the fluorescent probe, combined with a small imaging box and a smartphone, to achieve a rapid testing of histidine in human urine. The output image was analyzed in dual mode: RGB numerical analysis in pixel units and the direct measurement of the fluorescent strips length (limit of detection (LOD) is 0.021 and 0.5 mM, respectively), and improved antidistortion for visual fluorescent sensing. This strategy can overcome the distortion of a smartphone-visualized fluorescent image and shows great potential for rapid and convenient analysis.

Design, fabrication, and evaluation of a large-area hybrid solar simulator for remote sensing applications.

Solar irradiance variations have a direct effect on the accuracy and repeatability of identifying spectral signatures in the remote sensing field experiments. Solar simulators have been deployed to allow for testing under controlled and reproducible laboratory conditions. However, it is difficult and expensive to make a large-area solar simulation with the appropriate spectral content and spatial uniformity of irradiance. In this study, a hybrid solar simulator has been designed and constructed to provide large-area illumination for remote sensing simulation applications. A design method based on the two-phase genetic algorithm is proposed to improve the performance of the spectral match and spatial uniformity, which no longer relies on the traditional trial-and-error technique. The first phase is used to determine the most appropriate configuration of different lamps in order to represent the solar spectrum. The second phase is to accommodate an optimal placement of the multiple sources to achieve irradiance uniformity. Both numerical simulations and experiments were performed to verify the performances. The results showed that the solar simulator provided a good spectral match and spatial irradiance for simulating the variations in direct normal irradiance at different solar zenith angles. In addition, the modular design makes it possible to adjust irradiance on the target area without altering the spectral distribution. This work demonstrates the development and measurement of a hybrid solar simulator with a realizable optimal configuration of multiple lamps, and offers the prospect of a scalable, large-area solar simulation.

Artificial intelligence-based full aortic CT angiography imaging with ultra-low-dose contrast medium: a preliminary study.

OBJECTIVES: To further reduce the contrast medium (CM) dose of full aortic CT angiography (ACTA) imaging using the augmented cycle-consistent adversarial framework (Au-CycleGAN) algorithm. METHODS: We prospectively enrolled 150 consecutive patients with suspected aortic disease. All received ACTA scans of ultra-low-dose CM (ULDCM) protocol and low-dose CM (LDCM) protocol. These data were randomly assigned to the training datasets (n = 100) and the validation datasets (n = 50). The ULDCM images were reconstructed by the Au-CycleGAN algorithm. Then, the AI-based ULDCM images were compared with LDCM images in terms of image quality and diagnostic accuracy. RESULTS: The mean image quality score of each location in the AI-based ULDCM group was higher than that in the ULDCM group but a little lower than that in the LDCM group (all p < 0.05). All AI-based ULDCM images met the diagnostic requirements (score ≥ 3). Except for the image noise, the AI-based ULDCM images had higher attenuation value than the ULDCM and LDCM images as well as higher SNR and CNR in all locations of the aorta analyzed (all p < 0.05). Similar results were also seen in obese patients (BMI > 25, all p < 0.05). Using the findings of LDCM images as the reference, the AI-based ULDCM images showed good diagnostic parameters and no significant differences in any of the analyzed aortic disease diagnoses (all K-values > 0.80, p < 0.05). CONCLUSIONS: The required dose of CM for full ACTA imaging can be reduced to one-third of the CM dose of the LDCM protocol while maintaining image quality and diagnostic accuracy using the Au-CycleGAN algorithm. KEY POINTS: • The required dose of contrast medium (CM) for full ACTA imaging can be reduced to one-third of the CM dose of the low-dose contrast medium (LDCM) protocol using the Au-CycleGAN algorithm. • Except for the image noise, the AI-based ultra-low-dose contrast medium (ULDCM) images had better quantitative image quality parameters than the ULDCM and LDCM images. • No significant diagnostic differences were noted between the AI-based ULDCM and LDCM images regarding all the analyzed aortic disease diagnoses.

Bidirectional causal association between ischemic stroke and five mental disorders.

OBJECTIVE: To explore the bidirectional causal association between ischemic stroke and five mental disorders from a genetic perspective using two-sample Mendelian randomization (TSMR). METHODS: Single-nucleotide polymorphisms (SNPs) associated with ischemic stroke were obtained from the genome-wide association study (GWAS) database, and those closely related to the exposure phenotype and satisfying the three core assumptions of Mendelian randomization were selected as instrumental variables (IVs). The main TSMR analysis was conducted using the inverse variance-weighted (IVW) method, and the robustness of the results was assessed using the weighted median, weighted mode, and MR Egger methods. Heterogeneity test, pleiotropy test, and sensitivity analysis were also conducted to further ensure the accuracy and stability of the research results. RESULTS: This study found a positive correlation between ischemic stroke and depression [IVW method (FEM): OR = 1.002, 95%CI: 1.000-1.003, P = 0.023<0.05], but no significant causal association with schizophrenia, bipolar disorder, insomnia, or anxiety (P > 0.05). Reverse TSMR analysis showed no causal association between depression, schizophrenia, bipolar disorder, insomnia, anxiety, and ischemic stroke (P > 0.05). CONCLUSION: This study used TSMR to demonstrate from a genetic perspective that there is a positive correlation between ischemic stroke and depression, which increases the risk of depression. Proactive intervention for ischemic stroke might reduce the risk of depression.

Causal relationship between sex hormone-binding globulin and major depression: A Mendelian randomization study.

OBJECTIVE: This study aimed to explore the causal relationship between sex hormone-binding globulin (SHBG) and major depression using two-sample Mendelian randomization (MR) studies. METHODS: Based on the genome-wide association study (GWAS) summary data of SHBG and major depression in the European population, which included 214,989 female SHBG samples, 185,221 male SHBG samples, and 500,199 major depression samples, we used genetic factors as instrumental variables to conduct two-sample MR analyses. We used methods including inverse variance weighted (IVW), weighted median, weighted mode, and MR Egger to evaluate the bidirectional causal relationship between SHBG and major depression. RESULTS: The results showed that there was a causal relationship between female SHBG and major depression, which was positively correlated. The ORs were 1.056 (95% CI: 1.005-1.109, p = 0.031) for the weighted median and 1.067 (95% CI: 1.012-1.126, p = 0.021) for the weighted mode. There was no significant effect of male SHBG on major depression (p > 0.05), and there was no significant effect of major depression on female SHBG (p > 0.05). Major depression was negatively correlated with male SHBG, indicating that major depression could lead to a decrease in male SHBG. The OR was 0.954 (95% CI: 0.916-0.993, p = 0.023) for IVW. CONCLUSION: Female SHBG was positively correlated with the risk of major depression, however, major depression was found to be negatively correlated with serum SHBG levels in men, indicating that SHBG plays distinct roles in patients with major depression of different genders.

Molecular cloning and functional characterization of peroxiredoxin 4 (prx 4) in freshwater crayfish, Procambarus clarkii.

Peroxiredoxin (Prx), which is a newly discovered member of the antioxidant protein family, performs important biological functions in intracellular signal transduction. In the present study, a peroxiredoxin 4 gene was cloned from crayfish for the first time and named Pc-prx 4. According to the amino acid sequence signature, Pc-Prx 4 was identified as the typical 2-Cys Prx molecule, which possessed two conserved cysteines (Cys98 and Cys219). Time-course expression patterns post V. harveyi infection revealed that Pc-prx 4 was likely related to crayfish innate immune defense responses. In particular, the highest fold upregulation of the Pc-prx 4 mRNA transcript reached approximately 170 post V. harveyi infection in the crayfish hepatopancreas. The results of the mixed functional oxidase assay showed that rPc-Prx 4△ could resist the damaging effect of reactive oxygen species generated from the thiol/Fe3+/O2- reaction system to some extent. In addition, the results of the RNAi assay revealed that the crayfish survival rate was obviously increased post injection of V. harveyi when Pc-prx 4 was knocked down. Further study revealed that both hemolymph melanization and PO activity were strengthened to different degrees in the RNAi assay. Therefore, we speculated that the increase in the crayfish survival rate was likely due to the increase in hemolymph melanization. The obviously reinforced hemolymph melanization was directly caused by the upregulation of hemolymph PO activity, which was induced by the knockdown of Pc-prx 4. However, further studies are still indispensable for illuminating the molecular mechanism of Pc-prx 4 in the crayfish innate immune defense system.

Selection of reference genes for RT-qPCR analysis in developing chicken embryonic ovary.

BACKGROUND: Normalization of the expression profiling of target genes, in a tissue-specific manner and under different experimental conditions, requires stably expressed gene(s) to be used as internal reference(s). However, to study the molecular regulation of oocyte meiosis initiation during ovary development in chicken embryos, stable reference gene(s) still need to be compared and confirmed. METHODS AND RESULTS: Six candidate genes previously used as internal references for the chicken embryo (Actb, Cvh, Dazl, Eef1a, Gapdh and Rpl15) were chosen, and their expression profiles in left ovaries dissected at five chicken embryonic days (E12.5, E15.5, E17.5, E18.5 and E20.5) were evaluated, respectively. Separately, GeNorm, NormFinder, BestKeeper and Comparative ΔCt methods were used to assess the stability of candidate reference genes, and all results were combined to give the final rank by RefFinder. All methods identified that Eef1a and Rpl15 were the two most stable internal reference genes, whereas Cvh is the most unstable one. Moreover, expression levels of three marker genes for chicken oocyte meiosis entry (Stra8, Scp3 and Dmc1) were normalized, based on Eef1a, Rpl15, or their combinations, respectively. CONCLUSION: Our findings provide the most suitable internal reference genes (Eef1a and Rpl15), to investigate further molecular regulation of ovary development and oocyte meiosis initiation in chicken embryos.

Optical reflective metasurfaces enable spin-decoupled OAM and focusing.

Due to the physically unrestricted set of orthogonally helical modes of orbital angular momentum (OAM), it has contributed significantly to wireless communication and information capacity. Meanwhile, focusing has important applications in fields such as super-resolution microscopic imaging and optical integration. Plasmonic metasurfaces have a powerful ability to modulate electromagnetic (EM) waves, and diversified functionalities in them are strongly desired. As of today, few plasmonic metasurfaces are reported which have multi-function in a single flat device. Herein, by fine-tuning the geometric dimensions and orientation angle of the meta-atom, the geometric phase is combined with the propagation phase to produce an independent phase response when left-handed circular polarization (LCP) and right-handed circular polarization (RCP) waves illuminate the metasurface. This paper presents three plasmonic metasurfaces, and each of them implements multiple functions on a single plasmonic metasurface. Firstly, normal reflection of OAM and a focused beam is achieved. Secondly, we realize anomalous reflection of OAM by convolving a gradient sequence and implement computational focusing at any point. Finally, addition theorem is adopted to implement the above two functions, and this design contains normal and inclined output beams. Our work provides novel approaches for the integration of multifunctional EM modulation.

The correlation of Esketamine with specific adverse events: a deep dive into the FAERS database.

Analyzing the vast data from FAERS database to evaluate the association between Esketamine and specific adverse events to guide clinical practice and regulatory decisions. Data related to Esketamine adverse events from 2019 Q1 to 2023 Q1 were collected from FAERS database. After data standardization, various signal quantification technologies, such as ROR, PRR, BCPNN, and MGPS, were employed to identify and evaluate adverse reaction signals closely related to the use of Esketamine comprehensively. A total of 5061 reports with Esketamine as the primary suspected drug were obtained, identifying 117 adverse reaction terms (PT) involving 27 system organ class (SOC) categories. Apart from the adverse events already mentioned in the drug's instructions, this study identified some new, clinically valuable potential AE signals, such as Flashback, Tachyphylaxis, and Autoscopy. In addition, high-ranking results included euphoric mood, feeling of relaxation, and feeling drunk. Notably, the occurrence frequencies of suicidal ideation and suicide attempt were relatively high, so clinicians should be particularly vigilant about these potential adverse reactions when using Esketamine. Moreover, since this drug is administered as a nasal spray, issues such as drug monitoring procedure incorrectly performed and nasal discomfort may arise. This study underscores the potential adverse reactions and risks of Esketamine in clinical applications, especially regarding long-term efficacy, addiction risks, and suicidal risks.

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig.

As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber-type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process under spatio-temporal regulation, that is, the intermingled and concomitant proliferation, differentiation, migration and fusion of myoblasts. Recently, with the fast and continuous development of next-generation sequencing technology, the integration of quantitative trait loci mapping with genome-wide association studies (GWAS) has greatly helped animal geneticists to discover and explore thousands of functional or causal genetic elements underlying muscle growth and development. However, owing to the underlying complex molecular mechanisms, challenges to in-depth understanding and utilization remain, and the cost of large-scale sequencing, which requires integrated analyses of high-throughput omics data, is high. In this review, we mainly elaborate on research advances in integrative analyses (e.g. GWAS, omics) for identifying functional genes or genomic elements for longissimus dorsi muscle growth and development for different pig breeds, describing several successful transcriptome analyses and functional genomics cases, in an attempt to provide some perspective on the future functional annotation of genetic elements for muscle growth and development in pigs.

Single-cell RNA sequencing reveals blastomere heterogeneity of 2-cell embryos in pigs.

In mammals, single blastomeres from as early as 2-cell embryos demonstrate heterogeneous developmental capacity and fate decision into different cell lineages. However, mechanisms underlying blastomere heterogeneity of 2-cell embryos remain largely unresolved. Here, we analysed the molecular heterogeneity of full-length mRNAs and their 3'UTR regions, based on the single-cell RNA-seq data of pig 2-cell embryos generated from in vivo fertilization (in vivo), in vitro fertilization (in vitro) and parthenogenetic activation (PA), respectively. First, unsupervised clustering helped discover two different groups of blastomeres for 2-cell pig embryos. Between these two groups of blastomeres in pig 2-cell embryos, 35, 301 and 428 full-length mRNAs respectively in in vivo, in vitro and PA embryo types were identified to be differentially expressed (padj ≤ .05 and |log2 [fold change]| ≥1) (DE mRNAs), while 92, 89 and 42 mRNAs were shown to be with significantly different 3'UTR lengths (3'UTR DE) (padj ≤ .05). Gene enrichment for both DE mRNAs and 3'UTR DE mRNAs found multiple signalling pathways, including cell cycle, RNA processing. Few numbers of common DE mRNAs and 3'UTR DE mRNAs existed between in vitro and in vivo blastomeres derived from 2-cell embryos, indicating the larger differences between in vitro and in vivo fertilized embryos. Integrative genomics viewer analysis further identified that 3'UTRs of HSDL2 and SGTA (in vivo), FAM204A and phosphoserine phosphatase (in vitro), PRPF40A and RPIA (PA) had >100 nt average length changes. Moreover, numbers and locations of regulatory elements (polyadenylation site, cytoplasmic polyadenylation element and microRNA binding sites) within 3'UTRs of these DE mRNAs were predicted. These results indicate that molecular heterogeneity existed among blastomeres from different types of pig 2-cell embryos, providing useful information and novel insights into future functional investigation on its relationship with the subsequent embryo development and differentiation.

Integrated single cell transcriptome sequencing analysis reveals species-specific genes and molecular pathways for pig spermiogenesis.

Mammalian spermatogenesis is a highly complicated and intricately organized process involving spermatogonia propagation (mitosis) and meiotic differentiation into mature sperm cells (spermiogenesis). In pigs, spermatogonia development and the role of somatic cells in spermatogenesis were previously investigated in detail. However, the characterization of key molecules fundamental to pig spermiogenesis remains less explored. Here we compared spermatogenesis between humans and pigs, focusing on spermiogenesis, by integrative testicular single-cell RNA sequencing (scRNA-seq) analysis. Human and pig testicular cells were clustered into 26 different groups, with cell-type-specific markers and signalling pathways. For spermiogenesis, pseudo-time analysis classified the lineage differentiation routes for round, elongated spermatids and spermatozoa. Moreover, markers and molecular pathways specific to each type of spermatids were examined for humans and pigs, respectively. Furthermore, high-dimensional weighted gene co-expression network analysis (hdWGCNA) identified gene modules specific for each type of human and pig spermatids. Hub genes (pig: SNRPD2.1 related to alternative splicing; human: CATSPERZ, Ca[2+] ion channel) potentially involved in spermiogenesis were also revealed. Taken together, our integrative analysis found that human and pig spermiogeneses involve specific genes and molecular pathways and provided resources and insights for further functional investigation on spermatid maturation and male reproductive ability.