Multiple sequence alignment-based RNA language model and its application to structural inference.

Compared with proteins, DNA and RNA are more difficult languages to interpret because four-letter coded DNA/RNA sequences have less information content than 20-letter coded protein sequences. While BERT (Bidirectional Encoder Representations from Transformers)-like language models have been developed for RNA, they are ineffective at capturing the evolutionary information from homologous sequences because unlike proteins, RNA sequences are less conserved. Here, we have developed an unsupervised multiple sequence alignment-based RNA language model (RNA-MSM) by utilizing homologous sequences from an automatic pipeline, RNAcmap, as it can provide significantly more homologous sequences than manually annotated Rfam. We demonstrate that the resulting unsupervised, two-dimensional attention maps and one-dimensional embeddings from RNA-MSM contain structural information. In fact, they can be directly mapped with high accuracy to 2D base pairing probabilities and 1D solvent accessibilities, respectively. Further fine-tuning led to significantly improved performance on these two downstream tasks compared with existing state-of-the-art techniques including SPOT-RNA2 and RNAsnap2. By comparison, RNA-FM, a BERT-based RNA language model, performs worse than one-hot encoding with its embedding in base pair and solvent-accessible surface area prediction. We anticipate that the pre-trained RNA-MSM model can be fine-tuned on many other tasks related to RNA structure and function.

Y chromosome polymorphisms contribute to an increased risk of non-obstructive azoospermia: a retrospective study of 32,055 Chinese men.

PURPOSE: To investigate the prevalence of Y chromosome polymorphisms in Chinese men and analyze their associations with male infertility and female adverse pregnancy outcomes. METHODS: The clinical data of 32,055 Chinese men who underwent karyotype analysis from October 2014 to September 2019 were collected. Fisher's exact test, chi-square test, or Kruskal-Wallis test was used to analyze the effects of Y chromosome polymorphism on semen parameters, azoospermia factor (AZF) microdeletions, and female adverse pregnancy outcomes. RESULTS: The incidence of Y chromosome polymorphic variants was 1.19% (381/32,055) in Chinese men. The incidence of non-obstructive azoospermia (NOA) was significantly higher in men with the Yqh- variant than that in men with normal karyotype and other Y chromosome polymorphic variants (p < 0.050). The incidence of AZF microdeletions was significantly different among the normal karyotype and different Y chromosome polymorphic variant groups (p < 0.001). The detection rate of AZF microdeletions was 28.92% (24/83) in the Yqh- group and 2.50% (3/120) in the Y ≤ 21 group. The AZFb + c region was the most common AZF microdeletion (78.57%, 22/28), followed by AZFc microdeletion (7.14%,2/28) in NOA patients with Yqh- variants. There was no significant difference in the distribution of female adverse pregnancy outcomes among the normal karyotype and different Y chromosome polymorphic variant groups (p = 0.528). CONCLUSIONS: Patients with 46,XYqh- variant have a higher incidence of NOA and AZF microdeletions than patients with normal karyotype and other Y chromosome polymorphic variants. Y chromosome polymorphic variants do not affect female adverse pregnancy outcomes.

The Progress of Research on Genetic Factors of Recurrent Pregnancy Loss.

Recurrent pregnancy loss (RPL) is both mental and physical health problem affecting about 1-5% of women of childbearing age. The etiology of RPL is complex, involving chromosomal abnormalities, autoimmune diseases, metabolic disorders, and endometrial dysfunction. The causes of abortion are still unknown in more than 50% of these cases. With the development of science and technology, an increasing number of scholars focus on this field and find that genetic factors may play an essential role in unexplained RPL, such as embolism-related genes, immune factor-related genes, and chromosomal numeric, and structural variation. This review summarizes the genetic factors associated with RPL, including genetic mutations and genetic polymorphisms, chromosomal variants, and chromosomal polymorphisms. Many related genetic factors have been found to be demographically and geographically relevant, some of which can be used for risk prediction or screening for the etiology of RPL. However, it is difficult to predict and prevent RPL due to uncertain pathogenesis and highly variable clinical presentation. Therefore, the genetic factors of RPL still need plentiful research to obtain a more accurate understanding of its pathogenesis and to provide more detection means for the screening and prevention of RPL.

Sensory Recruitment Revisited: Ipsilateral V1 Involved in Visual Working Memory.

The "sensory recruitment hypothesis" posits an essential role of sensory cortices in working memory, beyond the well-accepted frontoparietal areas. Yet, this hypothesis has recently been challenged. In the present study, participants performed a delayed orientation recall task while high-spatial-resolution 3 T functional magnetic resonance imaging (fMRI) signals were measured in posterior cortices. A multivariate inverted encoding model approach was used to decode remembered orientations based on blood oxygen level-dependent fMRI signals from visual cortices during the delay period. We found that not only did activity in the contralateral primary visual cortex (V1) retain high-fidelity representations of the visual stimuli, but activity in the ipsilateral V1 also contained such orientation tuning. Moreover, although the encoded tuning was faded in the contralateral V1 during the late delay period, tuning information in the ipsilateral V1 remained sustained. Furthermore, the ipsilateral representation was presented in secondary visual cortex (V2) as well, but not in other higher-level visual areas. These results thus supported the sensory recruitment hypothesis and extended it to the ipsilateral sensory areas, which indicated the distributed involvement of visual areas in visual working memory.

High expression of CFTR in cumulus cells from mature oocytes is associated with high-quality of oocyte and subsequent embryonic development.

OBJECTIVE: The purpose of this study was to explore the association of expression of cystic fibrosis transmembrane conductance regulator (CFTR) in cumulus cells (CCs) from mature oocytes with oocyte quality and embryonic development. METHODS: A total of 338 infertile women who underwent ovarian stimulation cycle of oocyte retrieval in Zhejiang University School of Medicine were retrospectively enrolled in this study. The relative mRNA expression levels of CFTR, bone morphogenetic protein 15 (BMP15), and growth differentiation factor 9 (GDF9) in CCs were detected by qPCR technology. ROC curve was applied for the diagnosis of oocyte maturation. The serum levels of anti-Müllerian hormone (AMH), E2, follicle-stimulating hormone (FSH), luteinizing hormone (LH), and androstenedione were measured. Oocyte maturation rate, fertilization rate, cleavage rate, high-quality embryo formation rate, and implantation rate after embryo transfer were also determined. RESULTS: The mRNA expression levels of CFTR in CCs were significantly increased in metaphase II (MII) oocytes compared to that in metaphase I (MI) or germinal vesicle (GV) oocytes. The ROC curve analysis illustrated that CFTR mRNA expression could efficiently discriminate MII oocytes from MI or GV oocytes (AUC = 0.954), and revealed that 0.695 RQU is the optimal cut-off value for diagnosis. So the cut-off value of 2-ΔΔCT = 0.70 was used to divide the patients into two groups: low- (n = 114) and high-CFTR group (n = 224). The mRNA expression of CFTR in CCs was positively correlated with the antral follicular count (AFC), number of oocytes retrieved, number of MII oocytes, serum E2 level on hCG day, and BMP15 and GDF9 expression in CCs. Under continuous stimulation with the same dose of recombinant follicle-stimulating hormone (rFSH), the number of follicles, average recovered oocytes, recovered oocytes, MII oocytes, as well as the oocyte recovery rate, fertilization rate, oocyte cleavage rate, high-quality embryo formation rate, and implantation rate were decreased in patients with lower CFTR. CONCLUSIONS: This study suggests that CFTR expression in CCs is associated with the developmental potential of human oocytes.

Development and validation predictive models of sperm retrieval for azoospermic men undergoing testicular sperm aspiration: a multicentre, retrospective, cohort study.

PURPOSE: Testicular sperm aspiration (TESA) is widely used to retrieve sperm from testis. Diagnostic testicular biopsy should not be routinely performed for azoospermia. Therefore, a good predictive model is needed before TESA. METHODS: A total of 1972 azoospermia patients constituted the modelling set, and 260 azoospermia patients from two other centres constituted the validation set. An integrated predictive model was built using logistic regression. Receiver operating characteristic (ROC), calibration and decision curve analyses were performed to evaluate the performance of follicle-stimulating hormone (FSH), semen volume, testicular volume and the integrated model. RESULTS: The FSH level was the best univariate predictor for successful sperm retrieval (SSR) and was better than semen volume and testicular volume alone (p<0.001, threshold 6.17 IU/L, modelling set area under receiver operating characteristic curve (AUC) 0.80, accuracy 0.79; validation set AUC 0.87, accuracy 0.78). The integrated predictive model had excellent accuracy for predicting SSR (modelling set: AUC 0.93, accuracy 0.89; validation set: AUC 0.96, accuracy: 0.89). Calibration curve analysis indicated that the integrated model calibration was good and better than that of FSH, semen volume and testicular volume alone. Decision curve analysis indicated with a threshold probability between 0.05 and 0.98, the integrated model added more benefit than treating either all or no patients. CONCLUSIONS: The integrated model has excellent discrimination and good calibration. It can help azoospermic men make better decisions before TESA. It should be noted that TESA is not the first-line treatment for non-obstructive azoospermia because of a low sperm retrieval rate.

Sperm DNA fragmentation and male fertility: a retrospective study of 5114 men attending a reproductive center.

PURPOSE: The sperm DNA fragmentation index (DFI) was quantitatively measured and its relationship with age, semen quality, and infertility conditions was investigated. METHODS: Semen routine test and sperm DFI were performed in 2760 infertile male and 2354 male whose spouse experienced at least one unexplained miscarriage to analyze the correlation between sperm DNA damage, semen routine parameters, and age. RESULTS: Sperm DFI was significantly lower from patients whose wife experienced unexplained miscarriage compared to infertility males (p = 0.000). An inverse correlation between sperm DFI and sperm progressive motility was observed (rs = - 0.465, p = 0.000) and sperm DFI was positively correlated with age (rs = 0.255, p = 0.000). However, the correlation between sperm DFI and sperm concentration, semen volume, total sperm count, and motile sperm count were not proved. CONCLUSIONS: Sperm DFI is an important indicator for evaluating the quality of semen. Sperm DNA integrity testing is preferentially recommended to those who have decreased sperm progressive motility, especially older men. An integrative analysis of sperm DFI, sperm progressive motility, age, and infertility conditions can provide a more comprehensive assessment of male fertility.

Joint segmentation and detection of COVID-19 via a sequential region generation network.

The fast pandemics of coronavirus disease (COVID-19) has led to a devastating influence on global public health. In order to treat the disease, medical imaging emerges as a useful tool for diagnosis. However, the computed tomography (CT) diagnosis of COVID-19 requires experts' extensive clinical experience. Therefore, it is essential to achieve rapid and accurate segmentation and detection of COVID-19. This paper proposes a simple yet efficient and general-purpose network, called Sequential Region Generation Network (SRGNet), to jointly detect and segment the lesion areas of COVID-19. SRGNet can make full use of the supervised segmentation information and then outputs multi-scale segmentation predictions. Through this, high-quality lesion-areas suggestions can be generated on the predicted segmentation maps, reducing the diagnosis cost. Simultaneously, the detection results conversely refine the segmentation map by a post-processing procedure, which significantly improves the segmentation accuracy. The superiorities of our SRGNet over the state-of-the-art methods are validated through extensive experiments on the built COVID-19 database.

High-precision three dimensional atom localization via multiphoton quantum destructive interference.

We propose an effective scheme for high-precision three dimensional(3D) atom localization via measuring the population of excited state in a four-level atomic system driven by a probe field and three orthogonal standing-wave fields. In this scheme, the position-dependent multiphoton quantum destructive interference leads to multiphoton excitation of the excited state and enhances the fluorescence emission. We show that adjusting the frequency detuning and phase shifts associated with the standing-wave fields can modify the multiphoton quantum destructive interference and lead to a redistribution of the atoms. The maximal probability of finding the atom at the certain position in one period of the standing-wave fields can be 100% and the highest spatial precision is about 0.02λ.

NbB12-: a new member of half-sandwich type doped boron clusters with high stability.

A theoretical study of geometrical structures and electronic properties of niobium-doped boron clusters is performed using the CALYPSO approach for the global minimum search followed by density functional theory calculations. It is found that the global minima obtained for the neutral clusters correspond to the half-sandwich structures at n = 10-17 and the tubular-type structures at n = 18-20. The geometrical patterns in the anion series are more complex. The geometries undergo a transformation from the wheel-like structure of NbB10- to the half-sandwich ones beginning at n = 11 and finally to the drum-shaped structures at n ≥ 18. A fascinating NbB12- cluster is uncovered by our structural search, which shows robust stability and can be considered as a new member of the half-sandwich transition metal doped boron clusters. The chemical bond analysis indicates that the high stability is due to the strong interactions between the Nb atom and the B12 host as well as to the strong B-B covalent bonds. Our study will enrich the database of geometrical structures of transition metal doped boron clusters and will stimulate future synthesis of boron-based nanomaterials.

Exhaustive exploration of MgBn (n = 10-20) clusters and their anions.

To understand the effect of magnesium atom doping on boron clusters, here we report the lowest-lying energy structures and electronic properties of neutral and monoanionic magnesium-boron clusters, in which boron atoms range in size from 10 to 20, in the framework of a CALYPSO structural search and DFT calculations. One of the most stable combinations is MgB18, which adopts an unexpected tubular drum-shaped geometry that is found for the first time in boron clusters doped with alkaline-earth metal atoms. The stability of the MgB18 cluster mainly stems from the intense electrostatic interaction between the B18 skeleton and the Mg atom.

Seminal plasma neutral alpha-glucosidase activity as an early predictor of patency and natural pregnancy after microsurgical vasoepididymostomy.

Microsurgical vasoepididymostomy (MVE) is recommended as a first-line option for treatment of epididymal obstructive azoospermia (EOA). However, early indicators for predicting patency and natural pregnancy are unclear. Our aim was to explore the early predictive value of seminal plasma neutral alpha-glucosidase (NAG) activity for patency and natural pregnancy after MVE. Eighty-four patients with EOA who underwent MVE were enrolled in this study. The post-operative patency and natural pregnancy rates were 60.71% and 33.33% respectively. The presence of motile epididymal spermatozoa at the anastomosis site and NAG activity measured at the first month after MVE were early and independent predictors of patency and natural pregnancy. The areas under the receiver operating characteristic curves (AUCs) of NAG activity for prediction of patency and natural pregnancy were 0.78 (95% confidence interval [CI]: 0.68-0.88) and 0.82 (95% CI: 0.73-0.92). The best cut-off values of NAG activity for predicting patency and pregnancy were 15.9 and 17.0 m IU/ejaculate respectively. In conclusion， NAG activity measured at the first month after MVE is an early and independent predictor of patency and natural pregnancy.

Elevated RON protein expression in endometriosis and disease-associated ovarian cancers.

BACKGROUND: Recepteur d'origine nantais (RON) protein expression has been demonstrated to correlate with tumor progression, metastasis, and prognosis, and its mRNA expression increases in deeply infiltrating endometriotic lesions. However, it remains unclear whether RON protein expression also increases in endometriotic lesions, and may be a risk factor of malignant transformation in endometriotic lesions. METHODS: The protein expression of RON in control (n = 19), eutopic (n = 16), and ectopic (n = 51) endometria, as well as in endometriosis-associated ovarian cancers (EAOC, n = 16) was determined by immunohistochemical (IHC) staining. RESULTS: Endometriotic lesions expressed low levels of RON protein, but no RON protein expression appeared in matched eutopic or control endometrium. EAOC exhibited high levels of RON protein. The frequency and IHC score of RON protein expression were both significantly higher in EAOC [100.0% (14/14), 5.37 ± 0.74] than those in endometriotic lesions [51.0% (26/51), 2.15 ± 1.12; P = 0.002, 0.001]. Multivariate analysis of covariance only revealed a correlation of RON protein expression and EAOC (P = 0.006), but no correlations of RON protein expression and clinical parameters (P > 0.05). CONCLUSIONS: These obtained results suggest that increased RON expression might be involved in the pathogenesis of endometriosis and disease-associated ovarian cancers.

Indoor Trajectory Tracking Scheme Based on Delaunay Triangulation and Heuristic Information in Wireless Sensor Networks.

Object tracking and detection is one of the most significant research areas for wireless sensor networks. Existing indoor trajectory tracking schemes in wireless sensor networks are based on continuous localization and moving object data mining. Indoor trajectory tracking based on the received signal strength indicator (RSSI) has received increased attention because it has low cost and requires no special infrastructure. However, RSSI tracking introduces uncertainty because of the inaccuracies of measurement instruments and the irregularities (unstable, multipath, diffraction) of wireless signal transmissions in indoor environments. Heuristic information includes some key factors for trajectory tracking procedures. This paper proposes a novel trajectory tracking scheme based on Delaunay triangulation and heuristic information (TTDH). In this scheme, the entire field is divided into a series of triangular regions. The common side of adjacent triangular regions is regarded as a regional boundary. Our scheme detects heuristic information related to a moving object's trajectory, including boundaries and triangular regions. Then, the trajectory is formed by means of a dynamic time-warping position-fingerprint-matching algorithm with heuristic information constraints. Field experiments show that the average error distance of our scheme is less than 1.5 m, and that error does not accumulate among the regions.

Seminal plasma HSPA2 mRNA content is associated with semen quality.

PURPOSE: Cell-free mRNAs (cfmRNAs) were quantitatively measured in human seminal plasma and its relationship with semen quality was investigated. METHODS: Herein, a prospectively, controlled investigation was performed to study seminal plasma HSPA2 and uPA cfmRNA alterations between 21 asthenozoospermic patients and 16 normozoospermic individuals. Standard semen analysis was performed and seminal plasma cfmRNAs content was measured by real-time quantitative PCR. In addition, the regression analysis between seminal plasma cfmRNAs expression and semen parameters was performed. RESULTS: Seminal plasma HSPA2, but not uPA cfmRNA indicated significant difference between normozoospermia and asthenozoospermia men (P = 0.02444 and 0.07811, respectively). Negative correlation between HSPA2 cfmRNA and sperm motility (R (2) = 0.213, P = 0.004) as well as sperm concentration (R (2) = 0.133, P = 0.026) were revealed. However, no correlation was found between seminal plasma uPA cfmRNA content and semen parameters. CONCLUSIONS: Our data suggest that seminal plasma HSPA2 cfmRNA is different between asthenozoospermic and normozoospermic individuals and it might be an indicator for semen quality.

Ab Initio Search for Global Minimum Structures of Pure and Boron Doped Silver Clusters.

The global minimum structures of pure and boron doped silver clusters up to 16 atoms are determined through ab initio calculations and unbiased structure searching methods. The structural and electronic properties of neutral, anionic, and cationic Ag(n)B (n ≤ 15) and Ag(n)B2 (n ≤ 14) clusters are much distinct from those of the corresponding pure silver. Considering that Ag and B possess one and three valence electrons, respectively, both the single and the double boron-atom doped silver clusters with even number of valence electrons are more stable than those with odd number of electrons, a feature also observed in the pure silver clusters. We demonstrate that the species with a valence count of 8 and 14 appear to be magic numbers with enhanced stability irrespective of component or the charged state. A new putative global minimum structure of Ag13(-) cluster, with high symmetry of C(2v), is unexpectedly observed as the ground state, which is lower in energy than the previous suggested bilayer structure.

[Microsurgical treatment of obstructive azoospermia: a report of 76 cases].

OBJECTIVE: To investigate the clinical effect of microsurgical vasoepididymostomy and/or vasovasostomy in the treatment of obstructive azoospermia. METHODS: This study included 76 patients with obstructive azoospermia, 53 treated by bilateral vasoepididymostomy (8 involving the epididymal head, 18 involving the epididymal body, 5 involving the epididymal tail, and 22 involving the epididymal head, body and tail), 14 by unilateral vasoepididymostomy, and the other 9 by unilateral vasoepididymostomy + unilateral vasovasostomy (including cross anastomosis). We followed up the patients for 2 to 16 months for the patency rate, routine semen parameters, and pregnancy outcomes. RESULTS: The success rate of bilateral vasoepididymostomy, unilateral vasoepididymostomy, and unilateral vasoepididymostomy + unilateral vasovasostomy (including cross anastomosis) were 62.26% (33/53), 35.71% (5/14), and 77.78% (7/9), respectively. The average sperm concentrations in the three groups of patients were (27.9 +/- 5.74), (11.8 +/- 8.33), and (19.9 +/- 7.53) x 10(6)/ml, the average total sperm counts were (65.6 +/- 13.71), (28.0 +/- 15.86), and (69.2 +/- 28.59) x 10(6), and the mean rates of progressively motile sperm were (22.3 +/- 3.18), (11.0 +/- 9.77), and (15.8 +/- 5.05)%, respectively. The success rates of bilateral vasoepididymostomy that involved the epididymal head, body, tail, and all the three parts were 62.5, 72.22, 60, and 54.55%, respectively. Natural pregnancy was achieved in 8 (10.53%) of the total number of cases. CONCLUSION: Microsurgery is effective for the treatment obstructive azoospermia. Unilateral vasoepididymostomy + unilateral vasovasostomy is superior to the other procedures, followed by bilateral vasoepididymostomy. Bilateral vasoepididymostomy involving the epididymal body may achieve a slightly better effect than that involving the other epididymal parts.

Human sperm devoid of germinal angiotensin-converting enzyme is responsible for total fertilization failure and lower fertilization rates by conventional in vitro fertilization.

In conventional in vitro fertilization (IVF), complete failure of fertilization occurs in 5% to 15% of treatments. Although the causes may be unclear, sperm defects appear to be the major contributor. However, a convincing test is not yet available that can predict the risk of fertilization failure. In this study, we found that germinal angiotensin-converting enzyme (gACE) (also called testicular ACE) was undetectable in sperm from patients who had total fertilization failure (TFF) and lower fertilization rates (LFRs) by IVF based on Western blot and indirect immunofluorescence analyses. Additionally, almost all of the patients without gACE on sperm (23 of 25) manifested a TT genotype of the rs4316 single-nucleotide polymorphism of ACE. Overall, our results indicate that the absence of gACE expression is responsible for TFF and LFRs by IVF. The rs4316 polymorphism of ACE might be associated with infertility in those patients. We conclude that sperm lacking gACE may be recognized before commencing IVF and that the patients may be directed instead to consider intracytoplasmic sperm injection.

Soliton controlling and steering in asymmetric nonlocal media with optical lattices.

Existence and stability of the fundamental and higher-order solitons, which exist in nonlinear media with asymmetric response and periodic linear refractive index modulation, are presented. It is found that the existence of solitons results in the balance between linear refractive index modulation (optical lattices) and nonlinear refractive index induced by incident optical field. In addition, Dynamical properties of fundamental mode solitons are also investigated in detail, and may be applied in the fields of soliton controlling and steering.

Depression of HspA2 in human testis is associated with spermatogenic impairment and fertilization rate in ICSI treatment for azoospermic individuals.

PURPOSE: Heat shock protein A2 (HspA2) expression was quantitatively measured in human testis and its relationship with the spermatogenetic status and laboratory outcomes of intracytoplasmic sperm injection (ICSI) was investigated. METHODS: Testicular tissues of azoospermia men were divided into four groups according to histopahtology: normal spermatogenesiss, hypospermatogenesis, maturation arrest and Sertoli cell-only syndrome (SCOS). HspA2 immunostaining was measured by Image Pro-Plus (IPP) and laboratory outcomes were calculated. The regression analysis between HspA2 expression and Johnsen score of as well as fertilization, cleavage and high quality embryo rate was performed. RESULTS: HspA2 was strongly present in the cytoplasm of spermatocytes and spermatides in normal testis. However, hypospermatogenesis and maturation arrest testicular tissues demonstrated light staining and no staining for SCOS. Quantitative image analysis showed that there were significant differences among groups (P = 0.000 & P = 0.001). HspA2 exspression was founded significantly correlated spermatogenetic status (R(2) = 0.726, P = 0.000) as well as fertilization rate in ICSI (R(2) = 0.569, P = 0.000). CONCLUSIONS: The fertilization rate with ICSI is associated with HspA2 expression in the testis from which sperm retrieved and the alteration of HspA2 expression has been involved in spermatogenic impairment.