Self-supervised semantic segmentation of retinal pigment epithelium cells in flatmount fluorescent microscopy images.

MOTIVATION: Morphological analyses with flatmount fluorescent images are essential to retinal pigment epithelial (RPE) aging studies and thus require accurate RPE cell segmentation. Although rapid technology advances in deep learning semantic segmentation have achieved great success in many biomedical research, the performance of these supervised learning methods for RPE cell segmentation is still limited by inadequate training data with high-quality annotations. RESULTS: To address this problem, we develop a Self-Supervised Semantic Segmentation (S4) method that utilizes a self-supervised learning strategy to train a semantic segmentation network with an encoder-decoder architecture. We employ a reconstruction and a pairwise representation loss to make the encoder extract structural information, while we create a morphology loss to produce the segmentation map. In addition, we develop a novel image augmentation algorithm (AugCut) to produce multiple views for self-supervised learning and enhance the network training performance. To validate the efficacy of our method, we applied our developed S4 method for RPE cell segmentation to a large set of flatmount fluorescent microscopy images, we compare our developed method for RPE cell segmentation with other state-of-the-art deep learning approaches. Compared with other state-of-the-art deep learning approaches, our method demonstrates better performance in both qualitative and quantitative evaluations, suggesting its promising potential to support large-scale cell morphological analyses in RPE aging investigations. AVAILABILITY AND IMPLEMENTATION: The codes and the documentation are available at: https://github.com/jkonglab/S4_RPE.

Brachytherapy in craniopharyngiomas: a systematic review and meta-analysis of long-term follow-up.

OBJECTIVE: Brachytherapy has been indicated as an alternative option for treating cystic craniopharyngiomas (CPs). The potential benefits of brachytherapy for CPs have not yet been clarified. The purpose of this work was to conduct a meta-analysis to analyze the long-term efficacy and adverse reactions profile of brachytherapy for CPs. MATERIALS AND METHODS: The relevant databases were searched to collect the clinical trials on brachytherapy in patients with CPs. Included studies were limited to publications in full manuscript form with at least 5-year median follow-up, and adequate reporting of treatment outcomes and adverse reactions data. Stata 12.0 was used for data analysis. RESULTS: According to the inclusion and exclusion criteria, a total of 6 clinical trials involving 266 patients with CPs were included in this meta-analysis. The minimum average follow-up was 5 years. The results of the meta-analysis showed that 1-year, 2-3 years and 5 years progression free survival rates (PFS) are 75% (95%CI: 66-84%), 62% (95%CI: 52-72%) and 57% (95%CI: 22-92%), respectively. At the last follow-up, less than 16% of patients with visual outcomes worser than baseline in all included studies. While, for endocrine outcomes, less than 32% of patients worser than baseline level. CONCLUSION: In general, based on the above results, brachytherapy should be considered as a good choice for the treatment of CP.

Folded Digital Meta-Lenses for on-Chip Spectrometer.

In-plane diffractive optical networks based on meta-surfaces are promising for on-chip application. The design constraints of regular antenna unit place ultimate limits on the functionalities of the meta-systems. This fundamental limitation has been reflected by the large footprints of cascaded meta-surfaces. Here, we propose a digital meta-lens with a large degree of design freedom, enabling significantly improved beam focusing, collimation, and deflection capabilities. A highly dispersive and compact diffractive optical system is constructed for spectrometer via five layers of meta-lenses in a folded configuration. The device only occupies a 100 µm × 100 µm chip area on a silicon photonic platform. Sparse and continuous spectra reconstruction is achieved over a 35 nm bandwidth. Fine spectral lines separated by 0.14 nm are resolved. In addition to such a compact and high-resolution on-chip spectrometer, it is also expected to be promising for imaging, optical computing, and other applications due to the great versatility of the digital lens design.

On-chip Y-junction with adaptive power splitting toward ultrabroad bandwidth.

Growing research interests have been directed to the emerging optical communication band at 2-µm wavelengths. The silicon photonic components are highly desired to operate over a broad bandwidth covering both C-band and the emerging 2-µm wave band. However, the dispersions of the silicon waveguides eventually limit the optical bandwidth of the silicon photonic devices. Here, we introduce a topology-optimized Y-junction with a shallow-etched trench and its utility to reverse the detrimental dispersion effect. The shallow trench enables the Y-junction to have an adaptive splitting capability over a broad spectral range. The 0.2-dB bandwidth of the power splitter exceeds 800 nm from 1400 nm to 2200 nm. The device has a compact footprint of 3 µm × 1.64 µm. The device is characterized at the C-band and 2-µm band with a measured excess loss below 0.4 dB for a proof-of-concept demonstration.

Inverse design of a dual-mode 3-dB optical power splitter with a 445†nm bandwidth.

Optical power splitters are fundamental blocks for photonic integrated circuits. Conventional 3-dB power splitters are either constrained to single-mode regime or to the limited optical bandwidth. In this paper, an alternative design approach is proposed via combined method of topology optimizations on both analog and digital meta-structure. Based on this approach, a dual-mode power splitter is designed on silicon-on-insulator with an ultra-broad bandwidth from 1588 nm - 2033nm and an ultra-compact footprint of only 5.4 µm × 2.88 µm. The minimum feature size is 120 nm which can be compatible with silicon photonic foundry process. The simulated excess loss and crosstalk over this wavelength range for the two lowest TE modes are lower than 0.83 dB and -22 dB, respectively. To the best of our knowledge, this is a record large optical bandwidth for an integrated dual-mode 3-dB power splitter on silicon.

A high-performance SNP panel developed by machine-learning approaches for characterizing genetic differences of Southern and Northern Han Chinese, Korean, and Japanese individuals.

Population stratification analyses targeting genetically closely related East Asians have revealed that distinguishable differentiation exists between Han Chinese, Korean, and Japanese individuals, as well as between southern (S-) and northern (N-) Han Chinese. Previous studies offer a number of choices for ancestry informative single nucleotide polymorphisms (AISNPs) to discriminate East-Asian populations. In this study, we collected and examined the efficiency of 1185 AISNPs using frequency and genotype data from various publicly available databases. With the aim to perform fine-scale classification of S-Han, N-Han, Korean, and Japanese subjects, machine-learning methods (Softmax and Random Forest) were used to screen a panel of highly informative AISNPs and to develop a superior classification model. Stepwise classification was implemented to increase and balance the discrimination in the process of AISNP selection, first discriminating Han, Korean, and Japanese individuals, and then characterizing stratification between S-Han and N-Han. The final 272-AISNP panel is an alternative optimization of various previous works, which promises reliable and >90% accuracy in classification of the four East-Asian groups. This AISNP panel and the machine-learning model could be a useful and superior choice in medical genome-wide association studies and in forensic investigations for unknown suspect identity.

Evaluation of Hepatoprotective Effects of Piperlongumine Derivative PL 1-3-Loaded Albumin Nanoparticles on Lipopolysaccharide/d-Galactosamine-Induced Acute Liver Injury in Mice.

In recent years, piperlongumine (PL) having specific cytotoxicity has attracted considerable attention for anticancer activity. Through structural modification, the active derivative PL 1-3 shows potential anti-inflammatory activity and low cytotoxicity, but its water solubility is low. Here, PL 1-3-loaded bovine serum albumin nanoparticles (1-3 NPs) were prepared and characterized, which can improve the dissolution. 1-3 NPs exhibited effective hepatoprotective effects on lipopolysaccharide/d-galactosamine-induced acute liver injury of mice, which was similar to liver injury in clinical settings. 1-3 NPs treatment can inhibit inflammation, oxidative stress, and apoptosis via the downregulation of NF-κB signaling pathways, the activation of Nrf2/HO-1 signaling pathways, and the inhibition of expression of Bax and caspase 3 proteins. The above results demonstrated that PL 1-3-loaded bovine serum albumin nanoparticles possessed potential value in intervention of inflammation-based liver injury.

Phosphoproteome Profiling Revealed the Importance of mTOR Inhibition on CDK1 Activation to Further Regulate Cell Cycle Progression.

The mammalian target of rapamycin (mTOR) functions as a critical regulator of cell cycle progression. However, the underlying mechanism by which mTOR regulates cell cycle progression remains elusive. In this study, we used stable isotope labeling of amino acids in cell culture with a two-step strategy for phosphopeptide enrichment and high-throughput quantitative mass spectrometry to perform a global phosphoproteome analysis of mTOR inhibition by rapamycin. By monitoring the phosphoproteome alterations upon rapamycin treatment, downregulation of mTOR signaling pathway was detected and enriched. Further functional analysis of phosphoproteome revealed the involvement of cell cycle events. Specifically, the elevated profile of cell cycle-related substrates was observed, and the activation of CDK1, MAPK1, and MAPK3 kinases was determined. Second, pathway interrogation using kinase inhibitor treatment confirmed that CDK1 activation operated downstream from mTOR inhibition to further regulate cell cycle progression. Third, we found that the activation of CDK1 following 4-12 h of mTOR inhibition was accompanied by the activation of the Greatwall-endosulfine complex. In conclusion, we presented a high-confidence phosphoproteome map inside the cells upon mTOR inhibition by rapamycin. Our data implied that mTOR inhibition could contribute to CDK1 activation for further regulating cell cycle progression, which was mediated by the Greatwall-endosulfine complex.

Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.

Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan's molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.

49AISNP: a study on the ancestry inference of the three ethnic groups in the north of East Asia.

The ancestry inference of unknown samples plays an important role in forensic investigations. An ideal panel is a set of few markers with high ancestry inference accuracy. We collected 428 AISNP (ancestry informative SNP) that can distinguish the three ethnic groups in north of East Asia, including northern Han, Japanese and Korean. The genotypes of 428 AISNP in 307 samples from these three ethnic groups were obtained. Based on the information of Fst value and clustering by allele frequency, the panel was further refined into 49AISNP smart panel. Inference accuracy of the 49AISNP was verified by the leave-one-out method with 307 samples, and the results showed that its accuracy was higher than 99% in the northern Han, Japanese and Korean ethnic groups. This panel can also be helpful to further distinguish the ethnic sub-groups in East Asia.

Metabolism of polysaccharides in dynamic middle lamellae during cotton fibre development.

MAIN CONCLUSION: Evidence is presented that cotton fibre adhesion and middle lamella formation are preceded by cutin dilution and accompanied by rhamnogalacturonan-I metabolism. Cotton fibres are single cell structures that early in development adhere to one another via the cotton fibre middle lamella (CFML) to form a tissue-like structure. The CFML is disassembled around the time of initial secondary wall deposition, leading to fibre detachment. Observations of CFML in the light microscope have suggested that the development of the middle lamella is accompanied by substantial cell-wall metabolism, but it has remained an open question as to which processes mediate adherence and which lead to detachment. The mechanism of adherence and detachment were investigated here using glyco-microarrays probed with monoclonal antibodies, transcript profiling, and observations of fibre auto-digestion. The results suggest that adherence is brought about by cutin dilution, while the presence of relevant enzyme activities and the dynamics of rhamnogalacturonan-I side-chain accumulation and disappearance suggest that both attachment and detachment are accompanied by rhamnogalacturonan-I metabolism.

Involvement of Salicylic Acid in Anthracnose Infection in Tea Plants Revealed by Transcriptome Profiling.

Anthracnose is a major leaf disease in tea plant induced by Colletotrichum, which has led to substantial losses in yield and quality of tea. The molecular mechanism with regards to responses or resistance to anthracnose in tea remains unclear. A de novo transcriptome assembly dataset was generated from healthy and anthracnose-infected leaves on tea cultivars "Longjing-43" (LJ43) and "Zhenong-139" (ZN139), with 381.52 million pair-end reads, encompassing 47.78 billion bases. The unigenes were annotated versus Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), National Center for Biotechnology Information (NCBI) non-redundant protein sequences (Nr), evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Swiss-prot. The number of differential expression genes (DEGs) detected between healthy and infected leaves was 1621 in LJ43 and 3089 in ZN139. The GO and KEGG enrichment analysis revealed that the DEGs were highly enriched in catalytic activity, oxidation-reduction, cell-wall reinforcement, plant hormone signal transduction and plant-pathogen interaction. Further studies by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and high-performance liquid chromatography (HPLC) showed that expression of genes involved in endogenous salicylic acid biosynthesis and also accumulation of foliar salicylic acid are involved in the response of tea plant to anthracnose infection. This study firstly provided novel insight in salicylic acid acting as a key compound in the responses of tea plant to anthracnose disease. The transcriptome dataset in this study will facilitate to profile gene expression and metabolic networks associated with tea plant immunity against anthracnose.

Erratum to: The treatment effect of novel hGHRH homodimer to male infertility hamster.

[This corrects the article on p. 637 in vol. 22, PMID: 30402024.].

The Three Members of the Arabidopsis Glycosyltransferase Family 92 are Functional ß-1,4-Galactan Synthases.

Pectin is a major component of primary cell walls and performs a plethora of functions crucial for plant growth, development and plant-defense responses. Despite the importance of pectic polysaccharides their biosynthesis is poorly understood. Several genes have been implicated in pectin biosynthesis by mutant analysis, but biochemical activity has been shown for very few. We used reverse genetics and biochemical analysis to study members of Glycosyltransferase Family 92 (GT92) in Arabidopsis thaliana. Biochemical analysis gave detailed insight into the properties of GALS1 (Galactan synthase 1) and showed galactan synthase activity of GALS2 and GALS3. All proteins are responsible for adding galactose onto existing galactose residues attached to the rhamnogalacturonan-I (RG-I) backbone. Significant GALS activity was observed with galactopentaose as acceptor but longer acceptors are favored. Overexpression of the GALS proteins in Arabidopsis resulted in accumulation of unbranched ß-1, 4-galactan. Plants in which all three genes were inactivated had no detectable ß-1, 4-galactan, and surprisingly these plants exhibited no obvious developmental phenotypes under standard growth conditions. RG-I in the triple mutants retained branching indicating that the initial Gal substitutions on the RG-I backbone are added by enzymes different from GALS.

Pea Border Cell Maturation and Release Involve Complex Cell Wall Structural Dynamics.

The adhesion of plant cells is vital for support and protection of the plant body and is maintained by a variety of molecular associations between cell wall components. In some specialized cases, though, plant cells are programmed to detach, and root cap-derived border cells are examples of this. Border cells (in some species known as border-like cells) provide an expendable barrier between roots and the environment. Their maturation and release is an important but poorly characterized cell separation event. To gain a deeper insight into the complex cellular dynamics underlying this process, we undertook a systematic, detailed analysis of pea (Pisum sativum) root tip cell walls. Our study included immunocarbohydrate microarray profiling, monosaccharide composition determination, Fourier-transformed infrared microspectroscopy, quantitative reverse transcription-PCR of cell wall biosynthetic genes, analysis of hydrolytic activities, transmission electron microscopy, and immunolocalization of cell wall components. Using this integrated glycobiology approach, we identified multiple novel modes of cell wall structural and compositional rearrangement during root cap growth and the release of border cells. Our findings provide a new level of detail about border cell maturation and enable us to develop a model of the separation process. We propose that loss of adhesion by the dissolution of homogalacturonan in the middle lamellae is augmented by an active biophysical process of cell curvature driven by the polarized distribution of xyloglucan and extensin epitopes.

Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis.

Most glycosylation reactions require activated glycosyl donors in the form of nucleotide sugars to drive processes such as posttranslational modifications and polysaccharide biosynthesis. Most plant cell wall polysaccharides are biosynthesized in the Golgi apparatus from cytosolic-derived nucleotide sugars, which are actively transferred into the Golgi lumen by nucleotide sugar transporters (NSTs). An exception is UDP-xylose, which is biosynthesized in both the cytosol and the Golgi lumen by a family of UDP-xylose synthases. The NST-based transport of UDP-xylose into the Golgi lumen would appear to be redundant. However, employing a recently developed approach, we identified three UDP-xylose transporters in the Arabidopsis thaliana NST family and designated them UDP-XYLOSE TRANSPORTER1 (UXT1) to UXT3. All three transporters localize to the Golgi apparatus, and UXT1 also localizes to the endoplasmic reticulum. Mutants in UXT1 exhibit ∼30% reduction in xylose in stem cell walls. These findings support the importance of the cytosolic UDP-xylose pool and UDP-xylose transporters in cell wall biosynthesis.

The treatment effect of novel hGHRH homodimer to male infertility hamster.

Extra-hypothalamic growth hormone-releasing hormone (GHRH) plays an important role in reproduction. To study the treatment effect of Grin (a novel hGHRH homodimer), the infertility models of 85 male Chinese hamsters were established by intraperitoneally injecting 20 mg/kg of cyclophosphamide once in a week for 5 weeks and the treatment with Grin or human menopausal gonadotropin (hMG) as positive control was evaluated by performing a 3-week mating experiment. 2-8 mg/kg of Grin and 200 U/kg of hMG showed similar effect and different pathological characteristics. Compared to the single cyclophosphamide group (0%), the pregnancy rates (H-, M-, L-Grin 26.7, 30.8, 31.3%, and hMG 31.3%) showed significant difference, but there was no difference between the hMG and Grin groups. The single cyclophosphamide group presented loose tubules with pathologic vacuoles and significant TUNEL positive cells. Grin induced less weight of body or testis, compactly aligned tubules with little intra-lumens, whereas hMG caused more weight of body or testis, enlarging tubules with annular clearance. Grin presented a dose-dependent manner or cell differentiation-dependentincrease in testicular GHRH receptor, and did not impact the levels of blood and testicular GH, testosterone. Grin promotes fertility by proliferating and differentiating primitive cells through up-regulating testicular GHRH receptor without triggering GH secretion, which might solve the etiology of oligoasthenozoospermia.

Heteromannan and Heteroxylan Cell Wall Polysaccharides Display Different Dynamics During the Elongation and Secondary Cell Wall Deposition Phases of Cotton Fiber Cell Development.

The roles of non-cellulosic polysaccharides in cotton fiber development are poorly understood. Combining glycan microarrays and in situ analyses with monoclonal antibodies, polysaccharide linkage analyses and transcript profiling, the occurrence of heteromannan and heteroxylan polysaccharides and related genes in developing and mature cotton (Gossypium spp.) fibers has been determined. Comparative analyses on cotton fibers at selected days post-anthesis indicate different temporal and spatial regulation of heteromannan and heteroxylan during fiber development. The LM21 heteromannan epitope was more abundant during the fiber elongation phase and localized mainly in the primary cell wall. In contrast, the AX1 heteroxylan epitope occurred at the transition phase and during secondary cell wall deposition, and localized in both the primary and the secondary cell walls of the cotton fiber. These developmental dynamics were supported by transcript profiling of biosynthetic genes. Whereas our data suggest a role for heteromannan in fiber elongation, heteroxylan is likely to be involved in the regulation of cellulose deposition of secondary cell walls. In addition, the relative abundance of these epitopes during fiber development varied between cotton lines with contrasting fiber characteristics from four species (G. hirsutum, G. barbadense, G. arboreum and G. herbaceum), suggesting that these non-cellulosic polysaccharides may be involved in determining final fiber quality and suitability for industrial processing.

Exploring the nonlinear relationship between body mass index and health-related quality of life among adults: a cross-sectional study in Shaanxi Province, China.

INTRODUCTION: China is a country facing the "double burden" of both obesity and underweight. The objective of this study was to explore the relationship between body mass index (BMI) and health-related quality of life (HRQOL) in adults from Shaanxi Province. METHODS: The data were derived from the fifth Health Service Survey of Shaanxi Province, which was part of China's National Health Service Survey (NHSS), conducted in 2013. The HRQOL was assessed using the three-level EQ-5D questionnaire and scored based on a recently developed Chinese-specific tariff. Semiparametric regression models were adopted to explore the non-linear relationship between continuous BMI and overall HRQOL scores. Logistic regression models were further undertaken to assess the relationship between categorized BMI and five dimensions of HRQOL. RESULTS: Among the study sample (n = 37,902), 77% of men and 75 % of women were assigned to normal weight, according to the WHO International classification. There were statistical significant nonlinear relationships between BMI and HRQOL, with optimal HRQOL achieved at a BMI of near 23 kg/m2 for men and 24 kg/m2 for women. Before BMI reached optimal HRQOL, the EQ-5D utility scores were increasing faster among men than the women, whilst after the BMI value reached the optimal utility scores, women showed a faster decline in utility scores than men. With adjustments for socio-demographic, physical activity and co-morbidities, obese respondents were more likely to suffer from physical rather than mental problems. Underweight respondents were significantly more likely to report having any problems in all five dimensions of the EQ-5D, whilst the magnitudes of odds ratios were consistently larger for men than women. CONCLUSION: There was an inverse U-shaped association between continuous BMI and overall HRQOL scores, meaning that both underweight and obesity were associated with lower HRQOL. The relationship between BMI and HRQOL varied between sexes. Underweight respondents had a higher risk of suffering from both physical and mental problems. Interventions aimed to tackle the prevalence of underweight should be put into action in Shaanxi Province.

Research progress on the generation of NDMA by typical PPCPs in disinfection treatment of water environment in China: A review.

The drugs and personal care products in water sources are potential threats to the ecological environment and drinking water quality. In recent years, the presence of PPCPs has been detected in multiple drinking water sources in China. PPCPs are usually stable and resistant to degradation in aquatic environments. During chlorination, chloramination, and ozonation disinfection processes, PPCPs can act as precursor substances to generate N-nitrosodimethylamine (NDMA) which is the most widely detected nitrosamine byproduct in drinking water. This review provides a comprehensive overview of the impact of PPCPs in China's water environment on the generation of NDMA during disinfection processes to better understand the correlation between PPCPs and NDMA generation. Chloramine is the most likely to form NDMA with different disinfection methods, so chloramine disinfection may be the main pathway for NDMA generation. Activated carbon adsorption and UV photolysis are widely used in the removal of NDMA and its precursor PPCPs, and biological treatment is found to be a low-cost and high removal rate method for controlling the generation of NDMA. However, there are still certain regional limitations in the investigation and research on PPCPs, and other nitrosamine by-products such as NMEA, NDEA and NDBA should also be studied to investigate the formation mechanism and removal methods.