Patch-Based Convolutional Encoder: A Deep Learning Algorithm for Spectral Classification Balancing the Local and Global Information

Molecular vibrational spectroscopies, including infrared absorption and Raman scattering, provide molecular fingerprint information and are powerful tools for qualitative and quantitative analysis. They benefit from the recent development of deep-learning-based algorithms to improve the spectral, spatial, and temporal resolutions. Although a variety of deep-learning-based algorithms, including those to simultaneously extract the global and local spectral features, have been developed for spectral classification, the classification accuracy is still far from satisfactory when the difference becomes very subtle. Here, we developed a lightweight algorithm named patch-based convolutional encoder (PACE), which effectively improved the accuracy of spectral classification by extracting spectral features while balancing local and global information. The local information was captured well by segmenting the spectrum into patches with an appropriate patch size. The global information was extracted by constructing the correlation between different patches with depthwise separable convolutions. In the five open-source spectral data sets, PACE achieved a state-of-the-art performance. The more difficult the classification, the better the performance of PACE, compared with that of residual neural network (ResNet), vision transformer (ViT), and other commonly used deep learning algorithms. PACE helped improve the accuracy to 92.1% in Raman identification of pathogen-derived extracellular vesicles at different physiological states, which is much better than those of ResNet (85.1%) and ViT (86.0%). In general, the precise recognition and extraction of subtle differences offered by PACE are expected to facilitate vibrational spectroscopy to be a powerful tool toward revealing the relevant chemical reaction mechanisms in surface science or realizing the early diagnosis in life science.

Deep Learning-Enabled Raman Spectroscopic Identification of Pathogen-Derived Extracellular Vesicles and the Biogenesis Process

Pathogenic bacterial infections, exacerbated by increasing antimicrobial resistance, pose a major threat to human health worldwide. Extracellular vesicles (EVs), secreted by bacteria and acting as their "long-distance weapons", play an important role in the occurrence and development of infectious diseases. However, no efficient methods to rapidly detect and identify EVs of different bacterial origins are available. Here, label-free Raman spectroscopy in combination with a new deep learning model of the attentional neural network (aNN) was developed to identify pathogen-derived EVs at Gram^±, species, strain, and even down to physiological levels. By training the aNN model with a large Raman data set from six typical pathogen-derived EVs, we achieved the identification of EVs with high accuracies at all levels: exceeding 96% at the Gram and species levels, 93% at the antibiotic-resistant and sensitive strain levels, and still above 87% at the physiological level. aNN enabled Raman spectroscopy to interrogate the bacterial origin of EVs to a much higher level than previous methods. Moreover, spectral markers underpinning EV discrimination were uncovered from subtly different EV spectra via an interpretation algorithm of the integrated gradient. A further comparative analysis of the rich Raman biochemical signatures of EVs and parental pathogens clearly revealed the biogenesis process of EVs, including the selective encapsulation of biocomponents and distinct membrane compositions from the original bacteria. This developed platform provides an accurate and versatile means to identify pathogen-derived EVs, spectral markers, and the biogenesis process. It will promote rapid diagnosis and allow the timely treatment of bacterial infections.

Effects of soil protists on the antibiotic resistome under long term fertilization

Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.

[Cross-sectional study of association between dietary pattern and cognitive performance in people aged 50 and above years in Shanghai]

Objective: To investigate the association between dietary pattern and cognitive performance in local residents aged ≥50 years in Shanghai. Methods: Data were obtained from the second round of Study of Global Ageing and Adult Health (SAGE) survey in Shanghai. Dietary patterns were surveyed by factor analysis. Cognitive tests were conducted to assess subjects' cognitive performance, including verbal recall, verbal fluency and digit test. Multiple linear regression analysis was used to evaluate the relationship between dietary patterns and cognition performance. Results: A total of 4 132 subjects with complete dietary and cognitive performance test data were included. Factor analysis was used to obtain three dietary patterns: including plant-based pattern, high animal-food pattern, high salt-oil pattern. After controlling for gender, age, education level and other factors, it was found that plant-based pattern (β=0.26,95%CI: 0.17-0.36) and high animal-food pattern (β=0.18, 95%CI:0.06-0.29) were positively associated with total cognitive test score while high salt-oil pattern (β=-0.28, 95%CI:-0.85--0.07) was negatively associated with verbal fluency test score. Conclusion: A dietary pattern with high intake of plant food and appropriate intake of animal food might be associated with better cognitive function of residents aged ≥50 years.

[MiR-135b promotes proliferation of endometrial carcinoma cells by targeting FOXO1]

OBJECTIVE

To explore the expression of miR-135b in endometrial carcinoma and the mechanism by which miR-135b promotes the proliferation of endometrial cancer cells.

METHODS

The expressions of miR-135b and FOXO1 were using RT-PCR detected in 22 fresh endometrial cancer tissues and paired adjacent tissues and also in endometrial cancer cell lines JEC, Ishikawa, HEC-1-B, and RL-952. The RL-952 and Ishikawa cell lines were transfected with miR-135b mimics or inhibitors, and the changes in their proliferative activity were detected with MTT assay; the expressions of FOXO1 mRNA and protein were detected by RT-PCR and Western blotting, respectively.

RESULTS

The expression of miRNA135b was significantly up-regulated and FOXO1 expression was down-regulated in endometrial carcinoma tissues as compared with the adjacent tissues (P<0.05). The mRNA expression of miR-135b was negatively correlated with the expression of FOXO1 in endometrial carcinoma. In RL-952 and Ishikawa cell lines, transfection with miR-135b mimics obviously promoted the cell proliferation (P<0.05). Up-regulation of miR-135b significantly decreased the expressions of FOXO1 protein and mRNA (P<0.05), and down- regulation of miR-135b increased FOXO1 expressions (P<0.05).

CONCLUSIONS

MiR-135b plays an important role in the occurrence and development of endometrial carcinoma partially by regulating its target gene FOXO1.

Effects of perinatal hypothyroidism on rat behavior and its relation with apoptosis of hippocampus neurons

Thyroid hormone is an important factor for proper development of the mammalian brain. Perinatal hypothyroidism leads to long-term behavior and neuromotor competence alterations in humans and animals. Our study aimed to investigate the effects of perinatal hypothyroidism on behavior changes of rat pups and its relation with the apoptosis of hippocampus neurons. Behavior tests were taken to evaluate the effects caused by perinatal hypothyroidism. TUNEL staining was used to analyze the apoptosis of neurons on CA3 region of hippocampus. The study suggested that perinatal hypothyroidism affects behavior development, as well as leading to the decrease in spatial learning and memory capability. This condition can be improved with hormone substitute treatment. Furthermore, the changes of learning and memory capability are closely related to the increasing number of apoptotic neurons in the hippocampus.

[Association of transforming growth factor-alpha gene polymorphism and environment factors with nonsyndromic cleft lip with or without cleft palate in Han nationality]

OBJECTIVE

To study the association of transforming growth factor-alpha (TGF-alpha gene polymorphism and environment factors with nonsyndromic cleft lip with or without cleft palate (NSCLP) in Han nationality.

METHODS

Data related to infection, drug intake and folic acid supplement during pregnancy were gained through investigation of mothers. Polymerase chain reaction combined with restrict enzyme digestion was used to detect the target gene variation in 199 patients with NSCL/P and 203 healthy controls. Analysis was carried on the genotype and infection,drug intake and folic acid supplement.

RESULTS

The C2 allele frequency in patients with NSCL/P was significantly higher than that in healthy controls. There was a significant increase of patients with NSCL/P in pregnant women exposed to infection, drug intake and folic acid deficiency. There was an interaction between C1C2 genetype and infection, drug intake and folic acid supplement.

CONCLUSION

TGF-alpha gene polymorphism is associated with NSCL/P. Infection, drug intake and folic acid supplement during pregnancy were associated with the occurrence of NSCL/P. Individuals containing C2 allele were more sensitive to infection, drug intake and folic acid deficiency.

[Study of the detection characteristics of clozapine, N-desmethyl clozapine and olanzapine with high performance liquid chromatograph-electrochemical detector]

In order to analyze clozapine, N-desmethyl clozapine and olanzapine, their detection characteristics with high performance liquid chromatograph-electrochemical detector (HPLC-ECD) were investigated. The separation was performed on an ODS-3 column with the mobile phase of methanol and 0.1 mol/L phosphate buffer(60:40, V/V). The retention times of clozapine, N-desmethyl clozapine and olanzapine were all prolonged with higher pH of the mobile phase. These three compounds could be separated on the baseline at pH 4.56 and 5.56. The relationships of peak heights and detection voltages shown typical "S" shaped curves, and these curves shifted to the left with higher pH. To get stable detection current, the detection voltages for clozapine, N-desmethyl clozapine and olanzapine must be higher than 0.60 V, 0.60 V and 0.35 V at pH 4.56, and 0.48 V, 0.48 V and 0.30 V at pH 5.56, respectively. The typical "S" shaped ampere-volt curves were very important for the selection of suitable voltage for quantitative detection, and could be used for the qualitative detection of these three compounds.

Non-MHC-restricted cell-mediated lysis of human oligodendrocytes in vitro: relation with CD56 expression

Oligodendrocytes and their myelin membranes are the apparent target of the autoimmune response that characterizes the human adult central nervous system-demyelinating disease multiple sclerosis. Human oligodendrocytes do not express MHC class II molecules, a requirement for MHC-restricted injury mediated by myelin-reactive CD4+ T cells, the cell type implicated in initiating the disease process. In this study we observed that human adult central nervous system-derived oligodendrocytes can be susceptible to non-MHC-restricted lysis mediated by myelin basic protein-reactive CD4+ T cell lines. Cytotoxicity was significantly greater (37 +/- 4 vs 7 +/- 3%) with cell lines in which a high proportion of cells (mean, 28 +/- 6%) expressed CD56 compared with cytotoxicity mediated by low CD56 cell lines (8 +/- 2%). High CD56 cell lines, when rested in IL-2, lost cytotoxic activity and had reduced expression of CD56 (mean, 5 +/- 2%). CD4+ T cells isolated from short term (3-day) anti-CD3/IL-2-activated mononuclear cell cultures did not express CD56 and were not cytotoxic to oligodendrocytes unless lectin was added. In contrast, an enriched population of non-T cells extracted from the same activated MNC cultures expressed CD56 as well as other NK cell-associated surface molecules and was cytotoxic. These results indicate the potential susceptibility of human oligodendrocytes to non-MHC-restricted injury mediated by both Ag-reactive and nonspecific cellular immune effector cells, with CD56 expression being a common feature of the effector cells.

Effects of Ca2+ antagonists on glutamate release and Ca2+ influx in the hippocampus with in vivo intracerebral microdialysis

1. The extracellular glutamate content and Ca2+ level in vivo in rat hippocampus were measured by brain microdialysis following administration of two depolarizing agents (veratridine, KCl) and quinolinic acid (Quin). 2. The two depolarizing agents increased the extracellular glutamate level (to between 280 and 320% basal) and decreased the extracellular Ca2+ content (to 48% of basal). However, Quin did not change the glutamate level but decreased the Ca2+ content. 3. The effects of Ca2+ antagonists on the changes of glutamate and Ca2+ level were evaluated in this experimental model. At a dose of 0.5 mg kg-1, i.v., nimodipine (L-type channel blocker) did not produce significant changes in the stimulated-glutamate release. A statistically significant inhibition of Ca2+ influx was observed at a dose of 0.05 mg kg-1. In contrast, in those animals receiving the N-type Ca2+ antagonist, daurisoline (0.1, 1 or 5 mg kg-1, i.v.), a potent attenuation of both glutamate release and Ca2+ influx was found. 4. We propose that the pharmacological properties of Ca2+ influx and of neurotransmitter release differ and that nimodipine-sensitive L-type channels may not be very common in nerve terminals but are localized in cell soma. Daurisoline-sensitive N-type channels in nerve terminals have a much greater influence on excitatory amino acid release.

Determination of liver volume in vivo in rats using MRI

Accurate estimation of the liver volume may be important for the diagnosis of several pathological processes in patients and for the study of new therapies in experimental oncology. Although sonography and computed tomography (CT) have been used for this purpose in patients, the lack of spatial resolution and tissue differentiation is a source of measurement errors which, at present, makes it impossible to accept sonography and CT widely for the determination of the liver volume. In the present study, the liver volumes of seven rats were measured by magnetic resonance imaging (MRI) and an automated image analysis system before and after the animals were killed. Volume computation was carried out by adding up the individual volumes in the sequential MR sections. Adequate MR images with high contrast between the liver and surrounding structures were obtained with spin echo pulse sequence and retarded phase encoding while no contrast material was used. The mean volumes of the livers measured by MR in vivo and in cadavers were 11.91 +/- 0.40 and 11.92 +/- 0.45 ml, respectively. When compared with the actual liver volumes measured in vitro after resection, the errors of determinations in vivo and in cadavers were as small as 3.1 and 2.1%, respectively. These data indicate that MR imaging is an accurate means to determine the liver volume in vivo and that it may be potentially useful to measure small intrahepatic lesions in patients.

Experimental autoimmune encephalomyelitis in the maturing central nervous system. Transfer of myelin basic protein-specific T line lymphocytes to neonatal Lewis rats

We analyzed the effects of myelin basic protein (MBP)-specific encephalitogenic T line cells in neonatal syngeneic recipients before and after formation of central nervous system myelin. Lewis rat pups (postnatal days 0, 1, 2, 4, 8) were injected intraperitoneally with MBP-specific T cell line in doses which cause clinical and histologic changes of experimental autoimmune encephalomyelitis (EAE) in adult rats. We correlated the susceptibility to transferred EAE with the developmental appearance of MBP as demonstrated by immunohistochemical staining. MBP was barely demonstrable until postnatal day 2 but became definitely apparent on postnatal day 4. All newborn rats that were injected on postnatal day 0, 1, 2 failed to develop any apparent clinical signs, but histologically some recipients displayed slight inflammatory cell infiltration of the meninges and subpial lesions limited to the lower spinal cord. In striking contrast, rats that were injected on postnatal day 4 or 8, developed clinical signs and, in particular, many of the older recipients became moribund. Histologically, these animals displayed marked inflammatory cell infiltrations and white matter destruction within the spinal cord. Clinical and histologic severity clearly increased with the recipient's age. Histologically, there were some differences between adult rat EAE and newborn rat EAE. In contrast to adult rat EAE which displayed grey and white matter involvement with marked perivascular mononuclear cell infiltrations, newborn rat EAE typically showed very severe changes with edema formation selectively in the white matter and the cellular infiltrates were dominated by polymorphonuclear cells and macrophages. Newborn T line-mediated EAE thus strikingly resembles hyperacute EAE induced in immunocompromised (irradiated) recipients.

Resistance to experimental autoimmune encephalomyelitis induced by neonatal tolerization to myelin basic protein: clonal elimination vs. regulation of autoaggressive lymphocytes

The target autoantigen of experimental autoimmune encephalomyelitis (EAE), myelin basic protein (MBP), appears late in ontogeny. In the rat MBP is expressed first on days 2-3 post partum, at a development stage, when self tolerance to most other autoantigens has already developed. To shed light on the cellular mechanisms that lead to immunological self tolerance to MBP, we treated neonatal rats with high doses of MBP before ontogenetic appearance of this autoantigen. We found that high doses are required to confer MBP-specific tolerance lasting until the adult life. Neonatally tolerized, adult rats are completely resistant to induction of EAE by injection of MBP in complete Freund's adjuvant (CFA). Upon MBP CFA challenge, these animals develop a limited humoral response to MBP, but are completely unreactive to MBP on the T cell level. The function of antigen-presenting cells is unchanged by neonatal tolerization, and there is no evidence for the induction of suppressive mechanisms. Transfers of large numbers of tolerized lymphocytes to normal hosts fails to interfere with EAE inducibility. Moreover, neonatally tolerized lymphocytes do not reduce MBP reactivity of primed lymph node cells or T line cells in vitro. Finally, neonatally tolerized rats are susceptible to EAE transferred by activated primed lymphocytes or by in vitro-activated MBP-specific T line cells. The apparent deletion of MBP-specific T lymphocytes in neonatally tolerized rats is in striking contrast to the physiological self tolerance to MBP, which is characterized by the presence of MBP-specific clones in the normal immune repertoire.