Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing and Navigating ETDs Using Topic Models

Electronic theses and dissertations (ETDs) contain valuable knowledge that can be useful in a wide range of research areas. Accordingly, we are building electronic infrastructure leveraging advanced work on digital libraries, for discovering and accessing the knowledge buried in ETDs. In this paper we focus on our work to incorporate topic modeling into digital libraries for ETDs. We present ETD-Topics, a framework that extracts topics from a large text corpus in an unsupervised way. The representations learnt from topic models can be useful for downstream tasks such as searching and / or browsing documents by topic, document recommendation, topic recommendation, and describing temporal topic trends (e.g., from the perspective of disciplines or universities).
BECKER-GOTTLIEB TRANSFER FOR HOCHSCHILD COHOMOLOGY

Let G be a ﬁnite group. Over any ﬁnite G -poset P we may deﬁne a transporter category G ∝ P as the corresponding Grothendieck construction. There exists a Becker-Gottlieb transfer from the ordinary cohomology of G ∝ P to that of G . We shall construct it using module-theoretic methods and then extend it to a transfer from the Hochschild cohomology of k ( G ∝ P ) to that of kG , where k is a base ﬁeld.
Inferring the Causes of Real-World Rogue Waves

english Rogue waves are rare surface waves in the ocean that are signi cantly larger than the general wave population. Although they pose a serious threat to mariners, the causes of these waves in the real ocean are still poorly understood, and they remain hard to forecast. This is due to the lack of a high-quality observational dataset, the rarity of these waves and therefore required amounts of data, the di culty of analyzing said data, and the lack of a principled way to infer causation. This thesis consists of a collection of 3 articles that address all of these issues through a combination of data mining, interpretable machine learning, and causal analysis based on domain knowledge. The rst article describes the assembly of a comprehensive wave catalogue processing over 700 years of sea surface elevation time series from 158 buoy locations. The second article presents an analysis on the leadingorder e ects governing rogue wave formation based on interpretable machine learning. The third article extends this to a fully nonlinear predictive model by searching for a causally consistent neural network, and presents a path to an improved rogue wave forecast. Finally, I discuss the implications of our ndings for future rogue wave research, and outline how machine learning can augment the scienti c method and guide us towards scienti c discovery.
Association between dietary inflammation and erectile dysfunction among US adults: A cross-sectional analysis of the National Health and Nutrition Examination Survey 2001–2004

Background Although chronic low-grade inflammation has been linked to the development of erectile dysfunction (ED), the association between pro-inflammatory diets and ED is unclear. The dietary inflammation index (DII) is a novel method to quantify the inflammatory potential of a diet. Objective Our objective was to investigate the association between the DII and ED among US males. Design This cross-sectional study included 3,693 males 20–85 year of age from the National Health and Nutrition Examination Survey (NHANES) 2001–2004. Multivariable-adjusted logistic regression models were used to assess the association between the DII and ED. All analyses accounted for the complex sampling design. Results The mean ± SE of the DII was 0.8 ± 0.1 and 0.4 ± 0.1 among participants with and without ED, respectively. After adjusting for age, race/ethnicity, education, smoking status, physical activity, drinking status, hypertension, diabetes, cardiovascular disease, hypercholesterolemia, BMI, and eGFR, the DII score was associated with ED (odds ratio 1.12; 95% CI: 1.04–1.19). Moreover, this association was also stable in our subgroup analysis or sensitivity analyses. Conclusion Dietary inflammatory potential, as estimated by the DII score, is positively associated with ED among US males.
Symptomatic or asymptomatic SAR-CoV-2 positive divers should be medically evaluated before returning to scuba diving

Introduction: In order to allow the resumption of diving activities after a COVID-19 infection, French military divers are required to undergo a medical fitness to dive (FTD) assessment. We present here the results of this medical evaluation performed 1 month after the infection. Methods: We retrospectively analyzed between April 2020 and February 2021 200 records of divers suspected of COVID-19 contamination. Data collected included physical examination, ECG, blood biochemistry, chest CT scan and spirometry. Results: 145 PCR-positive subjects were included, representing 8.5% of the total population of French military divers. Two divers were hospitalized, one for pericarditis and the other for non-hypoxemic pneumonia. For the other 143 divers, physical examination, electrocardiogram and blood biology showed no abnormalities. However 5 divers (3.4%) had persistent subjective symptoms including fatigability, exertional dyspnea, dysesthesias and anosmia. 41 subjects (29%) had significant decreases in forced expiratory flows at 25–75% and 50% on spirometry (n = 20) or bilateral ground-glass opacities on chest CT scan (n = 24). Only 3 subjects were affected on both spirometry and chest CT. 45% of these abnormalities were found in subjects who were initially asymptomatic or had non-respiratory symptoms. In case of abnormalities, normalization was obtained within 3 months. The median time to return to diving was 45 days (IQR 30, 64). Conclusion: Our study confirms the need for standardized follow-up in all divers after COVID-19 infection and for maintaining a rest period before resuming diving activities.
Identification and validation of a signature based on macrophage cell marker genes to predict recurrent miscarriage by integrated analysis of single-cell and bulk RNA-sequencing

Recurrent miscarriage (RM) is a chronic, heterogeneous autoimmune disease that has serious social and personal consequences. No valid and reliable diagnostic markers or therapeutic targets for RM have been identified. Macrophages impact the innate immune system and can be used as diagnostic and prognostic markers for many diseases. We first collected 16 decidua and villi tissue samples from 5 normal patients and 3 RM patients for single-cell RNA sequencing data analysis and identified 1293 macrophage marker genes. We then screened a recurrent miscarriage cohort (GSE165004) for 186 macrophage-associated marker genes that were significantly differentially expressed between RM patients and the normal pregnancy endometrial tissues, and performed a functional enrichment analysis of differentially expressed genes. We then identified seven core genes (ACTR2, CD2AP, MBNL2, NCSTN, PUM1, RPN2, and TBC1D12) from the above differentially expressed gene group that are closely related to RM using the LASSO, Random Forest and SVM-RFE algorithms. We also used GSE26787 and our own collection of clinical specimens to further evaluate the diagnostic value of the target genes. A nomogram was constructed of the expression levels of these seven target genes to predict RM, and the ROC and calibration curves showed that our nomogram had a high diagnostic value for RM. These results suggest that ACTR2 and NCSTN may be potential targets for preventative RM treatments.
Imbalance hepatic metabolism homeostasis in the F1 generation of endometrial DNMT3B conditional knockout female mice

Numerous studies have suggested the possibility of explaining the etiology of metabolic syndrome through DNA methylation. DNA methyltransferase 3B (DNMT3B) plays an important role in de novo DNA methylation. There was an alteration in maternal (F0) endometrial function, which might lead to growth and developmental disorder in offspring (F1). In this study, we investigated the effect of maternal endometrial DNMT3B deficiency on the metabolism in offspring. We constructed endometrial DNMT3B conditional knockout female mice (cKO) which were mated with normal C57BL/6 male mice to obtain the F1 generation. Further, to study the development of these offspring, we observed them at three different life stages which included the 6-week-old juvenile, 9-week-old sub-adult and 12-week-old adult. Follow the detection of a range of metabolism-related indicators, we found that in the cKO F1 generation, liver triglyceride level was significantly elevated in 9-week-old female mice, lipid droplet deposition was significantly increased in 9-week-old and 12-week-old mice, and the expression of lipid metabolism key factors in the liver was markedly decreased except of 6-week-old male mice. These results indicate that maternal endometrial DNMT3B conditional knockout leads to imbalance in hepatic metabolism in F1 generation, the mechanism of which requires further discussion.
Face yourself: The social neuroscience of mirror gazing

In philosophical and psychological accounts alike, it has been claimed that mirror gazing is like looking at ourselves as others. Social neuroscience and social psychology offer support for this view by showing that we use similar brain and cognitive mechanisms during perception of both others’ and our own face. I analyse these premises to investigate the factors affecting the perception of one’s own mirror image. I analyse mechanisms and processes involved in face perception, mimicry, and emotion recognition, and defend the following argument: because perception of others’ face is affected by our feelings toward them, it is likely that feelings toward ourselves affect our responses to the mirror image. One implication is that negative self-feelings can affect mirror gazing instantiating a vicious cycle where the negative emotional response reflects a previously acquired attitude toward oneself. I conclude by discussing implications of this view for psychology and social studies.
Using strengths to attack weaknesses – The effect of comparative advertising on purchasing intention of green products

Firms increasingly use comparative advertising in green marketing to convey information of green products to consumers, but there is still a lack of research on the effect and mechanism of comparative advertising in the green products field. Across four experimental studies, we show that comparative advertising facilitates consumers’ purchase intention of green products (PIGP), because comparative advertising lead to higher perceived diagnosticity of Information. Yet, comparative advertising does not always bring high intention to buy green products. When using egoistic appeals, the perceived diagnosticity of information and purchase intention of green products were higher in comparative advertising than in non-comparative advertising. When utilizing altruistic appeals, there was no significant difference between the two kinds of advertising. In addition, individual differences of consumers also affect the effect of comparative advertising. The positive effect of comparative advertising on the purchase intention of green products is weakened for consumers with high green involvement. Our findings advance existing knowledge about the use of comparative advertising in green marketing and provide enlightening suggestions for how firms can promote consumers to buy green products.
Identification of plant leaf diseases by deep learning based on channel attention and channel pruning

Plant diseases cause significant economic losses and food security in agriculture each year, with the critical path to reducing losses being accurate identification and timely diagnosis of plant diseases. Currently, deep neural networks have been extensively applied in plant disease identification, but such approaches still suffer from low identification accuracy and numerous parameters. Hence, this paper proposes a model combining channel attention and channel pruning called CACPNET, suitable for disease identification of common species. The channel attention mechanism adopts a local cross-channel strategy without dimensionality reduction, which is inserted into a ResNet-18-based model that combines global average pooling with global max pooling to effectively improve the features’ extracting ability of plant leaf diseases. Based on the model’s optimum feature extraction condition, unimportant channels are removed to reduce the model’s parameters and complexity via the L1-norm channel weight and local compression ratio. The accuracy of CACPNET on the public dataset PlantVillage reaches 99.7% and achieves 97.7% on the local peanut leaf disease dataset. Compared with the base ResNet-18 model, the floating point operations (FLOPs) decreased by 30.35%, the parameters by 57.97%, the model size by 57.85%, and the GPU RAM requirements by 8.3%. Additionally, CACPNET outperforms current models considering inference time and throughput, reaching 22.8 ms/frame and 75.5 frames/s, respectively. The results outline that CACPNET is appealing for deployment on edge devices to improve the efficiency of precision agriculture in plant disease detection.
Application of amide proton transfer imaging for the diagnosis of neonatal hypoxic–ischemic encephalopathy

Objective This study aimed to evaluate cerebral amide proton transfer signal intensity (SI) among controls, hypoxic–ischemic encephalopathy (HIE) neonates with normal conventional magnetic resonance imaging (HIE/MRI−) findings, and HIE neonates with abnormal conventional MRI (HIE/MRI+) findings. Methods Forty neonates diagnosed with neonatal HIE and sixteen normal neonates were evaluated. All neonates underwent conventional MRI scans and APT imaging. Cerebral APT SIs were compared to identify cerebral regions with significant APT changes among sixteen controls, thirteen HIE/MRI− patients, and twenty–seven HIE/MRI+ patients. Results Significantly increased APT SIs were observed in the HIE/MRI− group compared with controls, in the left insula, right occipital lobe, left cingulate gyrus (posterior part), and corpus callosum. Significantly increased APT SIs were found in the HIE/MRI+ group compared with controls, in the right anterior temporal lobe (medial part), anterior parts of the right parahippocampal and ambient gyri, left superior temporal gyrus (middle part), left insula, left cingulate gyrus (posterior part), and right lentiform nucleus. No significant APT SI differences were observed in the cerebellum and brainstem among the three groups. Conclusion Amide proton transfer imaging plays an important role in detecting hypoxic–ischemic encephalopathy regardless of conventional MRI findings. Changes in APT signal intensity may provide important insights into the characterization of the cerebral internal environment. This study suggests that APT imaging could be used as a complement to conventional MRI in the detection of hypoxic–ischemic encephalopathy in clinical practice.
Short-term head-down bed rest microgravity simulation alters salivary microbiome in young healthy men

Microgravity influences are prevalent during orbital flight and can adversely affect astronaut physiology. Notably, it may affect the physicochemical properties of saliva and the salivary microbial community. Therefore, this study simulates microgravity in space using a ground-based −6° head-down bed rest (HDBR) test to observe the effects of microgravity on oral salivary secretion function and the salivary microbiome. Sixteen healthy young male volunteers were recruited for the 15-day −6° HDBR test. Non-stimulated whole saliva was collected on day 1 (pre-HDBR), on days 5, 10, and 15 of HDBR, and day 6 of recovery. Salivary pH and salivary flow rate were measured, and the V3–V4 region of the 16S rRNA gene was sequenced and analyzed in 80 saliva samples. The results showed that there were no significant differences in salivary pH, salivary flow rate, and alpha diversity between any two time points. However, beta diversity analysis revealed significant differences between pre-HDBR and the other four time points. After HDBR, the relative abundances of Actinomyces, Parvimonas, Peptostreptococcus, Porphyromonas, Oribacterium, and Capnocytophaga increased significantly, whereas the relative abundances of Neisseria and Haemophilus decreased significantly. However, the relative abundances of Oribacterium and Capnocytophaga did not recover to the pre-HDBR level on day 6 of recovery. Network analysis revealed that the number of relationships between genera decreased, and the positive and negative correlations between genera changed in a complex manner after HDBR and did not reach their original levels on day 6 of recovery. PICRUSt analysis demonstrated that some gene functions of the salivary microbiome also changed after HDBR and remained significantly different from those before HDBR on day 6 of recovery. Collectively, 15 days of −6° HDBR had minimal effect on salivary secretion function but resulted in significant changes in the salivary microbiome, mainly manifested as an increase in oral disease-related bacteria and a decrease in oral health-related commensal bacteria. Further research is required to confirm these oral microbial changes and explore the underlying pathological mechanisms to determine the long-term effects on astronauts embarking on long-duration voyages to outer space.
Fusion assays for screening of fusion inhibitors targeting SARS-CoV-2 entry and syncytia formation

Virus fusion process is evolutionarily conserved and provides a promising pan-viral target. Cell-cell fusion leads to syncytial formation and has implications in pathogenesis, virus spread and immune evasion. Drugs that target these processes can be developed into anti-virals. Here, we have developed sensitive, rapid, adaptable fusion reporter gene assays as models for plasma membrane and alternative fusion pathways as well as syncytial fusion in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have confirmed their specificity using neutralizing antibodies and specific protease inhibitors. The fusion report gene assays are more sensitive and unbiased than morphological fusion assay. The fusion assays can differentiate between transmembrane serine protease 2 (TMPRSS2)-dependency in TMPRSS2(+) cells and trypsin-dependency in angiotensin-converting enzyme 2 (ACE2)(+)TMPRSS2(-) cells. Moreover, we have identified putative novel fusion processes that are triggered by an acidic pH with and without trypsin. Coupled with morphological fusion criteria, we have found that syncytia formation is enhanced by TMPRSS2 or trypsin. By testing against our top drug hits previously shown to inhibit SARS-CoV-2 pseudovirus infection, we have identified several fusion inhibitors including structurally related lopsided kite-shaped molecules. Our results have important implications in the development of universal blockers and synergistic therapeutics and the small molecule inhibitors can provide important tools in elucidating the fusion process.
Peroxisome proliferator-activated receptor-γ as the gatekeeper of tight junction in Clostridioides difficile infection

Clostridioides difficile is a major causative pathogen of nosocomial antibiotic-associated diarrhea and severe colitis. Despite the use of vancomycin and fidaxomicin as standard drugs for the treatment of C. difficile infection (CDI), clinical relapse rates remain high. Therefore, new alternative therapeutics to treat CDI are urgently required. The nuclear receptor, peroxisome proliferator-activated receptor-γ (PPAR-γ), is mainly expressed in the adipose tissue and modulates lipid metabolism and insulin sensitization. Previous studies have shown that PPAR-γ is highly expressed in colonic tissues and regulates tight junction function in epithelial cells. However, the role of PPAR-γ in CDI pathogenesis remains unclear. In this study, we used a mouse model of CDI and found that both expression levels of PPAR-γ and the tight junction protein, occludin, were decreased in colonic tissues. Furthermore, to investigate the role of PPAR-γ in CDI, we used PPAR-γ defective mice and found that intestinal permeability and bacterial dissemination in these mice were significantly higher than those in wild-type mice during CDI. Administration of the PPAR-γ agonist, pioglitazone, to activate PPAR-γ activity improved the phenotypes of CDI, including bodyweight loss, inflammation, and intestinal integrity. Taken together, these results demonstrate that PPAR-γ is a potential therapeutic target in CDI, as it modulates colonic inflammation and integrity.
Integrative sperm DNA methylation and miRomics analysis highlights interaction of two epigenetic patterns of pseudomale inheritance in teleost

Proper DNA methylation in spermatozoa is essential for the normal development of fertilized embryos through gene expression regulation. Abnormal sperm DNA methylation is associated with male fertility impairment, offspring quality decline, and disease susceptibility. Compared with other epigenetic regulatory mechanisms (e.g., histone modification), DNA methylation is a stable regulator for the long-term transcriptional activity of genes. Sperm DNA methylation is crucial to offspring’s survival, development, and reproduction. However, it has not been well studied in teleost to a large extent, especially in some species with sex deviation or congenital sex abnormality in offspring. In the present study, DNA methylation profiles of pseudomale (ZW) and male (ZZ) tongue sole (Cynoglossus semilaevis) spermatozoa were characterized for differential methylation regions (DMRs) screening. The global methylation levels of the two sperm groups were highly methylated with no significant differences. For all kinds of genomic elements, the mean methylation level of the ZW group was higher than that of the ZZ group. The total numbers of Covered C annotated on the W chromosome of both groups were extremely small, suggesting that W-type sperm did not exist in pseudomales. A comparison of methylation levels on 20 sex-related genes between sperm and gonad showed that the heterogeneity between tissue resources was greater than that between sexes, and the methylation level of most genes in gonads was lower than that in sperm. For integrative analysis of DNA methylation and miRomic profiles, 11 sex-related DMRs associated with 15 differentials micro RNAs (miRNAs) in spermatozoa were identified to present targeting relationships and regulatory trends of the two distinct epigenetic patterns. This study provides valuable and potential targets of coordination between two epigenetic mechanisms in the process of C. semilaevis sex congenital bias.
Research on the dynamic spillover of stock markets under COVID-19—Taking the stock markets of China, Japan, and South Korea as an example

Examining stock market interactions between China (mainland China and Hong Kong), Japan, and South Korea, this study employs a framework that includes 239 economic variables to identify the spillover effects among these three countries, and empirically simulates the dynamic time-varying non-linear relationship between the stock markets of different countries. The findings are that in recent decades, China's stock market relied on Hong Kong's as a window to the exchange of price information with Japan and South Korea. More recently, the China stock market's spillover effect on East Asia has expanded. The spread of the crisis has strengthened co-movement between the stock markets of China, Japan, and South Korea.