Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring optimized configurations of plasmonic nanoparticles

Finite difference time domain (FDTD) simulations are used to find the electric field intensity at the center of a cluster of plasmonic nanoparticles irradiated by a planewave source. We use an iterative optimization algorithm to maximize the electric field intensity. The resulting optimized configurations are found to be non-symmetric and non-intuitive, and cannot be obtained by analytical calculation methods. Experimentally, we investigate a novel technique using angle evaporation to produce plasmonic nanostructures with gap sizes of 1-2 nm. We evaluate the plasmonic activity of these nanoparticles both experimentally using surface enhanced Raman spectroscopy (SERS) measurements and theoretically using FDTD simulations. These simulations predict an electric field intensity enhancement of 82,400 at the center of the nanoparticle dimer, and an electromagnetic SERS enhancement factor of 109-1010.
Effects of traditional Chinese herb hot compress combined with therapeutic exercise on pain, proprioception, and functional performance among older adults with knee osteoarthritis: A randomized controlled trial

Background: Knee osteoarthritis (KOA) is one of the most common chronic progressive diseases with degenerative destruction of articular cartilage and bone, leading to knee pain, impaired proprioception, and reduced functional performance. This study was to investigate the effects of an 8-week Traditional Chinese herb hot compress (TCHHC) combined with therapeutic exercise (TE) on pain, proprioception, and functional performance among older adults with KOA. Methods: Twenty-seven older adults with KOA were recruited and randomly assigned to the TCHHC + TE or TE groups. Thirteen participants received TCHHC + TE, and fourteen received TE. At pre- (week 0) and post-intervention (week 9), their pain, joint proprioception, and functional performance were measured. Two-way ANOVA with repeated measures was adopted to analyze the data. Results: Compared with week 0, the pain score, proprioception thresholds of knee extension and ankle plantarflexion, and the times of TUG and 20-m walk tests decreased more significantly in the TCHHC + TE group than in the TE group at week 9. Conclusion: Compared with TE, the 8-week TCHHC + TE was superior in relieving pain, recovering proprioception, and improving functional performance among older adults with KOA. It is recommended that TCHHC should be adopted prior to TE to enhance the effects of KOA rehabilitation.
Identification of prognosis-related gene features in low-grade glioma based on ssGSEA

Low-grade gliomas (LGG) are commonly seen in clinical practice, and the prognosis is often poor. Therefore, the determination of immune-related risk scores and immune-related targets for predicting prognoses in patients with LGG is crucial. A single-sample gene set enrichment analysis (ssGSEA) was performed on 22 immune gene sets to calculate immune-based prognostic scores. The prognostic value of the 22 immune cells for predicting overall survival (OS) was assessed using the least absolute shrinkage and selection operator (LASSO) and univariate and multivariate Cox analyses. Subsequently, we constructed a validated effector T-cell risk score (TCRS) to identify the immune subtypes and inflammatory immune features of LGG patients. We divided an LGG patient into a high-risk–score group and a low-risk–score group based on the optimal cutoff value. Kaplan–Meier survival curve showed that patients in the low-risk–score group had higher OS. We then identified the differentially expressed genes (DEGs) between the high-risk–score group and low-risk-score group and obtained 799 upregulated genes and 348 downregulated genes. The analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) show that DEGs were mainly concentrated in immune-related processes. In order to further explore the immune-related genes related to prognosis, we constructed a protein–protein interaction (PPI) network using Cytoscape and then identified the 50 most crucial genes. Subsequently, nine DEGs were found to be significantly associated with OS based on univariate and multivariate Cox analyses. It was further confirmed that CD2, SPN, IL18, PTPRC, GZMA, and TLR7 were independent prognostic factors for LGG through batch survival analysis and a nomogram prediction model. In addition, we used an RT-qPCR assay to validate the bioinformatics results. The results showed that CD2, SPN, IL18, PTPRC, GZMA, and TLR7 were highly expressed in LGG. Our study can provide a reference value for the prediction of prognosis in LGG patients and may help in the clinical development of effective therapeutic agents.
IRAS galaxies versus potent mass: Density fields, biasing and omega

A comparison of the galaxy density field extracted from a complete redshift survey of IRAS galaxies brighter than 1.936 Jy with the mass-density field reconstructed by the POTENT procedure from the observed peculiar velocities of 493 objects is presented. A strong correlation is found between the galaxy and mass-density fields; both feature the Great Attractor, part of the Perseus-Pisces supercluster, and the large void between them. Monte Carlo noise simulations show that the data are consistent with the hypotheses that the smoothed fluctuations of galaxy and mass densities at each point are proportional to each other with the 'biasing' factor of IRAS galaxies, b(I), and that the peculiar velocity field is related to the mass-density field as expected according to the gravitational instability theory. Under these hypotheses, the two density fields can be related by specifying b(I) and the cosmological density parameter, Omega.
A U-shaped association of tracheostomy timing with all-cause mortality in mechanically ventilated patients admitted to the intensive care unit: A retrospective cohort study

Objectives To evaluate the association of tracheostomy timing with all-cause mortality in patients with mechanical ventilation (MV). Method It’s a retrospective cohort study. Adult patients undergoing invasive MV who received tracheostomy during the same hospitalization based on the Medical Information Mart for Intensive Care-III (MIMIC-III) database, were selected. The primary outcome was the relationship between tracheostomy timing and 90-day all-cause mortality. A restricted cubic spline was used to analyze the potential non-linear correlation between tracheostomy timing and 90-day all-cause mortality. The secondary outcomes included free days of MV, incidence of ventilator-associated pneumonia (VAP), free days of analgesia/sedation in the intensive care unit (ICU), length of stay (LOS) in the ICU, LOS in hospital, in-ICU mortality, and 30-day all-cause mortality. Results A total of 1,209 patients were included in this study, of these, 163 (13.5%) patients underwent tracheostomy within 4 days after intubation, while 647 (53.5%) patients underwent tracheostomy more than 11 days after intubation. The tracheotomy timing showed a U-shaped relationship with all-cause mortality, patients who underwent tracheostomy between 5 and 10 days had the lowest 90-day mortality rate compared with patients who underwent tracheostomy within 4 days and after 11 days [84 (21.1%) vs. 40 (24.5%) and 206 (31.8%), P < 0.001]. Conclusion The tracheotomy timing showed a U-shaped relationship with all-cause mortality, and the risk of mortality was lowest on day 8, but a causal relationship has not been demonstrated.
Cotton disease identification method based on pruning

Deep convolutional neural networks (DCNN) have shown promising performance in plant disease recognition. However, these networks cannot be deployed on resource-limited smart devices due to their vast parameters and computations. To address the issue of deployability when developing cotton disease identification applications for mobile/smart devices, we compress the disease recognition models employing the pruning algorithm. The algorithm uses the γ coefficient in the Batch Normalization layer to prune the channels to realize the compression of DCNN. To further improve the accuracy of the model, we suggest two strategies in combination with transfer learning: compression after transfer learning or transfer learning after compression. In our experiments, the source dataset is famous PlantVillage while the target dataset is the cotton disease image set which contains images collected from the Internet and taken from the fields. We select VGG16, ResNet164 and DenseNet40 as compressed models for comparison. The experimental results show that transfer learning after compression overall surpass its counterpart. When compression rate is set to 80% the accuracies of compressed version of VGG16, ResNet164 and DenseNet40 are 90.77%, 96.31% and 97.23%, respectively, and the parameters are only 0.30M, 0.43M and 0.26M, respectively. Among the compressed models, DenseNet40 has the highest accuracy and the smallest parameters. The best model (DenseNet40-80%-T) is pruned 75.70% of the parameters and cut off 65.52% of the computations, with the model size being only 2.2 MB. Compared with the version of compression after transfer learning, the accuracy of the model is improved by 0.74%. We further develop a cotton disease recognition APP on the Android platform based on the model and on the test phone, the average time to identify a single image is just 87ms.
Advances in fermented foods revealed by multi-omics: A new direction toward precisely clarifying the roles of microorganisms

Fermented foods generally comprise a complex micro-ecosystem with beneficial microbiota, functional products, and special flavors and qualities that are welcomed globally. Single-omics analysis allows for a comprehensive characterization of the main microbial factors influencing the function, flavor, and quality of fermented foods. However, the species, relative abundance, viability, growth patterns, and metabolic processes of microorganisms vary with changes in processing and environmental conditions during fermentation. Furthermore, the mechanisms underlying the complex interaction among microorganisms are still difficult to completely understand and analyze. Recently, multi-omics analysis and the integration of multiple types of omics data allowed researchers to more comprehensively explore microbial communities and understand the precise relationship between fermented foods and their functions, flavors, and qualities. Multi-omics approaches might help clarify the mechanisms underpinning the fermentation processes, metabolites, and functional components of these communities. This review clarified the recent advances in the roles of microorganisms in fermented foods based on multi-omics data. Current research achievements may allow for the precise control of the whole industrial processing technology of fermented foods, meeting consumers’ expectations of healthy products.
Integrative proteomics and metabolomics approach to identify the key roles of icariin-mediated protective effects against cyclophosphamide-induced spermatogenesis dysfunction in mice

The alkylating antineoplastic agent cyclophosphamide (CP) is known to be toxic to the male reproductive system, but there are no effective prevention or treatment options. The flavonoid icariin (ICA), which is used in Chinese medicine, has been shown to have a number of biological functions, including testicular protection. The current study looked into the protective effects of ICA in preventing CP-induced spermatogenesis dysfunction. The current study looked into the role of ICA in preventing testicular dysfunction caused by CP. For 5 days, healthy adult mice were given saline or a single dose of CP (50 mg/kg) intraperitoneally (i.p). For the next 30 days, mice were given ICA (80 mg/kg) by gavage. Animals were euthanized 12 h after receiving ICA, and testes were removed for biochemical, histopathological, sperm evaluation, and transmission electron microscope analysis (TEM). We also investigated the potential biological effects of ICA on CP-induced spermatogenesis dysfunction in mice using an integrated proteomic and metabolomic approach. The levels of 8309 proteins and 600 metabolites were measured. The majority of the differential proteins and metabolites were found to be enriched in a variety of metabolic pathways, including the PI3K-Akt signaling pathway, necroptosis, the mTOR signaling pathway, glycerophospholipid metabolism, and ABC transporters, implying that ICA may have molecular mechanisms that contribute to CP-induced spermatogenesis dysfunction in the testis. Taken together, these findings show that ICA effectively reduces testis injury, implying that ICA may have a role in male infertility preservation.
An evaluation of the rat intestinal monoamine biogeography days following exposure to acute stress

Stress-induced abnormalities in gut monoamine levels (e.g., serotonin, dopamine, norepinephrine) have been linked to gastrointestinal (GI) dysfunction, as well as the worsening of symptoms in GI disorders. However, the influence of stress on changes across the entire intestinal monoamine biogeography has not been well-characterized, especially in the days following stress exposure. Therefore, the aim of this study was to comprehensively assess changes to monoamine neurochemical signatures across the entire rat intestinal tract days after exposure to an acute stressor. To the end, adult male F344 rats were subjected to an episode of unpredictable tail shocks (acute stress) or left undisturbed. Forty-eight hours later rats were euthanized either following a 12 h period of fasting or 30 min of food access to evaluate neurochemical profiles during the peri- and early postprandial periods. Monoamine-related neurochemicals were measured via UHPLC in regions of the small intestine (duodenum, jejunum, ileum), large intestine (cecum, proximal colon, distal colon), cecal contents, fecal contents, and liver. The results suggest a relatively wide-spread increase in measures of serotonin activity across intestinal regions can be observed 48 h after exposure to acute stress, however some evidence was found supporting localized differences in serotonin metabolization. Moreover, acute stress exposure reduced catecholamine-related neurochemical concentrations most notably in the ileum, and to a lesser extent in the cecal contents. Next, stress-related fecal serotonin concentrations were consistent with intestinal profiles. However, fecal dopamine was elevated in association with stress, which did not parallel findings in any other intestinal area. Finally, stress exposure and the food access period together only had minor effects on intestinal monoamine profiles. Taken together, these data suggest nuanced differences in monoaminergic profiles exist across intestinal regions the days following exposure to an acute stressor, highlighting the importance of assessments that consider the entire intestinal tract biogeography when investigating stress-related biological outcomes that may be relevant to GI pathophysiology.
Valorization of whey proteins and beetroot peels to develop a functional beverage high in proteins and antioxidants

Introduction Adequate protein and antioxidant intake are crucial for everyone, particularly athletes, to promote muscle performance and prevent muscle damage. Whey proteins are high-quality proteins with high digestibility and bioavailability; beetroot peels are an abundant antioxidant source. Methods The present study was designated to develop a functional beverage based on mixing whey protein isolate (5%) with different concentrations of beetroot peel water extract (1, 2.5, and 5%) and flavored with strawberries puree (5%). In addition, we examined the stability of the physicochemical parameters and the bioactive components of the beverages during cold storage (4°C) for 14 days. Results and discussion Whey protein isolates enriched the juices with stable protein content during the storage (4.65–4.69%). Besides, the extract revealed a concentration-dependent effect on the bioactive components, the antioxidant activity, and the microbial load of the juices; it distinguished the fresh juices by high betalains and nitrate content, 87.31–106.44 mg/L and 94.29–112.59 mg/L, respectively. Beverages with 2.5% peel extract (T2) had the preferable sensory attributes compared to control and other treatments. On day 0, phenolics and flavonoids increased in T2 by 44 and 31% compared to the control, which elevated the scavenging activity of the juice (T2) (P < 0.05). At the end of the storage period (14 days), phenolics and flavonoids of T2 recorded their lowest values, 26.23 and 21.75 mg/mL, respectively. However, they stood higher than phenolics (22.21 mg/mL) (p < 0.05) and flavonoids (18.36 mg/mL) (p > 0.05) of control. Similarly, betalains degraded by 45% to reach 47.46 mg/L in T2, which reduced the redness (a*) and increased the yellowness (b*) values. Conclusion Consequently, whey/strawberry/beetroot peel (5: 5: 2.5 w/v/w) in d.H2O is a functional beverage that provides the body with a high-quality protein and a considerable amount of antioxidants.
Evaluating breast ultrasound S-detect image analysis for small focal breast lesions

Background S-Detect is a computer-assisted, artificial intelligence-based system of image analysis that has been integrated into the software of ultrasound (US) equipment and has the capacity to independently differentiate between benign and malignant focal breast lesions. Since the revision and upgrade in both the breast imaging-reporting and data system (BI-RADS) US lexicon and the S-Detect software in 2013, evidence that supports improved accuracy and specificity of radiologists’ assessment of breast lesions has accumulated. However, such assessment using S-Detect technology to distinguish malignant from breast lesions with a diameter no greater than 2 cm requires further investigation. Methods The US images of focal breast lesions from 295 patients in our hospital from January 2019 to June 2022 were collected. The BI-RADS data were evaluated by the embedded program and as manually modified prior to the determination of a pathological diagnosis. The receiver operator characteristic (ROC) curves were constructed to compare the diagnostic accuracy between the assessments of the conventional US images, the S-Detect classification, and the combination of the two. Results There were 326 lesions identified in 295 patients, of which pathological confirmation demonstrated that 239 were benign and 87 were malignant. The sensitivity, specificity, and accuracy of the conventional imaging group were 75.86%, 93.31%, and 88.65%. The sensitivity, specificity, and accuracy of the S-Detect classification group were 87.36%, 88.28%, and 88.04%, respectively. The assessment of the amended combination of S-Detect with US image analysis (Co-Detect group) was improved with a sensitivity, specificity, and accuracy of 90.80%, 94.56%, and 93.56%, respectively. The diagnostic accuracy of the conventional US group, the S-Detect group, and the Co-Detect group using area under curves was 0.85, 0.88 and 0.93, respectively. The Co-Detect group had a better diagnostic efficiency compared with the conventional US group (Z = 3.882, p = 0.0001) and the S-Detect group (Z = 3.861, p = 0.0001). There was no significant difference in distinguishing benign from malignant small breast lesions when comparing conventional US and S-Detect techniques. Conclusions The addition of S-Detect technology to conventional US imaging provided a novel and feasible method to differentiate benign from malignant small breast nodules.
Time evolution and transfer of entanglement between an isolated atom and a Jaynes–Cummings atom

We investigate the entanglement dynamics of two space-separated atoms, one of them in Jaynes–Cummings cavity and the other isolated completely. We show analytically that initial entanglement has an interesting subsequent time evolution and transfer, including the so-called sudden death effect. A little inconsistency of concurrence and negativity is indicated qualitatively to measure the two-qubit states.
Successful treatment of dupilumab in Kimura disease independent of IgE: A case report with literature review

Kimura disease (KD) is a rare and benign chronic inflammatory disease of unknown cause. It is characterized by subcutaneous granuloma of soft tissues in the head and neck region, increased eosinophil count, and elevated serum IgE. Currently, no definitive treatments are recommended. A 57-year-old Chinese man was diagnosed with KD after 7 years of slow subcutaneous masses growth. The patient underwent treatment of oral glucocorticoids for 1 year, but the masses recurred as the dosage was tapered down. Subsequent anti-IgE therapy of omalizumab administered subcutaneously at 450 mg/day at a 4-week interval did not show improvement. The size of masses and serum IgE and circulating eosinophils did not decrease significantly after 19 cycles of continuous treatment. Ultimately, switched strategy of dupilumab was applied at an initial dose of 600 mg, followed by 300 mg every 2 weeks for 4 months. This treatment demonstrated dramatical effects with reduced masses in each area and fast dropdown of eosinophil counts, while the high level of serum IgE remained without changes. Recently, different biologics including anti-IgE, anti-IL-5, and anti-IL-4/IL-13 have been applied to treat KD with satisfied results and help to explore the pathogenesis of this rare disease. To our knowledge, this is the first report that demonstrates the effects of two different biologics in the same patient and reveals the impressive clinical efficacy of dupilumab to treat KD independent of IgE. Therefore, further investigation of the underlying mechanism and the development of diagnosis and treatment of KD is valuable.
Association between healthy food environment and metabolic syndrome, waist circumference, and systolic blood pressure in older adults in Southern Brazil

The aim of this study was to investigate the association between healthy food outlet proximity, metabolic syndrome (MS), and two of its components, waist circumference (WC) and systolic blood pressure (SBP), in older adults (63–107 years old, median age 73 years) living in Florianópolis, South Brazil in 2013–2014. This is a cross-sectional analysis of the second wave of the EpiFloripa Aging Cohort Study. Individual-level data on MS, WC, SBP, and socio-demographic and health-related characteristics were collected from face to face interviews. The healthy food environment was assessed via the number and types of establishments present. The residences of older adult participants were georeferenced using Geographical Information System (GIS) software. The number of each type of food establishment in a 500 m buffer around the each residence was determined. Multivariate linear regression was used to test association between food outlet proximity and continuous outcomes (SBP and WC), and multiple logistic regression was used to examine the relations between the predictor variables and the dichotomous outcome of MS (yes/no). The study revealed that greater frequency of supermarkets and restaurants in the neighborhood was associated with a lower likelihood of having MS. WC was lower in individuals living in places with greater availability of greengrocers’ shops and restaurants. The results demonstrated that the number of establishments in a neighborhood is associated with cardiometabolic outcomes, and the likelihood of MS and increased WC is lower for older adults who live in neighborhoods with more access to establishments that sell foundational components of a healthy diet.