Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Selective Bacterial Colonization by Polyethylene and Polyethylene Terephthalate Microplastics

In this study, we report the biodiversity and functional characteristics of microplastic-attached biofilms originating from two freshwater bacterial communities. Even though the microplastic-biofilm (MPB) diversities are mostly determined by original bacteria instead of microplastic types, the results from 16S rRNA amplicon sequencing still showed that the dynamic biofilm successions on different microplastics were highly dissimilar. Furthermore, the analysis of biomarkers indicated distinct bacterial species with significant dissimilarities between different MPBs, which further determined the associated functions. The co-occurrence networks showed distinct interconnective characteristics in different MPBs: The structure of MPB incubated in the lake water sample was more robust under environmental stresses, and bacteria in the tap water MPB interacted more cooperatively. Regarding this cooperative interaction, the analysis of functional prediction, in this study, also showed that more symbionts and parasites colonized on microplastics in the tap water than in the lake water. Moreover, it was suggested that MPBs were more easily formed in the tap water sample. The overall results revealed significant dissimilarities in bacterial diversity, succession, and associated functions between MPBs, in which bacterial species with specific functions should be taken seriously.
Network Pharmacology-Based and Experimental Identification of the Effects of Paeoniflorin on Major Depressive Disorder

Objective: Major depressive disorder (MDD) is one of the most common psychiatric disorders, the diagnosis and treatment of MDD are major clinical issues. However, there is a lack of effective biomarkers and drugs diagnosis and therapeutics of MDD. In the present study, bioinformatics analysis combined with an experimental verification strategy was used to identify biomarkers and paeoniflorin targets for MDD diagnosis and treatment. Methods: Based on network pharmacology, we obtained potential targets and pathways of paeoniflorin as an antidepressant through multiple databases. We then constructed a protein-protein interaction network and performed enrichment analyses. According to the results, we performed in vivo and in vitro experimental validation. Results: The results showed that paeoniflorin may exert an antidepressant effect by regulating cell inflammation, synaptic function, NF-κB signaling pathway, and intestinal inflammation. Conclusion: NPM1, HSPA8, HSPA5, HNRNPU, and TNF are the targets of paeoniflorin treatment. In addition, we demonstrated that paeoniflorin inhibits inflammatory cytokine production via the p38MAPK/NF-κB pathway and has neuroprotective effects on the synaptic structure. Our findings provide valuable evidence for the diagnosis and treatment of MDD.
Immune Reconstitution Following Autologous Hematopoietic Stem Cell Transplantation for Multiple Sclerosis: A Review on Behalf of the EBMT Autoimmune Diseases Working Party

Multiple sclerosis (MS) is a central nervous system (CNS) disorder, which is mediated by an abnormal immune response coordinated by T and B cells resulting in areas of inflammation, demyelination, and axonal loss. Disease-modifying treatments (DMTs) are available to dampen the inflammatory aggression but are ineffective in many patients. Autologous hematopoietic stem cell transplantation (HSCT) has been used as treatment in patients with a highly active disease, achieving a long-term clinical remission in most. The rationale of the intervention is to eradicate inflammatory autoreactive cells with lympho-ablative regimens and restore immune tolerance. Immunological studies have demonstrated that autologous HSCT induces a renewal of TCR repertoires, resurgence of immune regulatory cells, and depletion of proinflammatory T cell subsets, suggesting a “resetting” of immunological memory. Although our understanding of the clinical and immunological effects of autologous HSCT has progressed, further work is required to characterize the mechanisms that underlie treatment efficacy. Considering that memory B cells are disease-promoting and stem-like T cells are multipotent progenitors involved in self-regeneration of central and effector memory cells, investigating the reconstitution of B cell compartment and stem and effector subsets of immunological memory following autologous HSCT could elucidate those mechanisms. Since all subjects need to be optimally protected from vaccine-preventable diseases (including COVID-19), there is a need to ensure that vaccination in subjects undergoing HSCT is effective and safe. Additionally, the study of vaccination in HSCT-treated subjects as a means of evaluating immune responses could further distinguish broad immunosuppression from immune resetting.
Diffuse Large B-Cell Lymphoma: Clinical Presentation and Treatment Outcomes From the OncoCollect Lymphoma Registry

Background Diffuse large B-cell lymphoma (DLBCL) is the commonest subtype of lymphoma, standard CHOP was the treatment of choice, 42% of patients received rituximab, and 29% of patients were lost to follow-up during therapy, were reported in a study that collected retrospective data at 13 public and private hospitals for patients diagnosed with lymphoma between January 2005 and December 2009. The OncoCollect Registry was set up in 2017 to address the challenges in the collection of retrospective data through chart review, recording access to anthracycline and rituximab-based treatment, and to study outcomes and any improvement in the patient follow-up. Methodology The OncoCollect Lymphoma group registry was set up at a national level with 9 participating centers. Lymphoma patients registered at these centers between 2011 and 2017 were included. The clinical features, prognostic stratification, associated comorbidities, response to first-line treatment, and 3-year outcomes of adult patients with DLBCL were analyzed. Results Of the 5,886 lymphoma patients registered in the OncoCollect registry, 2,581 (44%) had DLBCL. A total of 1,961 were evaluable for frontline therapy. The median age at presentation was 57 years. Gender ratio was 1.6:1. At presentation, 43% were early stage, 70% had low and low intermediate IPI, 53% had extranodal disease, and 30.9% had one or more comorbidities (data available for 1,136 patients). The commonest extra nodal site was gastro-intestinal (23.98%) followed by head and neck (19.24%). The overall response rate was 79.29%. Complete remission was seen in 61.75%, partial response in 17.5%, stable disease in 4.3%, and progression in 7.9%. Patients who received anthracycline-based therapy (86.7%) and rituximab-based therapy (83.7%) had a 3-year event-free survival (EFS) of 69.67% and 68.48%, respectively. With a median follow-up of 33 months, the 3-year overall Survival (OS) and EFS were 75.37% and 66.58%, respectively. Conclusions DLBCL remains the commonest (44%) lymphoma subtype and is curable with standard anthracycline- and rituximab-based therapies. The availability of rituximab has increased the proportion of patients receiving standard chemoimmunotherapy.
Random Network and Non-rich-club Organization Tendency in Children With Non-syndromic Cleft Lip and Palate After Articulation Rehabilitation: A Diffusion Study

Objective The neuroimaging pattern in brain networks after articulation rehabilitation can be detected using graph theory and multivariate pattern analysis (MVPA). In this study, we hypothesized that the characteristics of the topology pattern of brain structural network in articulation-rehabilitated children with non-syndromic cleft lip and palate (NSCLP) were similar to that in healthy comparisons. Methods A total of 28 children with NSCLP and 28 controls with typical development were scanned for diffusion tensor imaging on a 3T MRI scanner. Structural networks were constructed, and their topological properties were obtained. Besides, the Chinese language clear degree scale (CLCDS) scores were used for correlation analysis with topological features in patients with NSCLP. Results The NSCLP group showed a similar rich-club connection pattern, but decreased small-world index, normalized rich-club coefficient, and increased connectivity strength of connections compared to controls. The univariate and multivariate patterns of the structural network in articulation-rehabilitated children were primarily in the feeder and local connections, covering sensorimotor, visual, frontoparietal, default mode, salience, and language networks, and orbitofrontal cortex. In addition, the connections that were significantly correlated with the CLCDS scores, as well as the weighted regions for classification, were chiefly distributed in the dorsal and ventral stream associated with the language networks of the non-dominant hemisphere. Conclusion The average level rich-club connection pattern and the compensatory of the feeder and local connections mainly covering language networks may be related to the CLCDS in articulation-rehabilitated children with NSCLP. However, the patterns of small-world and rich-club structural organization in the articulation-rehabilitated children exhibited a random network and non-rich-club organization tendency. These findings enhanced the understanding of neuroimaging patterns in children with NSCLP after articulation rehabilitation.
Factors Associated With E. coli Levels in and Salmonella Contamination of Agricultural Water Differed Between North and South Florida Waterways

The microbial quality of agricultural water is often assessed using fecal indicator bacteria (FIB) and physicochemical parameters. The presence, direction, and strength of associations between microbial and physicochemical parameters, and the presence of human pathogens in surface water vary across space (e.g., region) and time. This study was undertaken to understand these associations in two produce-growing regions in Florida, USA, and to examine the pathogen ecology in waterways used for produce production. The relationship between Salmonella presence, and microbial and physicochemical water quality; as well as weather and land use factors were evaluated. Water samples were collected from six sites in North Florida (N = 72 samples) and eight sites in South Florida (N = 96 samples) over 12 sampling months. Land use around each sampling site was characterized, and weather and water quality data were collected at each sampling. Salmonella, generic Escherichia coli, total coliform, and aerobic plate count bacteria populations were enumerated in each sample. Univariable and multivariable regression models were then developed to characterize associations between microbial water quality (i.e., E. coli levels and Salmonella presence), and water quality, weather, and land use factors separately for North and South Florida. The E. coli and total coliforms mean concentrations (log10 MPN/100 mL) were 1.8 ± 0.6 and >3.0 ± 0.4 in North and 1.3 ± 0.6 and >3.3 ± 0.2 in South Florida waterways, respectively. While Salmonella was detected in 23.6% (17/72) of North Florida and 28.1% (27/96) of South Florida samples, the concentration ranged between <0.48 and 1.4 log10 MPN/100 mL in North Florida, and <0.48 and 3.0 log10 MPN/100 mL in South Florida. Regression analyses showed no evidence of a correlation between either log10 total coliforms or E. coli levels, and if a sample was Salmonella-positive. The factors associated with Salmonella presence and log10 E. coli levels in North Florida differed from those in South Florida; no factors retrained in multivariable regression models were the same for the North and South Florida models. The differences in associations between regions highlight the complexity of understanding pathogen ecology in freshwater environments and suggest substantial differences between intra-state regions in risk factors for Salmonella contamination of agricultural water.
Genome-Wide Identification and Comparative Analysis of WRKY Transcription Factors Related to Momilactone Biosynthesis in Calohypnum plumiforme

Momilactones are diterpenoid phytoalexins with allelopathic functions, which have been found in the widely distributed bryophyte Calohypnum plumiforme. Clustered genes containing CpDTC1/HpDTC1, CpCYP970A14, CpCYP964A1, and CpMAS are involved in momilactone biosynthesis. Besides, momilactone concentration in C. plumiforme is affected by heavy metal treatment such as CuCl2. However, transcription factors which might regulate momilactone biosynthesis are unclear. WRKY transcription factors (TFs) regulate phytoalexin biosynthesis in many plant species. In this study, a systematic analysis of the WRKY TFs was performed according to the C. plumiforme genome. A total of 19 CpWRKY genes were identified and categorized into five subgroups based on their phylogenetic relationship. Conserved domain and motif analysis suggested that the WRKY domain was highly conserved, but there were some variations. Cis-acting elements and binding sites analysis implied that CpWRKY genes might be induced by stress and further regulate the biosynthesis of momilactones. Our study lays a foundation for further functional characterization of the candidate CpWRKY genes involved in the regulation of momilactone biosynthesis, and provides new strategies for increasing momilactone production.
Network Meta-Analysis of the Effects of Different Types of Traditional Chinese Exercises on Pulmonary Function, Endurance Capacity and Quality of Life in Patients With COPD

Background In recent years, Chinese and international studies have reported that traditional Chinese exercises (TCEs) have good therapeutic effects on pulmonary function, endurance capacity, and quality of life in patients with chronic obstructive pulmonary disease (COPD). However, only a few studies have reported the differences in the efficacy of different TCEs in the treatment of COPD. Objective The objective of this study is to compare the effects of five TCEs on patients with COPD, including Taijiquan (TJQ), Baduanjin (BDJ), Liuzijue (LZJ), Wuqinxi (WQX), and Yijinjing (YJJ). Methods All randomized controlled trials (RCTs) of TCEs for patients with COPD were searched in PubMed, Web of Science, Cochrane Library, Excerpt Medica Database (EMBASE), China National Knowledge Infrastructure (CNKI), China Biology Medicine database (CBM), China Scientific Journal Database (VIP), and Wanfang database. The search period was from the establishment of each database to August 16, 2021. The quality of the included studies was assessed according to the Cochrane handbook of systematic review, and the network meta-analysis was conducted with R 4.0. 2 (Ross Ihaka, Auckland, New Zealand) and ADDIS 1.16. 8 (Gert vsn Valkenhoef, Groningen, Netherlands). The effect size was evaluated using the mean difference (MD) and 95% confidence interval (CI). Results A total of 53 RCTs involving 3,924 patients were included. The network meta-analysis results showed that WQX was the most effective in improving FEV1/FVC% score and 6-MWT score. The difference was statistically significant (MD = 8.62, 95% CI 4.46 to 13.04, P < 0.05), (MD = 74.29, 95% CI 47.67 to 102.24, P < 0.05). However, YJJ was the most effective in reducing the CAT score, and the difference was statistically significant (MD = −8.38, 95% CI −13.24 to −3.28, P < 0.05). Conclusion The existing evidence shows that WQX has advantages over other TCEs in improving pulmonary function and endurance capacity in patients with COPD, while YJJ has advantages in improving the quality of life. Although TCEs show no significant adverse effects, more large-scale, double-blind, and high-quality RCTs are needed in the future to verify the findings of this study. Systematic Review Registration: https://www.crd. york.ac. uk/PROSPERO/, identifier: CRD42021293640.
Differentiating Melancholic and Non-melancholic Major Depressive Disorder Using Fractional Amplitude of Low-Frequency Fluctuations

Background Melancholic major depressive disorder (MDD) is a network-based brain disorder. However, whether or not network-based changes can be applied to differentiate melancholic (MEL) from non-melancholic (NMEL) MDD remains unclear. Methods Thirty-one MEL patients, 28 NMEL patients, and 32 matched healthy controls (HCs) were scanned using resting-state functional magnetic resonance imaging. Patients were assessed by the Chinese version of Snaith–Hamilton Pleasure Scale (SHAPS-C) and Temporal Experience of Pleasure Scale (TEPS). Fractional amplitude of low-frequency fluctuations (fALFF) and correlation analysis were used to analyze the data. Results Compared with HCs, the MEL group had significantly higher fALFF values in the bilateral inferior frontal gyrus and right supplementary motor area (SMA) and significantly lower fALFF values in the right inferior occipital gyrus (IOG), right middle temporal gyrus (MTG)/left IOG, and bilateral superior occipital gyrus (SOG)/MTG. On the other hand, the NMEL group showed significantly higher fALFF values in the bilateral SMA and significantly lower fALFF values in the bilateral posterior cingulate cortex/precuneus relative to HCs. Compared with the NMEL group, the MEL group showed significantly lower fALFF values in the left anterior cingulate cortex (ACC). A correlation was found between the fALFF values of the right SMA and the SHAPS-C in the MEL group. In addition, correlations were observed between the fALFF values of the left ACC and the TEPS contextual consummatory and total scores in all patients. Conclusion Our study uncovered that MDD exhibited altered brain activity in extensive brain networks, including the default-mode network, frontal-striatal network, reward system, and frontal-limbic network. Decreased fALFF in the left ACC might be applied to differentiate the two subtypes of MDD.
Nanoliposome-Encapsulated and Non-Encapsulated Phenolics From Achillea millefolium and Their Biological Function in Mice Challenged by Campylobacter jejuni: A Comparative Study

The objective of this research was to develop the nanoliposome-encapsulated phenolic rich fraction from Achillea millefolium (A. millefolium) and to investigate its antibacterial and health-promoting activities in mice challenged by pathogenic foodborne Campylobacter jejuni. The A. millefolium was extracted and the ethyl acetate fraction was found to be the phenolic-rich fraction (PRF) containing 14.72 ± 2.39 mg gallic acid equivalent (GAE)/g dry weight (DM). Base on the results, the synthesized nanoliposome-loaded PRF (PRF-NLs) with the size of 187.2 nm exhibited homogeneous dispersion (PDI 0.213) and moderate stability behavior in colloidal dispersions (Zeta potential −37.45). The non-encapsulated PRF and PRF-NLs were gavaged orally in the mice for 28 days, and mice were challenged with C. jejuni on day 21. The results indicated that the dietary supplementation of non-encapsulated PRF and PRF-NLs significantly (p < 0.05) improved the average daily weight gain, food intake, liver function, antioxidant status, and morphostructural characteristics of the ileum. However, the PRF-NLs appeared to be more potent as compared to non-encapsulated PRF. The higher biological activity of PRF-NLs could be associated with the higher intestinal solubility and absorption of nanoliposome-encapsulated PRF. Thereby, the nanoliposome-encapsulated PRF could be considered as a natural antibiotic alternative called phytobiotic to prevent intestinal infection caused by enteropathogenic C. jejuni.
Immune Characteristics of LYN in Tumor Microenvironment of Gliomas

The prognosis of gliomas is poor and there are limited therapeutic approaches. Immunotherapy has become a promising treatment for gliomas. Here, we explored the expression pattern of Lck/yes-related protein tyrosine kinase (LYN) in gliomas and assessed its value as an immunotherapy biomarker. Transcriptional data was mined from two publicly available datasets, TCGA and CGGA, and used to investigate the correlation between LYN and clinical characteristics including patient prognosis, somatic mutation, and immune infiltrating features in gliomas. Besides, the correlation between LYN and classical immune checkpoint molecules was explored. Glioma samples obtained from the Xiangya Hospital cohort were used for immunohistochemistry staining. High expression level of LYN was observed in advanced gliomas and other cancer types, which predicted a worse prognosis. LYN stratified patients’ survival in the Xiangya cohort and was also significantly associated with infiltrating immune cell types and inflammatory activities in the tumor microenvironment. LYN was involved in tumor mutation, correlated with the regulation of oncogenic genes, and also showed a significant positive correlation with PD-L1. LYN can be a potential diagnostic marker and immunotherapy marker in gliomas.
Toward Engineered Nanoparticle-Doped Optical Fibers for Sensor Applications

Nanoparticle-doped optical fibers, investigated first as fiber lasers and fiber amplifiers, have gained tremendous interest over the past few years as fiber sensors. One of the main interests of such fibers relies on the ability to develop a distributed sensor, allowing real-time measurement with multiplexed architecture. To go beyond the actual proof of concept, we discuss in this perspective paper three main challenges to tackle: understanding light propagation in heterogeneous materials, controlling nanoparticle formation in glass, and engineering nanoparticle characteristics. Identified as the main directions to follow, they will contribute to promote nanoparticle-doped fiber sensors in the next few years.
A Mini-Review of Pediatric Anthropometrics as Predictors of Future Insulin Resistance

The impact of rising rates of childhood obesity is far reaching. Metabolic syndrome in children is increasing, yet for most children the consequences of excess adiposity will manifest in adulthood. Excess early fat accrual is a risk factor for future insulin resistance. However, certain types of fat and patterns of fat distribution are more relevant than others to metabolic risk. Therefore, adiposity measures are important. The link between childhood obesity and future insulin resistance was initially established with body mass index (BMI), but BMI is an in imperfect measure of adiposity. It is worthwhile to evaluate other anthropometrics as they may more accurately capture metabolic risk. While measures such as waist to height ratio are established as superior screening measures in adulthood - the findings are not as robust in pediatrics. Emerging evidence suggests that alternative anthropometrics may be slightly superior to BMI in identifying those youth most at risk of developing insulin resistance, but the clinical significance of that superiority appears limited. Increasing study is needed in longitudinal and varied cohorts to identify which pediatric anthropometric best predicts adult insulin resistance. We review alternative anthropometrics as predictors of future insulin resistance and identify current gaps in knowledge and potential future directions of inquiry.