Miracle-dz/UniFAR-FTUs huggingface dataset:
Bifidobacterium breve Exopolysaccharide Blocks Dendritic Cell Maturation and Activation of CD4+ T Cells

Exopolysaccharide (EPS) is a bacterial extracellular carbohydrate moiety which has been associated with immunomodulatory activity and host protective effects of several gut commensal bacteria. Bifidobacterium breve are early colonizers of the human gastrointestinal tract (GIT) but the role of EPS in mediating their effects on the host has not been investigated for many strains. Here, we characterized EPS production by a panel of human B. breve isolates and investigated the effect of EPS status on host immune responses using human and murine cell culture-based assay systems. We report that B. breve EPS production is heterogenous across strains and that immune responses in human THP-1 monocytes are strain-specific, but not EPS status-specific. Using wild type and isogenic EPS deficient mutants of B. breve strains UCC2003 and JCM7017 we show that EPS had strain-specific divergent effects on cytokine responses from murine bone marrow derived macrophages (BMDMs) and dendritic cells (BMDCs). The B. breve UCC2003 EPS negative (EPS–) strain increased expression of cytokine genes (Tnfa, Il6, Il12a, and Il23a) relative to untreated BMDCs and BMDCs treated with wild type strain. B. breve UCC2003 and JCM7017 EPS– strains increased expression of dendritic cell (DC) activation and maturation marker genes (Cd80, Cd83, and Cd86) relative to untreated BMDCs. Consistent with this, BMDCs co-cultured with B. breve UCC2003 and JCM7017 EPS– strains engineered to express OVA antigen activated OVA-specific OT-II CD4+ T-cells in a co-culture antigen-presentation assay while EPS proficient strains did not. Collectively, these data indicate that B. breve EPS proficient strains use EPS to prevent maturation of DCs and activation of antigen specific CD4+ T cells responses to B. breve. This study identifies a new immunomodulatory role for B. breve EPS and suggests it may be important for immune evasion of adaptive immunity by B. breve and contribute to host-microbe mutualism.
Feline Stool-Associated Circular DNA Virus (FeSCV) in Diarrheic Cats in China

Feline stool-associated circular DNA virus (FeSCV) is an unclassified circular replication-associated protein-encoding single-stranded (CRESS) DNA virus that was discovered in cats in Japan in 2018. Few studies on the genomic characteristics and prevalence of FeSCV have been conducted. To investigate whether FeSCV has been circulating in domestic cats in Guangdong, China, fecal samples were collected from cats with diarrhea in an animal hospital in 2018 to promote research on FeSCV. The FeSCV genome was obtained by PCR amplification and sequencing, and the detected virus was named PY4 (GenBank No. MT732515). The genome of PY4 was 2,034 nt in size, which was 12 nt smaller than the reported genome of Japanese FeSCV strains (KU7, KU8, KU9, KU14) (2,046 nt). The PY4 strain shared 95.1 ~ 95.5% homology with Japanese FeSCV strains. Notably, the Cap protein of PY4 was mutated at 15 amino acid sites, and the PY4 genome contained a unique open reading frame 3. In addition, there were two additional base insertions in the stem-loop structure of PY4, and the nucleotide homology of the spacer region was not high. A phylogenetic tree based on Rep proteins showed that PY4, Japanese FeSCVs and rodent stool-associated circular viruses (RodSCVs) clustered together, suggesting that they might share a similar origin in their phylogenetic evolution. In this study, samples collected in Guangzhou, China, in 2018 were subjected to an etiological investigation, and 20% (2/10) of the samples were positive for FeSCV. The ORFs, stem-loop structures, Cap proteins and intergenic region sequences of PY4 were significantly different from those reported in Japan. This is the first report of FeSCV in domestic cats with diarrhea in China, and further epidemiological studies are urgently needed to assess the impact of the virus on cats.
Specialization for Tachinid Fly Pollination in the Phenologically Divergent Varieties of the Orchid Neotinea ustulata

Despite increased focus on elucidating the various reproductive strategies employed by orchids, we still have only a rather limited understanding of deceptive pollination systems that are not bee- or wasp-mediated. In Europe, the orchid Neotinea ustulata has been known to consist of two phenologically divergent varieties, neither of which provide rewards to its pollinators. However, detailed studies of their reproductive biology have been lacking. Our study aimed to characterize and understand the floral traits (i.e., morphology, color, and scent chemistry) and reproductive biology of N. ustulata. We found that the two varieties differ in all their floral traits; furthermore, while Neotinea ustulata var. ustulata appears to be pollinated by both bees (e.g., Anthophora, Bombus) and flies (e.g., Dilophus, Tachina), var. aestivalis is pollinated almost entirely by flies (i.e., Nowickia, Tachina). Tachinids were also found to be much more effective than bees in removing pollinaria, and we show experimentally that they use the characteristic dark inflorescence top as a cue for approaching inflorescences. Our results thus suggest that while both N. ustulata varieties rely on tachinids for pollination, they differ in their degree of specialization. Further studies are, however, needed to fully understand the reproductive strategy of N. ustulata varieties.
Heart and Head: Profiles and Predictors of Self-Assessed Cognitive and Affective Empathy in a Sample of Medical and Health Professional Students

For medical and health professions, students learning to respond to others' distress with well-regulated empathy is an important developmental skill linked to positive health outcomes and professionalism. Our study aimed to investigate the sociodemographic, psychological, and psychosocial differences between medical (MS) and health professional (HPS) students and their empathic abilities, since both populations share common stressors, namely, dealing with suffering people. Additionally, we were interested in assessing the psychological and psychosocial predictors of empathy of MS compared to HPS. One hundred thirty MS and 86 HPS were administered the Patient Health Questionnaire-9, Interpersonal Reactivity Index, Integrative Hope Scale, and UCLA Loneliness Scale. The two groups showed differences in their contextual characteristics, with the HPS group having larger families, lower parents' education levels, and lower family income compared to the MS group. In both groups, ~15% of students reported previous contact for psychological problems. A higher proportion of HPS (23.3%) reported depressive symptoms than MS (10%), and female HPS reported more intense feelings of loneliness than other subgroups of students. No differences were found between the two groups in self-assessed cognitive and affective empathy. In both groups, women showed greater affective scores than men and, at the same time, seemed to be particularly prone to personal distress. The cognitive empathic dimension of “perspective taking” was predicted by young age (OR, 612; 95% CI, 1.395–15.242) and the overall socioeconomic status (OR, 3.175; 95% CI, 1.154–8.734) of the HPS. Self-assessed affective competence was predicted by female gender (OR, 3.112; 95% CI, 1.328–7.288), depressive symptomatology (OR, 2.777; 95% CI, 1.004–7.681), higher mother's level of education (OR, 2.764; 95% CI, 1.147–6.659), and feeling of hope related to social relationships (OR, 1.367; 95% CI, 1.152–1.622). Risk factors for poor self-assessed affective emphatic skills were previous contact for psychological problems (OR, 3.263; 95% CI, 1.238–8.601) and feelings of loneliness (OR, 1.18; 95% CI, 1.09–1.276). Our findings emphasize the need to test psychosocial models to better understand empathic skills.
Imaging the Pathophysiology of Essential Tremor—A Systematic Review

Background: The pathophysiology underlying essential tremor (ET) still is poorly understood. Recent research suggests a pivotal role of the cerebellum in tremor genesis, and an ongoing controversy remains as to whether ET constitutes a neurodegenerative disorder. In addition, mounting evidence indicates that alterations in the gamma-aminobutyric acid neurotransmitter system are involved in ET pathophysiology. Here, we systematically review structural, functional, and metabolic neuroimaging studies and discuss current concepts of ET pathophysiology from an imaging perspective. Methods: We conducted a PubMed and Scopus search from 1966 up to December 2020, entering essential tremor in combination with any of the following search terms and their corresponding abbreviations: positron emission tomography (PET), single-photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), magnetic resonance spectroscopy (MRS), and gamma-aminobutyric acid (GABA). Results: Altered functional connectivity in the cerebellum and cerebello-thalamico-cortical circuitry is a prevalent finding in functional imaging studies. Reports from structural imaging studies are less consistent, and there is no clear evidence for cerebellar neurodegeneration. However, diffusion tensor imaging robustly points toward microstructural cerebellar changes. Radiotracer imaging suggests that the dopaminergic axis is largely preserved in ET. Similarly, measurements of nigral iron content and neuromelanin are unremarkable in most studies; this is in contrast to Parkinson's disease (PD). PET and MRS studies provide limited evidence for cerebellar and thalamic GABAergic dysfunction. Conclusions: There is robust evidence indicating that the cerebellum plays a key role within a multiple oscillator tremor network which underlies tremor genesis. However, whether cerebellar dysfunction relies on a neurodegenerative process remains unclear. Dopaminergic and iron imaging do not suggest a substantial overlap of ET with PD pathophysiology. There is limited evidence for alterations of the GABAergic neurotransmitter system in ET. The clinical, demographical, and genetic heterogeneity of ET translates into neuroimaging and likely explains the various inconsistencies reported.
AVUBDI: A Versatile Usable Big Data Infrastructure and Its Monitoring Approaches for Process Industry

The amount of sensors in process industry is continuously increasing as they are getting faster, better and cheaper. Due to the rising amount of available data, the processing of generated data has to be automatized in a computationally efficient manner. Such a solution should also be easily implementable and reproducible independently of the details of the application domain. This paper provides a suitable and versatile usable infrastructure that deals with Big Data in the process industry on various platforms using efficient, fast and modern technologies for data gathering, processing, storing and visualization. Contrary to prior work, we provide an easy-to-use, easily reproducible, adaptable and configurable Big Data management solution with a detailed implementation description that does not require expert or domain-specific knowledge. In addition to the infrastructure implementation, we focus on monitoring both infrastructure inputs and outputs, including incoming data of processes and model predictions and performances, thus allowing for early interventions and actions if problems occur.
Tuning the Kinetics and Energetics of Diels−Alder Cycloaddition Reactions to Improve Poling Efficiency and Thermal Stability of High-Temperature Cross-Linked Electro-Optic Polymers

A comprehensive theoretical and experimental study of the bromo effect on Diels−Alder (DA) and retro-Diels−Alder (rDA) reactions between the anthracene-containing dienes and maleimide dienophile has been conducted to improve thermal stability and poling efficiency of electro-optic (EO) polymers. Calculations with density functional theory (DFT) reveal that the bromo substitution on anthracene-based dienes leads to significantly increased cycloaddition exothermicities (9−12 kcal/mol) but has a minor effect on their activation barriers (0.6−3 kcal/mol) when reacted with N-phenylmaleimide dienophile. These calculated values correlate very well with the experimental results obtained from a series of model compounds. The DA/rDA cross-linking protocols based on these compounds can be applied to several nonlinear optical (NLO) polymers and result in large EO coefficients (r33) (as high as 69 pm/V) and greatly improved thermal stability (up to 250 °C). This demonstrates that controlled DA/rDA reactions can be use.
Tumor Immune Microenvironment Components and Checkpoint Molecules in Anaplastic Variant of Diffuse Large B-Cell Lymphoma

Background Anaplastic diffuse large B-cell lymphoma(A-DLBCL) is a rare morphological subtype characterized by the presence of polygonal, bizarre-shaped tumor cells. Our previous research found that A-DLBCL displays many genetic alterations and biological features that differ greatly from those of ordinary DLBCL. However, the status of tumor immune microenvironment components and checkpoint molecules in A-DLBCL remains unclear. Methods Thirty A-DLBCL patients were enrolled to study tumor immune microenvironment components and checkpoint molecules and their associations with clinicopathological features and prognosis. Results Patients with A-DLBCL presented higher expression of PD-L1 (40% vs 10%, P=0.004) than patients with ordinary DLBCL. FISH analysis showed that extra copies of PD-L1 were more frequent in A-DLBCL cases than in ordinary DLBCL cases (23.3% vs 4.0%, P=0.001). The numbers of PD-1+ TILs (tumor infiltrating lymphocytes) and CD8+T cells were significantly lower in A-DLBCL versus ordinary DLBCL. In contrast, the numbers of GATA3+ Th2 cells, FOXP3+ Tregs and CD33+ myeloid-derived suppressor cells (MDSCs) were significantly higher in A-DLBCL than in ordinary DLBCL. The associations between clinicopathological features and tumor immune microenvironment cell frequency were analyzed in A-DLBCL patients. Briefly, the number of PD-1+ TILs was lower and the number of CD33+ MDSCs was higher in patients with mutated TP53 compared to those with wild-type TP53. The number of FOXP3+ Tregs was much lower in patients with a noncomplete response (CR) to chemotherapy than in those with a complete response. The number of CD8+ T cells showed a decreasing trend in patients with high International Prognostic Index (IPI) scores and in those with concurrent MYC and BCL2 and/or BCL6 abnormalities. Univariate survival analysis showed that patients with PD-L1+, mPD-L1+(PD-L1+ nonmalignant stromal cells) or mPD-L1+ status had a significantly poorer overall survival (OS) than those with PD-L1- status. An increase in the number of CD3+ T cells, FOXP3+ Treg cells and T-bet+ Th1 cells was significantly associated with prolonged OS in patients with A-DLBCL. Conclusion Our study suggests that A-DLBCL displays a distinct pattern of tumor immune microenvironment components and checkpoint molecules that distinguish it from ordinary DLBCL. The analysis of tumor immune microenvironment components and checkpoint molecules could help in predicting the prognosis of A-DLBCL patients and determining therapeutic strategies targeting the tumor immune microenvironment.
Analysis of Methylation Dynamics Reveals a Tissue-Specific, Age-Dependent Decline in 5-Methylcytosine Within the Genome of the Vertebrate Aging Model Nothobranchius furzeri

Erosion of the epigenetic DNA methylation landscape is a widely recognized hallmark of aging. Emerging advances in high throughput sequencing techniques, in particular DNA methylation data analysis, have resulted in the establishment of precise human and murine age prediction tools. In vertebrates, methylation of cytosine at the C5 position of CpG dinucleotides is executed by DNA methyltransferases (DNMTs) whereas the process of enzymatic demethylation is highly dependent on the activity of the ten-eleven translocation methylcytosine dioxygenase (TET) family of enzymes. Here, we report the identification of the key players constituting the DNA methylation machinery in the short-lived teleost aging model Nothobranchius furzeri. We present a comprehensive spatio-temporal expression profile of the methylation-associated enzymes from embryogenesis into late adulthood, thereby covering the complete killifish life cycle. Data mining of the N. furzeri genome produced five dnmt gene family orthologues corresponding to the mammalian DNMTs (DNMT1, 2, 3A, and 3B). Comparable to other teleost species, N. furzeri harbors multiple genomic copies of the de novo DNA methylation subfamily. A related search for the DNMT1 recruitment factor UHRF1 and TET family members resulted in the identification of N. furzeri uhrf1, tet1, tet2, and tet3. Phylogenetic analysis revealed high cross-species similarity on the amino acid level of all individual dnmts, tets, and uhrf1, emphasizing a high degree of functional conservation. During early killifish development all analyzed dnmts and tets showed a similar expression profile characterized by a strong increase in transcript levels after fertilization, peaking either at embryonic day 6 or at the black eye stage of embryonic development. In adult N. furzeri, DNA methylation regulating enzymes showed a ubiquitous tissue distribution. Specifically, we observed an age-dependent downregulation of dnmts, and to some extent uhrf1, which correlated with a significant decrease in global DNA methylation levels in the aging killifish liver and muscle. The age-dependent DNA methylation profile and spatio-temporal expression characteristics of its enzymatic machinery reported here may serve as an essential platform for the identification of an epigenetic aging clock in the new vertebrate model system N. furzeri.
Investigating the Role of Root Exudates in Recruiting Streptomyces Bacteria to the Arabidopsis thaliana Microbiome

Streptomyces species are saprophytic soil bacteria that produce a diverse array of specialized metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant Arabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing cpr5 plants are colonized more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonization by Streptomyces bacteria as the wild-type plants. We then tested eight genome sequenced Streptomyces endophyte strains in vitro and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used 13CO2 DNA stable isotope probing to test whether Streptomyces species can feed off a wider range of plant metabolites but found that Streptomyces bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.
Disparity in Access to Oncology Precision Care: A Geospatial Analysis of Driving Distances to Genetic Counselors in the U.S.

In the US, the growing demand for precision medicine, particularly in oncology, continues to put pressure on the availability of genetic counselors to meet that demand. This is especially true in certain geographic locations due to the uneven distribution of genetic counselors throughout the US. To assess these disparities, access to genetic counselors of all specialties is explored by geography, cancer type, and social determinants of health. Geospatial technology was used to combine and analyze genetic counselor locations and cancer incidence at the county level across the US, with a particular focus on tumors associated with BRCA mutations including ovarian, pancreatic, prostate and breast. Access distributions were quantified, and associations with region, cancer type, and socioeconomic variables were investigated using correlational tests. Nationally, in 2020, there were 4,813 genetic counselors, or 1.49 genetic counselors per 100,000 people, varying between 0.17 to 5.7 per 100,000 at the state level. Seventy-one percent of U.S. residents live within a 30-minute drive-time to a genetic counselor. Drive-times, however, are not equally distributed across the country – while 82% of people in metropolitan areas are 30 minutes from a genetic counselor, only 6% of people in nonmetro areas live within 30 minutes’ drive time. There are statistically significant differences in access across geographical regions, socioeconomics and cancer types. Access to genetic counselors for cancer patients differs across groups, including regional, socioeconomic, and cancer type. These findings highlight areas of the country that may benefit from increased genetic counseling provider supply, by increasing the number of genetic counselors in a region or by expanding the use of telegenetics a term used to describe virtual genetic counseling consults that occur via videoconference. Policy intervention to allow genetic counselors to bill for their services may be an effective route for increasing availability of genetic counselors’ services However, genetic counselors in direct patient care settings also face other challenges such as salary, job satisfaction, job recognition, overwork/burnout, and appropriate administrative/clinical support, and addressing these issues should also be considered along with policy support. These results could support targeted policy reform and alternative service models to increase access to identified pockets of unmet need, such as telemedicine. Data and analysis are available to the public through an interactive dashboard 1 .