Miracle-dz/UniFAR-FTUs huggingface dataset:
Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data

The advent of high throughput sequencing has enabled in-depth characterization of human and environmental microbiomes. Determining the taxonomic origin of microbial sequences is one of the first, and frequently only, analysis performed on microbiome samples. Substantial research has focused on the development of methods for taxonomic annotation, often making trade-offs in computational efficiency and classification accuracy. A side-effect of these efforts has been a reexamination of the bacterial taxonomy itself. Taxonomies developed prior to the genomic revolution captured complex relationships between organisms that went beyond uniform taxonomic levels such as species, genus, and family. Driven in part by the need to simplify computational workflows, the bacterial taxonomies used most commonly today have been regularized to fit within a standard seven taxonomic levels. Consequently, modern analyses of microbial communities are relatively coarse-grained. Few methods make classifications below the genus level, impacting our ability to capture biologically relevant signals. Here, we present ATLAS, a novel strategy for taxonomic annotation that uses significant outliers within database search results to group sequences in the database into partitions. These partitions capture the extent of taxonomic ambiguity within the classification of a sample. The ATLAS pipeline can be found on GitHub [https://github.com/shahnidhi/outlier_in_BLAST_hits]. We demonstrate that ATLAS provides similar annotations to phylogenetic placement methods, but with higher computational efficiency. When applied to human microbiome data, ATLAS is able to identify previously characterized taxonomic groupings, such as those in the class Clostridia and the genus Bacillus. Furthermore, the majority of partitions identified by ATLAS are at the subgenus level, replacing higher-level annotations with specific groups of species. These more precise partitions improve our detection power in determining differential abundance in microbiome association studies.
Does the addition of a supportive chatbot promote user engagement with a smoking cessation app? An experimental study

Objective The objective of this study was to assess whether a version of the Smoke Free app with a supportive chatbot powered by artificial intelligence (versus a version without the chatbot) led to increased engagement and short-term quit success. Methods Daily or non-daily smokers aged ≥18 years who purchased the ‘pro’ version of the app and set a quit date were randomly assigned (unequal allocation) to receive the app with or without the chatbot. The outcomes were engagement (i.e. total number of logins over the study period) and self-reported abstinence at a one-month follow-up. Unadjusted and adjusted negative binomial and logistic regression models were fitted to estimate incidence rate ratios (IRRs) and odds ratios (ORs) for the associations of interest. Results A total of 57,214 smokers were included (intervention: 9.3% (5339); control: 90.7% (51,875). The app with the chatbot compared with the standard version led to a 101% increase in engagement (IRRadj = 2.01, 95% confidence interval (CI) = 1.92–2.11, p < . 001). The one-month follow-up rate was 10.6% (intervention: 19.9% (1,061/5,339); control: 9.7% (5,050/51,875). Smokers allocated to the intervention had greater odds of quit success (missing equals smoking: 844/5,339 vs. 3,704/51,875, ORadj = 2.38, 95% CI = 2.19–2.58, p < .001; follow-up only: 844/1,061 vs. 3,704/5,050, ORadj = 1.36, 95% CI = 1.16–1.61, p < .001). Conclusion The addition of a supportive chatbot to a popular smoking cessation app more than doubled user engagement. In view of very low follow-up rates, there is low quality evidence that the addition also increased self-reported smoking cessation.
Extracellular RNA in Central Nervous System Pathologies

The discovery of extracellular RNA (exRNA) has shifted our understanding of the role of RNA in complex cellular functions such as cell-to-cell communication and a variety of pathologies. ExRNAs constitute a heterogenous group of RNAs ranging from small (such as microRNAs) and long non-coding to coding RNAs or ribosomal RNAs. ExRNAs can be liberated from cells in a free form or bound to proteins as well as in association with microvesicles (MVs), exosomes, or apoptotic bodies. Their composition and quantity depend heavily on the cellular or non-cellular component, the origin, and the RNA species being investigated; ribosomal RNA provides the majority of exRNA and miRNAs are predominantly associated with exosomes or MVs. Several studies showed that ribosomal exRNA (rexRNA) constitutes a proinflammatory and prothrombotic alarmin. It is released by various cell types upon inflammatory stimulation and by damaged cells undergoing necrosis or apoptosis and contributes to innate immunity responses. This exRNA has the potential to directly promote the release of cytokines such as tumor necrosis factor factor-α (TNF-α) or interleukin-6 from immune cells, thereby leading to a proinflammatory environment and promoting cardiovascular pathologies. The potential role of exRNA in different pathologies of the central nervous system (CNS) has become of increasing interest in recent years. Although various exRNA species including both ribosomal exRNA as well as miRNAs have been associated with CNS pathologies, their precise roles remain to be further elucidated. In this review, the different entities of exRNA and their postulated roles in CNS pathologies including tumors, vascular pathologies and neuroinflammatory diseases will be discussed. Furthermore, the potential role of exRNAs as diagnostic markers for specific CNS diseases will be outlined, as well as possible treatment strategies addressing exRNA inhibition or interference.
Acupuncture Treatment Reverses Retinal Gene Expression Induced by Optic Nerve Injury via RNA Sequencing Analysis

Glaucoma and traumatic optic nerve crush (ONC) injury result in progressive loss of retinal ganglion cells (RGCs) and defects in visual function. In clinical trials of Traditional Chinese Medicine, acupuncture has been widely used for the treatment of ocular diseases. However, the molecular mechanisms of acupuncture treatment are still unclear. In this study, we used technique of RNA sequencing (RNA-seq) to study the effects of acupuncture treatment on retinal transcriptome after axotomy injury. RNA-seq results revealed that 436 genes including 31 transcription factors (TFs) were changed after injury, among them were many well-known neural degeneration related TFs such as Jun, Ddit3, Atf3, and Atf4. Interestingly, acupuncture treatment at acupoint GB20 (Fengchi) significantly reversed a series of differential expressed genes (DEGs) induced by optic nerve injury. While treatments at BL1 (Jingming) or GB20 sham control acupoint-GV16 (Fengfu), led to limited DEG reversal. In contrast, treatments at these two sites further enhanced the trend of DEG expression induced by axotomy injury. At last, retina immunostaining results revealed that only GB20 acupoint treatment increased RGC survival, in consistent with RNA-seq results. Therefore, our study first reported that acupuncture treatment regulated retinal transcriptome and reversed the gene expression induced by axotomy injury, and GB20 acupoint treatment increased RGC survival, which will provide novel therapeutic targets for treatment of ocular diseases.
Complexity and Simplification in Understanding Travel Preferences Among Tourists

Travel preferences are complex phenomena, and thus cumbersome to deal with in full width in diagnostic and strategic planning processes. The aim of the present investigation was to explore to what extent individual preferences can be simplified into structures, and if tourists can be grouped into preference clusters that are viable and practically applicable for tourism planning. Building on prior studies that have validated survey instruments designed to measure different tourist role orientations, we used a factor analytical approach to develop a simplified structure of individual preferences, and a standard clustering technique for grouping tourists into preference clusters. Further analyses indicated that preference clusters based on reduced factor preference-data are to some extent related to context-specific valuations, perceptions, and revisit intentions; however, the magnitude of differences between groups was rather small. Overall findings provide reason to suggest that the identified preference clusters are insufficient when it comes to explaining variability in which aspects tourists emphasize as part of their vacation. Possible managerial implications and methodological limitations of the present investigation are noted.
A Jack of All Trades: Impact of Glucocorticoids on Cellular Cross-Talk in Osteoimmunology

Glucocorticoids (GCs) are known to have a strong impact on the immune system, metabolism, and bone homeostasis. While these functions have been long investigated separately in immunology, metabolism, or bone biology, the understanding of how GCs regulate the cellular cross-talk between innate immune cells, mesenchymal cells, and other stromal cells has been garnering attention rather recently. Here we review the recent findings of GC action in osteoporosis, inflammatory bone diseases (rheumatoid and osteoarthritis), and bone regeneration during fracture healing. We focus on studies of pre-clinical animal models that enable dissecting the role of GC actions in innate immune cells, stromal cells, and bone cells using conditional and function-selective mutant mice of the GC receptor (GR), or mice with impaired GC signaling. Importantly, GCs do not only directly affect cellular functions, but also influence the cross-talk between mesenchymal and immune cells, contributing to both beneficial and adverse effects of GCs. Given the importance of endogenous GCs as stress hormones and the wide prescription of pharmaceutical GCs, an improved understanding of GC action is decisive for tackling inflammatory bone diseases, osteoporosis, and aging.
Compressive Sensing Inference of Neuronal Network Connectivity in Balanced Neuronal Dynamics

Determining the structure of a network is of central importance to understanding its function in both neuroscience and applied mathematics. However, recovering the structural connectivity of neuronal networks remains a fundamental challenge both theoretically and experimentally. While neuronal networks operate in certain dynamical regimes, which may influence their connectivity reconstruction, there is widespread experimental evidence of a balanced neuronal operating state in which strong excitatory and inhibitory inputs are dynamically adjusted such that neuronal voltages primarily remain near resting potential. Utilizing the dynamics of model neurons in such a balanced regime in conjunction with the ubiquitous sparse connectivity structure of neuronal networks, we develop a compressive sensing theoretical framework for efficiently reconstructing network connections by measuring individual neuronal activity in response to a relatively small ensemble of random stimuli injected over a short time scale. By tuning the network dynamical regime, we determine that the highest fidelity reconstructions are achievable in the balanced state. We hypothesize the balanced dynamics observed in vivo may therefore be a result of evolutionary selection for optimal information encoding and expect the methodology developed to be generalizable for alternative model networks as well as experimental paradigms.
Age-Related Reductions in Cerebrovascular Reactivity Using 4D Flow MRI

Cerebrovascular reactivity (CVR), is important for determining future risk of cerebrovascular disease. It is unclear if primary aging is associated with reductions in CVR because previous studies often include participants with vascular risk factors. Additionally, the inconsistency in the literature may be due to the inherent difficulty in quantifying intracranial cerebral blood flow and CVR. To address these limitations, we determined the effect of age on CVR in the large intracranial vessels in adults with low vascular risk using state-of-the-art MRI techniques. We also determined if the effect of age on CVR was sex-specific. Young (n = 20; 25 ± 3 years) and older (n = 19; 61 ± 5 years) healthy, physically active adults participated in the study. CVR was measured in response to hypercapnia using 4D flow MRI, which allows for simultaneous angiographic and quantitative blood flow measurements in the intracranial arteries. Older adults had lower global CVR and CVR in multiple intracranial arteries [right and left internal carotid arteries (ICA), right and left middle cerebral arteries (MCA), and basilar artery (BA)] compared with young adults (p < 0.05 for all). In addition, the MCA dilated significantly in response to hypercapnia in young (p < 0.05), but not older adults. Young men demonstrated higher global CVR and CVR in multiple intracranial arteries (ICAs, MCAs, and BA) compared with young women and older men (p < 0.05 for both); however, CVR did not differ between young women and older women. Our results demonstrate that, using 4D flow MRI, primary aging is associated with lower CVR in adults with low vascular risk. In addition, the effect of age on CVR may be driven by men. The 4D flow MRI technique may provide a promising new alternative to measure cerebrovascular physiology without the limitations of commonly used techniques. Future studies could utilize this MRI technique to examine interventions to maintain CVR with advancing age. This study was registered under clinicaltrials.gov # NCT02840851.
Unveiling the smallest – systematics, classification and a new subfamily of featherwing beetles based on larval morphology (Coleoptera : Ptiliidae)

The higher-level systematics of featherwing beetles (Coleoptera: Ptiliidae), the smallest non-parasitic insects and abundant in the world’s forests, is poorly known. Based on larval morphology, the systematic relationships and internal classification are revised and analysed from a comparative, evolutionary and phylogenetic perspective. We introduce 37 morphological characters of all instars and of strong phylogenetic signal in a first-ever maximum parsimony phylogenetic family analysis, providing support for the erection of Nossidiinae, subfam. nov., keeping Cephaloplectinae within Ptiliidae and sinking Acrotrichini as a tribe into a revised subfamily Ptiliinae. Full homology of characters between Ptiliidae and its sister taxon Hydraenidae is demonstrated and miniaturisation effects on the larval exoskeleton reviewed. Keeping generalised mouthparts adapted to sapro-mycophagy through geological time made three evolutionarily independent invasion events of marine littorals possible in Ptiliidae. Keys to larval instars, subfamilies, tribes and species are presented for the first time, supplemented by model descriptions of multiple hierarchical levels (species, genus, tribe, subfamily, family), introducing many phylogenetically informative characters. The conservative larval morphology/chaetotaxy proves particularly useful for analysis on the family-group taxon level, as exemplified by caudal urogomphi, a key character in ptiliid systematics. The revised nomenclature and classification improves systematic predictability and better reflects natural relationships within Ptiliidae.
Notoginsenoside R1 for Organs Ischemia/Reperfusion Injury: A Preclinical Systematic Review

Notoginsenoside R1 (NGR1) exerts pharmacological actions for a variety of diseases such as myocardial infarction, ischemic stroke, acute renal injury, and intestinal injury. Here, we conducted a preclinical systematic review of NGR1 for ischemia reperfusion (I/R) injury. Eight databases were searched from their inception to February 23rd, 2019; Review Manager 5.3 was applied for data analysis. CAMARADES 10-item checklist and cell 10-item checklist were used to evaluate the methodological quality. Twenty-five studies with 304 animals and 124 cells were selected. Scores of the risk of bias in animal studies ranged from 3 to 8, and the cell studies ranged from 3 to 5. NGR1 had significant effects on decreasing myocardial infarct size in myocardial I/R injury, decreasing cerebral infarction volume and neurologic deficit score in cerebral I/R injury, decreasing serum creatinine in renal I/R injury, and decreasing Park/Chiu score in intestinal I/R injury compared with controls (all P < 0.05 or P < 0.01). The multiple organ protection of NGR1 after I/R injury is mainly through the mechanisms of antioxidant, anti-apoptosis, and anti-inflammatory, promoting angiogenesis and improving energy metabolism. The findings showed the organ protection effect of NGR1 after I/R injury, and NGR1 can potentially become a novel drug candidate for ischemic diseases. Further translation studies are needed.
Measurement of Personality Structure by the OPD Structure Questionnaire Can Help to Discriminate Between Subtypes of Eating-Disorders

Background Differentiation between purging type (AN-P) and restricting type (AN-R) is common in anorexia nervosa (AN) and relevant for clinical practice. However, differences of personality pathology in eating disorders (ED) and their subtypes, which can be captured by the operationalized psychodynamic diagnosis (OPD) system, have not been systematically investigated to date. Objectives The aim of this study was to explore differences in personality structure between the subtypes of AN and bulimia nervosa (BN) using the OPD structure questionnaire (OPD-SQ). In addition, the ability of the instrument to support the classification of eating disorders was examined. Materials and Methods We conducted a retrospective, exploratory study in a subset sample of a larger validation study. The OPD-SQ had been collected from n = 60 patients with AN or BN. Patients were assigned to the ED groups by clinical assessment. Statistical analyses included multivariate analysis of variance (MANOVA) and discriminant analysis. Results Differences between ED groups were observed on 5 OPD-SQ main scales and 9 subscales, as well as on the global scale. AN-P patients demonstrated the lowest personality structure on most of the main scales and subscales, whereas AN-R patients showed a higher personality structure level as compared to both BN and AN-P patients. The OPD-SQ scales with the largest differences include self-perception, object perception, and attachment to internal objects. Discriminant analysis resulted in satisfactory assignment to ED groups by OPD-SQ subscales. Conclusions Personality structure was found to be less developed in patients with BN and AN-P as compared to patients with AN-R. Although the results have to be proven in larger prospective studies, these results suggest that the OPD-SQ may be used to support the clinical assessment and classification in patients with EDs.
Continuous Cultivation as a Method to Assess the Maximum Specific Growth Rate of Photosynthetic Organisms

Modeling the growth of photosynthetic organisms is challenging, due to the complex role of light, which can be limiting because of self-shading, or photoinhibiting in the case of high intensities. A case of particular interest is represented by nitrogen-fixing cyanobacteria, whose growth is controlled not only by the light intensity, but also by the availability of atmospheric nitrogen in the liquid medium. The determination of the maximum specific growth rate is often affected by many variables that, in batch growth systems, may change significantly. On the other hand, in a continuous system, once the steady state is reached the values of all the process variables remain constant, including the biomass concentration and the specific light supply rate. In this work, the diazotrophic cyanobacterium Anabaena PCC 7122 was cultivated in continuous photobioreactors, to investigate the role of nitrogen, light and residence time on growth kinetics, and to retrieve the value of the maximum specific growth rate of this organism. In addition, the kinetic parameters for temperature and the half saturation constant for nitrogen (3 mg L−1) were measured by respirometric tests. Based on the results of continuous experiments, the specific maintenance rate was found to depend on the light intensity supplied to the reactor, ranging between 0.5 and 0.8 d−1. All these parameters were used to develop a kinetic model able to describe the biomass growth in autotrophic conditions. The maximum specific growth rate could hence be determined by applying the kinetic model in the material balances of the continuous photobioreactor, and resulted equal to 8.22 ± 0.69 d−1.
Development and Preliminary Validation of the Youth Leadership Potential Scale

To address the need for a valid and reliable scale of youth leadership potential based on the development theory of leadership, the current study developed the Youth Leadership Potential Scale (YLPS) and investigated its factor structure and psychometric properties in a sample of 696 students (grades 7–9) in China. Exploratory structural equation modeling (ESEM) identified a five-factor solution comprising leadership information, leadership attitude, communication skills, decision-making skills, and stress management skills. ESEM within confirmatory factor analysis demonstrated an adequate fit for this structure. The scale showed good composite reliability and measurement invariance across different gender and grade/age groups. The scale also showed sufficient concurrent validity with the Coping Self-Efficacy Scale, the Chinese Roets Rating Scale for Leadership, and the Leadership Skills Inventory. Furthermore, criterion-related validity was supported by the relationship between YLPS scores and the length of student leadership positions. The results suggest that the YLPS is a valid and pragmatic measure for assessing youth leadership potential. The current study is the first to develop a youth leadership potential scale based on the development theory of leadership.
Cardiovascular risk factors after renal transplantation. The impact of treatment with cyclosporine A

textabstractRenal transplantation is presently the renal replacement therapy ol choice lor most patients suffering lrom end-stage renal lailure, mainly because ol the gain in quality ol lile after successlul allografting. During the past decade the results ol renal transplantation, in terms ol incidence ol rejection episodes and graft loss because ol acute rejection, have improved substantially due to the introduction ol cyclosporine A. However, it appears that, despite the decrease in morbidity rates lollowing renal transplantation, in the long run the improvement in patient survival is rather limited (1). The success in terms ol graft survival wilhout a parallel improvement in patient survival, also emphasizes th at comorbid conditions such as cardiovascular disease, become increasingly important lor the longterm prospeets ol this patient group.