Miracle-dz/UniFAR-FTUs huggingface dataset:
Hidden Microatelectases Increase Vulnerability to Ventilation-Induced Lung Injury

Mechanical ventilation of lungs suffering from microatelectases may trigger the development of acute lung injury (ALI). Direct lung injury by bleomycin results in surfactant dysfunction and microatelectases at day 1 while tissue elastance and oxygenation remain normal. Computational simulations of alveolar micromechanics 1-day post-bleomycin predict persisting microatelectases throughout the respiratory cycle and increased alveolar strain during low positive end-expiratory pressure (PEEP) ventilation. As such, we hypothesize that mechanical ventilation in presence of microatelectases, which occur at low but not at higher PEEP, aggravates and unmasks ALI in the bleomycin injury model. Rats were randomized and challenged with bleomycin (B) or not (H = healthy). One day after bleomycin instillation the animals were ventilated for 3 h with PEEP 1 (PEEP1) or 5 cmH2O (PEEP5) and a tidal volume of 10 ml/kg bodyweight. Tissue elastance was repetitively measured after a recruitment maneuver to investigate the degree of distal airspace instability. The right lung was subjected to bronchoalveolar lavage (BAL), the left lung was fixed for design-based stereology at light- and electron microscopic level. Prior to mechanical ventilation, lung tissue elastance did not differ. During mechanical ventilation tissue elastance increased in bleomycin-injured lungs ventilated with PEEP = 1 cmH2O but remained stable in all other groups. Measurements at the conclusion of ventilation showed the largest time-dependent increase in tissue elastance after recruitment in B/PEEP1, indicating increased instability of distal airspaces. These lung mechanical findings correlated with BAL measurements including elevated BAL neutrophilic granulocytes as well as BAL protein and albumin in B/PEEP1. Moreover, the increased septal wall thickness and volume of peri-bronchiolar-vascular connective tissue in B/PEEP1 suggested aggravation of interstitial edema by ventilation in presence of microatelectases. At the electron microscopic level, the largest surface area of injured alveolar epithelial was observed in bleomycin-challenged lungs after PEEP = 1 cmH2O ventilation. After bleomycin treatment cellular markers of endoplasmic reticulum stress (p-Perk and p-EIF-2α) were positive within the septal wall and ventilation with PEEP = 1 cmH2O ventilation increased the surface area stained positively for p-EIF-2α. In conclusion, hidden microatelectases are linked with an increased pulmonary vulnerability for mechanical ventilation characterized by an aggravation of epithelial injury.
Alteration of Gut Microbiota in Patients With Epilepsy and the Potential Index as a Biomarker

Objective To explore the structure and composition of the fecal microbiota of patients with epilepsy. Methods Variations in the fecal microbiota between patients with epilepsy and healthy controls (HCs) from the same household were investigated and validated by utilizing 16S ribosomal RNA sequencing in two independent cohorts [exploration cohort (N = 55 patients and N = 46 HCs) and validation cohort (N = 13 patients and N = 10 HCs)]. Results The alpha diversity indexes of the specimens from patients with epilepsy were much lower than those from the HCs (p < 0.05). The structure and composition of the fecal microbiota differed between patients with different clinical prognoses and between patients and HCs (Adonis: p < 0.05). Microbiome alterations in patients with epilepsy included increases in Actinobacteria and Verrucomicrobia and decreases in Proteobacteria at the phylum level and increases in Prevotella_9, Blautia, Bifidobacterium, and others at the genus level [linear discriminant analysis (LDA): 3.5] Patients with drug-resistant epilepsy showed enrichment of bacterial taxa in Actinobacteria, Verrucomicrobia, and Nitrospirae and the genera Blautia, Bifidobacterium, Subdoligranulum, Dialister, and Anaerostipes (Kruskal-Wallis test: p < 0.05). Analysis of gut microbiome indicated predictive ability for disease diagnosis, with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.97 (95% CI, 0.84–0.98). Applying the model to our validation cohort resulted in an AUC of 0.96 (95% CI, 0.75–0.97). Notably, the model could distinguish drug-resistant from drug-sensitive epilepsy (AUC = 0.85, 95% CI: 0.69–0.94). Conclusion Patients with epilepsy exhibit substantial alterations of fecal microbiota composition, and specific gut commensal strains are altered depending on different clinical phenotypes and thus could serve as potential biomarkers for disease diagnosis.
Diverse Bacterial Communities From Qaidam Basin of the Qinghai–Tibet Plateau: Insights Into Variations in Bacterial Diversity Across Different Regions

The Qaidam Basin of the Qinghai–Tibet Plateau is a cold, hyper-arid desert that presents extreme challenges to microbial communities. As little is known about variations between surface and subsurface microbial communities, high-throughput DNA sequencing was used in this study to profile bacterial communities of the soil samples collected at different depths in three regions in the Qaidam Basin. The α-diversity indices (Chao, Shannon, and Simpson) indicated that bacterial abundance and diversity were higher in the east and the high-elevation regions compared to the west region. In general, Firmicutes was dominant in the west region, while Proteobacteria and Acidobacteria were dominant in the east and the high-elevation regions. The structure of the bacterial communities differed greatly across regions, being strongly correlated with total organic carbon (TOC) and total nitrogen (TN) content. The differences in bacterial communities between the surface and the subsurface soil samples were smaller than the differences across the regions. Network analyses of environmental factors and bacterial genera indicated significant positive correlations in all regions. Overall, our study provides evidence that TOC and TN are the best predictors of both surface and subsurface bacterial communities across the Qaidam Basin. This study concludes that the bacterial community structure is influenced by both the spatial distance and the local environment, but environmental factors are the primary drivers of bacterial spatial patterns in the Qaidam Basin.
Propionic Acid Targets the TLR4/NF-κB Signaling Pathway and Inhibits LPS-Induced Intestinal Barrier Dysfunction: In Vitro and In Vivo Studies

Intestinal barrier dysfunction contributes to the development of intestinal diseases. Propionic acid (PA), a metabolite generated by anaerobic fermentation of dietary fiber in the intestinal cavity, has been proved to exert anti-inflammatory effects in a variety of diseases. However, the exact role of PA in LPS-induced intestinal barrier dysfunction is still unclear. Accordingly, we examined the latent mechanism of PA and its protective role in LPS-induced intestinal barrier dysfunction by both in vitro and in vivo experiments. In vitro, we identified that PA treatment could strongly promote cell migration, inhibit activation of NLRP3 inflammasome and maintain intestinal barrier function in LPS-induced IEC-6 cells, indicating the protective effect on the intestinal barrier function of PA. Further investigation of the mechanism involved revealed that PA could suppress the activation of TLR4/NF-κB pathway. In vivo, in a LPS-induced rat model, PA-induced protective effects in intestinal barrier dysfunction could be detected. In summary, our findings clarify the role of PA in intestinal barrier dysfunction and suggest that it is promising for the treatment of LPS-related intestinal diseases.
MicroRNA-7 Targets the KLF4 Gene to Regulate the Proliferation and Differentiation of Chicken Primary Myoblasts

The proliferation and differentiation of chicken primary myoblasts (CPMs) play an important role in the development of skeletal muscle. In our previous research, RNA-seq analysis showed that microRNA-7 (miR-7) was relatively highly expressed in the proliferation phase of CPMs, but its expression level decreased significantly after CPMS-induced differentiation. Meanwhile, the mechanism by which the miR-7 regulates the proliferation and differentiation of CPMs is still unknown. In this study, we found that the expression levels of miR-7 and the Krüppel-like factor 4 (KLF4) gene were negatively correlated during the embryonic phase, and in vitro induced differentiation. A dual-luciferase assay and a rescue experiment show that there is a target relationship between miR-7 and the KLF4 gene. Meanwhile, the results show that overexpression of miR-7 inhibited the proliferation and differentiation of CPMs, while inhibition of miR-7 had the opposite effects. Furthermore, overexpression of the KLF4 gene was found to significantly promote the proliferation and differentiation of CPMs. Conversely, inhibition of the KLF4 gene was able to significantly decrease the proliferation and differentiation of CPMs. Our results demonstrate, for the first time, that miR-7 inhibits the proliferation and differentiation of myoblasts by targeting the KLF4 gene in chicken primary myoblasts.
Rhythmic Physical Activity Intervention: Exploring Feasibility and Effectiveness in Improving Motor and Executive Function Skills in Children

Introduction Increasing literature has emerged investigating the importance of considering the qualitative characteristics of physical activity (PA) interventions and sports as well as considering the role of motor competence in the exercise–cognition interplay. The purpose of this pilot study was to examine the feasibility and effectiveness of a rhythmic PA intervention compared to a standard physical education program, on motor and hot and cool executive function (EF) skills. Methods Children ages 6–11 were enrolled in one of the two programs: a rhythmic program (n = 22) and a physical education program (n = 17), both meeting for 30 min, twice per week, for 7 weeks. The rhythmic program emphasized moving to the beat of music and moving in various rhythmic patterns with whole body movements, clapping, and drumsticks. The children also created their own rhythmic patterns and socially engaged with other children by working in pairs and sharing their routines with the group. The physical education group engaged in ball skills, locomotor patterns, team sports, and moving through stations in small groups, with no emphasis on rhythm. Pretest and posttest measurements included measurement of balance (Movement ABC-2), cool and hot EF (Flanker, SWAN), and social factors, whereas throughout the implementation period data on affective valence, enjoyment, cognitive engagement, perceived exertion, and PA levels were collected at every lesson in both groups. Results The rhythmic program used in this study was feasible, scalable, affordable, and able to be implemented with minimal preparatory time. Children in both groups (rhythmic and physical education) engaged in a similar level of PA and had similar positive experiences from the programs. Both groups improved in balance and cool EF, and there were significant correlations in the change scores between balance and cool EF, as well as between cool EF with hot EF and socio-emotional factors. Discussion This study contributes to the literature by exploring the potential value of rhythmic programs as a vehicle in helping children develop motor and EF skills while deriving joy and positive social interactions from the program.
Big Data and the Little Big Bang: An Epistemological (R)evolution

Starting from an analysis of frequently employed definitions of big data, it will be argued that, to overcome the intrinsic weaknesses of big data, it is more appropriate to define the object in relational terms. The excessive emphasis on volume and technological aspects of big data, derived from their current definitions, combined with neglected epistemological issues gave birth to an objectivistic rhetoric surrounding big data as implicitly neutral, omni-comprehensive, and theory-free. This rhetoric contradicts the empirical reality that embraces big data: (1) data collection is not neutral nor objective; (2) exhaustivity is a mathematical limit; and (3) interpretation and knowledge production remain both theoretically informed and subjective. Addressing these issues, big data will be interpreted as a methodological revolution carried over by evolutionary processes in technology and epistemology. By distinguishing between forms of nominal and actual access, we claim that big data promoted a new digital divide changing stakeholders, gatekeepers, and the basic rules of knowledge discovery by radically shaping the power dynamics involved in the processes of production and analysis of data.
Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico

Oil reservoirs contain microbial populations that are both autochthonously and allochthonously introduced by industrial development. These microbial populations are greatly influenced by external factors including, but not limited to, salinity and temperature. In this study, we used metagenomics to examine the microbial populations within five wells of the same hydrocarbon reservoir system in the Gulf of Mexico. These elevated salinity (149–181 ppt salinity, 4–5× salinity of seawater) reservoirs have limited taxonomic and functional microbial diversity dominated by methanogens, Halanaerobium and other Firmicutes lineages, and contained less abundant lineages such as Deltaproteobacteria. Metagenome assembled genomes (MAGs) were generated and analyzed from the various wells. Methanogen MAGs were closely related to Methanohalophilus euhalobius, a known methylotrophic methanogen from a high salinity oil environment. Based on metabolic reconstruction of genomes, the Halanaerobium perform glycine betaine fermentation, potentially produced by the methanogens. Industrial introduction of methanol to prevent methane hydrate formation to this environment is likely to be consumed by these methanogens. As such, this subsurface oil population may represent influences from industrial processes.
BCIAUT-P300: A Multi-Session and Multi-Subject Benchmark Dataset on Autism for P300-Based Brain-Computer-Interfaces

There is a lack of multi-session P300 datasets for Brain-Computer Interfaces (BCI). Publicly available datasets are usually limited by small number of participants with few BCI sessions. In this sense, the lack of large, comprehensive datasets with various individuals and multiple sessions has limited advances in the development of more effective data processing and analysis methods for BCI systems. This is particularly evident to explore the feasibility of deep learning methods that require large datasets. Here we present the BCIAUT-P300 dataset, containing 15 autism spectrum disorder individuals undergoing 7 sessions of P300-based BCI joint-attention training, for a total of 105 sessions. The dataset was used for the 2019 IFMBE Scientific Challenge organized during MEDICON 2019 where, in two phases, teams from all over the world tried to achieve the best possible object-detection accuracy based on the P300 signals. This paper presents the characteristics of the dataset and the approaches followed by the 9 finalist teams during the competition. The winner obtained an average accuracy of 92.3% with a convolutional neural network based on EEGNet. The dataset is now publicly released and stands as a benchmark for future P300-based BCI algorithms based on multiple session data.
Reactive Oxygen Species Penetrate Persister Cell Membranes of Escherichia coli for Effective Cell Killing

Persister cells are difficult to eliminate because they are tolerant to antibiotic stress. In the present study, using artificially induced Escherichia coli persister cells, we found that reactive oxygen species (ROS) have greater effects on persister cells than on exponential cells. Thus, we examined which types of ROS could effectively eliminate persister cells and determined the mechanisms underlying the effects of these ROS. Ultraviolet (UV) light irradiation can kill persister cells, and bacterial viability is markedly increased under UV shielding. UV induces the production of ROS, which kill bacteria by moving toward the shielded area. Electron spin resonance-based analysis confirmed that hydroxyl radicals are produced by UV irradiation, although singlet oxygen is not produced. These results clearly revealed that ROS sterilizes persister cells more effectively compared to the sterilization of exponential cells (**p < 0.01). These ROS do not injure the bacterial cell wall but rather invade the cell, followed by cell killing. Additionally, the sterilization effect on persister cells was increased by exposure to oxygen plasma during UV irradiation. However, vapor conditions decreased persister cell sterilization by reducing the levels of hydroxyl radicals. We also verified the effect of ROS against bacteria in biofilms that are more resistant than planktonic cells. Although UV alone could not completely sterilize the biofilm bacteria, UV with ROS achieved complete sterilization. Our results demonstrate that persister cells strongly resist the effects of antibiotics and starvation stress but are less able to withstand exposure to ROS. It was shown that ROS does not affect the cell membrane but penetrates it and acts internally to kill persister cells. In particular, it was clarified that the hydroxy radical is an effective sterilizer to kill persister cells.
SMART Work Design: Accelerating the Diagnosis of Rare Diseases in the Western Australian Undiagnosed Diseases Program

The accurate and efficient diagnosis of rare diseases, many of which include congenital anomalies, depends largely on the specialists who diagnose them – including their ability to work alongside specialists from other fields and to take full advantage of cutting-edge precision medicine technologies and precision public health approaches. However, highly specialized clinicians operating within a historically-siloed healthcare system is antithetical to the multi-disciplinary, collaborative, and creative approach that facilitates the diagnosis of rare diseases. The Western Australian Undiagnosed Diseases Program (UDP-WA) successfully re-designed the work of the involved clinicians to facilitate teamworking across silos. To understand the effectiveness of the Western Australian program, we draw on a SMART work design perspective (i.e., work that involves Stimulation, Mastery, Agency, Relations, and Tolerable demands). We propose that the redesign was successful in part because it improved crucial psychosocial work characteristics that are less prevalent in the broader work system, as identified in the SMART model. Based on the effectiveness of UDP-WA and its SMART design, we provide a framework that clinicians, healthcare managers, and policymakers can consider when they re-design work so that they can create SMART jobs within healthcare.
A Database of Chinese-English Bilingual Speakers: Ratings of the Age of Acquisition and Familiarity

Recently, considerable attention has been given to the effect of the age of acquisition (AoA) on learning a second language (L2); however, the scarcity of L2 AoA ratings has limited advancements in this field. We presented the ratings of L2 AoA in late, unbalanced Chinese-English bilingual speakers and collected the familiarity of the L2 and the corresponding Chinese translations of English words. In addition, to promote the cross-language comparison and motivate the AoA research on Chinese two-character words, data on AoA, familiarity, and concreteness of the first language (L1) were also collected from Chinese native speakers. We first reported the reliability of each rated variable. Then, we described the validity by the following three steps: the distributions of each rated variable were described, the correlations between these variables were calculated, and regression analyses were run. The results showed that AoA, familiarity, and concreteness were all significant predictors of lexical decision times. The word database can be used by researchers who are interested in AoA, familiarity, and concreteness in both the L1 and L2 of late, unbalanced Chinese-English bilingual speakers. The full database is freely available for research purposes.
Neural Correlates of Repetition Priming: A Coordinate-Based Meta-Analysis of fMRI Studies

Repetition priming is a form of implicit memory, whereby classification or identification of a stimulus is improved by prior presentation of the same stimulus. Repetition priming is accompanied with a deceased fMRI signal for primed vs. unprimed stimuli in various brain regions, often called “repetition suppression,” or RS. Previous studies proposed that RS in posterior regions is associated with priming of perceptual processes, whereas RS in more anterior (prefrontal) regions is associated with priming of conceptual processes. To clarify which regions exhibit reliable RS associated with perceptual and conceptual priming, we conducted a quantitative meta-analysis using coordinate-based activation likelihood estimation. This analysis included 65 fMRI studies that (i) employed visual repetition priming during either perceptual or conceptual tasks, (ii) demonstrated behavioral priming, and (iii) reported the results from whole-brain analyses. Our results showed that repetition priming was mainly associated with RS in left inferior frontal gyrus and fusiform gyrus. Importantly, RS in these regions was found for both perceptual and conceptual tasks, and no regions show RS that was selective to one of these tasks. These results question the simple distinction between conceptual and perceptual priming, and suggest consideration of other factors such as stimulus-response bindings.
Accounting for Expected Adjusted Effect

The point that adjustment for confounders do not always guarantee protection against spurious findings and type 1-errors has been made before. The present simulation study indicates that for traditional regression methods, this risk is accentuated by a large sample size, low reliability in the measurement of the confounder, and high reliability in the measurement of the predictor and the outcome. However, this risk might be attenuated by calculating the expected adjusted effect, or the required reliability in the measurement of the possible confounder, with equations presented in the present paper.
The Effect of Ambiguity Awareness on Second Language Learners’ Prosodic Disambiguation

Three tasks were reported to examine the effect of ambiguity awareness on Chinese-speaking English learners’ use of prosody in resolving prepositional-phrase attachment ambiguity. In the first (Task 1) and second (Task 2) tasks, listeners were not informed of the syntactic ambiguity. In the third task (Task 3), listeners were given the specific information about syntactic ambiguity. The analysis of the overall accuracy rate showed that before receiving specific information about syntactic ambiguity, learners did not detect the ambiguity within the structure and tended to interpret the sentence in a “good-enough” heuristic to reduce the computational burden. After being aware of the syntactic ambiguity, they could use prosodic cues to resolve the ambiguity. However, the finding that the learners reversed their parsing bias from verb phrase attachment (VP-attachment) toward noun phrase attachment (NP-attachment) indicated their difficulty in integrating prosodic information to syntactic structure efficiently. The analysis of individual accuracy rate demonstrated learners’ individual variations in using prosodic cues. The result suggests that learners’ failure to use prosodic cues may be attributed to a lack of ambiguity awareness and difficulty in information integration, rather than their low sensitivity to prosodic cues.