Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing

Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools. Importance Cultivation is the definitive tool to understand a microorganism’s physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.
Chlorothalonil in a Quartz Sand Soil: Wetting Effects on Sorption Capacity and Bound Residue

Chlorothalonil has been found to persist but not leach in some quartz sandy soils. For this effect to be understood, it is necessary for the numbers of occupied and empty surface sorption sites to be known. This requires that the labile surface sorption capacity θC, which is the total number of sites, be measured. Wetting effects might however, affect θC. The measurement of θC has been done only recently by very few laboratories, and the wetting effects have seldom been investigated. New analytical chemical methods are therefore required. On − line HPLC micro extraction has been used in the present work to develop a method for the titration of chlorothalonil onto the labile surface sorption sites. Two conclusions have been drawn from the measurements. The first is that θC is one to 2 orders of magnitude greater than it is for the previously reported cases. Second, the effect of wetting on bound residue formation reported by Belliveau and Langford (9) has been confirmed. These effects help to explain the b.
APPLICATION OF THE EMBEDDED FIBER OPTIC PROBE IN HIGH EXPLOSIVE DETONATION STUDIES: PBX-9502 AND LX-17

The Embedded Fiber Optic probe directly measures detonation speed continuously in time, without the need to numerically differentiate data, and is a new tool for measuring time-dependent as well as steady detonation speed to high accuracy. It consists of a custom-design optical fiber probe embedded in high explosive. The explosive is detonated and a refractive index discontinuity is produced in the probe at the location of the detonation front by the compression of the detonation. Because this index-jump tracks the detonation front a measurement of the Doppler shift of laser light reflected from the jump makes it possible to continuously measure detonation velocity with high spatial and temporal resolution. We have employed this probe with a Fabry-Perot-type laser Doppler velocimetry system additionally equipped with a special filter for reducing the level of non-Doppler shifted light relative to the signal. This is necessary because the index-jump signal is relatively weak compared to the return expected from a well-prepared surface in the more traditional and familiar example of material interface velocimetry. Our observations were carried out on a number of explosives but this work is focused on our results on PBX-9502 (95% TATB, 5% Kel-F) and LX-17 (92.5% TATB, 7.5% Kel-F) atmore » varying initial charge density. Our measurements reveal a density dependence significantly lower than previous quoted values and lower than theoretical calculations. Our limited data on detonation speed dependence on wave curvature is in reasonable agreement with previous work using more standard methods and confirms deviation from the Wood-Kirkwood theoretical formula. « less
Individual-level Anxiety Detection and Prediction from Longitudinal YouTube and Google Search Engagement Logs

Anxiety disorder is one of the world's most prevalent mental health conditions, arising from complex interactions of biological and environmental factors and severely interfering one's ability to lead normal life activities. Current methods for detecting anxiety heavily rely on in-person interviews, which can be expensive, time-consuming, and blocked by social stigmas. In this work, we propose an alternative method to identify individuals with anxiety and further estimate their levels of anxiety using personal online activity histories from YouTube and the Google Search engine, platforms that are used by millions of people daily. We ran a longitudinal study and collected multiple rounds of anonymized YouTube and Google Search logs from volunteering participants, along with their clinically validated ground-truth anxiety assessment scores. We then developed explainable features that capture both the temporal and contextual aspects of online behaviors. Using those, we were able to train models that (i) identify individuals having anxiety disorder with an average F1 score of 0.83 and (ii) assess the level of anxiety by predicting the gold standard Generalized Anxiety Disorder 7-item scores (ranges from 0 to 21) with a mean square error of 1.87 based on the ubiquitous individual-level online engagement data. Our proposed anxiety assessment framework is cost-effective, time-saving, scalable, and opens the door for it to be deployed in real-world clinical settings, empowering care providers and therapists to learn about anxiety disorders of patients non-invasively at any moment in time.
Deep Manifold Transformation for Dimension Reduction.

Nonlinear dimensionality reduction (NLDR) plays an important role in feature extraction and visualization of high dimensional data. It transforms patterns of interest, or manifolds, in data to regions in a lower-dimensional latent space. When the manifolds are highly complicated, the NLDR transformation has to provide sufficient nonlinearity for downstream tasks. This paper proposes a novel method, called {\em deep manifold transformation} (DMT), to tackle this problem. As a multi-layer neural network, DMT can support a higher degree of nonlinearity than single-layer methods. Continuation strategy is applied during training to address the local minimum problem common in manifold learning algorithms. Such a learned DMT network can generalize to unseen data whereas traditional manifold learning methods only provide an embedding of the training data. Extensive experiments, comparisons, and ablation studies demonstrate that DMT can deliver results superior to UMAP and t-SNE, and other leading manifold-based NLDR methods.
An Agile Approach to Service Innovation: Creating Valuable Service Innovation with Agile Resource Integration

Value creation through service innovation is challenging in complex, changing markets. Agility may be the key to understanding resource integration in dynamic contexts and what drives and enables service innovation. To understand service innovation, 12 interviews were conducted in four innovative companies. This study’s findings indicate that agility links adaptive and creative resource integration efforts in organizations, enabling actors to function smoothly together in dynamic contexts while engaging in disruptive activities. Creative resource integration is experimenting and reusing resources and practices in new contexts for the purpose of improving value creation. In retrospect, creative resource integration activities, which may not be considered innovative in the moment, are labelled as innovation based on aggregation. Being truly innovative requires the ability to be agile by proactively and reactively balancing adaptive and creative resource integration, the drive to constantly improve, and embracing a culture for agility congruent throughout the organization.
Determination of the Solubility, Dissolution Enthalpy, and Entropy of Icariin in Acetone, Acetoacetate, Chloroform, and Light Petroleum

The solubility of icariin in acetone, acetoacetate, chloroform, and light petroleum in the 283.2‐318.2 K range was measured by ultraviolet-visible spectrophotometry. As the temperature increased, the solubility of icariin in the 4 solvents gradually increased. The solubility data correlated with the modified Apelblat equation. The dissolution enthalpy and entropy of icariin were determined using van’t Hoff plots. The dissolution enthalpy and entropy of icariin in the 4 solvents increases as acetone >acetoacetate >chloroform >light petroleum, which can be explained by the difference of the polarity indices between them. The polarity indices of the solvents affect the solubility behavior.
Infection, Sepsis and the Inflammatory Response: Mechanisms and Therapy

Sepsis secondary to bacterial infection remains a significant cause of morbidity and mortality globally. Recent decades have seen the evolution of international collaborations to improve care for these patients and identify areas for research. In this article we discuss the pathophysiology underlying the condition, review the current recommended management strategies, discuss areas of controversy, and highlight the need for ongoing research, particularly in diagnostics.
Identification of EMT-Related Gene Signatures to Predict the Prognosis of Patients With Endometrial Cancer

Background Endometrial cancer (EC) is one of the most common gynecological cancers. Epithelial–mesenchymal transition (EMT) is believed to be significantly associated with the malignant progression of tumors. However, there is no relevant study on the relationship between EMT-related gene (ERG) signatures and the prognosis of EC patients. Methods We extracted the mRNA expression profiles of 543 tumor and 23 normal tissues from The Cancer Genome Atlas database. Then, we selected differentially expressed ERGs (DEERGs) among these mRNAs. Next, univariate and multivariate Cox regression analyses were performed to select the ERGs with predictive ability for the prognosis of EC patients. In addition, risk score models were constructed based on the selected genes to predict patients’ overall survival (OS), progression-free survival (PFS), and disease-free survival (DFS). Finally, nomograms were constructed to estimate the OS and PFS of EC patients, and pan-cancer analysis was performed to further analyze the functions of a certain gene. Results Six OS-, ten PFS-, and five DFS-related ERGs were obtained. By constructing the prognostic risk score model, we found that the OS, PFS, and DFS of the high-risk group were notably poorer. Last, we found that AQP5 appeared in all three gene signatures, and through pan-cancer analysis, it was also found to play an important role in immunity in lower grade glioma (LGG), which may contribute to the poor prognosis of LGG patients. Conclusions We constructed ERG signatures to predict the prognosis of EC patients using bioinformatics methods. Our findings provide a thorough understanding of the effect of EMT in patients with EC and provide new targets and ideas for individualized treatment, which has important clinical significance.
Genetically Different Isolates of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis Induce Differential Responses to Stress in Cassava

Water scarcity negatively impacts global crop yields and climate change is expected to greatly increase the severity of future droughts. The use of arbuscular mycorrhizal fungi (AMF) can potentially mitigate the effects of water stress in plants. Cassava is a crop that feeds approximately 800 million people daily. Genetically different isolates of the AMF R. irregularis as well as their clonal progeny have both been shown to greatly alter cassava growth in field conditions. Given that cassava experiences seasonal drought in many of the regions in which it is cultivated, we evaluated whether intraspecific variation in R. irregularis differentially alters physiological responses of cassava to water stress. In a first experiment, conducted in field conditions in Western Kenya, cassava was inoculated with two genetically different R. irregularis isolates and their clonal progeny. All cassava plants exhibited physiological signs of stress during the dry period, but the largest differences occurred among plants inoculated with clonal progeny of each of the two parental fungal isolates. Because drought had not been experimentally manipulated in the field, we conducted a second experiment in the greenhouse where cassava was inoculated with two genetically different R. irregularis isolates and subjected to drought, followed by re-watering, to allow recovery. Physiological stress responses of cassava to drought differed significantly between plants inoculated with the two different fungi. However, plants that experienced higher drought stress also recovered at a faster rate following re-watering. We conclude that intraspecific genetic variability in AMF significantly influences cassava physiological responses during water stress. This highlights the potential of using naturally existing variation in AMF to improve cassava tolerance undergoing water stress. However, the fact that clonal progeny of an AMF isolate can differentially affect how cassava copes with natural drought stress in field conditions, highlights the necessity to understand additional factors, beyond genetic variation, which can account for such large differences in cassava responses to drought.
Build with intrinsic security: Trusted autonomy security system

Security of Internet of things network is difficult to manage because Internet of things devices are heterogeneous and always deployed in remote places. Based on these features, attacks against Internet of things network like distributed denial-of-service and system intrusion are easier than traditional network. In order to enhance Internet of things network’s security, in this article we propose the concept of intrinsic security to establish a trusted and autonomy Internet of things network. Intrinsic security emphasizes that network itself must be trusted and security autonomous to address the security problems which are caused by remote and heterogeneous. Based on this thought, we designed the architecture of Trusted Autonomy Security System. Trusted Autonomy Security System maintains a LAN characterized by trusted and security autonomy, in which all Internet of things network gateways formed a decentralized autonomy system to evaluate if other gateways or Internet of things devices are secure. Compared to traditional Internet of things networks, this architecture uses trusted computing technique to build the basic of security, and makes Internet of things network available to manage security automatically. In addition, the decentralized architecture could reduce security risks caused by compromise of single node in Internet of things network. With these advantages, it can be expected that this novel idea will have more development in Internet of things scenarios with high security requirements.
Tumor-Associated Neutrophils and Macrophages—Heterogenous but Not Chaotic

Tumor-associated macrophages (TAMs) and tumor-associated neutrophils (TANs) have been extensively studied. Their pleotropic roles were observed in multiple steps of tumor progression and metastasis, and sometimes appeared to be inconsistent across different studies. In this review, we collectively discussed many lines of evidence supporting the mutual influence between cancer cells and TAMs/TANs. We focused on how direct interactions among these cells dictate co-evolution involving not only clonal competition of cancer cells, but also landscape shift of the entire tumor microenvironment (TME). This co-evolution may take distinct paths and contribute to the heterogeneity of cancer cells and immune cells across different tumors. A more in-depth understanding of the cancer-TAM/TAN co-evolution will shed light on the development of TME that mediates metastasis and therapeutic resistance.
The Epigenetics of Glioma Stem Cells: A Brief Overview

Glioma stem cells (GSCs) are crucial in the formation, perpetuation and recurrence of glioblastomas (GBs) due to their self-renewal and proliferation properties. Although GSCs share cellular and molecular characteristics with neural stem cells (NSCs), GSCs show unique transcriptional and epigenetic features that may explain their relevant role in GB and may constitute druggable targets for novel therapeutic approaches. In this review, we will summarize the most important findings in GSCs concerning epigenetic-dependent mechanisms.
Citizen Science, Education, and Learning: Challenges and Opportunities

Citizen science is a growing field of research and practice, generating new knowledge and understanding through the collaboration of citizens in scientific research. As the field expands, it is becoming increasingly important to consider its potential to foster education and learning opportunities. Although progress has been made to support learning in citizen science projects, as well as to facilitate citizen science in formal and informal learning environments, challenges still arise. This paper identifies a number of dilemmas facing the field—from competing scientific goals and learning outcomes, differing underlying ontologies and epistemologies, diverging communication strategies, to clashing values around advocacy and activism. Although such challenges can become barriers to the successful integration of citizen science into mainstream education systems, they also serve as signposts for possible synergies and opportunities. One of the key emerging recommendations is to align educational learning outcomes with citizen science project goals at the planning stage of the project using co-creation approaches to ensure issues of accessibility and inclusivity are paramount throughout the design and implementation of every project. Only then can citizen science realise its true potential to empower citizens to take ownership of their own science education and learning.
Skin Immunity to Dermatophytes: From Experimental Infection Models to Human Disease

Dermatophytoses (ringworms) are among the most frequent skin infections and are a highly prevalent cause of human disease worldwide. Despite the incidence of these superficial mycoses in healthy people and the compelling evidence on chronic and deep infections in immunocompromised individuals, the mechanisms controlling dermatophyte invasion in the skin are scarcely known. In the last years, the association between certain primary immunodeficiencies and the susceptibility to severe dermatophytosis as well as the evidence provided by novel experimental models mimicking human disease have significantly contributed to deciphering the basic immunological mechanisms against dermatophytes. In this review, we outline the current knowledge on fungal virulence factors involved in the pathogenesis of dermatophytoses and recent evidence from human infections and experimental models that shed light on the cells and molecules involved in the antifungal cutaneous immune response. The latest highlights emphasize the contribution of C-type lectin receptors signaling and the cellular immune response mediated by IL-17 and IFN-γ in the anti-dermatophytic defense and skin inflammation control.
Application of Referencing Techniques in EEG-Based Recordings of Contact Heat Evoked Potentials (CHEPS)

Evoked potentials in the amplitude-time spectrum of the electroencephalogram are commonly used to assess the extent of brain responses to stimulation with noxious contact heat. The magnitude of the N- and P-waves are used as a semi-objective measure of the response to the painful stimulus: the higher the magnitude, the more painful the stimulus has been perceived. The strength of the N-P-wave response is also largely dependent on the chosen reference electrode site. The goal of this study was to examine which reference technique excels both in practical and theoretical terms when analyzing noxious contact heat evoked potentials (CHEPS) in the amplitude-time spectrum. We recruited 21 subjects (10 male, 11 female, mean age of 55.79 years). We applied seven noxious contact heat stimuli using two temperatures, 51°C, and 54°C, to each subject. During EEG analysis, we aimed to identify the referencing technique which produces the highest N-wave and P-wave amplitudes with as little artifactual influence as possible. For this purpose, we applied the following six referencing techniques: mathematically linked A1/A2 (earlobes), average reference, REST, AFz, Pz, and mathematically linked PO7/PO8. We evaluated how these techniques impact the N-P amplitudes of CHEPS based on our data from healthy subjects. Considering all factors, we found that mathematically linked earlobes to be the ideal referencing site to use when displaying and evaluating CHEPS in the amplitude-time spectrum.
Asymmetry in the Qy Fluorescence and Absorption Spectra of Chlorophyll a Pertaining to Exciton Dynamics

Significant asymmetry found between the high-resolution Qy emission and absorption spectra of chlorophyll-a is herein explained, providing basic information needed to understand photosynthetic exciton transport and photochemical reactions. The Qy spectral asymmetry in chlorophyll has previously been masked by interference in absorption from the nearby Qx transition, but this effect has recently been removed using extensive quantum spectral simulations or else by analytical inversion of absorption and magnetic circular dichroism data, allowing high-resolution absorption information to be accurately determined from fluorescence-excitation spectra. To compliment this, here, we measure and thoroughly analyze the high-resolution differential fluorescence line narrowing spectra of chlorophyll-a in trimethylamine and in 1-propanol. The results show that vibrational frequencies often change little between absorption and emission, yet large changes in line intensities are found, this effect also being strongly solvent dependent. Among other effects, the analysis in terms of four basic patterns of Duschinsky-rotation matrix elements, obtained using CAM-B3LYP calculations, predicts that a chlorophyll-a molecule excited into a specific vibrational level, may, without phase loss or energy relaxation, reemit the light over a spectral bandwidth exceeding 1,000 cm−1 (0.13 eV) to influence exciton-transport dynamics.