Miracle-dz/UniFAR-FTUs huggingface dataset:
Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis

Aim: Clostridia are relevant commensals of the human gut due to their major presence and correlations to the host. In this study, we investigated intestinal Clostridia of 51 healthy subjects and reconstructed their taxonomy and phylogeny. The relatively small number of intestinal Clostridia allowed a systematic whole genome approach based on average amino acid identity (AAI) and core genome with the aim of revising the current classification into genera and determining evolutionary relationships. Methods: 51 healthy subjects’ metagenomes were retrieved from public databases. After the dataset’s validation through comparison with Human Microbiome Project (HMP) samples, the metagenomes were profiled using MetaPhlAn3 to identify the population ascribed to the class Clostridia. Intestinal Clostridia genomes were retrieved and subjected to AAI analysis and core genome identification. Phylogeny investigation was conducted with RAxML and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithms, and SplitsTree for split decomposition. Results: 225 out of 406 bacterial taxonomic units were ascribed to Bacillota [Firmicutes], among which 124 were assigned to the class Clostridia. 77 out of the 124 taxonomic units were referred to a species, altogether covering 87.7% of Clostridia abundance. According to the lowest AAI genus boundary set at 55%, 15 putative genera encompassing more than one species (G1 to G15) were identified, while 19 species did not cluster with any other one and each appeared to belong to a diverse genus. Phylogenetic investigations highlighted that most of the species clustered into three main evolutive clades. Conclusion: This study shed light on the species of Clostridia colonizing the gut of healthy adults and pinpointed several gaps in knowledge regarding the taxonomy and the phylogeny of Clostridia.
Automated Industrial Composite Fiber Orientation Inspection Using Attention-Based Normalized Deep Hough Network

Fiber-reinforced composites (FRC) are widely used in various fields due to their excellent mechanical properties. The mechanical properties of FRC are significantly governed by the orientation of fibers in the composite. Automated visual inspection is the most promising method in measuring fiber orientation, which utilizes image processing algorithms to analyze the texture images of FRC. The deep Hough Transform (DHT) is a powerful image processing method for automated visual inspection, as the “line-like” structures of the fiber texture in FRC can be efficiently detected. However, the DHT still suffers from sensitivity to background anomalies and longline segments anomalies, which leads to degraded performance of fiber orientation measurement. To reduce the sensitivity to background anomalies and longline segments anomalies, we introduce the deep Hough normalization. It normalizes the accumulated votes in the deep Hough space by the length of the corresponding line segment, making it easier for DHT to detect short, true “line-like” structures. To reduce the sensitivity to background anomalies, we design an attention-based deep Hough network (DHN) that integrates attention network and Hough network. The network effectively eliminates background anomalies, identifies important fiber regions, and detects their orientations in FRC images. To better investigate the fiber orientation measurement methods of FRC in real-world scenarios with various types of anomalies, three datasets have been established and our proposed method has been evaluated extensively on them. The experimental results and analysis prove that the proposed methods achieve the competitive performance against the state-of-the-art in F-measure, Mean Absolute Error (MAE), Root Mean Squared Error (RMSE).
Atom localization via electromagnetically induced transparency

We propose a simple scheme of atom localization based on probe absorption in which the atom interacts with a classical standing-wave field. By employing a three-level A system, it is shown that the position of an atom inside the standing-wave field depends on the detuning of the coupling field, detuning of the probe laser field, and the position-dependent Rabi frequency of the coupling field.
Learning Behavior Trees From Planning Experts Using Decision Tree and Logic Factorization

The increased popularity of Behavior Trees (BTs) in different fields of robotics requires efficient methods for learning BTs from data instead of tediously handcrafting them. Recent research in learning from demonstration reported encouraging results that this letter extends, improves and generalizes to arbitrary planning domains. We propose BT-Factor as a new method for learning expert knowledge by representing it in a BT. Execution traces of previously manually designed plans are used to generate a BT employing a combination of decision tree learning and logic factorization techniques originating from circuit design. We test BT-Factor in an industrially-relevant simulation environment from a mining scenario and compare it against a state-of-the-art BT learning method. The results show that our method generates compact BTs easy to interpret, and capable to capture accurately the relations that are implicit in the training data.
Low Pre-Season Hamstring-to-Quadriceps Strength Ratio Identified in Players Who Further Sustained In-Season Hamstring Strain Injuries: A Retrospective Study from a Brazilian Serie A Team

A common pre-season injury prevention assessment conducted by professional football clubs is the hamstring-to-quadriceps (H:Q) strength ratio calculated by peak torque (PT). However, it is debatable whether players that present low pre-season H:Q ratios are more susceptible to further sustaining in-season hamstring strain injuries (HSI). Based upon retrospective data from a Brazilian Serie A football squad, a particular season came to our attention as ten out of seventeen (~59%) professional male football players sustained HSI. Therefore, we examined the pre-season H:Q ratios of these players. H:Q conventional (CR) and functional (FR) ratios, and the respective knee extensor/flexor PT from the limbs of players further sustaining in-season HSI (injured players, IP) were compared to the proportional number of dominant/non-dominant limbs from uninjured players (UP) in the squad. FR and CR were ~18–22% lower (p < 0.01), whereas quadriceps concentric PT was ~25% greater for IP than UP (p = 0.002). Low scores of FR and CR were correlated (p < 0.01) with high levels of quadriceps concentric PT (r = −0.66 to −0.77). In conclusion, players who sustained in-season HSI had lower pre-season FR and CR compared to UP, which appears to be associated with higher levels of quadriceps concentric torque than hamstring concentric or eccentric torque.
Nonpolar III-nitride vertical-cavity surface-emitting laser with a photoelectrochemically etched air-gap aperture

We demonstrate a III-nitride nonpolar vertical-cavity surface-emitting laser (VCSEL) with a photoelectrochemically (PEC) etched aperture. The PEC lateral undercut etch is used to selectively remove the multi-quantum well (MQW) region outside the aperture area, defined by an opaque metal mask. This PEC aperture (PECA) creates an air-gap in the passive area of the device, allowing one to achieve efficient electrical confinement within the aperture, while simultaneously achieving a large index contrast between core of the device (the MQW within the aperture) and the lateral cladding of the device (the air-gap formed by the PEC etch), leading to strong lateral confinement. Scanning electron microscopy and focused ion-beam analysis is used to investigate the precision of the PEC etch technique in defining the aperture. The fabricated single mode PECA VCSEL shows a threshold current density of ∼22 kA/cm2 (25 mA), with a peak output power of ∼180 μW, at an emission wavelength of 417 nm. The near-field emission p.
Considerations for at-home upper-limb rehabilitation technology following stroke: Perspectives of stroke survivors and therapists

Introduction This study investigated the needs of stroke survivors and therapists, and how they may contrast, for the design of robots for at-home post stroke rehabilitation therapy, in the Ontario, Canada, context. Methods Individual interviews were conducted with stroke survivors (n = 10) and therapists (n = 6). The transcripts were coded using thematic analysis inspired by the WHO International Classification of Functioning, Disability, and Health. Results Design recommendations, potential features, and barriers were identified from the interviews. Stroke survivors and therapists agreed on many of the needs for at-home robotic rehabilitation; however, stroke survivors had more insights into their home environment, barriers, and needs relating to technology, while therapists had more insights into therapy methodology and patient safety and interaction. Both groups felt a one-size-fits-all approach to rehabilitation robot design is inappropriate. Designs could address a broader range of impairments by incorporating household items and breaking activities down into their component motions. Designs should incorporate hand and wrist supports and activities. Designs should monitor trunk and shoulder motion and consider incorporating group activities. Conclusion While therapists can provide insight in the early stages of design of rehabilitation technology, stroke survivors’ perspectives are crucial to designing for the home environment.
Vasorelaxant Effect of Moroccan Cannabis sativa Threshing Residues on Rat Mesenteric Arterial Bed is Endothelium and Muscarinic Receptors Dependent

Introduction Ethanolic fraction of Moroccan Cannabis sativa threshing residues (EFCS) was evaluated for its vasorelaxant activity. The current work aims to identify the active metabolites in the ethanolic fraction of the EFCS and illustrate their mechanism of action. Methods Free radical scavenging capacity of EFCS was assessed using DPPH method. The EFCS vasodilation activities in phenylephrine-precontracted isolated rat mesenteric arterial beds were investigated in presence of L-NAME (nitric oxide synthase inhibitor), indomethacin (cyclooxygenase inhibitor), potassium channel blockers (namely tetraetylamonium, barium chloride, and glibenclamide), and atropine. Nitric oxide vascular release was measured by electron paramagnetic resonance (EPR) using a spin trap in rat aortic rings. Results EFCS induced dose-dependent vasorelaxation on mesenteric vascular bed. Incubation of the preparations with L-NAME, ODQ (a soluble guanylyl cyclase inhibitor), or potassium channel blockers reduced the fall of perfusion pressure caused by EFCS. Endothelial denudation or atropine abolished the EFCS's vasorelaxant effect, suggesting involvement of muscarinic receptors and endothelium-relaxing factors. The extract induced nitric oxide release in aortic rings in a similar manner as acetylcholine suggesting an effect of EFCS on the muscarinic receptor and the conductance arteries. Chemical investigation of EFCS identified potential active components namely apigenin and derivatives of luteolin skeleton and also additional components such as neophytadiene, squalene, and β-sitosterol. In conclusion, the vasorelaxant effect of EFCS on rat mesenteric arterial bed, which is dependent of muscarinic receptor activation, nitric oxide, and EDHF, can account for potential therapeutic use against high blood pressure related cardiovascular diseases.
Design and Implementation of a Time-Restricted Eating Intervention in a Randomized, Controlled Eating Study

The efficacy of time-restricted eating for weight loss has not been established, as prior studies were limited by a lack of controlled isocaloric designs. This study describes the design and implementation of interventions in a controlled eating study evaluating time-restricted eating. We designed a randomized, controlled, parallel-arm eating study comparing time-restricted eating (TRE) to a usual eating pattern (UEP) for the primary outcome of weight change. Participants were aged 21–69 years with prediabetes and obesity. TRE consumed 80% of calories by 1300 h (military time), and UEP consumed ≥ 50% of calories after 1700 h (military time). Both arms consumed identical macro- and micro-nutrients based on a healthy, palatable diet. We calculated individual calorie requirements, which were maintained throughout the intervention. The desired distribution of calories across eating windows in both arms was achieved, as were the weekly averages for macronutrients and micronutrients. We actively monitored participants and adapted diets to facilitate adherence. We provide the first report, to our knowledge, on the design and implementation of eating study interventions that isolated the effect of meal timing on weight while maintaining constant caloric intake and identical diets during the study period.
An Adaptive Fast Non Local Image Denoising Algorithm

This paper makes some improvements on Non Local Means(NL-Means) image denoising algorithm.A quantitative method is given to estimate the optimal filter parameter h.Noise variance is estimated from noise image,and h parameter is estimated from this variance and noise image standard deviation.Based on the symmetry of weighted Euclidean distance,the most complex distance computation was halved for every pair of pixels,so the computation complexity was reduced to about half of original NL-Means without performance decline.Experimental results on several images show that our adaptive non local means algorithm(ANL-Means) gives nearly best performance with only about half computation time if using original NL-Means.
Regulation of nerve cells using conductive nanofibrous scaffolds for controlled release of Lycium barbarum polysaccharides and nerve growth factor

Abstract Currently, more and more patients suffer from peripheral nerve injury due to trauma, tumor and other causes worldwide. Biomaterial-based nerve conduits are increasingly recognized as a potential alternative to nerve autografts for the treatment of peripheral nerve injury. However, an ideal nerve conduit must offer topological guidance and biochemical and electrical signal transduction mechanisms. In this work, aligned conductive nanofibrous scaffolds comprising polylactic-co-glycolic acid and multiwalled carbon nanotubes (MWCNTs) were fabricated via coaxial electrospinning, and nerve growth factor (NGF) and Lycium barbarum polysaccharides (LBP) purified from the wolfberry were loaded on the core and shell layers of the nanofibers, respectively. LBP were confirmed to accelerate long-distance axon regeneration after severe peripheral nerve injury. In addition, the synergistic promotion of LBP and NGF on nerve cell proliferation and neurite outgrowth was demonstrated. MWCNTs were introduced into the aligned fibers to further increase the electrical conductivity, which promoted the directional growth and neurite extension of neurons in vitro. Further, the combination of conductive fibrous scaffolds with electrical stimulation that mimics endogenous electric fields significantly promoted the differentiation of PC12 cells and the axon outgrowth of neurons. Based on robust cell-induced behaviors, conductive composite fibers with optimized fiber alignment may be used for the promotion of nerve recovery.
Decentralized Inverse Transparency With Blockchain

Employee data can be used to facilitate work, but their misusage may pose risks for individuals. Inverse transparency therefore aims to track all usages of personal data, allowing individuals to monitor them to ensure accountability for potential misusage. This necessitates a trusted log to establish an agreed-upon and non-repudiable timeline of events. The unique properties of blockchain facilitate this by providing immutability and availability. For power asymmetric environments such as the workplace, permissionless blockchain is especially beneficial as no trusted third party is required. Yet, two issues remain: (1) In a decentralized environment, no arbiter can facilitate and attest to data exchanges. Simple peer-to-peer sharing of data, conversely, lacks the required non-repudiation. (2) With data governed by privacy legislation such as the GDPR, the core advantage of immutability becomes a liability. After a rightful request, an individual’s personal data need to be rectified or deleted, which is impossible in an immutable blockchain. To solve these issues, we present Kovacs , a decentralized data exchange and usage logging system for inverse transparency built on blockchain. Its new-usage protocol ensures non-repudiation, and therefore accountability, for inverse transparency. Its one-time pseudonym generation algorithm guarantees unlinkability and enables proof of ownership, which allows data subjects to exercise their legal rights regarding their personal data. With our implementation, we show the viability of our solution. The decentralized communication impacts performance and scalability, but exchange duration and storage size are still reasonable. More importantly, the provided information security meets high requirements. We conclude that Kovacs realizes decentralized inverse transparency through secure and GDPR-compliant use of permissionless blockchain.
Effects of Drought and Flooding on Phytohormones and Abscisic Acid Gene Expression in Kiwifruit

Environmental extremes, such as drought and flooding, are becoming more common with global warming, resulting in significant crop losses. Understanding the mechanisms underlying the plant water stress response, regulated by the abscisic acid (ABA) pathway, is crucial to building resilience to climate change. Potted kiwifruit plants (two cultivars) were exposed to contrasting watering regimes (water logging and no water). Root and leaf tissues were sampled during the experiments to measure phytohormone levels and expression of ABA pathway genes. ABA increased significantly under drought conditions compared with the control and waterlogged plants. ABA-related gene responses were significantly greater in roots than leaves. ABA responsive genes, DREB2 and WRKY40, showed the greatest upregulation in roots with flooding, and the ABA biosynthesis gene, NCED3, with drought. Two ABA-catabolic genes, CYP707A i and ii were able to differentiate the water stress responses, with upregulation in flooding and downregulation in drought. This study has identified molecular markers and shown that water stress extremes induced strong phytohormone/ABA gene responses in the roots, which are the key site of water stress perception, supporting the theory kiwifruit plants regulate ABA to combat water stress.
Home-Based Preoperative Exercise Training for Lung Cancer Patients Undergoing Surgery: A Feasibility Trial

Background: Clinical guidelines recommend prehabilitation with exercise training to optimize recovery after lung cancer surgery. However, the lack of access to facility-based exercise programs is a major barrier to routine participation. This study aimed to assess the feasibility of a home-based exercise intervention before lung cancer resection. Methods: We conducted a prospective, two-site feasibility study, including patients scheduled for lung cancer surgery. Exercise prescription involved aerobic and resistance training with telephone-based supervision. The primary endpoint was overall feasibility (recruitment rate, retention rate, intervention adherence and acceptability). Secondary endpoints included safety and effects on health-related quality of life (HRQOL) and physical performance, evaluated at baseline, after the exercise intervention and 4–5 weeks after surgery. Results: Over three months, 15 patients were eligible, and all agreed to participate (recruitment rate: 100%). A total of 14 patients completed the exercise intervention, and 12 patients were evaluated postoperatively (retention rate: 80%). The median length of the exercise intervention was 3 weeks. Patients performed an aerobic and resistance training volume higher than prescribed (median adherence rates of 104% and 111%, respectively). A total of nine adverse events occurred during the intervention (Grade 1, n = 8; Grade 2, n = 1), the most common being shoulder pain. After the exercise intervention, significant improvements were observed in the HRQOL summary score (mean difference, 2.9; 95% confidence interval [CI], from 0.9 to 4.8; p = 0.049) and the five-times sit-to-stand test score (median difference, −1.5; 95% CI, from −2.1 to −0.9; p = 0.001). After surgery, no significant effects on HRQOL and physical performance were observed. Conclusion: A short-term preoperative home-based exercise intervention is feasible before lung cancer resection and may enhance accessibility to prehabilitation. Clinical effectiveness should be investigated in future studies.
Diagnosing Primary Students’ Reading Progression: Is Cognitive Diagnostic Computerized Adaptive Testing the Way Forward?

Cognitive diagnostic computerized adaptive testing (CD-CAT) is a cutting-edge technology in educational measurement that targets at providing feedback on examinees’ strengths and weaknesses while increasing test accuracy and efficiency. To date, most CD-CAT studies have made methodological progress under simulated conditions, but little has applied CD-CAT to real educational assessment. The present study developed a Chinese reading comprehension item bank tapping into six validated reading attributes, with 195 items calibrated using data of 28,485 second to sixth graders and the item-level cognitive diagnostic models (CDMs). The measurement precision and efficiency of the reading CD-CAT system were compared and optimized in terms of crucial CD-CAT settings, including the CDMs for calibration, item selection methods, and termination rules. The study identified seven dominant reading attribute mastery profiles that stably exist across grades. These major clusters of readers and their variety with grade indicated some sort of reading developmental mechanisms that advance and deepen step by step at the primary school level. Results also suggested that compared to traditional linear tests, CD-CAT significantly improved the classification accuracy without imposing much testing burden. These findings may elucidate the multifaceted nature and possible learning paths of reading and raise the question of whether CD-CAT is applicable to other educational domains where there is a need to provide formative and fine-grained feedback but where there is a limited amount of test time.
Determination of the focused beam waist of lasers with weak measurements

In this Letter, a method for detecting the focused beam waist of lasers is proposed by using weak measurements based on the so-called weak-value amplification. We establish a propagation model to describe the quantitative relation between the beam waist and the amplified shift of the spin Hall effect of light(SHEL), which is sensitive to the variation of the beam waist. We experimentally measure the amplified shift corresponding to a different beam waist and the experimental data agrees well with theoretical calculation. These results confirm the rationality and feasibility of our method.