Miracle-dz/UniFAR-FTUs huggingface dataset:
Abattoir-based study of Salmonella prevalence in pigs at slaughter in Great Britain

Abstract Consumption of pork and pork products can be associated with outbreaks of human salmonellosis. Salmonella infection is usually subclinical in pigs, and farm-based control measures are challenging to implement. To obtain data on Salmonella prevalence, samples can be collected from pigs during the slaughter process. Here we report the results of a Great Britain (GB) based abattoir survey conducted by sampling caecal contents from pigs in nine British pig abattoirs during 2019. Samples were collected according to a randomised stratified scheme, and pigs originating from 286 GB farms were included in this survey. Salmonella was isolated from 112 pig caecal samples; a prevalence of 32.2% [95% confidence interval (CI) 27.4–37.4]. Twelve different Salmonella serovars were isolated, with the most common serovars being S. 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium (36.6% of Salmonella-positive samples), followed by S. Derby (25.9% of Salmonella-positive samples). There was no significant difference compared to the estimate of overall prevalence (30.5% (95% CI 26.5–34.6)) obtained in the last abattoir survey conducted in the UK (2013). Abattoir-based control measures are often effective in the reduction of Salmonella contamination of carcasses entering the food chain. In this study, the effect of abattoir hygiene practices on the prevalence of Salmonella on carcasses was not assessed. Continuing Salmonella surveillance at slaughter is recommended to assess effect of farm-based and abattoir-based interventions and to monitor potential public health risk associated with consumption of Salmonella-contaminated pork products.
Xylopidimers A–E, Five New Guaiane Dimers with Various Carbon Skeletons from the Roots of Xylopia vielana

Five new guaiane dimers, xylopidimers A–E (1–5), were isolated and identified from the roots of Xylopia vielana. The structures of 1–5 were elucidated by spectroscopic analysis and further confirmed by single-crystal X-ray diffraction. On the basis of the results of single-crystal X-ray analysis, 1–5 showed different carbon skeletons. Among these compounds, the unique connecting patterns of 1 and 2 caused significant differences on their carbon skeletons, which have not been reported. Moreover, 3–5 were also three new guaiane dimers. Among these compounds, 4 exhibited potent inhibitory activity against the production of nitric oxide with an IC50 value of 4.59 μM in RAW264.7 cells stimulated by lipopolysaccharide.
MotionRing: Creating Illusory Tactile Motion around the Head using 360°  Vibrotactile Headbands

We present MotionRing, a vibrotactile headband that creates illusory tactile motion around the head by controlling the timing of a 1-D, 360° sparse array of vibration motors. Its unique ring shape enables symmetric and asymmetric haptic motion experiences, such as when users pass through a medium and when an object passes nearby in any direction. We first conducted a perception study to understand how factors such as vibration motor timing, spacing, duration, intensity, and head region affect the perception of apparent tactile motion. Results showed that illusory tactile motion around the head can be achieved with 12 and 16 vibration motors with angular speed between 0.5-4.9 revolutions per second. We developed a symmetric and an asymmetric tactile motion pattern to enhance the experience of teleportation in VR and dodging footballs, respectively. We conducted a user study to compare the experience of MotionRing vs. static vibration patterns and visual-only feedback. Results showed that illusory tactile motion significantly improved users’ perception of directionality and enjoyment of motion events, and was most preferred by users.
Simultaneous temporal and spatial deep attention for imaged skeleton-based action recognition

The use of skeletons as a modality to represent and recognize human actions has gained interest thanks to the compactness of the data, their reliable representativeness in addition to their strong robustness. The deep learning based recognition approaches which are based on it often propose to improve the recognition pipeline by integrating the concept of attention in their modeling. The idea is to allow the model to focus on the relevant information of the action instead of attempting some kind of blind modeling. In this article, we propose an action recognition approach integrating simultaneously both spatial and temporal attentions. We first perform a transformation of the input sequence data into a color matrix, called imaged skeleton, comprising Cartesian and rotational information. Then, this new representation is given as input to an architecture composed of a main trunk, that allows features extraction and classification, and several attention branches. Different experimental evaluations on two popular benchmark databases, namely UT-Kinect [1] and SBU Kinect Interaction [2], are conducted to verify the interest of our proposed approach, where better performances are reported. Index: convolutional neural network, spatio-temporal, skeleton-based action recognition, deep attention.
Face anti-spoofing by using Feature Fusion

Security issues have attracted more and more attention with the application of face recognition technology. Face anti-spoofing has become an important derivative subject in the current research of face recognition, More and more researchers are devoted to the research of face anti-spoofing by the increase of fake face types. Even face anti-spoofing has been studied from different angles, some of the methods have significant effects, while there are still some deficiencies and can not get satisfactory results, How to effectively distinguish between real faces and fake faces and improve the accuracy of classification is the focus of current research.
Matrix Completion using Block Toeplitz Matrix for Recovering an Incomplete Path-Tracing Image

This paper introduces a novel matrix completion method to recover an incomplete path tracing image using a block Toeplitz matrix (BTM). The BTM provides an efficient numerical approach to create a low rank matrix from a single patch from an input image, which enables the recovery of missing pixels in the patch using matrix completion. Matrix completion is solved using weighted nuclear norm minimization with a parameter adjustment strategy. Previous approaches create a low rank matrix for matrix completion using similar patches across an image for every iteration of the optimization. Our method avoids this similar patch finding and the sophisticated initialization steps by using the BTM, improving the overall performance of matrix completion. We show efficient recovery of missing pixels of an incomplete path tracing image and partially damaged or occluded photograph.
TypeBoard: Identifying Unintentional Touch on Pressure-Sensitive Touchscreen Keyboards

Text input is essential in tablet computer interaction. However, tablet software keyboards face the problem of misrecognizing unintentional touch, which affects efficiency and usability [29, 49]. In this paper, we proposed TypeBoard, a pressure-sensitive touchscreen keyboard that prevents unintentional touches. The TypeBoard allows users to rest their fingers on the touchscreen, which changes the user behavior: on average, users generate 40.83 unintentional touches every 100 keystrokes. The TypeBoard prevents unintentional touch with an accuracy of 98.88%. A typing study showed that the TypeBoard reduced fatigue (p < 0.005) and typing errors (p < 0.01), and improved the touchscreen keyboard’ typing speed by 11.78% (p < 0.005). As users could touch the screen without triggering responses, we added tactile landmarks on the TypeBoard, allowing users to locate the keys by the sense of touch. This feature further improves the typing speed, outperforming the ordinary tablet keyboard by 21.19% (p < 0.001). Results show that pressure-sensitive touchscreen keyboards can prevent unintentional touch, improving usability from many aspects, such as avoiding fatigue, reducing errors, and mediating touch typing on tablets.
The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean

Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase of the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure and UV-protection, nervous system and behavior, organ development, metabolism and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
Extremely thermophilic endospores germinate and metabolise organic carbon in sediments heated to above 80°C

Endospores of thermophilic bacteria are widespread in cold seabed environments where they remain dormant during initial burial in accumulating sediments. The temperature increase during sedimentation can be simulated in experimental heating of sediments, resulting in the temperature-dependent activation of different endospore populations from the microbial seed bank. Here we investigated the response of endospore populations to heating at extreme high temperature (80– 99°C). Metabolites for germination and organic matter degradation (dipicolinic acid and organic acids) revealed both endospore germination and subsequent metabolism at ≥80°C. Endospore-forming Firmicutes with the genomic potential for organic carbon and nitrogen transformation were recovered by genome-resolved metagenomics. Genomes from Symbiobacteriales, Thermosediminibacteriales, Moorellales and Calditerricolales encode multiple mechanisms for high temperature degradation of sedimentary organic carbon and features of necromass that accumulate during sediment burial including saccharides, amino and nucleic acids. The results provide insight into the metabolism of novel carbon cycling microorganisms activated at high temperature, and suggest that extremely thermophilic Firmicutes dispersed in the ocean are poised to germinate in response to sediment heating during burial and transform a wide range of organic substrates.
Application of machine learning methods in clinical trials for precision medicine

Objective A key component for precision medicine is a good prediction algorithm for patients’ response to treatments. We aim to implement machine learning (ML) algorithms into the response-adaptive randomization (RAR) design and improve the treatment outcomes. Materials and Methods We incorporated nine ML algorithms to model the relationship of patient responses and biomarkers in clinical trial design. Such a model predicted the response rate of each treatment for each new patient and provide guidance for treatment assignment. Realizing that no single method may fit all trials well, we also built an ensemble of these nine methods. We evaluated their performance through quantifying the benefits for trial participants, such as the overall response rate and the percentage of patients who receive their optimal treatments. Results Simulation studies showed that the adoption of ML methods resulted in more personalized optimal treatment assignments and higher overall response rates among trial participants. Compared with each individual ML method, the ensemble approach achieved the highest response rate and assigned the largest percentage of patients to their optimal treatments. For the real-world study, we successfully showed the potential improvements if the proposed design had been implemented in the study. Conclusion In summary, the ML-based RAR design is a promising approach for assigning more patients to their personalized effective treatments, which makes the clinical trial more ethical and appealing. These features are especially desirable for late-stage cancer patients who have failed all the FDA-approved treatment options and only can get new treatments through clinical trials.
Identification of sex chromosomes using genomic and cytogenetic methods in a range-expanding spider, Argiope bruennichi (Araneae: Araneidae)

Differences between sexes in growth, ecology and behavior strongly shape species biology. In some animal groups, such as spiders, it is difficult or impossible to identify the sex of juveniles based on external morphology. This information would be useful for field surveys, behavioral experiments, and ecological studies on e.g. sex ratios and dispersal. In species with sex chromosomes, sex can be determined based on the specific sex chromosome complement. Additionally, information on the sequence of sex chromosomes provides the basis for studying sex chromosome evolution. We combined cytogenetic and genomic data to identify the sex chromosomes in the sexually dimorphic spider Argiope bruennichi, and designed RT-qPCR sex markers. We found that genome size and GC content of this spider falls into the range reported for the majority of araneids. The male karyotype is formed by 24 acrocentric chromosomes with an X1X20 sex chromosome system, with little similarity between X chromosomes, suggesting origin of these chromosomes by X chromosome fission or early duplication of an X chromosome and subsequent independent differentiation of the copies. Our data suggest similarly sized X chromosomes in A. bruennichi. They are smaller chromosomes of the complement. Our findings open the door to new directions in spider evolutionary and ecological research.
Cell Adhesion-Dependent Biphasic Axon Outgrowth Elucidated by Femtosecond Laser Impulse

Axon outgrowth is promoted by the mechanical coupling between F-actin and adhesive substrates via clutch and adhesion molecules in an axonal growth cone. In this study, we utilized a femtosecond laser-induced impulse to break the coupling between the growth cone and the substrate, enabling us to evaluate the strength of the binding between the growth cone and a laminin on the substrate, and also determine the contribution of adhesion strength to axon outgrowth and traction force for the outgrowth. We found that the adhesion strength of axonal L1 cell adhesion molecule (L1CAM)-laminin binding increased with the laminin density on the substrate. In addition, fluorescent speckle microscopy revealed that the retrograde flow of F-actin in the growth cone was dependent on the laminin density such that the flow speed reduced with increasing L1CAM-laminin binding. However, axon outgrowth and the traction force did not increase monotonically with increased L1CAM-laminin binding but rather exhibited biphasic behavior, in which the outgrowth was suppressed by excessive L1CAM-laminin binding. Our quantitative evaluations suggest that the biphasic outgrowth is regulated by the balance between traction force and adhesion strength. These results imply that adhesion modulation is key to the regulation of axon guidance.
Assessing the Live Decellularized Renal Microvasculature Post-Transplantation Using Intravital Microscopy

Transplantation is the ideal solution for end-stage renal failure, but the growing mismatch between organ supply and demand accentuates the need for alternative solutions like the bioartificial kidney. Several approaches to developing this technology have been demonstrated, and whole organ decellularization appears to be a promising methodology. One major challenge to this strategy is maintaining vascular integrity and functionality post-transplantation. Most models to examine the microvasculature have primarily utilized in vitro or in vivo techniques that are incapable of providing adequate spatial and temporal resolution. Here, we show that decellularized scaffolds orthotopically transplanted into rats initially retain microvascular structure in vivo using intravital two-photon microscopy, as previously identified in vitro. Large molecular weight dextran molecules also provide real-time evidence of the onset of ischemia and increases in microvascular permeability, support substantial translocation of dextran macromolecules from glomerular and peritubular capillary tracks as early as 12 hours after transplantation. Macromolecular extravasation continued across a week, at which time the decellularized microarchitecture was significantly compromised. These results indicate that a in vivo method capable of tracking microvascular integrity represents a powerful interdisciplinary approach for studying scaffold viability and identifying ways to promote scaffold longevity and angiogenesis in bioartificial organs.
Chapter 8. Role of the Stomach in Anthocyanin Absorption

The influence of dietary flavonoids on human physiology and ageing is a subject of high interest, involving consumers, food producers, the medical community, and the drug industry. Anthocyanins make up a distinct class of flavonoids, conferring orange-to-blue colour to fruits and vegetables. The anthocyanins are among the few known molecules that are absorbed from the stomach and could serve as a case study for a deeper understanding of the physiology of the stomach and the pharmacology of drugs and natural compounds. “Can we identify elements and factors in the anatomy, histology, and physiology of the stomach that may rationally support the concept that some selected compounds can indeed be absorbed from this organ? ” This is the main question that this chapter attempts to address by first providing a description of the multiple levels of structural organisation and functioning of the stomach. Subsequently, it focuses on evidence of gastric absorption of compounds other than anthocyanins in the belief that a given property should be seen as a general rule rather than an exception. If molecules can travel from the lumen to the blood across the gastric mucus and epithelium, then it is useful to consider if these layers act as either barriers or breaches. Finally, reports on gastric absorption of anthocyanins are critically examined with respect to the highlighted aspects of the stomach anatomy and physiology.
Visual Research Methods: Recognising the Social Identities and Behaviour of Non-Smokers and Smokers

Abstract This article presents the visual research methods (VRM), a procedure containing an iterative circle for detecting smokers and non-smokers among adolescents and young adults. Qualitative and quantitative approaches were used to develop the theoretical framework and questionnaires, conduct workshops, content analysis and statistical modelling, and to examine and interpret the results. The visual context that detects smokers and non-smokers concerns the social norms and environment, attitudes, beliefs, role models, individual factors, situational context and healthy vs. unhealthy lifestyle. VRM provide precise results regarding the phenomenon and offer a sympathetic, considerate and suitable way to examine it. The interpretations of the visual context of smoking generates valuable information for smoking prevention methods compared with the traditional verbal questionnaire.
Design and Optimization of a Linear Wavenumber Spectrometer with Cylindrical Optics for Line Scanning Optical Coherence Tomography

We report the design of a high-efficiency spectral-domain spectrometer with cylindrical optics for line scanning optical coherence tomography (OCT). The spectral nonlinearity in k space (wavenumber) lowers the depth-dependent signal sensitivity of the spectrometers. For linearizing, in this design, grating and prism have been introduced. For line scanning, a cylindrical mirror is utilized in the scanning part. Line scanning improves the speed of imaging compared to fly-spot scanning. Line scanning OCT requires a spectrometer that utilizes cylindrical optics. In this work, an optical design of a linear wavenumber spectrometer with cylindrical optics is introduced. While there are many works using grating and prism to linearize the K space spectrometer design, there is no work on linearizing the k-space spectrometer with cylindrical optics for line scanning that provides high sensitivity and high-speed imaging without the need for resampling. The design of the spectrometer was achieved through MATLAB and ZEMAX simulations. The spectrometer design is optimized for the broadband light source with a center wavelength of 830 ± 100 nm (8.607 μm−1− 6.756 μm−1 in k-space). The variation in the output angle with respect to the wavenumber can be mentioned as a nonlinearity error. From our design results, it is observed that the nonlinearity error reduced from 147.0115 to 0.0149 Δθ*μm within the wavenumber range considered. The use of the proposed reflective optics for focusing reduces the chromatic aberration and increases image quality (measured by the Strehl ratio (SR)). The complete system will provide clinicians a powerful tool for real-time diagnosis, treatment, and guidance in surgery with high image quality for in-vivo applications.
Thermal Characterization of New 3D-Printed Bendable, Coplanar Capacitive Sensors

In this paper a new low-cost stretchable coplanar capacitive sensor for liquid level sensing is presented. It has been 3D-printed by employing commercial thermoplastic polyurethane (TPU) and conductive materials and using a fused filament fabrication (FFF) process for monolithic fabrication. The sensor presents high linearity and good repeatability when measuring sunflower oil level. Experiments were performed to analyse the behaviour of the developed sensor when applying bending stimuli, in order to verify its flexibility, and a thermal characterization was performed in the temperature range from 10 °C to 40 °C to evaluate its effect on sunflower oil level measurement. The experimental results showed negligible sensitivity of the sensor to bending stimuli, whereas the thermal characterization produced a model describing the relationship between capacitance, temperature, and oil level, allowing temperature compensation in oil level measurement. The different temperature cycles allowed to quantify the main sources of uncertainty, and their effect on level measurement was evaluated.