Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Paracoccidioides brasiliensis by gold nanoprobes

Paracoccidioides brasiliensis (P. brasiliensis) is a thermal dimorphic fungus and causal agent of paracoccidioidomycosis. Epidemiological data shows that it is mainly concentrated in Central and South America countries, with most registered cases in Colombia, Brazil, and Venezuela. The histopathological similarity with others fungal infection makes the diagnosis of P. brasiliensis more complicated. Therefore, the aim of this work was to find a positive and negative test for P. brasiliensis using gold nanoprobes as a new tool for P. brasiliensis detection. Gold nanoparticles were synthesized by reduction of gold chloride with sodium citrate. The results of this procedure is a wine-red solution with a maximum absorption in the range of ~520-530nm. A specific P. brasiliensis sequence of oligonucleotide was bonded to the nanoparticles, which maintained the wine-red color. The color changes from red to blue for negative diagnostic and is unchanged for a positive test. The H-bond interaction of DNA with the complementary DNA keeps strands together and forms double helical structure, maintaining the colloid stability. However, for non-complimentary DNA sequence the nanoprobes merge into a cluster, changing the light absorption.
Microbioreactors for nutrient‐controlled microbial cultures: Bridging the gap between bioprocess development and industrial use

It is common practice in the development of bioprocesses to genetically modify a microorganism and study a large number of resulting mutants in order to select the ones that perform best for use at the industrial scale. At industrial scale, strict nutrient‐controlled growth conditions are imposed to control the metabolic activity and growth rate of the microorganism, thereby enhancing the expression of the product of interest. Although it is known that microorganisms that perform best under these strictly controlled conditions are not the same as the ones that perform best under uncontrolled batch conditions, screening, and selection is predominantly performed under batch conditions. Tools that afford high throughput on the one hand and dynamic control over cultivation conditions on the other hand are not yet available. Microbioreactors offer the potential to address this problem, resolving the gap between bioprocess development and industrial scale use. In this review, we highlight the current state‐of‐the‐art of microbioreactors that offer the potential to screen microorganisms under dynamically controlled conditions. We classify them into: (i) microtiter plate‐based platforms, (ii) microfluidic chamber‐based platforms, and (iii) microfluidic droplet‐based platforms. We conclude this review by discussing the opportunities of nutrient‐fed microbioreactors in the field of biotechnology.
Improvement of Turbine Vane Film Cooling Performance by Double Flow-Control Devices

This study deals with the studies of the effect of flow control double device (DFCD) on a turbine vane film cooling. Aiming for improving film effectiveness, two semi-elliptical DFCDs per a pitch were attached obliquely upstream of the cooling hole. Since the DFCDs were applied to flat plate film cooling in the previous study, the applicability to the turbine vane was investigated in this study. In order to observe a flow field in detail, RANS CFD was conducted first. The DFCDs were installed upstream of each cooling hole of the pressure and suction sides of the vane to investigate the effect of the device position. In this paper, the effects of blowing ratio and cooling hole pitch were also investigated. The results obtained by CFD showed that the vortex generated from DFCD suppressed lift off of the secondary air. As a result, the film effectiveness became significantly higher than that without DFCD condition at high blowing ratio. Moreover, the improvement in the film effectiveness by DFCD was observed by both of the pressure and suction sides of the turbine vane. Based on the findings through RANS simulation, adiabatic effectiveness and total pressure loss coefficient measurement were performed in a linear cascade test facility. The experiment confirmed that the film effectiveness improved when DFCDs existed.
Coevolutionary analysis of Forkhead box protein P3 and its physical binary interactors E3 ubiquitin‐protein ligase CHIP, Zfp‐90, and nuclear receptor ROR‐α

Forkhead box protein P3 (FOXP3) is known to orchestrate the development and maintenance of T regulatory cells, a cell population specialized in immune suppression and peripheral immune tolerance. FOXP3 activity is fine‐tuned through its interaction with several protein‐binding partners. By using IntAct database, we retrieved three physical binary interactors: E3 ubiquitin‐protein ligase CHIP, Zfp‐90, and nuclear receptor ROR‐α. Coevolution clusters between FOXP3 and its interactors were identified with the use of iBIS2 algorithm, the iterative version of BIS/BIS2. Most of the coevolving pairs came from some species of monotremes and marsupials, as well as from a group of bats, thus suggesting that protein interactions of FOXP3 with its partners may be changed and/or modulated during mammalian speciation. Furthermore, our analysis would suggest the occurrence of a determinant role of FOXP3 in suppressing pregnancy alloreactions in placental mammals. Similarly, FOXP3, through its interaction with different protein interaction mechanisms, would explain the unique control of inflammatory response to infections in bats. By identifying several inter‐protein clusters between the different protein pairs, our findings may provide a guide for new therapeutic approaches to modulate T regulatory suppression and/or enhance immune tolerance.
APPLICABLE FORM OF FUZZY REASONING BY DNA COMPUTING

With the advent of fuzzy reasoning based on fuzzy logic as proposed by Zadeh there are several domains of science and engineering which have been enriched by its successful applications. Being motivated by the tremendous potentiality of fuzzy reasoning based on fuzzy logic we pick up this tool for its further enhancement. Fuzzy reasoning proposed by Zadeh is extended by Mizumoto and finally there is an applicable form of fuzzy reasoning for development of expert system package under vague and uncertain environment. In this paper we propose an alternative approach to applicable form of fuzzy reasoning by DNA computing with an aim to add a new dimension to the existing applicable form of fuzzy reasoning method by bringing it down to nano scale computing. We replace the logical aspect of fuzzy reasoning by DNA chemistry. To achieve this goal we first fuzzify the synthetic DNA
Biophysical model of muscle spindle encoding

Muscle spindles encode mechanosensory information by mechanisms that remain only partially understood. Their complexity is expressed in mounting evidence of various molecular mechanisms that play essential roles in muscle mechanics, mechanotransduction and intrinsic modulation of muscle spindle firing behaviour. Biophysical modelling provides a tractable approach to achieve more comprehensive mechanistic understanding of such complex systems that would be difficult/impossible by more traditional, reductionist means. Our objective here was to construct the first integrative biophysical model of muscle spindle firing. We leveraged current knowledge of muscle spindle neuroanatomy and in vivo electrophysiology to develop and validate a biophysical model that reproduces key in vivo muscle spindle encoding characteristics. Crucially, to our knowledge, this is the first computational model of mammalian muscle spindle that integrates the asymmetric distribution of known voltage‐gated ion channels (VGCs) with neuronal architecture to generate realistic firing profiles, both of which seem likely to be of great biophysical importance. Results predict that particular features of neuronal architecture regulate specific characteristics of Ia encoding. Computational simulations also predict that the asymmetric distribution and ratios of VGCs is a complementary and, in some instances, orthogonal means to regulate Ia encoding. These results generate testable hypotheses and highlight the integral role of peripheral neuronal structure and ion channel composition and distribution in somatosensory signalling.
Noninvasive respiratory support following extubation in preterm infants

The use of noninvasive respiratory support is widespread in newborn infants with respiratory distress. As the use of noninvasive respiratory support has increased, so too have the number of modes available. Among these modes, low‐flow nasal cannula and nasal continuous positive airway pressure (NCPAP) have been used for a long time and have known efficacy and safety in newborn infants needing respiratory support. High‐flow nasal cannula (HFNC) has been newly introduced, and its efficacy and safety are currently being investigated. Bilevel nasal continuous positive airway pressure and nasal intermittent positive‐pressure ventilation are often used when NCPAP or HFNC therapy fails. More recently, noninvasive neurally adjusted ventilatory assist and noninvasive high‐frequency oscillatory ventilation have been introduced, and their efficacy and safety are currently under evaluation. Comparison of the efficacy and safety among various modes of noninvasive respiratory support after extubation in preterm infants is helping to clarify the position of each mode. The clarification of the strength and characteristics of each device within the same mode will become important as a future direction of noninvasive respiratory support after extubation in such subjects. However, no research has yet reported on long‐term outcomes in preterm infants receiving noninvasive respiratory support after extubation. Therefore, further research is needed to evaluate the long‐term outcomes.
Memory feedback control for linear time-delay system with adaptation to delay parameter

The controller design of linear time delay system with delayed state is derived via compound memory and memoryless feedback. When the delay constant is not precisely known for linear delay system, the feedback control with adaptation to delay parameter is first given. The adaptive controller, which satisfied the requirement of design, is obtained by solving an LMI. Finally an example is presented to show the effectiveness of our results.
Entanglement and the shareability of quantum states

This brief review discusses the problem of determining whether a given quantum state is separable or entangled. I describe an established approach to this problem that is based on the monogamy of entanglement, which is the observation that a pair of quantum systems that are strongly entangled must be uncorrelated with the rest of the world. Unentangled states on the other hand involve correlations that can be shared with many other parties. Checking whether a given quantum state is shareable involves constructing certain symmetric quantum state extensions and I discuss how to do this using a class of optimizations known as semidefinite programs. An attractive feature of this approach is that it generates explicit entanglement witnesses that can be measured to demonstrate the entanglement experimentally. In recent years analysis of this approach has greatly increased our understanding of the complexity of determining whether a given quantum state is entangled and this review aims to give a unified discussion of these developments. Specifically, I describe how to use finite quantum de Finetti theorems to prove that highly shareable states are nearly separable and use these results to understand the computational complexity of the problem. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘50 years of Bell’s theorem’.
Effect of instant surgery compared with traditional management on paediatric complicated acute appendicitis post‐surgery wound: A meta‐analysis

A meta‐analysis study to assess the influence of instant surgery (IS) compared with conservative therapy (CT) on paediatric complicated acute appendicitis (CAA) post‐surgery wounds. A comprehensive literature examination until January 2023 was implemented, and 2098 linked studies were appraised. The picked studies contained 66 674 subjects with paediatric CAA post‐surgery wounds in the picked studies' baseline; 64 643 of them were using IS, and 2031 were using CT. The odds ratio (OR) in addition to 95% confidence intervals (CIs) were used to calculate the consequence of the IS compared with the CT on paediatric CAA post‐surgery wounds using the dichotomous and continuous styles and a fixed or random model. The IS had a significantly higher wound infection (OR, 4.97; 95% CI, 2.35–10.54, P < .001) with moderate heterogeneity (I2 = 57%) compared with the CT in a paediatric CAA post‐surgery wound. However, no significant difference was found between IS and CT in total antibiotic duration (MD, −5.34; 95% CI,−12.67 to −1.98, P = .15) with high heterogeneity (I2 = 95%) in paediatric CAA post‐surgery wounds. The IS had a significantly higher wound infection; however, no significant difference was found in total antibiotic duration compared with the CT in paediatric CAA post‐surgery wounds. Although precautions should be taken when commerce with the consequences because most of the studies picked for this meta‐analysis had low sample sizes.
Ca2+ ions facilitate the organization of the Annexin A2/S100A10 heterotetramer

Annexin A2 (A2) is a member of the Annexin family, which contains Ca2+‐regulated phospholipid‐binding proteins. Annexins associate with S100 proteins to form heterotetramers. The A2/S100A10 heterotetramer (A2t) is the most extensively studied of these heterotetramers. It induces membrane microdomain formation, causes membrane budding, and facilitates proliferation of some cancers. In this work, the first molecular dynamics (MD) study on the complete A2t of 868 amino acids was performed. MD trajectories of more than 600 ns each were generated for complete A2t complexes with and without Ca2+ ions. The outward extension of membrane‐binding residues A2‐K279 and A2‐K281 was shown to be inhibited in the absence of Ca2+ as they were captured by Ca2+‐binding residue D322. F‐actin binding residue A2‐D339 was observed to occupy either an exposed or buried state in the absence of Ca2+, while it only occupied the buried state in the presence of Ca2+. The observed motions of the A2t subunits are highly organized with a strongly correlated central region which is negatively correlated with the periphery of the complex. The central region contains the S100A10 (p11) dimer, A2‐N, and A2‐I, while the periphery contains A2‐II, A2‐III, and A2‐IV. Novel interactions between A2 and p11 were identified. A2 residues outside of A2‐N (K80, R77, E82, and R145) had strong interactions with p11. Residue R145 of A2 may have a significant effect on the dynamics of the system, with its interaction resulting in asymmetric motions of A2. The presented results provide novel insights to inform future experimental studies.
Molecular testing of DNA damage response pathways in prostate cancer patients

Purpose of review Personalizing prostate cancer therapy requires germline and tumor molecular tests that predict who will respond to specific treatments and who may not. The review covers molecular testing of DNA damage response pathways, the first biomarker-driven precision target with clinical utility for treatment selection in patients with castration resistant prostate cancer (CRPC). Recent findings Recurrent somatic and germline variants cause deficiency of the mismatch repair (MMR) or homologous recombination (HR) pathways in about a quarter of CRPC patients. In prospective clinical trials, patients with deleterious variants in the MMR pathway more frequently experience a therapeutic response to immune checkpoint inhibitors (ICI). Similarly, somatic and germline events affecting HR predict response to poly(ADP) ribose polymerase inhibitor (PARPi) therapy. Molecular testing of these pathways currently involves assaying for loss of function variants in individual genes and for the genome-wide consequences of repair deficiency. Summary DNA damage response pathways are the first major area of molecular genetic testing in CRPC settings and offer insights into this new paradigm. Our hope is that eventually an arsenal of molecularly-guided therapies will be developed across many pathways to enable precision medicine options for most men with prostate cancer.
Three unrelated chemoreceptors provide Pectobacterium atrosepticum with a broad‐spectrum amino acid sensing capability

Amino acids are important nutrients and also serve as signals for diverse signal transduction pathways. Bacteria use chemoreceptors to recognize amino acid attractants and to navigate their gradients. In Escherichia coli two likely paralogous chemoreceptors Tsr and Tar detect 9 amino acids, whereas in Pseudomonas aeruginosa the paralogous chemoreceptors PctA, PctB and PctC detect 18 amino acids. Here, we show that the phytobacterium Pectobacterium atrosepticum uses the three non‐homologous chemoreceptors PacA, PacB and PacC to detect 19 proteinogenic and several non‐proteinogenic amino acids. PacB recognizes 18 proteinogenic amino acids as well as 8 non‐proteinogenic amino acids. PacB has a ligand preference for the three branched chain amino acids L‐leucine, L‐valine and L‐isoleucine. PacA detects L‐proline next to several quaternary amines. The third chemoreceptor, PacC, is an ortholog of E. coli Tsr and the only one of the 36 P. atrosepticum chemoreceptors that is encoded in the cluster of chemosensory pathway genes. Surprisingly, in contrast to Tsr, which primarily senses serine, PacC recognizes aspartate as the major chemoeffector but not serine. Our results demonstrate that bacteria use various strategies to sense a wide range of amino acids and that it takes more than one chemoreceptor to achieve this goal.
Prediction-based uncertainty quantification for exchangeable sequences

Prediction has a central role in the foundations of Bayesian statistics and is now the main focus in many areas of machine learning, in contrast to the more classical focus on inference. We discuss that, in the basic setting of random sampling—that is, in the Bayesian approach, exchangeability—uncertainty expressed by the posterior distribution and credible intervals can indeed be understood in terms of prediction. The posterior law on the unknown distribution is centred on the predictive distribution and we prove that it is marginally asymptotically Gaussian with variance depending on the predictive updates, i.e. on how the predictive rule incorporates information as new observations become available. This allows to obtain asymptotic credible intervals only based on the predictive rule (without having to specify the model and the prior law), sheds light on frequentist coverage as related to the predictive learning rule, and, we believe, opens a new perspective towards a notion of predictive efficiency that seems to call for further research. This article is part of the theme issue ‘Bayesian inference: challenges, perspectives, and prospects’.
IMETA: An Interactive Mobile Eye Tracking Annotation Method for Semi-automatic Fixation-to-AOI mapping

Mobile eye tracking studies involve analyzing areas of interest (AOIs) and visual attention to these AOIs to understand how people process visual information. However, accurately annotating the data collected for user studies can be a challenging and time-consuming task. Current approaches for automatically or semi-automatically analyzing head-mounted eye tracking data in mobile eye tracking studies have limitations, including a lack of annotation flexibility or the inability to adapt to specific target domains. To address this problem, we present IMETA, an architecture for semi-automatic fixation-to-AOI mapping. When an annotator assigns an AOI label to a sequence of frames based on the respective fixation points, an interactive video object segmentation method is used to estimate the mask proposal of the AOI. Then, we use the 3D reconstruction of the visual scene created from the eye tracking video to map these AOI masks to 3D. The resulting 3D segmentation of the AOI can be used to suggest labels for the rest of the video, with the suggestions becoming increasingly accurate as more samples are provided by an annotator using interactive machine learning (IML). IMETA has the potential to reduce the annotation workload and speed up the evaluation of mobile eye tracking studies.
WATAA: Web Alternative Text Authoring Assistant for Improving Web Content Accessibility

Alternative (alt) text is essential for people with visual impairments to acquire information about image content through a screen reader. However, collecting images and creating alt text requires time and effort. To deal with this problem, automatically collecting images that have no alt text is essential to ensure that all image content in a web page has their alt text. Additionally, automatic alt text has limitations in accuracy and quality compared to human-created alt text despite the improvements in image recognition and natural language process technology. We present WATAA, a web alt text authoring assistant that collects images containing no alt text and suggests automatic alt text to help human alt text authors improve a web page’s accessibility.
Motivating People to Move More with Personalized Activity and Tip Recommendations: a Randomized Controlled Trial

As current mobile health interventions often suffer from user dropout and a lack of motivation, this study investigates motivation of insufficiently active people when receiving personalized recommendations to move more. We developed a content-based recommender system, based on our two datasets for physical activities and tips to break sedentary behavior with descriptive attributes, implemented in an Android app. A longitudinal user study was conducted with 25 participants over eight weeks, following a randomized controlled trial study design in which the experimental group receives personalized recommendations based on the user’s mood, preference history, and estimated current situation (e.g., work or free time), while the control group receives non-personalized, random recommendations. Our results show that rating feedback was on average . 596 out of 5 stars higher, and motivation to move on average . 929 out of 4 higher in the experimental group. Additionally, 53 participants initially started the study and there was lower dropout after eight weeks in the experimental group. As our results confirm that the experimental group had more motivation to move, we propose integrating our personalization algorithm in future mobile health interventions as a solution to the challenge of keeping users engaged and motivated.
Tuning the energy levels of self-assembled inas quantum dots by rapid thermal annealing

We studied the photoluminescence spectra of rapid-thermal-annealed self-assembled InAs quantum dots at 10 K. For annealing temperatures ranging from 700 to 950 °C, we observed a blueshift in the interband transition energies, a decrease in the intersublevel spacing energies, and a narrowing of photoluminescence linewidths. In this letter, we demonstrate that the tuning of the InAs quantum dots interband transition and intersublevel spacing energies can be achieved by 30 s of rapid thermal annealing. The relation between interband transition energy changes and the intersublevel spacing energies is found to be linear, with a slope close to the ratio of the dots’ height to their diameter.