Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrete vs continuum level simulations of radiative transfer in semitransparent two-phase media

abstract The mathematical formulation of the continuum approach to radiative transfer model-ing in two-phase semi-transparent media is numerically validated by comparingradiative ﬂuxes computed by (i) direct, discrete-scale and (ii) continuum-scaleapproaches. The analysis is based on geometrical optics. The discrete-scale approachuses the Monte Carlo ray-tracing applied directly to real 3D geometry measured bycomputed tomography. The continuum-scale approach is based on a set of continuum-scale radiative transfer equations and associated radiative properties, and employs theMonte Carlo ray-tracing for computations of radiative ﬂuxes and for computations ofthe radiative properties. The model two-phase media are reticulate porous ceramicsand a particle packed bed, each composed of semitransparent solid and ﬂuid phases.The results obtained by the two approaches are in good agreement within the limits ofstatistical uncertainty. The continuum-scale approach leads to a reduction in computa-tional time by approximately one order of magnitude, and is therefore suited to treatradiative transfer problems in two-phase media in a wide range of engineeringapplications.Published by Elsevier Ltd.
Deprescribing and medicines optimisation, two sides of the same coin? Considerations for design of interventional studies

Interventions to promote deprescribing are an important focus of research. Key decisions for such interventions are whether to target one or multiple medicines, and whether the intervention scope is deprescribing, or also extends to other aspects of medicines optimisation. This article reflects on how these decisions impact on developing interventions and measuring outcomes. Many behavioural strategies are common to deprescribing and medicines optimisation, however operationalisation may differ. Aspects to consider include the burden of multiple simple interventions versus one complex intervention, the extent to which the approach to deprescribing can be specified as part of the intervention, and variability in how the intervention is delivered across patients and providers. Outcomes should be selected based on the intervention target and scope and the audience for whom evidence is being produced. These may include medication changes, and process outcomes to assess intervention delivery. Targeting single medications may allow for a focus on specific clinical or symptom-related outcomes, but a broader perspective may be needed in a generalist setting in the context of multimorbidity and which also considers the patient's priorities. Cost-related outcomes are also important to inform implementation decisions, and modelling approaches may be more feasible for interventions targeting single medications.
PhAT: A Flexible Open‐Source GUI‐Driven Toolkit for Photometry Analysis

Photometry approaches detect sensor‐mediated changes in fluorescence as a proxy for rapid molecular changes within the brain. As a flexible technique with a relatively low cost to implement, photometry is rapidly being incorporated into neuroscience laboratories. Yet, although multiple data acquisition systems for photometry now exist, robust analytical pipelines for the resulting data remain limited. Here we present the Photometry Analysis Toolkit (PhAT)—a free open‐source analysis pipeline that provides options for signal normalization, incorporation of multiple data streams to align photometry data with behavior and other events, calculation of event‐related changes in fluorescence, and comparison of similarity across fluorescent traces. A graphical user interface (GUI) enables use of this software without prior coding knowledge. In addition to providing foundational analytical tools, PhAT is designed to readily incorporate community‐driven development of new modules for more bespoke analyses, and enables data to be easily exported to enable subsequent statistical testing and/or code‐based analyses. In addition, we provide recommendations regarding technical aspects of photometry experiments, including sensor selection and validation, reference signal considerations, and best practices for experimental design and data collection. We hope that the distribution of this software and protocols will lower the barrier to entry for new photometry users and improve the quality of collected data, increasing transparency and reproducibility in photometry analyses. © 2023 Wiley Periodicals LLC.
A gene‐nutrient interaction between vitamin B6 and serine hydroxymethyltransferase (SHMT) affects genome integrity in Drosophila

Pyridoxal 5′‐phosphate (PLP), the catalytically active form of vitamin B6, participates as a cofactor to one carbon (1C) pathway that produces precursors for DNA metabolism. The concerted action of PLP‐dependent serine hydroxymethyltransferase (SHMT) and thymidylate synthase (TS) leads to the biosynthesis of thymidylate (dTMP), which plays an essential function in DNA synthesis and repair. PLP deficiency causes chromosome aberrations (CABs) in Drosophila and human cells, rising the hypothesis that an altered 1C metabolism may be involved. To test this hypothesis, we used Drosophila as a model system and found, firstly, that in PLP deficient larvae SHMT activity is reduced by 40%. Second, we found that RNAi‐induced SHMT depletion causes chromosome damage rescued by PLP supplementation and strongly exacerbated by PLP depletion. RNAi‐induced TS depletion causes severe chromosome damage, but this is only slightly enhanced by PLP depletion. dTMP supplementation rescues CABs in both PLP‐deficient and PLP‐proficient SHMTRNAi. Altogether these data suggest that a reduction of SHMT activity caused by PLP deficiency contributes to chromosome damage by reducing dTMP biosynthesis. In addition, our work brings to light a gene‐nutrient interaction between SHMT decreased activity and PLP deficiency impacting on genome stability that may be translated to humans.
ANALYSIS OF SIMPLIFICATION ERRORS FOR WATER DISTRIBUTION MODELS

Information, data and maps required to analyze water distribution networks are commonly available nowadays. Furthermore, the use of information technology and geographical information systems has become part of normal mapping and management tasks in the water industry. In particular, improved descriptions of both network topology (number and position of the property connections along water mains) and its boundary conditions (e.g. demands, leakage, etc.) permit a more detailed analysis for different management purposes. These facts increase considerably the complexity of the network analysis and the size of the system hydraulic models and related mathematical problems. For example, the mathematical description of the actual demand pattern along a water main could be potentially achieved by adding one interior node for each connection point, but this will normally increase the size of the hydraulic model by more than one order of magnitude. Thus, simplification of the network model is vital for achieving an acceptable computational efficiency level that allows effective investigation. In this paper, network simplification is achieved by using the recently developed Enhanced Global Gradient Algorithm (EGGA). EGGA simplifies the network topology by automatically removing interior/serial nodes, which are those adjacent to two nodes only, thus reducing the total number of demand nodes and pipes in the analyzed hydraulic model whilst preserving original mass and energy balance. The EGGA formulation shows clearly that the sensitivity of the algorithm results to the uncertainties of the boundary conditions is unchanged with respect to classical GGA. Thus, this paper analyses two simplification strategies based on EGGA and applying them to a case study.
Rethinking a delayed choice quantum eraser experiment: A simple baseball model

In a double slit experiment, you can see an interference fringe pattern or you can know which slit the photon came through, but not both. There are two diametrically opposite theories about why this happens. One is complementarity. The other is the proposal made in this article. An experiment, published in 2000 [Y. -H. Kim et al., Phys. Rev. Lett. 8, 1 (2000)] allegedly supports the idea of complementarity. With different starting assumptions, we arrive at opposite conclusions: complementarity is irrelevant to this experiment. Our assumptions come from the Theory of Elementary Waves. Waves are assumed to travel in the opposite direction: from the detector to the laser. All wave interference is located at the laser. All decisions of importance are located at the laser, not at the detectors. The “decisions” concern which of several elementary rays a photon chooses to follow (this is a probabilistic decision). If a photon is emitted in response to one such impinging ray, all wave interference is then complete. The photon will follow backwards that ray alone, with a probability of one, back to the pair of detectors from which that ray originated. Based on these assumptions, the experiment has nothing to do with complementarity. There is also no delayed choice and no quantum eraser. Conclusion: complementarity is not the only way to understand this experiment. VC 2013 Physics Essays Publication. [http://dx.doi. org/10.4006/0836-1398-26.1. 100] Résumé: Une expérience à double fente vous permet soit d’observer une figure de franges d’interférences, soit de savoir de quelle fente vient le photon, mais pas les deux. Actuellement, deux théories diamétralement opposées expliquent ce fait. L’une parle de complémentarité, l’autre est décrite dans cet article. Une expérimentation publiée en 2000 [Y. -H. Kim et al., Phys. Rev. Lett. 8, 1 (2000)] soutiendrait la théorie de la complémentarité. Mais différentes hypothèses de départ nous conduisent à d’autres conclusions: La théorie de la complémentarité est insignifiant dans le cadre de cette expérience. Nous avons basé nos hypothèses sur la théorie des ondes élémentaires. Les ondes voyageraient dans la direction opposée: du détecteur vers le laser. Toute interférence des ondes est localisée dans le laser. Toutes les décisions importantes se prennent dans le laser, et non pas dans les détecteurs. Le terme “décisions” désigne le choix que fait le photon lorsqu’il décide de suivre un seul rayon élémentaire parmi d’autres (il s’agit d’une décision probabiliste). Si un photon est émis en réponse à un tel rayon incident, il n’y a plus aucune interférence d’ondes. Le photon suivra ce seul rayon, avec une probabilité de un, vers les deux détecteurs d’où provient ce rayon. Selon ces hypothèses, l’expérience ne relève donc pas de la théorie de la complémentarité. De plus, il n’y a aucun choix retardé, ni gomme quantique. En conclusion, la complémentarité n’est pas la seule théorie permettant de comprendre cette expérience.
Chest Radiography of Tuberculosis: Determination of Activity Using Deep Learning Algorithm

Background Inactive or old, healed tuberculosis (TB) on chest radiograph (CR) is often found in high TB incidence countries, and to avoid unnecessary evaluation and medication, differentiation from active TB is important. This study develops a deep learning (DL) model to estimate activity in a single chest radiographic analysis. Methods A total of 3,824 active TB CRs from 511 individuals and 2,277 inactive TB CRs from 558 individuals were retrospectively collected. A pretrained convolutional neural network was fine-tuned to classify active and inactive TB. The model was pretrained with 8,964 pneumonia and 8,525 normal cases from the National Institute of Health (NIH) dataset. During the pretraining phase, the DL model learns the following tasks: pneumonia vs. normal, pneumonia vs. active TB, and active TB vs. normal. The performance of the DL model was validated using three external datasets. Receiver operating characteristic analyses were performed to evaluate the diagnostic performance to determine active TB by DL model and radiologists. Sensitivities and specificities for determining active TB were evaluated for both the DL model and radiologists. Results The performance of the DL model showed area under the curve (AUC) values of 0.980 in internal validation, and 0.815 and 0.887 in external validation. The AUC values for the DL model, thoracic radiologist, and general radiologist, evaluated using one of the external validation datasets, were 0.815, 0.871, and 0.811, respectively. Conclusion This DL-based algorithm showed potential as an effective diagnostic tool to identify TB activity, and could be useful for the follow-up of patients with inactive TB in high TB burden countries.
Effects of N‐ and C‐terminal regions on oligomeric formation of blue light sensor protein SyPixD

A sensor of blue‐light using flavin adenine dinucleotide (BLUF) is a typical blue light photoreceptor domain that is found in many photosensor proteins in bacteria and some eukaryotic algae. SyPixD in Synechocystis is one of the well‐studied BLUF proteins. In the dark state, it forms a decamer and, upon photoexcitation, a dissociation reaction takes place to yield dimers. Such change in the intermolecular interactions of the protomers is important for the biological function. The effect of the N‐ and C‐terminal sequences on the stability of SyPixD oligomeric states and photoreactions of SyPixD were studied to understand how the oligomeric form is maintained with weak interaction. It was found that a few residues that frequently persist at the N‐terminus after removing a tag for purification are sensitive to the stability of the decamer structure. Even two or three residues at the N‐terminus considerably reduces decamer stability, whereas four or more residues completely prevent decamer formation. Unexpectedly, truncating C‐terminal sequences, which locate far from any protomer interface and of which structure is undetermined in crystal structure, also destabilizes the decamer structure. This destabilization is also apparent from the dissociation reaction dynamics detected by the transient grating and transient absorption measurements. The dissociation reaction is faster and the yield increases when the C‐terminus does not contain seven amino acid residues. Photoexcitation induces a conformational change in the C‐terminus of the decamer but not the dimer.
Progressive structural damage in sleep‐related hypermotor epilepsy

This study aimed to explore the alterations in gray matter volume (GMV) based on high‐resolution structural data and the temporal precedence of structural alterations in patients with sleep‐related hypermotor epilepsy (SHE). After preprocessing of T1 structural images, the voxel‐based morphometry and source‐based morphometry (SBM) methods were applied in 60 SHE patients and 56 healthy controls to analyze the gray matter volumetric alterations. Furthermore, a causal network of structural covariance (CaSCN) was constructed using Granger causality analysis based on structural data of illness duration ordering to assess the causal impact of structural changes in abnormal gray matter regions. The GMVs of SHE patients were widely reduced, mainly in the bilateral cerebellums, fusiform gyri, the right angular gyrus, the right postcentral gyrus, and the left parahippocampal gyrus. In addition to those regions, the results of the SBM analysis also found decreased GMV in the bilateral frontal lobes, precuneus, and supramarginal gyri. The analysis of CaSCN showed that along with disease progression, the cerebellum was the prominent node that tended to affect other brain regions in SHE patients, while the frontal lobe was the transition node and the supramarginal gyrus was the prominent node that may be easily affected by other brain regions. Our study found widely affected regions of decreased GMVs in SHE patients; these regions underlie the morphological basis of epileptic networks, and there is a temporal precedence relationship between them.
PitA Controls the H2- and H3-T6SSs through PhoB in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogenic bacterium that causes acute and chronic infections in humans. The type VI secretion systems (T6SSs) have been shown to associate with chronic infections. ABSTRACT Pseudomonas aeruginosa possesses three type VI secretion systems (T6SSs) that are involved in interspecies competition, internalization into epithelial cells, and virulence. Host-derived mucin glycans regulate the T6SSs through RetS, and attacks from other species activate the H1-T6SS. However, other environmental signals that control the T6SSs remain to be explored. Previously, we determined PitA to be a constitutive phosphate transporter, whose mutation reduces the intracellular phosphate concentration. Here, we demonstrate that mutation in the pitA gene increases the expression of the H2- and H3-T6SS genes and enhances bacterial uptake by A549 cells. We further found that mutation of pitA results in activation of the quorum sensing (QS) systems, which contributes to the upregulation of the H2- and H3-T6SS genes. Overexpression of the phosphate transporter complex genes pstSCAB or knockdown of the phosphate starvation response regulator gene phoB in the ΔpitA mutant reduces the expression of the QS genes and subsequently the H2- and H3-T6SS genes and bacterial internalization. Furthermore, growth of wild-type PA14 in a low-phosphate medium results in upregulation of the QS and H2- and H3-T6SS genes and bacterial internalization compared to those in cells grown in a high-phosphate medium. Deletion of the phoB gene abolished the differences in the expression of the QS and T6SS genes as well as bacterial internalization in the low- and high- phosphate media. Overall, our results elucidate the mechanism of PitA-mediated regulation on the QS system and H2- and H3-T6SSs and reveal a novel pathway that regulates the T6SSs in response to phosphate starvation. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogenic bacterium that causes acute and chronic infections in humans. The type VI secretion systems (T6SSs) have been shown to associate with chronic infections. Understanding the mechanism used by the bacteria to sense environmental signals and regulate virulence factors will provide clues for developing novel effective treatment strategies. Here, we demonstrate a relationship between a phosphate transporter and the T6SSs and reveal a novel regulatory pathway that senses phosphate limitation and controls bacterial virulence factors in P. aeruginosa.
Astrocytic A2A receptors silencing negatively impacts hippocampal synaptic plasticity and memory of adult mice

Astrocytes are wired to bidirectionally communicate with neurons namely with synapses, thus shaping synaptic plasticity, which in the hippocampus is considered to underlie learning and memory. Adenosine A2A receptors (A2AR) are a potential candidate to modulate this bidirectional communication, since A2AR regulate synaptic plasticity and memory and also control key astrocytic functions. Nonetheless, little is known about the role of astrocytic A2AR in synaptic plasticity and hippocampal‐dependent memory. Here, we investigated the impact of genetic silencing astrocytic A2AR on hippocampal synaptic plasticity and memory of adult mice. The genetic A2AR silencing in astrocytes was accomplished by a bilateral injection into the CA1 hippocampal area of a viral construct (AAV5‐GFAP‐GFP‐Cre) that inactivate A2AR expression in astrocytes of male adult mice carrying “floxed” A2AR gene, as confirmed by A2AR binding assays. Astrocytic A2AR silencing alters astrocytic morphology, typified by an increment of astrocytic arbor complexity, and led to deficits in spatial reference memory and compromised hippocampal synaptic plasticity, typified by a reduction of LTP magnitude and a shift of synaptic long‐term depression (LTD) toward LTP. These data indicate that astrocytic A2AR control astrocytic morphology and influence hippocampal synaptic plasticity and memory of adult mice in a manner different from neuronal A2AR.
Monorchiids (Digenea, Trematoda) of fishes in the Yucatán Peninsula, Mexico, with the description of three new species based on morphological and molecular data

Adult specimens of monorchiids (Digenea) were collected from the intestines of the white grunt, Haemulon plumierii Lacepède (Haemulidae), and the white mullet, Mugil curema Valenciennes (Mugilidae) from five localities off the Yucatán Peninsula and one locality in the Gulf of Mexico. Some specimens were photographed and sequenced for two molecular markers, the large subunit (LSU) of nuclear rDNA and the cytochrome c oxidase subunit 1 (cox1) of mitochondrial DNA. Other specimens were processed for morphological analyses. Newly generated sequences were aligned with other sequences available in GenBank. Bayesian inference and maximum likelihood analyses were implemented using the data sets of LSU and cox1 independently. Reciprocal monophyly evidenced through phylogenetic analyses, sequence divergence values for both molecular markers, and detailed morphological analyses, including scanning electron microscopy photomicrographs, revealed three new genetic lineages, i.e., species, as parasites of M. curema. The three new species are Sinistroporomonorchis mexicanus n. sp. , Sinistroporomonorchis yucatanensis n. sp. , and Sinistroporomonorchis minutus n. sp. Two additional species of monorchiids were sampled, characterised molecularly, and re-described, namely Sinistroporomonorchis glebulentus (Overstreet, 1971) from the white mullet, and Alloinfundiburictus haemuli (Overstreet, 1969), from the white grunt.
Input‐output based fault estimation for linear systems with partially dynamic uncertainty and actuator faults

This paper is concentrated on the problem of fault estimation for a class of linear systems with partially dynamic uncertainty and actuator faults. A novel input–output‐based fault estimation approach is proposed, by which the estimates can asymptotically converge to the magnitudes of the actuator faults, and the asymptotic convergence of the estimation is theoretically proved. Some important properties related to the corresponding fault errors are obtained. The proposed input–output‐based fault estimation method can exponentially weaken the effects of the fault derivatives on the fault error dynamics. Based on the online estimates, a corresponding robust fault‐tolerant control policy is designed, so that the closed‐loop system is asymptotically stable and the control output curves can asymptotically trace to the normal control output curves. Finally, three examples are given to show the effectiveness, merits, and applications of the proposed methods. Copyright © 2016 John Wiley & Sons, Ltd.
Scattering From $(p,q)$-Strings in $\text{AdS}_5 \times \text{S}^5$

Motivated by understanding the scattering of gravitons and their superpartners from extended $(p, q)$-strings in type IIB string theory via AdS/CFT, we study an integrated two-point function of stress tensor multiplet operators in the presence of a half-BPS line defect in ${\cal N} = 4$ $SU(N)$ super-Yang-Mills theory. We determine this integrated correlator at the five lowest non-trivial orders in $1/\sqrt{N}$ at fixed Yang-Mills coupling and $\theta$ angle. Our calculations are performed explicitly when the line defect is a Wilson line, in which case we find a finite number of perturbative contributions at each order in $1/\sqrt{N}$, as well as instanton contributions. Using $SL(2, \mathbb{Z})$ transformations, our results can also be applied to Wilson-'t Hooft line defects dual to extended $(p, q)$-strings in the bulk. We analyze features of these integrated correlators in the weak coupling expansion by comparing with open-closed amplitudes of type IIB string theory on $\text{AdS}_5\times \text{S}^5$, as well as in its flat space limit. We predict new higher-derivative interaction vertices on the D1-brane and, more generally, on $(p,q)$-strings.