Miracle-dz/UniFAR-FTUs huggingface dataset:
Data-driven discovery of partial differential equations

Researchers propose sparse regression for identifying governing partial differential equations for spatiotemporal systems. We propose a sparse regression method capable of discovering the governing partial differential equation(s) of a given system by time series measurements in the spatial domain. The regression framework relies on sparsity-promoting techniques to select the nonlinear and partial derivative terms of the governing equations that most accurately represent the data, bypassing a combinatorially large search through all possible candidate models. The method balances model complexity and regression accuracy by selecting a parsimonious model via Pareto analysis. Time series measurements can be made in an Eulerian framework, where the sensors are fixed spatially, or in a Lagrangian framework, where the sensors move with the dynamics. The method is computationally efficient, robust, and demonstrated to work on a variety of canonical problems spanning a number of scientific domains including Navier-Stokes, the quantum harmonic oscillator, and the diffusion equation. Moreover, the method is capable of disambiguating between potentially nonunique dynamical terms by using multiple time series taken with different initial data. Thus, for a traveling wave, the method can distinguish between a linear wave equation and the Korteweg–de Vries equation, for instance. The method provides a promising new technique for discovering governing equations and physical laws in parameterized spatiotemporal systems, where first-principles derivations are intractable.
COMPARATIVE STUDIES ON QUALITY ANALYSIS OF FREEZE DRIED AND CROSS FLOW DRIED AMLA POWDER

Amla is known as wonder fruit for health. Due to its therapeutic properties, there is a great demand for the amla. It is as well as one of the richest sources of Vitamin C. Several value added products have been reported from Amla. Drying can be used as a means of increasing product stability and increasing ease of distribution and storage of this product and products derived from it. Freeze-drying is a technique that results in high-quality dehydrated products due to the absence of liquid water and the low temperatures required in the process. Use of a cabinet dryer is an alternative drying method that both decreases the drying time and improves the quality of the final product. The present work was undertaken to get good quality of amla powder by comparing the drying techniques of freeze dryer and cross flow dryer. Work were carried to produce amla powder by using amla juice but in this study instead of drying amla juice, directly amla chunks/ segments were used to produce powder. For easier consumer consumption and longer shelf life, amla can be dried and powdered. The powdered amla can be packed and can be used for longer days, mostly during the periods when the availability of amla fruits are less.
NOD2 up-regulates TLR2-mediated IL-23p19 expression via NF-κB subunit c-Rel in Paneth cell-like cells

IL-23p19 plays important roles in intestinal antimicrobial immunity, while its over-expression can lead to intestinal inflammation. However, the bacterial compounds and the type of pattern recognition receptor involved in the inducible expression of IL-23p19 in Paneth cells remain unclear. Here we show that the mRNA expression of IL-23p19 was increased in Paneth cell (PC)-like cells stimulated by Toll-like receptor 2 (TLR2) ligands, peptidoglycan (PGN) and Pam3CSK4, and was further increased in the presence of nucleotide-binding oligomerization domain 2 (NOD2)-ligand muramyl dipeptide (MDP). However, its mRNA expression was decreased in NOD2-knockdown PC-like cells. Additionally, the c-Rel activation was increased in Pam3CSK4- or PGN-stimulated PC-like cells, but the PGN-induced c-Rel activation was decreased in NOD2-knockdown PC-like cells and had no significant difference compared with Pam3CSK4-induced c-Rel activation. Our results suggest that NOD2 up-regulates TLR2-mediated IL-23p19 expression via increasing c-Rel activation in PC-like cells. This finding might provide us with a novel therapeutic target for inflammatory bowel disease to inhibit IL-23p19 over-expression via the NOD2-c-Rel pathway.
DEVELOPMENT AND PROPERTIES OF LOW-CALCIUM FLY ASH-BASED GEOPOLYMER CONCRETE

This Research Report describes the first part of the work carried out by the geopolymer research group at Curtin University of Technology. It describes the development and properties of heat-cured low-calcium fly ash-based geopolymer concrete. This Report will be followed by two other Reports describing the long-term properties of geopolymer concrete, and the behaviour of reinforced geopolymer concrete beams and columns.
How to determine an impaired health status in COPD: Results from a population-based study.

BACKGROUND Chronic obstructive pulmonary disease (COPD) is associated with a significantly impaired health status and lost work productivity across all degrees of airflow limitation. The current study investigated whether an impaired health status is better represented by the recommended COPD Assessment Test (CAT) cut-point of 10 points, or the 95th percentile of the CAT score in a non-COPD population. Additionally, the impact of COPD on health status in a Dutch population, after stratification for work status, was measured. METHODS Demographics, clinical characteristics, post-bronchodilator spirometry, and CAT were assessed in subjects from the Longitudinal Aging Study Amsterdam (LASA), a large Dutch population-based study. Normative values for the CAT score were described by percentiles using the mean, standard deviation, median and range. RESULTS In total, 810 COPD and non-COPD subjects (50.4% male, mean age 60.5 ±; 2.9 years) were analysed. Significant differences were observed in CAT scores between non-COPD and COPD subjects (6.7 ±; 5.2 vs. 9.5 ±; 5.9, p < 0.001 respectively). The proportion of COPD subjects with an impaired health status differed between applying the CAT ≥ 10 cut-point (50.0%) and applying the 95th percentile of CAT in non-COPD subjects (> 18 cut-point; 7.6%). Higher CAT scores were seen in working COPD patients compared with working non-COPD subjects (9.3 ±; 5.2 vs. 6.0 ±; 4.6, p < 0.001). CONCLUSION We suggest a CAT cut-point of > 18 points to indicate an impaired health status in COPD. This would imply an adaptation of the current GOLD classification of the disease.
Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria

Significance Phosphorothioate (PT) modification of the DNA sugar-phosphate backbone is an important microbial epigenetic modification governed by DndABCDE, which together with DndFGH, constitutes a restriction-modification system. We show that up to 45% of 1,349 identified bacterial dnd systems exhibit the form of solitary dndABCDE without the restriction counterparts of dndFGH. The combination of epigenomics, transcriptome analysis, and metabolomics suggests that in addition to providing a genetic barrier against invasive DNA, PT modification is a versatile player involved in the epigenetic control of gene expression and the maintenance of cellular redox homeostasis. This finding provides evolutionary and functional insights into this unusual epigenetic modification. Our results imply that PT systems might evolve similar to other epigenetic modification systems with multiple cellular functions. The chemical diversity of physiological DNA modifications has expanded with the identification of phosphorothioate (PT) modification in which the nonbridging oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together with DndFGH as cognate restriction enzymes, DNA PT modification, which is catalyzed by the DndABCDE proteins, functions as a bacterial restriction-modification (R-M) system that protects cells against invading foreign DNA. However, the occurrence of dnd systems across a large number of bacterial genomes and their functions other than R-M are poorly understood. Here, a genomic survey revealed the prevalence of bacterial dnd systems: 1,349 bacterial dnd systems were observed to occur sporadically across diverse phylogenetic groups, and nearly half of these occur in the form of a solitary dndBCDE gene cluster that lacks the dndFGH restriction counterparts. A phylogenetic analysis of 734 complete PT R-M pairs revealed the coevolution of M and R components, despite the observation that several PT R-M pairs appeared to be assembled from M and R parts acquired from distantly related organisms. Concurrent epigenomic analysis, transcriptome analysis, and metabolome characterization showed that a solitary PT modification contributed to the overall cellular redox state, the loss of which perturbed the cellular redox balance and induced Pseudomonas fluorescens to reconfigure its metabolism to fend off oxidative stress. An in vitro transcriptional assay revealed altered transcriptional efficiency in the presence of PT DNA modification, implicating its function in epigenetic regulation. These data suggest the versatility of PT in addition to its involvement in R-M protection.
Low-energy defibrillation with multi-electrodes stimulation: A simulation study

The objective of this study is to explore the possible ways to reduce defibrillation energy and further reveal the mechanism of electric defibrillation. A bidomain simulation study was performed on a rabbit whole-ventricle electrophysiological model and the feasibility of the defibrillation strategy with multi-electrodes stimulation was verified. Simulation results indicate that the new approach is effective in low-energy defibrillation.
Selective targeting of mutant adenomatous polyposis coli (APC) in colorectal cancer

A small molecule specifically kills cancer cells with APC truncations and spares cells with wild-type APC. Truncating colorectal cancer The adenomatous polyposis gene (APC), which is a tumor suppressor, is commonly mutated in colon cancer and cannot be directly targeted by existing therapeutics. Zhang et al. identified a drug called TASIN-1, which specifically targets cells with APC truncations, the most common APC mutation seen in colorectal cancer. The authors showed that this drug interferes with cholesterol biosynthesis and that it selectively kills APC-truncated cancer cells in vitro and in mouse models without any detectable toxicity, paving the way for further development of TASIN-1. Mutations in the adenomatous polyposis coli (APC) gene are common in colorectal cancer (CRC), and more than 90% of those mutations generate stable truncated gene products. We describe a chemical screen using normal human colonic epithelial cells (HCECs) and a series of oncogenically progressed HCECs containing a truncated APC protein. With this screen, we identified a small molecule, TASIN-1 (truncated APC selective inhibitor–1), that specifically kills cells with APC truncations but spares normal and cancer cells with wild-type APC. TASIN-1 exerts its cytotoxic effects through inhibition of cholesterol biosynthesis. In vivo administration of TASIN-1 inhibits tumor growth of CRC cells with truncated APC but not APC wild-type CRC cells in xenograft models and in a genetically engineered CRC mouse model with minimal toxicity. TASIN-1 represents a potential therapeutic strategy for prevention and intervention in CRC with mutant APC.
Sample size and classification error for Bayesian change-point models with unlabelled sub-groups and incomplete follow-up

Many medical (and ecological) processes involve the change of shape, whereby one trajectory changes into another trajectory at a specific time point. There has been little investigation into the study design needed to investigate these models. We consider the class of fixed effect change-point models with an underlying shape comprised two joined linear segments, also known as broken-stick models. We extend this model to include two sub-groups with different trajectories at the change-point, a change and no change class, and also include a missingness model to account for individuals with incomplete follow-up. Through a simulation study, we consider the relationship of sample size to the estimates of the underlying shape, the existence of a change-point, and the classification-error of sub-group labels. We use a Bayesian framework to account for the missing labels, and the analysis of each simulation is performed using standard Markov chain Monte Carlo techniques. Our simulation study is inspired by cognitive decline as measured by the Mini-Mental State Examination, where our extended model is appropriate due to the commonly observed mixture of individuals within studies who do or do not exhibit accelerated decline. We find that even for studies of modest size (n = 500, with 50 individuals observed past the change-point) in the fixed effect setting, a change-point can be detected and reliably estimated across a range of observation-errors.
A statics-dynamics equivalence through the fluctuation–dissipation ratio provides a window into the spin-glass phase from nonequilibrium measurements

Significance The unifying feature of glass formers (such as polymers, supercooled liquids, colloids, granulars, spin glasses, superconductors, etc.) is a sluggish dynamics at low temperatures. Indeed, their dynamics are so slow that thermal equilibrium is never reached in macroscopic samples: in analogy with living beings, glasses are said to age. Here, we show how to relate experimentally relevant quantities with the experimentally unreachable low-temperature equilibrium phase. This relation is made quantitative via a statics-dynamics dictionary, established for spin glasses. In our dictionary, the aging response to a magnetic field is related to the spin-glass order parameter as obtained on samples small enough to equilibrate. We remark that all of the observables we consider can be measured with current experimental methods. We have performed a very accurate computation of the nonequilibrium fluctuation–dissipation ratio for the 3D Edwards–Anderson Ising spin glass, by means of large-scale simulations on the special-purpose computers Janus and Janus II. This ratio (computed for finite times on very large, effectively infinite, systems) is compared with the equilibrium probability distribution of the spin overlap for finite sizes. Our main result is a quantitative statics-dynamics dictionary, which could allow the experimental exploration of important features of the spin-glass phase without requiring uncontrollable extrapolations to infinite times or system sizes.
Lung deposition predictions of airborne particles and the emergence of contemporary diseases Part-I

Inhaled particles can cause a variety of pulmonary illnesses such as asthma, bronchitis, chronic obstructive pulmonary diseases (COPD) and even secondary organismic diseases. Thus, predictions of inhaled aerosol deposition in the respiratory tract are essential not only to assess their possible consequences but also to optimize drug delivery using pharmaceutical aerosols. Deposition of inhaled aerosols is a complex phenomenon that depends on the physico-chemical properties of the particles, lung anatomy, and respiratory patterns of the subject. Hence, the prediction of particle deposition for an individual person poses real challenges. Different conceptual particle deposition models are employed for the estimation of deposition fraction in different region of the lung. However, these deposition fractions vary with the above mentioned parameters in addition to the modeling and computational technique. Part-I of this review article briefly describes the deposition behaviour of inhaled particulate matter and the currently available approaches for the prediction of aerosol deposition in the respiratory tract. Part-II continues this thread and provides a broad view of the health-related issues of particle exposure.
Population Pharmacokinetic Modeling as a Tool To Characterize the Decrease in Ciprofloxacin Free Interstitial Levels Caused by Pseudomonas aeruginosa Biofilm Lung Infection in Wistar Rats

ABSTRACT Biofilm formation plays an important role in the persistence of pulmonary infections, for example, in cystic fibrosis patients. So far, little is known about the antimicrobial lung disposition in biofilm-associated pneumonia. This study aimed to evaluate, by microdialysis, ciprofloxacin (CIP) penetration into the lungs of healthy and Pseudomonas aeruginosa biofilm-infected rats and to develop a comprehensive model to describe the CIP disposition under both conditions. P. aeruginosa was immobilized into alginate beads and intratracheally inoculated 14 days before CIP administration (20 mg/kg of body weight). Plasma and microdialysate were sampled from different animal groups, and the observations were evaluated by noncompartmental analysis (NCA) and population pharmacokinetic (popPK) analysis. The final model that successfully described all data consisted of an arterial and a venous central compartment and two peripheral distribution compartments, and the disposition in the lung was modeled as a two-compartment model structure linked to the venous compartment. Plasma clearance was approximately 32% lower in infected animals, leading to a significantly higher level of plasma CIP exposure (area under the concentration-time curve from time zero to infinity, 27.3 ± 12.1 μg · h/ml and 13.3 ± 3.5 μg · h/ml in infected and healthy rats, respectively). Despite the plasma exposure, infected animals showed a four times lower tissue concentration/plasma concentration ratio (lung penetration factor = 0.44 and 1.69 in infected and healthy rats, respectively), and lung clearance (CLlung) was added to the model for these animals (CLlung = 0.643 liters/h/kg) to explain the lower tissue concentrations. Our results indicate that P. aeruginosa biofilm infection reduces the CIP free interstitial lung concentrations and increases plasma exposure, suggesting that plasma concentrations alone are not a good surrogate of lung concentrations.
Expressive Spectral Error Visualization for Enhanced Spectral Unmixing

A major issue in multispectral data analysis stems from the concept of spectral mixture analysis, i.e. the fact that a pixel does not cover only one material but corresponds to a mixture of materials. Even though many automatic methods for spectral unmixing exist, in many practical applications, domain experts have to verify the result and sometimes have to manually adjust the set of determined materials to achieve proper spectral reconstructions. In this paper, we propose an approach to enhance the very tedious and time-consuming task of manual veriﬁcation of the unmixing and optional reﬁnement of the materials. Our visual analysis approach comprises different techniques for an expressive spectral error visualization, efﬁciently guiding the user towards spectra in the dataset which are potentially missing materials. Here, combined views allow comprehensive, local and global error in-spections in parallel. We present results of our proposed approach for two domains.
Identification of Vaccinia Virus Replisome and Transcriptome Proteins by Isolation of Proteins on Nascent DNA Coupled with Mass Spectrometry

ABSTRACT Poxviruses replicate within the cytoplasm and encode proteins for DNA and mRNA synthesis. To investigate poxvirus replication and transcription from a new perspective, we incorporated 5-ethynyl-2′-deoxyuridine (EdU) into nascent DNA in cells infected with vaccinia virus (VACV). The EdU-labeled DNA was conjugated to fluor- or biotin-azide and visualized by confocal, superresolution, and transmission electron microscopy. Nuclear labeling decreased dramatically after infection, accompanied by intense labeling of cytoplasmic foci. The nascent DNA colocalized with the VACV single-stranded DNA binding protein I3 in multiple puncta throughout the interior of factories, which were surrounded by endoplasmic reticulum. Complexes containing EdU-biotin-labeled DNA cross-linked to proteins were captured on streptavidin beads. After elution and proteolysis, the peptides were analyzed by mass spectrometry to identify proteins associated with nascent DNA. The known viral replication proteins, a telomere binding protein, and a protein kinase were associated with nascent DNA, as were the DNA-dependent RNA polymerase and intermediate- and late-stage transcription initiation and elongation factors, plus the capping and methylating enzymes. These results suggested that the replicating pool of DNA is transcribed and that few if any additional viral proteins directly engaged in replication and transcription remain to be discovered. Among the host proteins identified by mass spectrometry, topoisomerases IIα and IIβ and PCNA were noteworthy. The association of the topoisomerases with nascent DNA was dependent on expression of the viral DNA ligase, in accord with previous proteomic studies. Further investigations are needed to determine possible roles for PCNA and other host proteins detected. IMPORTANCE Poxviruses, unlike many well-characterized animal DNA viruses, replicate entirely within the cytoplasm of animal cells, raising questions regarding the relative roles of viral and host proteins. We adapted newly developed procedures for click chemistry and iPOND (Isolation of proteins on nascent DNA) to investigate vaccinia virus (VACV), the prototype poxvirus. Nuclear DNA synthesis ceased almost immediately following VACV infection, followed swiftly by the synthesis of viral DNA within discrete cytoplasmic foci. All viral proteins known from genetic and proteomic studies to be required for poxvirus DNA replication were identified in the complexes containing nascent DNA. The additional detection of the viral DNA-dependent RNA polymerase and intermediate and late transcription factors provided evidence for a temporal coupling of replication and transcription. Further studies are needed to assess the potential roles of host proteins, including topoisomerases IIα and IIβ and PCNA, which were found associated with nascent DNA.
Altered corticospinal function during movement preparation in humans with spinal cord injury

In uninjured humans, transmission in the corticospinal pathway changes in a task‐dependent manner during movement preparation. We investigated whether this ability is preserved in humans with incomplete chronic cervical spinal cord injury (SCI). Our results show that corticospinal excitability is altered in the preparatory phase of an upcoming movement when there is a need to suppress but not to execute rapid index finger voluntary contractions in individuals with SCI compared with controls. This is probably related to impaired transmission at a cortical and spinal level after SCI. Overall our findings indicate that deficits in corticospinal transmission in humans with chronic incomplete SCI are also present in the preparatory phase of upcoming movements.