Miracle-dz/UniFAR-FTUs huggingface dataset:
Describing oxymethylene ether synthesis based on the application of non-stoichiomsetric Gibbs minimisation

The synthesis of short chain poly oxymethylene dimethyl ethers, also known as oxymethylene ethers (OME; molecular formula: H3CO–(CH2O)n–CH3 where n = 1–8) is described through the application of non-stoichiometric Gibbs minimisation (NSGM) to a synthesis based on methanol and anhydrous formaldehyde. The presented approach shows several synthesis efficiency and economic advantages as demonstrated through a simulation platform based on MATLAB® (where the two main reactors models are implemented) and the NSGM, which utilises stochastic global optimisation (SGO) to perform an unconstrained minimisation and convergence of the complex OME reaction system (comprising >31 reactants and also recycling of non-reacted components). A complimentary experimental validation is provided for the OME reaction equilibrium model based on the use of different feeds, namely 1) CH3OH/CH2O and 2) H3C–O–(CH2O)1–CH3/(CH2O)3. The presented results demonstrate the robustness of the applied NSGM for this multi-reaction system. With regard to the overall evaluation of the presented process, key performance indicators (KPIs) are discussed based on the material balance results of the simulation platform. A cost model for the OME synthesis process based on different feeds is also presented based on an annual production of one million metric tonnes of OME3–5. The cost of 571 € per tonne demonstrates the economic potential of the presented OME production process.
In Vivo Evaluation of a Pectin-Honey Hydrogel Coating on Polypropylene Mesh in a Rat Model of Acute Hernia

Investigations about ventral hernia repair are focused on improving the quality, resistance, and biocompatibility of mesh. This study compared plain polypropylene mesh with a pectin-honey hydrogel-coated polypropylene mesh in an acute hernia model in rats. Forty Wistar rats, randomly assigned to two groups, were submitted to laparotomy, and a 1 cm × 2 cm fascial defect was created, centered on the midline. Uncoated (group C) or coated mesh (group T) was inserted in an inlay fashion to repair the defect. After 30 days, the rats were euthanized, and the presence of adhesions to the mesh was macroscopically evaluated. Histology and measurement of COX-2 as tissue inflammation markers were used to assess fascia tissue healing. Grades of adhesion were not different between groups. Histological score and COX-2 expression were not significantly different between groups, except for the higher inflammatory response demonstrated in group T. The pectin-hydrogel coated mesh could not reduce adhesion formation compared to uncoated polypropylene mesh but improved peritoneal regeneration and tissue healing.
Effect of Addition of Chokeberry Juice Concentrate and Foaming Agent on the Physical Properties of Agar Gel

This study aimed to determine the effect of the addition of chokeberry juice concentrate (CJC) and foaming agent (egg albumin) with different percentages on the selected physical properties of agar gel. The agar gels with the addition of 5, 10, and 20% concentrations of chokeberry juice concentrate and with fructose addition were prepared. In addition, the foamed gels with different concentrations of egg albumin (in the range 0.5–2.0%) and CJC were produced. The water content, colour, density, hold-up and some mechanical and TPA (Texture Profile Analysis) descriptors as well some structural and acoustic emission parameters of non-aerated and foamed gels were analysed. The addition of CJC changed the colour of agar gel with fructose, the attractive appearance of the aerated gel was also linked with the addition of concentrate. The addition of 20% of CJC and foaming agent created samples with very low hardness, cohesiveness, and gumminess, and the structure of the aerated samples was characterised by the larger bubble diameter and the wider distribution of their size. The more promising texture and structure properties were obtained for samples with aerated gels with 5 and 10% addition of chokeberry juice concentrate.
Genetic Determinants of Non-Syndromic Enlarged Vestibular Aqueduct: A Review

Hearing loss is the most common sensorial deficit in humans and one of the most common birth defects. In developed countries, at least 60% of cases of hearing loss are of genetic origin and may arise from pathogenic sequence alterations in one of more than 300 genes known to be involved in the hearing function. Hearing loss of genetic origin is frequently associated with inner ear malformations; of these, the most commonly detected is the enlarged vestibular aqueduct (EVA). EVA may be associated to other cochleovestibular malformations, such as cochlear incomplete partitions, and can be found in syndromic as well as non-syndromic forms of hearing loss. Genes that have been linked to non-syndromic EVA are SLC26A4, GJB2, FOXI1, KCNJ10, and POU3F4. SLC26A4 and FOXI1 are also involved in determining syndromic forms of hearing loss with EVA, which are Pendred syndrome and distal renal tubular acidosis with deafness, respectively. In Caucasian cohorts, approximately 50% of cases of non-syndromic EVA are linked to SLC26A4 and a large fraction of patients remain undiagnosed, thus providing a strong imperative to further explore the etiology of this condition.
Mesenchymal Stromal Cells Enhance Vascularization and Epithelialization within 7 Days after Gingival Augmentation with Collagen Matrices in Rabbits

Soft gingival tissue deficiency remains a severe problem leading to postoperative recession, peri-implantitis, and bone resorption. The use of collagen matrices does not always lead to complete rebuilding of the gingiva volume. The application of mesenchymal stromal cells (MSCs) simultaneously with collagen materials represents a promising approach for the restoration of soft gingival tissues. However, short-term effects of MSCs-enriched collagen grafts after gingival augmentation have not yet been studied properly. Mucograft and Mucoderm matrices were implanted in rabbits (n = 12) simultaneously with the intraoperative injection of rabbit bone marrow-derived mesenchymal stromal cells (BM-MSCs) or without cells. Collagen matrices were implanted under the flap or by the surface technique without intentional primary closure. The samples were harvested seven days after implantation, histological staining with hematoxylin and eosin, and immunohistochemical staining for VEGF, IGF1, and TGF were performed. The use of Mucoderm led to better augmentation outcomes on day 7 compared with Mucograft (p < 0.0001). Gingival augmentation in combination with the local administration of BM-MSCs led to better regeneration of the soft gingival tissues independently of the type of implanted collagen matrices (p < 0.0001). Furthermore, injection of BM-MSCs significantly enhanced gingival vascularization and epithelization with a clear positive correlation between vascular growth and epithelial response. Administration of BM-MSCs in combination with various collagen materials may potentially improve gingiva regeneration.
In Situ Quantification of Polyhydroxybutyrate in Photobioreactor Cultivations of Synechocystis sp. Using an Ultrasound-Enhanced ATR-FTIR Spectroscopy Probe

Polyhydroxybutyrate (PHB) is a very promising alternative to most petroleum-based plastics with the huge advantage of biodegradability. Biotechnological production processes utilizing cyanobacteria as sustainable source of PHB require fast in situ process analytical technology (PAT) tools for sophisticated process monitoring. Spectroscopic probes supported by ultrasound particle traps provide a powerful technology for in-line, nondestructive, and real-time process analytics in photobioreactors. This work shows the great potential of using ultrasound particle manipulation to improve spectroscopic attenuated total reflection Fourier-transformed mid-infrared (ATR-FTIR) spectra as a monitoring tool for PHB production processes in photobioreactors.
An Electrochemical Enzyme Biosensor for Ammonium Detection in Aquaculture Using Screen-Printed Electrode Modified by Gold Nanoparticle/Polymethylene Blue

A SPEC/AuNPs/PMB modified electrode was prepared by electrodeposition and electro-polymerization. The electrochemical behavior of reduced nicotinamide adenine dinucleotide (NADH) on the surface of the modified electrode was studied by cyclic voltammetry. A certain amount of substrate and glutamate dehydrogenase (GLDH) were coated on the modified electrode to form a functional enzyme membrane. The ammonia nitrogen in the water sample could be calculated indirectly by measuring the consumption of NADH in the reaction. The results showed that the strength of electro-catalytic current signal was increased by two times; the catalytic oxidation potential was shifted to the left by 0.5 V, and the anti-interference ability of the sensor was enhanced. The optimum substrate concentration and enzyme loading were determined as 1.3 mM NADH, 28 mM α-Ketoglutarate and 2.0 U GLDH, respectively. The homemade ceramic heating plate controlled the working electrode to work at 37 °C. A pH compensation algorithm based on piecewise linear interpolation could reduce the measurement error to less than 3.29 μM. The biosensor exhibited good linearity in the range of 0~300 μM with a detection limit of 0.65 μM NH4+. Compared with standard Nessler’s method, the recoveries were 93.71~105.92%. The biosensor was found to be stable for at least 14 days when refrigerated and sealed at 4 °C.
Arteriovenous Fistula Flow Dysfunction Surveillance: Early Detection Using Pulse Radar Sensor and Machine Learning Classification

Vascular Access (VA) is often referred to as the “Achilles heel” for a Hemodialysis (HD)-dependent patient. Both the patent and sufficient VA provide adequacy for performing dialysis and reducing dialysis-related complications, while on the contrary, insufficient VA is the main reason for recurrent hospitalizations, high morbidity, and high mortality in HD patients. A non-invasive Vascular Wall Motion (VWM) monitoring system, made up of a pulse radar sensor and Support Vector Machine (SVM) classification algorithm, has been developed to detect access flow dysfunction in Arteriovenous Fistula (AVF). The harmonic ratios derived from the Fast Fourier Transform (FFT) spectrum-based signal processing technique were employed as the input features for the SVM classifier. The result of a pilot clinical trial showed that a more accurate prediction of AVF flow dysfunction could be achieved by the VWM monitor as compared with the Ultrasound Dilution (UD) flow monitor. Receiver Operating Characteristic (ROC) curve analysis showed that the SVM classification algorithm achieved a detection specificity of 100% at detection thresholds in the range from 500 to 750 mL/min and a maximum sensitivity of 95.2% at a detection threshold of 750 mL/min.
Étude de la contamination des sols par les éléments traces métalliques : influence de la profondeur de la contamination sur la croissance de plantes indigènes et évaluation de la mobilité du zinc

Distribution and concentration of metals became a major environmental issue because of their massive utilization to support the development of the society. Trace metals elements are easily adsorbed by organic matter and soil’s minerals in such a way that they accrue in the first soil layers. But wat happens when this layer is buried deeper? This work is based on experimental lysimeters where polluted soil layer is placed at various depths (none, on the surface, 25-cm and 50-cm deep). The aim is to study the capacity development of three local plants (Sinapis alba, Echium vulgare, Tanacetum vulgare) in these conditions. In a second time, the evolution of the zinc concentration is derived from the soil’s solution at various heights. The results show no significative difference in the development plants between the practical details. However, one can see a trend of higher percentages of plants germination when the polluted soil is on the surface and also a smaller final height for the same disposition compared to the three other configurations. As regards the zinc levels, the observations show that polluted soil layers release few amounts of zinc whatever the depth. The highest concentrations in percolation water were found for lysimeters without polluted soil, where only sand and industrial compost were used.
Collective memory and the populist cause: The Ulucanlar Prison Museum in Turkey

This article focuses on how political actors appropriate the past by utilizing collective traumas for their populist cause. We demonstrate how the Ulucanlar Prison Museum in Turkey and the oppression of military interventions, for which it served as a backyard, became a tool for the AKP’s (Adalet ve Kalkınma Partisi-Justice and Development Party) populist agenda. Through a particular narration of history embedded in the museum, the AKP aimed to forge an internal frontier within the society between an envisioned homogenous body of people on the one hand and the elite on the other. Situating itself as the people’s authentic voice against this elite, the AKP tried to further its popular appeal and legitimize its extension of power. What appeared as coming to terms with the past was instead the instrumentalization of the past for a singular political agenda, eager to remove the complexities and pluralism of the past for the sake of telling a politically useful story.
Initial contact shapes the perception of friction

Significance Humans have the remarkable ability to manipulate a large variety of objects, regardless of how fragile, heavy, or slippery they are. To correctly scale the grip forces, the nervous system gauges the slipperiness of the surface. This information is present at the instant we first touch an object, even before any lateral force develops. However, how friction could be estimated without slippage only from the fingertip skin deformation is not understood, either in neuroscience or engineering disciplines. This study demonstrates that a radial tensile strain of the skin is involved in the perception of slipperiness during this initial contact. These findings can inform the design of advanced tactile sensors for robotics or prosthetics and for improving haptic human–machine interactions. Humans efficiently estimate the grip force necessary to lift a variety of objects, including slippery ones. The regulation of grip force starts with the initial contact and takes into account the surface properties, such as friction. This estimation of the frictional strength has been shown to depend critically on cutaneous information. However, the physical and perceptual mechanism that provides such early tactile information remains elusive. In this study, we developed a friction-modulation apparatus to elucidate the effects of the frictional properties of objects during initial contact. We found a correlation between participants’ conscious perception of friction and radial strain patterns of skin deformation. The results provide insights into the tactile cues made available by contact mechanics to the sensorimotor regulation of grip, as well as to the conscious perception of the frictional properties of an object.
Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference

Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs, and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail, and by analyzing five additional datasets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other datasets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.
Oligomerization of the FliF Domains Suggests a Coordinated Assembly of the Bacterial Flagellum MS Ring

The bacterial flagellum is a complex, self-assembling macromolecular machine that powers bacterial motility. It plays diverse roles in bacterial virulence, including aiding in colonization and dissemination during infection. The flagellum consists of a filamentous structure protruding from the cell, and the basal body, a large assembly that spans the cell envelope. The basal body is comprised of over 10 different proteins, forming several concentric ring structures, termed the M- S- L- P- and C-rings, respectively. In particular, the MS rings are formed by a single protein FliF, which consists of two trans-membrane helices anchoring it to the inner membrane and surrounding a large periplasmic domain. Assembly of the MS ring, through oligomerization of FliF, is one of the first steps of basal body assembly. Previous computational analysis had shown that the periplasmic region of FliF consists of three structurally similar domains, termed Ring-Building Motif (RBM)1, RBM2 and RBM3. The structure of the MS-ring has been reported recently, and unexpectedly shown that these three domains adopt different symmetries, with RBM3 having a 34-mer stoichiometry, while RBM2 adopts two distinct positions in the complex, including a 23-mer ring. This observation raises some important question on the assembly of the MS ring, and the formation of this symmetry mis-match within a single protein. In this study, we analyze the oligomerization of the individual RBM domains in isolation, in the Salmonella typhimurium FliF orthologue. We demonstrate that the periplasmic domain of FliF assembles into the MS ring, in the absence of the trans-membrane helices. We also report that the RBM2 and RBM3 domains oligomerize into ring structures, but not RBM1. Intriguingly, we observe that a construct encompassing RBM1 and RBM2 is monomeric, suggesting that RBM1 interacts with RBM2, and inhibits its oligomerization. However, this inhibition is lifted by the addition of RBM3. Collectively, this data suggests a mechanism for the controlled assembly of the MS ring.
Mosaic Evolution of Beta Barrel Porin Encoding Genes in Escherichia coli

Bacterial porins serve as the interface interacting with extracellular environment, and are often found under positive selection to fit in different environmental stresses. Local recombination has been identified in a handful of porin genes to facilitate the rapid adaptation of bacterial cells. It remains unknown whether it is a common evolutionary mechanism in gram-negative bacteria for all or a majority of the outer membrane proteins. In this research, we investigated the β-barrel porin encoding genes in Escherichia coli that were reported under positive Darwinia selection. Besides fhuA that was found with ingenic local recombination predominantly previously, we identified four other genes, i.e., lamB, ompA, ompC and ompF, all showing the similar mosaic evolution patterns as in fhuA. Comparative analysis of the protein sequences disclosed a list of highly variable regions in each protein family, which are mostly located in the convex of extracellular loops and coinciding with the binding sites of various bacteriophages. For each of the porin family, mosaic recombination leads to various combinations of the HVRs with different sequence patterns, generating diverse protein groups. Structure modeling further indicated the conserved global topology for various groups of each porin family, but the extracellular surface varies a lot that is formed by individual or combinatorial HVRs. The conservation of global tertiary structure ensures the channel activity while the wide diversity of HVRs may assist bacteria avoiding the invasion of phages, antibiotics or immune surveillance factors. In summary, the study identified multiple bacterial porin genes with mosaic evolution, a likely general strategy, by which outer membrane proteins could facilitate the host bacteria to both maintain normal life processes and evade the attack of unflavored environmental factors rapidly. Importance Microevolution studies can disclose more elaborate evolutionary mechanisms of genes, appearing especially important for genes with multifaceted function such as those encoding outer membrane proteins. However, in most cases, the gene is considered as a whole unit and the evolutionary patterns are disclosed. In this research, we reported that multiple bacterial porin proteins follow mosaic evolution, with local ingenic recombination combined with spontaneous mutations based positive Darwinia selection, and conservation for most of the other regions. It could represent a common mechanism for bacterial outer membrane proteins. The study also provides insights on development of new anti-bacterial agent or vaccines.
Regulation of immune receptor kinases plasma membrane nanoscale landscape by a plant peptide hormone and its receptors

Spatial partitioning is a propensity of biological systems orchestrating cell activities in space and time. The dynamic regulation of plasma membrane nano-environments has recently emerged as a key fundamental aspect of plant signaling, but the molecular components governing it are still mostly unclear. The receptor kinase FERONIA (FER) controls complex formation of the immune receptor kinase FLAGELLIN SENSING 2 (FLS2) with its co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1), and this function is inhibited by the FER ligand RAPID ALKALANIZATION FACTOR 23 (RALF23). Here, we show that FER regulates the plasma membrane nanoscale organization of FLS2 and BAK1. Our study demonstrates that akin to FER, leucine-rich repeat (LRR) extensin (LRXs) proteins contribute to RALF23 responsiveness, regulate BAK1 nanoscale organization and immune signaling. Furthermore, RALF23 perception leads to rapid modulation of FLS2 and BAK1 nanoscale organization and its inhibitory activity on immune signaling relies on FER kinase activity. Our results suggest that perception of RALF peptides by FER and LRXs actively modulates the plasma membrane nanoscale landscape to regulate cell surface signaling by other receptor kinases.