Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico Analysis of Changes in Predicted Metabolic Capabilities of Intestinal Microbiota after Fecal Microbial Transplantation for Treatment of Recurrent Clostridioides difficile Infection

Importance: Although highly effective in treating recurrent Clostridioides difficile infection (RCDI), the mechanisms of action of fecal microbial transplantation (FMT) are not fully understood. Aim: The aim of this study was to explore microbially derived products or pathways that could contribute to the therapeutic efficacy of FMT. Methods: Stool shotgun metagenomic sequencing data from 18 FMT-treated RCDI patients at 4 points in time were used for the taxonomic and functional profiling of their gut microbiome. The abundance of the KEGG orthology (KO) groups was subjected to univariate linear mixed models to assess the significance of the observed differences between 0 (pre-FMT), 1, 4, and 12 weeks after FMT. Results: Of the 59,987 KO groups identified by shotgun metagenomic sequencing, 27 demonstrated a statistically significant change after FMT. These KO groups are involved in many cellular processes, including iron homeostasis, glycerol metabolism, and arginine regulation, all of which have been implicated to play important roles in bacterial growth and virulence in addition to modulating the intestinal microbial composition. Conclusion: Our findings suggest potential changes in key KO groups post-FMT, which may contribute to FMT efficacy beyond the restored microbial composition/diversity and metabolism of bile acids and short-chain fatty acids. Future larger studies that include a fecal metabolomics analysis combined with animal model validation work are required to further elucidate the molecular mechanisms.
Hierarchical simulation for rare events

A speed-up technique for the simulation of very rare events (p 10 -9 ) is proposed. Developed as part of research on cell losses in ATM switching nodes, it extends the classical importance sampling. It is to be applied when a set of cut-off points can be identified in a Markov chain that in an orderly way imply each other and the rare events as well. A batch mean technique is used for estimating the Cv's of the primary estimators. Thus, the size of the simulation to be run is easily determined. And, second but not least, an algorithmic choice for the intermediate conditioning events is to be inferred from those Cv's. Some side-optimizations are also proposed. An analytically solvable example is then addressed for illustrating and checking purpose. A good concordance is found, especially between the estimated Cv's and the explicitly calculated standard deviations. The paper ends with a discussion of the limitations and applicability of the proposed method.
Polar Decomposition of a Matrix

The matrix representation of systems reveals many useful and fascinating properties of linear transformations. One such representation is the polar decomposition. This paper will investigate the polar decomposition of matrices. The polar decomposition is analogous to the polar form of coordinates. We will begin with a definition of the decomposition and then a proof of its existence. We will then move on to the construction of the decomposition and some interesting properties including a guest appearance by the singular value decomposition. The final component of the paper will be a discussion of the geometric underpinnings of the polar decomposition through an example.
Cellulases: From Lignocellulosic Biomass to Improved Production

Cellulases are enzymes that are attracting worldwide attention because of their ability to degrade cellulose in the lignocellulosic biomass and transform it into highly demanded bioethanol. The enzymatic hydrolysis of cellulose by cellulases into fermentable sugars is a crucial step in biofuel production, given the complex structure of lignocellulose. Due to cellulases’ unique ability to hydrolyze the very recaltricant nature of lignocellulosic biomass, the cellulase market demand is rapidly growing. Although cellulases have been used in industrial applications for decades, constant effort is being made in the field of enzyme innovation to develop cellulase mixtures/cocktails with improved performance. Given that the main producers of cellulases are of microbial origin, there is a constant need to isolate new microorganisms as potential producers of enzymes important for biofuel production. This review provides insight into current research on improving microbial cellulase production as well as the outlook for the cellulase market with commercial cellulase preparation involved in industrial bioethanol production.
Molecular Genetic Analysis of the Autosomal Recessive Non-Syndromic Inherited Retinitis Pigmentosa

Introduction: 90% of visually impaired people live in developing countries. There are various types of vision impairment, but the focus of the current study is retinitis pigmentosa (RP). Up to now, 150 mutations have been reported that are linked with RP. Methodology: Healthy and affected members from two Pakistani families (RP01 and RP02) segregating autosomal recessive RP were selected for DNA extraction. PCR was conducted, and the amplified PCR products were analyzed using Polyacrylamide Gel Electrophoresis (PAGE) and visualized in the Gel Doc system for linkage analysis. The Gene Hunter 2.1r5 tool in the Simple Linkage v5.052 beta software suite was used to conduct multipoint parametric linkage analysis on the two consanguineous families examined on the 6K Illumina array. Exons and intron-exon borders of all known arRP genes found in homozygous areas were sequenced in the matching probands using a 3130 automated sequencer and the Big Dye Terminator Cycle Sequencing Kit v3.1. The mutation study was carried out using the AlaMut 1.5 program. Results: In both families, linkage analysis was performed using microsatellite marker DIS422 for gene crumbs homolog 1 (CRB1) and microsatellite marker D8S2332 for gene Retinitis Pigmentosa 1 (RP1). Multipoint linkage analysis identifies genomic regions that could potentially contain the genetic defect. In family RP01, only a single peak with a maximal multipoint LOD score of 3.00 was identified on chromosome 1, whereas in family RP02, multiple peaks with multipoint LOD scores of 1.80 were identified on chromosome 8. Analysis of the CRB1 gene revealed a homozygous substitution of glycine for valine (c.1152T>G; p.V243G), whereas the RP1 gene demonstrated that leucine was substituted for proline as a result of cytosine to thymine transfer (c.3419C>T; p. P1035L). Conclusion: Homozygosity mapping is a powerful method for finding genetic abnormalities that are both precise and comprehensive for identifying harmful variations in consanguineous families. This method is invaluable for providing accurate clinical diagnostic and genetic advice in remote regions of Pakistan while also increasing knowledge about autosomal recessive diseases and the dangers of mixing.
Organic-inorganic composites for THz device fabrication

In this paper, several organic-inorganic composites were prepared for Terahertz (THz) devices fabrication. First, a two-layer structure was designed for femtosecond (fs) laser/THz radiation separation. The top layer was made by sintered 20-40 nm hollow quartz particles which can diffuse the incident fs laser thus decrease the power intensity. The bottom layer comprised of silicon 100 nm particles and cycle-olefine polymer (COP), by which the fs laser light can be greatly scattered and absorbed but THz radiation can propagate insusceptibly. With this two-layer structure a high efficient fs-laser/THz filter was fabricated successfully. Second, titania–polymer composites with a very high refractiveindex tunability and high transparency in the THz region were prepared. By controlling the blending ratio of the titania particle, a broad refractive-index tuning range from 1.5 to 3.1 was realized. Then, the composites were used to fabricate antireflective (AR) layers on a high-resistivity silicon (HR-Si) substrate. By utilizing the thermoplasticity of the titania– polymer composite, a graded-index structure was fabricated via a hot-embossing method. Because of the good refractive-index matching between the composite and the HR-Si substrate, a broadband AR layer was fabricated.
Regulation of Ras-GTPase Signaling and Localization by Post-Translational Modifications

Ras, a GTP-GDP binary switch protein, transduces signals from diverse receptors to regulate various signaling networks. Three Ras genes encode for protein isoforms, namely, Harvey Ras (H-Ras), Kirsten Ras (K-Ras, with two splice variants, K-Ras4A and K-Ras4B), and Neuroblastoma Ras (N-Ras). The isoforms undergo a series of post-translational modifications that enable their membrane attachment and biological activity. The activation of Ras isoforms is tightly regulated, and any dysregulation affects cellular processes, such as cell division, apoptosis, differentiation, cell migration, etc. The Ras gene is highly prone to mutation, and ~30% of cancers carry somatic mutations in Ras, whereas germline mutations clinically manifest as various rasopathies. In addition to regulation by the Guanine nucleotide exchange factors and the GTPase activation proteins, Ras signaling, and localization are also regulated by phosphorylation-dephosphorylation, ubiquitination, nitrosylation, and acetylation. Herein, we review the regulation of Ras signaling and localization by various regulatory enzymes in depth and assess the current status of Ras drug discovery targeting these regulatory enzymes.
Mise en œuvre de schémas numériques pour l'étude d'écoulements diphasiques instationnaires

Cet article propose la mise en œuvre de schemas numeriques permettant le calcul d'ecoulements diphasiques liquide-vapeur monodimensionnels instationnaires. Les cas tests classiques sont decrits avec leur etude de convergence. Des comparaisons avec des resultats experimentaux stationnaires sont aussi donnees.
KernGPLM – A Package for Kernel-Based Fitting of Generalized Partial Linear and Additive Models

Marlene Müller Aim of this Talk analysis of highdimensional data by semiparametric (generalized) regression models • compare different approaches to additive models (AM) and generalized additive models (GAM) • include categorical variables =⇒ partial linear terms (combination of AM/PLM and GAM/GPLM) • provide software ⇒ R package KernGPLM • focus on kernel-based techniques for high-dimensional data
UMA CIDADE CRIATIVA PARA POTENCIALIZAR O DESENVOLVIMENTO LOCAL SUSTENTÁVEL

RESUMO O argumento do texto é que a cidade criativa apresenta potencial para impulsionar a capacidade humana de cocriar soluções para os problemas urbanos e promover o desenvolvimento local sustentável. Para que as cidades adotem essa nova lógica territorial, os gestores e planejadores devem primeiro entender como a criatividade se origina e sua rede interacional. Embora haja uma crescente literatura sobre o tema, pouca atenção tem sido dedicada à produção do espaço criativo. Para tanto, faz-se necessária a compreensão conceitual de espaço, território e sociabilidades, a partir de uma perspectiva sociológica. Desse modo, foi realizada uma revisão bibliográfica e documental. Os resultados apontam a demanda por gestão da criatividade pelas cidades e, em especial, algumas experiências brasileiras estão apenas priorizando aspectos econômicos em vez de mitigar a problemática urbana. A cidade criativa em sua essência transcende a classe criativa e a economia criativa, em que trata-se de um modelo urbano multidimensional. Vê-se que o espaço criativo é uma produção social que reflete a sociedade que o produz, contudo, é benéfico uma melhor formulação de políticas que visam promovê-lo e também a necessidade da realização de futuros estudos empíricos diante da emergência do fenômeno urbano.
Health Disparities in Multiple Sclerosis among Hispanic and Black Populations in the United States

Multiple sclerosis (MS) is an acquired demyelinating disease of the central nervous system (CNS). Historically, research on MS has focused on White persons with MS. This preponderance of representation has important possible implications for minority populations with MS, from developing effective therapeutic agents to understanding the role of unique constellations of social determinants of health. A growing body of literature involving persons of historically underrepresented races and ethnicities in the field of multiple sclerosis is assembling. Our purpose in this narrative review is to highlight two populations in the United States: Black and Hispanic persons with multiple sclerosis. We will review the current understanding about the patterns of disease presentation, genetic considerations, response to treatment, roles of social determinants of health, and healthcare utilization. In addition, we explore future directions of inquiry as well as practical methods of meeting these challenges.
On the Stability of Conjunctive Boolean Networks

Boolean networks have been used extensively in modeling many biological systems. In this paper, we study the stability of conjunctive Boolean networks, which consist of canalyzing functions using only the logic AND operator. To analyze the stability of such networks, we develop a method that decomposes the wiring diagram into a number of components each of which is an irreducible subgraph. In particular, we show that the system may switch from one limit cycle to another under certain conditions, when one of the variables fails to follow the coordinate function. It is also shown that for conjunctive Boolean networks whose wiring diagram is strongly connected, the number of limit cycles can be computed using the binary necklace model.
Chitosan-based mixed matrix membranes: effect of different fillers on membrane properties and performance in hydrophilic pervaporation

Abstract Pervaporation is still regarded as an emergent process, with a great potential to be an alternative to classical separation processes, with technical advantages. Chitosan is considered a promising material in next-generation pervaporation membranes, especially hybrid and mixed matrix membranes. This study aimed to evaluate the effect of fillers such as calcium carbonate, kaolinite, graphene, and graphene oxide, added separately at the concentration of 1 wt. %, on the mechanic and physical-chemical properties, microstructure, and hydrophilic pervaporation performance of chitosan membranes cross-linked with glutaraldehyde. The fillers influenced the mechanical and physicochemical properties of the membranes differently. Relative to the hydrophilic pervaporation tests, the presence of calcium carbonate and kaolinite increased membrane efficiency (αW/E of 1,777 and 1,225 against 611 in the control), whereas graphene reduced the permeate flux (0.341 kg·m−2·h−1 against 0.397 kg·m−2·h−1 in the control). The addition of graphene oxide increased the flux and permeability of ethanol (0.089 kg·m−2·h−1 and 8.66·10−14 kg·m−1·s−1·Pa−1 against 0.019 kg·m−2·h−1 and 1.74·10−14 kg·m−1·s−1·Pa−1 in the control), unlike the other fillers, which had no significant influence on this parameter. Thus, the membranes containing the fillers calcium carbonate and kaolinite were more suited for use in hydrophilic pervaporation (PSI of 842 and 561 against 228 in the control). Graphene did not affect membrane properties (αW/E of 398 and PSI of 127). Graphene oxide (αW/E of 174 and PSI of 72) may be considered as an alternative and starting point for the development and research of mixed matrix membranes based on chitosan to be used in target-organophilic pervaporation.
MUREN: MUltistage Recursive Enhanced Network for Coal-Fired Power Plant Detection

The accurate detection of coal-fired power plants (CFPPs) is meaningful for environmental protection, while challenging. The CFPP is a complex combination of multiple components with varying layouts, unlike clearly defined single objects, such as vehicles. CFPPs are typically located in industrial districts with similar backgrounds, further complicating the detection task. To address this issue, we propose a MUltistage Recursive Enhanced Detection Network (MUREN) for accurate and efficient CFPP detection. The effectiveness of MUREN lies in the following: First, we design a symmetrically enhanced module, including a spatial-enhanced subnetwork (SEN) and a channel-enhanced subnetwork (CEN). SEN learns the spatial relationships to obtain spatial context information. CEN provides adaptive channel recalibration, restraining noise disturbance and highlighting CFPP features. Second, we use a recursive construction set on top of feature pyramid networks to receive features more than once, strengthening feature learning for relatively small CFPPs. We conduct comparative and ablation experiments in two datasets and apply MUREN to the Pearl River Delta region in Guangdong province for CFPP detection. The comparative experiment results show that MUREN improves the mAP by 5.98% compared with the baseline method and outperforms by 4.57–21.38% the existing cutting-edge detection methods, which indicates the promising potential of MUREN in large-scale CFPP detection scenarios.
Effects of defatted walnut meal as a potential ingredient in bread: physicochemical, rheological, functional and sensory properties

Potential functional ingredients, resulting after partial oil extraction by cold pressing, present a promising direction with perspective for the nutritional improvement of traditional bakery products and may enhance their health-promoting properties. The current study sought to determine the effect of wheat flour substitution with walnut (Juglans regia L.) meal by 0, 2, 4, and 6% of the total amount. The influence of partially defatted walnut meal (BWF) incorporation on dough physicochemical, and rheological properties, as well as the final sensory properties of the bread was investigated. Mixolab test results indicated an increase in dough development time and stability, a reduction of hydration capacity, free water content, enzymatic activity as well as a reduction of the shelf life of the enriched bread. Physical and sensory analyses showed that substitution of wheat flour with partially defatted walnut meal below 6% (on a flour basis) in bread manufacturing recipes yielded products with an enhanced porosity (72.2 to 74.5%), titratable acidity (1.4 to 2.3 degrees), freshness (2.0 to 7.8%) and polyphenol content (0.09 to 2.20 μg GAE/100 g product). All samples show specific positive characteristics, well defined, without defects, with a total acceptability of 4.54 - 4.88. The samples with 2% and 4% BWF show better quality indicators, therefore they can be recommended to consumers as products with high nutritional value.
Direction information is more influential than distance information in memory for location relative to landmarks

ABSTRACT Our results suggest that direction information is more influential than distance information in memory for the locations of objects relative to landmarks. Participants viewed target objects in conjunction with pairs of landmarks and then attempted to place the targets in the correct locations relative to the landmarks. The locations of the landmarks at test were slightly different from their locations at study. This dissociated the locations in which the targets would be placed if they were remembered solely on the basis of distance and direction, respectively. Participants placed the targets closer to the “direction-predicted” locations than to the “distance-predicted” locations.
Uncertainty calculation of the effective emissivity of cylinder-conical blackbody cavities

A numerical and geometrical model for calculating the local effective emissivity of isothermal blackbody cylinder-conical cavities with lid, assuming diffuse reflection, is described. This has been developed by generalizing previous models based on conical and cylindrical geometries. The model has been validated by determining the diffusely reflected photon trajectories and the corresponding experimental view factors between given pairs of surface elements. Differences compared to theoretical values, were subsequently analyzed in terms of the model’s intrinsic uncertainty. A well-defined numerical function that calculates the effective emissivity as a function of its natural variables, intrinsic emissivity and geometrical parameters, is established. In order to calculate the probability distribution of the output quantity, we use the Monte Carlo method for the propagation of the probability distributions that characterize our knowledge concerning the values of the influence variables. The model is applied to heat-pipe black bodies installed at our laboratory, previously characterized at the PTB. A comparison with published uncertainty results, obtained by applying classical uncertainty propagation techniques, is also made.
Steatosis and Metabolic Disorders Associated with Synergistic Activation of the CAR/RXR Heterodimer by Pesticides

The nuclear receptor, constitutive androstane receptor (CAR), which forms a heterodimer with the retinoid X receptor (RXR), was initially reported as a transcription factor that regulates hepatic genes involved in detoxication and energy metabolism. Different studies have shown that CAR activation results in metabolic disorders, including non-alcoholic fatty liver disease, by activating lipogenesis in the liver. Our objective was to determine whether synergistic activations of the CAR/RXR heterodimer could occur in vivo as described in vitro by other authors, and to assess the metabolic consequences. For this purpose, six pesticides, ligands of CAR, were selected, and Tri-butyl-tin (TBT) was used as an RXR agonist. In mice, CAR’s synergic activation was induced by dieldrin associated with TBT, and combined effects were induced by propiconazole, bifenox, boscalid, and bupirimate. Moreover, a steatosis, characterized by increased triglycerides, was observed when TBT was combined with dieldrin, propiconazole, bifenox, boscalid, and bupirimate. Metabolic disruption appeared in the form of increased cholesterol and lowered free fatty acid plasma levels. An in-depth analysis revealed increased expression of genes involved in lipid synthesis and lipid import. These results contribute to the growing understanding of how environmental contaminants can influence nuclear receptor activity and associated health risks.
Expression of the Populus Orthologues of AtYY1, YIN and YANG Activates the Floral Identity Genes AGAMOUS and SEPALLATA3 Accelerating Floral Transition in Arabidopsis thaliana

YIN YANG 1 (YY1) encodes a dual-function transcription factor, evolutionary conserved between the animal and plant kingdom. In Arabidopsis thaliana, AtYY1 is a negative regulator of ABA responses and floral transition. Here, we report the cloning and functional characterization of the two AtYY1 paralogs, YIN and YANG (also named PtYY1a and PtYY1b) from Populus (Populus trichocarpa). Although the duplication of YY1 occurred early during the evolution of the Salicaceae, YIN and YANG are highly conserved in the willow tree family. In the majority of Populus tissues, YIN was more strongly expressed than YANG. Subcellular analysis showed that YIN-GFP and YANG-GFP are mainly localized in the nuclei of Arabidopsis. Stable and constitutive expression of YIN and YANG resulted in curled leaves and accelerated floral transition of Arabidopsis plants, which was accompanied by high expression of the floral identity genes AGAMOUS (AG) and SEPELLATA3 (SEP3) known to promote leaf curling and early flowering. Furthermore, the expression of YIN and YANG had similar effects as AtYY1 overexpression to seed germination and root growth in Arabidopsis. Our results suggest that YIN and YANG are functional orthologues of the dual-function transcription factor AtYY1 with similar roles in plant development conserved between Arabidopsis and Populus.