Miracle-dz/UniFAR-FTUs huggingface dataset:
DYNAMIC RELATIONSHIP BETWEEN MECHANICAL PROPERTIES AND CHEMICAL COMPOSITION DISTRIBUTION OF WOOD CELL WALLS

Wood is a natural composite material with a complex structure. Its mechanical properties are mainly due to the cell walls. In order to investigate the relationship between mechanical properties and chemical composition of wood cell wall. Nanoindentation and Raman imaging were used to characterize the longitudinal mechanical properties and chemical composition distribution of wood fibers of three years old fast-growing poplar (Populus×euramericana cv. ‘74 /76’) during the growing season at different times. The results were showed that the content and distribution of cellulose and lignin are closely related to the mechanical properties of wood fiber cell walls, especially the cellulose for the longitudinal elastic modulus and the lignin for the hardness of cell walls. It was also demonstrated that the longitudinal elastic modulus and hardness of the secondary wall 2 layer (S2) were strongly correlated to the micro fibril angle (MFA) and crystallinity of cellulose during the active phase.
Pulsed Neutron Diffraction of Phosphorous Acid and its Aqueous Solution with Inactivation Capability of Activated Oxygen

Pulsed neutron diffraction was carried out to analyze an intramolecular structure of D3PO3 and an orientational characteristic of adjacent molecules in D3PO3–nD2O ( n = 0, 1 and 20) solutions by using the high intensity total scattering spectrometer in High Energy Accelerator Research Organization (KEK) at Tsukuba, Japan. The radial distribution method and the correlation method were employed for the analysis of structural parameters such as interatomic distances, coordination numbers and temperature factors, being consulted with those by simulations. The intramolecular structure of the phosphorous acid in the liquid state did not differ much from that in the crystalline state. In the liquid phosphorous acid, two intramolecular P-O bonds were recognized, the shorter P-O bond being assigned to the P-O double bond and the longer P-O to the single bond. On addition of heavy water, the coordination numbers of the intramolecular P-O correlations, i.e. both the shorter P-O double bond and the longer P-O single .
Optimization of neural network computations by reducing the precision of numbers

The current generation of neural networks requires a lot of resources in terms of storage and computing time. Due to the high number of parameters needed in this networks and the high precision of numbers (integers and ﬂoating point numbers) representing the weights and bias, the computations take a lot of time. it’s hard to imagine integrating this generation of neural networks in embedded systems, such as drones or microcontrollers that do not have a high power. Having noted this problem, new research has looked into the possibility of reducing the number of bits on which neural networks parameters are represented in order to reduce computing time and memory requirements. Thus, in this paper we present the formulations mathematics of two of them: the binarization which consists in reducing weights and outputs in the binary set {− 1 , + 1 } , and the ternarization which consists in reducing weights into the set {− 1 , 0 , + 1 } . We explain in this paper how to implement these types of neural networks, efﬁcient in terms of memory and computation time, based on research and open source projects related to this issue. We also present a learning algorithm adapted to these neural networks. And ﬁnally, we’re redeﬁning the arithmetic operations to ﬁt the operands of the set {− 1 , + 1 } , so that they can be used in simpliﬁed systems that operate in binary.
Breaking Writer’s Block: Low-cost Fine-tuning of Natural Language Generation Models

It is standard procedure these days to solve Information Extraction task by fine-tuning large pre-trained language models. This is not the case for generation task, which relies on a variety of techniques for controlled language generation. In this paper, we describe a system that fine-tunes a natural language generation model for the problem of solving writer’s block. The fine-tuning changes the conditioning to also include the right context in addition to the left context, as well as an optional list of entities, the size, the genre and a summary of the paragraph that the human author wishes to generate. Our proposed fine-tuning obtains excellent results, even with a small number of epochs and a total cost of USD 150. The system can be accessed as a web-service and all the code is released. A video showcasing the interface and the model is also available.
Synthesis and self-organization of Au nanoparticles

Monodisperse (diameter 10 nm) Au nanoparticles have been synthesized by the reduction of AuCl3 at high temperatures, in commercial oleyl amine, in the presence of tri-octyl phosphine oxide (TOPO). The oleyl amine molecule has multiple roles, acting as high-boiling-point solvent, capping agent and reducing agent. The Au nanocrystalline particles have been studied by powder x-ray diffraction (XRD) and transmission electron microscopy (TEM). The nanoparticles can disperse well in non-polar solvents such as hexane, toluene and chloroform. The as-received Au nanoparticles, capped with the alkylamine-TOPO molecules, form two-dimensional superlattices via solvent evaporation. Moreover, they can be converted into a water-soluble derivative via a simple procedure based on the formation of a physisorbed layer of an ionic (cationic or anionic) surfactant around the capped surface. The charged particles can assemble in aqueous solution into three-dimensional structures via electrostatic interactions.
Recent Advances in Docking and Scoring

This review is focused on recent advances and new aspects in the field of molecular docking and scoring, and it covers multiple applications and case studies. Basic requirements and different algorithms for docking are briefly discussed. Moreover, parameters that influence docking results, combination of different docking algorithms and scoring functions, performance of scoring functions, docking using homology models, and ligand and protein flexibility are examined to give an overview of the state-of-the-art methods and a survey of innovative approaches in molecular docking and scoring. Regarding the enormous amount of literature in this field we restrict ourselves on an overview of several important advances in docking and scoring techniques published within the last two years, i.e. we considered publications ranging from 2002 to 2004.
The mass balance model perfectly fits both Hall et al. underfeeding data and Horton et al. overfeeding data

Abstract Background & Aims Recently, the validity of mass balance model (MBM) was questioned based on two feeding studies. Thus, we simulated both of these feeding trials. Methods MBM describes the temporal evolution of body weight and body composition under a wide variety of feeding experiments. This computational study simulated, utilizing MBM, the underfeeding trial by Hall et al. (Cell Metab. 2015;22:427-36) and the overfeeding trial by Horton et al. (Am J Clin Nutr. 1995;62:19-29). Results Our simulation results indicate that data from both of these feeding trials perfectly match MBM-based predictions, i.e., MBM gives a remarkably accurate description of experimental data. Conclusions It is becoming increasingly clear that our model (MBM) is perfectly able to predict body weight and body composition fluctuations under a wide variety of feeding experiments.
Vapor Phosphorylation of Cellulose by Phosphorus Trichlo-Ride: Selective Phosphorylation of 6-Hydroxyl Function—The Synthesis of New Antimicrobial Cellulose 6-Phosphate(III)-Copper Complexes

This research is focused on a synthesis of copper-cellulose phosphates antimicrobial complexes. Vapor-phase phosphorylations of cellulose were achieved by exposing microcrystalline cellulose to phosphorus trichloride (PCl3) vapors. The cellulose-O-dichlorophosphines (Cell-O-PCl2) formed were hydrolyzed to cellulose-O-hydrogenphosphate (P(III)) (Cell-O-P(O)(H)(OH)), which, in turn, were converted into corresponding copper(II) complexes (Cell-O-P(O)(H)(OH)∙Cu2+). The analysis of the complexes Cell-O-P(O)(H)(OH)∙Cu2+ covered: scanning electron microscopy (SEM), attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), atomic absorption spectrometry with flame excitation (FAAS), and bioactivity tests against representative Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Staphylococcus aureus). The antimicrobial tests of synthesized Cell-O-P(O)(H)(OH)∙Cu2+ revealed their potential applications as an antibacterial material.
The Benefits and Hazards of Intravitreal Mesenchymal Stem Cell (MSC) Based-Therapies in the Experimental Ischemic Optic Neuropathy

Mesenchymal stem cell (MSC) therapy has been investigated intensively for many years. However, there is a potential risk related to MSC applications in various cell niches. Methods: The safety of intravitreal MSC application and the efficacy of MSC-derived conditioned medium (MDCM) were evaluated in the normal eye and the diseased eye, respectively. For safety evaluation, the fundus morphology, visual function, retinal function, and histological changes of the retina were examined. For efficacy evaluation, the MDCM was intravitreally administrated in a rodent model of anterior ischemic optic neuropathy (rAION). The visual function, retinal ganglion cell (RGC) density, and neuroinflammation were evaluated at day 28 post-optic nerve (ON) infarct. Results: The fundus imaging showed that MSC transplantation induced retinal distortion and venous congestion. The visual function, retinal function, and RGC density were significantly decreased in MSC-treated eyes. MSC transplantation induced astrogliosis, microgliosis, and macrophage infiltration in the retina due to an increase in the HLA-DR-positive MSC proportion in vitreous. Treatment with the MDCM preserved the visual function and RGC density in rAION via inhibition of macrophage infiltration and RGC apoptosis. Conclusions: The vitreous induced the HLA-DR expression in the MSCs to cause retinal inflammation and retina injury. However, the MDCM provided the neuroprotective effects in rAION.
Predictors of Progression and Mortality in Patients with Prevalent Rheumatoid Arthritis and Interstitial Lung Disease: A Prospective Cohort Study

Objectives: To describe a prospective cohort of patients with rheumatoid arthritis associated with interstitial lung disease (RA-ILD) and identify risk factors associated with disease progression and mortality in this cohort. Patients and methods: We performed a multicenter, prospective, observational study of patients with RA-ILD receiving disease-modifying antirheumatic drugs (DMARDs) between 2015 and 2020. The patients were assessed using high-resolution computed tomography and pulmonary function tests at baseline and at 60 months. The main endpoint was “Progression to ILD at the end of follow-up” in terms of the following outcomes: (1) improvement (i.e., improvement in forced vital capacity (FVC) ≥10% or diffusing capacity of the lungs for carbon monoxide (DLCO) ≥15% and absence of radiological progression); (2) nonprogression (stabilization or improvement in FVC ≤10% or diffusing capacity of the lungs for carbon monoxide (DLCO) <15% and absence of radiological progression); (3) progression (worsening of FVC >10% or DLCO >15% and radiological progression); or (4) death. We recorded demographic and clinical characteristics, lung function, and the incidence of adverse events. A Cox regression analysis was performed to identify factors associated with the worsening of ILD. Results: After 60 months, lung disease had stabilized in 66 patients (56.9%), improved in 9 (7.8%), and worsened in 23 (19.8%). Eighteen patients (15.5%) died, with a mean survival of 71.8 (1.9) months after diagnosis of ILD. The Cox multivariate analysis revealed the independent predictors of worsening of RA-ILD to be usual interstitial pneumonia (hazard ratio (HR), 2.6 (95%CI, 1.0–6.7)), FVC <80% (HR, 3.8 (95%CI, 1.5–6.7)), anticitrullinated protein antibody titers (HR, 2.8 (95%CI, 1.1–6.8)), smoking (HR, 2.5 (95%CI, 1.1–6.2)), and treatment with abatacept, tocilizumab, or rituximab (HR, 0.4 (95%CI, 0.2–0.8)). During follow-up, 79 patients (68%) experienced an adverse event, mostly infection (61%). Infection was fatal in 10/18 patients (55.5%) during follow-up. Conclusions: Lung function is stable in most patients with RA-ILD receiving treatment with disease-modifying anti-rheumatic drugs (DMARDs), although one-third worsened or died. Identifying factors associated with worsening in RA-ILD is important for clinical management.
Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity

For decades, bacteriophage purification has followed structured protocols focused on generating high concentrations of phage in manageable volumes. As research moves toward understanding complex phage populations, purification needs have shifted to maximize the amount of phage while maintaining diversity and activity. The effects of standard phage purification procedures such as polyethylene glycol (PEG) precipitation and cesium chloride (CsCl) density gradients on both diversity and activity of a phage population are not known. We have examined the effects of PEG precipitation and CsCl density gradients on a number of known phage (M13, T4, and ΦX 174) of varying structure and size, individually and as mixed sample. Measurement of phage numbers and activity throughout the purification process was performed. We demonstrate that these methods, used routinely to generate “pure” phage samples, are in fact detrimental to retention of phage number and activity; even more so in mixed phage samples. As such, minimal amounts of processing are recommended to introduce less bias and maintain more of a phage population.
Microbial Biofilms in the Food Industry—A Comprehensive Review

Biofilms, present as microorganisms and surviving on surfaces, can increase food cross-contamination, leading to changes in the food industry’s cleaning and disinfection dynamics. Biofilm is an association of microorganisms that is irreversibly linked with a surface, contained in an extracellular polymeric substance matrix, which poses a formidable challenge for food industries. To avoid biofilms from forming, and to eliminate them from reversible attachment and irreversible stages, where attached microorganisms improve surface adhesion, a strong disinfectant is required to eliminate bacterial attachments. This review paper tackles biofilm problems from all perspectives, including biofilm-forming pathogens in the food industry, disinfectant resistance of biofilm, and identification methods. As biofilms are largely responsible for food spoilage and outbreaks, they are also considered responsible for damage to food processing equipment. Hence the need to gain good knowledge about all of the factors favouring their development or growth, such as the attachment surface, food matrix components, environmental conditions, the bacterial cells involved, and electrostatic charging of surfaces. Overall, this review study shows the real threat of biofilms in the food industry due to the resistance of disinfectants and the mechanisms developed for their survival, including the intercellular signalling system, the cyclic nucleotide second messenger, and biofilm-associated proteins.
Effect of cadmium-contaminated soils on dry matter yield and mineral composition of raya (Brassica juncea) and spinach (Spinacia oleracea).

Raya (Brassica juncea) and spinach (Spinacia oleracea), grown as leafy vegetables, are known to accumulate large amounts of heavy metals in their shoots and roots because of their high biomass and root proliferation. In a pot experiment, a sandy loam soil was polluted with cadmium (Cd) at rates of 0, 5, 10, 20, 40 and 80 mg kg−1 soil to assess the accumulation pattern and its effect on the dry matter yield and mineral composition of these vegetables. There was a decrease in dry matter yield due to the phytotoxic effect of Cd. The rate of Cd application at which a significant decline in root and shoot dry matter yield occurred varied depending on the vegetable. It was 20 mg Cd kg−1 soil in the shoots for both crops. However, the roots of raya were found to be more tolerant of Cd toxicity than those of spinach, as is evident from the fact that a significant decline in dry matter yield occurred at 20 and 10 mg Cd kg−1 soil, respectively. Since no visual toxic symptoms were observed on the leaves of raya in a.
Promising Molecular Targets for the Targeted Therapy of Biliary Tract Cancers: An Overview

Abstract Biliary tract cancer (BTC) is a leading cause of cancer-related death, due to the limited benefits of current systematic therapies and the heterogeneity of the tumor itself. High heterogeneity means that the clinical and molecular features vary between different subtypes of BTC, while the underlying molecular mechanisms remain unclear. Targeted therapy, where inhibitors are developed to selectively combine with targeted molecules in order to block abnormal signaling pathways in BTC, has shown promise as an emerging form of treatment for various types of cancer. In this article, a comprehensive review is conducted to examine potential molecular targets for BTC targeted therapy and their mechanisms. Furthermore, preliminary data published from clinical trials is utilized to analyze the main drugs used to combat BTC. The collective information presented in this article has provided useful insights into the current understanding of BTC.
Female Germ Cell Development, Functioning and Associated Adversities under Unfavorable Circumstances

In the present era, infertility is one of the major issues which restricts many couples to have their own children. Infertility is the inability to achieve a clinical pregnancy after regular unprotected sexual intercourse for the period of one year or more. Various factors including defective male or female germ cell development, unhealthy and improper lifestyles, diseases like cancer and associated chemo-or-radiation therapies, congenital disorders, etc., may be responsible for infertility. Therefore, it is highly important to understand the basic concepts of germ cell development including primordial germ cell (PGC) formation, specification, migration, entry to genital ridges and their molecular mechanisms, activated pathways, paracrine and autocrine signaling, along with possible alteration which can hamper germ cell development and can cause adversities like cancer progression and infertility. Knowing all these aspects in a proper way can be very much helpful in improving our understanding about gametogenesis and finding possible ways to cure related disorders. Here in this review, various aspects of gametogenesis especially female gametes and relevant factors causing functional impairment have been thoroughly discussed.
The History of Colistin Resistance Mechanisms in Bacteria: Progress and Challenges

Since 2015, the discovery of colistin resistance genes has been limited to the characterization of new mobile colistin resistance (mcr) gene variants. However, given the complexity of the mechanisms involved, there are many colistin-resistant bacterial strains whose mechanism remains unknown and whose exploitation requires complementary technologies. In this review, through the history of colistin, we underline the methods used over the last decades, both old and recent, to facilitate the discovery of the main colistin resistance mechanisms and how new technological approaches may help to improve the rapid and efficient exploration of new target genes. To accomplish this, a systematic search was carried out via PubMed and Google Scholar on published data concerning polymyxin resistance from 1950 to 2020 using terms most related to colistin. This review first explores the history of the discovery of the mechanisms of action and resistance to colistin, based on the technologies deployed. Then we focus on the most advanced technologies used, such as MALDI-TOF-MS, high throughput sequencing or the genetic toolbox. Finally, we outline promising new approaches, such as omics tools and CRISPR-Cas9, as well as the challenges they face. Much has been achieved since the discovery of polymyxins, through several innovative technologies. Nevertheless, colistin resistance mechanisms remains very complex.
Anti-MRSA Constituents from Ruta chalepensis (Rutaceae) Grown in Iraq, and In Silico Studies on Two of Most Active Compounds, Chalepensin and 6-Hydroxy-rutin 3′,7-Dimethyl ether

Ruta chalepensis L. (Rutaceae), a perennial herb with wild and cultivated habitats, is well known for its traditional uses as an anti-inflammatory, analgesic, antipyretic agent, and in the treatment of rheumatism, nerve diseases, neuralgia, dropsy, convulsions and mental disorders. The antimicrobial activities of the crude extracts from the fruits, leaves, stem and roots of R. chalepensis were initially evaluated against two Gram-positive and two Gram-negative bacterial strains and a strain of the fungus Candida albicans. Phytochemical investigation afforded 19 compounds, including alkaloids, coumarins, flavonoid glycosides, a cinnamic acid derivative and a long-chain alkane. These compounds were tested against a panel of methicillin-resistant Staphylococcus aureus (MRSA) strains, i.e., ATCC 25923, SA-1199B, XU212, MRSA-274819 and EMRSA-15. The MIC values of the active compounds, chalepin (9), chalepensin (10), rutamarin (11), rutin 3′-methyl ether (14), rutin 7,4′-dimethyl ether (15), 6-hydroxy-rutin 3′,7-dimethyl ether (16) and arborinine (18) were in the range of 32–128 µg/mL against the tested MRSA strains. Compounds 10 and 16 were the most active compounds from R. chalepensis, and were active against four out of six tested MRSA strains, and in silico studies were performed on these compounds. The anti-MRSA activity of compound 16 was comparable to that of the positive control norfloxacin (MICs 32 vs 16 μg/mL, respectively) against the MRSA strain XU212, which is a Kuwaiti hospital isolate that possesses the TetK tetracycline efflux pump. This is the first report on the anti-MRSA property of compounds isolated from R. chalepensis and relevant in silico studies on the most active compounds.