Search results for: molecular characterization

Authors: Jan Bohata, Stanislav Zvanovec, Matej Komanec, Jakub Jaros, David Hruby

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Even though there is a rapid development in new optical networks, still optical communication infrastructures remain composed of thousands of kilometers of aging optical cables. Many of them are located in a harsh environment which contributes to an increased attenuation or induced birefringence of the fibers leading to the increase of polarization mode dispersion (PMD). In this paper, we report experimental results from environmental optical cable tests and characterization in the climate chamber. We focused on the evaluation of optical network reliability in a harsh environment. For this purpose, a special thermal chamber was adopted, targeting to the large temperature changes between -60 °C and 160 C° with defined humidity. Single mode optical cable 230 meters long, having six tubes and a total number of 72 single mode optical fibers was spliced together forming one fiber link, which was afterward tested in the climate chamber. The main emphasis was put to the polarization mode dispersion (PMD) changes, which were evaluated by three different PMD measuring methods (general interferometry technique, scrambled state-of-polarization analysis and polarization optical time domain reflectometer) in order to fully validate obtained results. Moreover, attenuation and chromatic dispersion (CD), as well as the PMD, were monitored using 17 km long single mode optical cable. Results imply a strong PMD dependence on thermal changes, imposing the exceeding 200 % of its value during the exposure to extreme temperatures and experienced more than 20 dB insertion losses in the optical system. The derived statistic is provided in the paper together with an evaluation of such as optical system reliability, which could be a crucial tool for the optical network designers. The environmental tests are further taken in context to our previously published results from long-term monitoring of fundamental parameters within an optical cable placed in a harsh environment in a special outdoor testbed. Finally, we provide a correlation between short-term and long-term monitoring campaigns and statistics, which are necessary for optical network safety and reliability.

Keywords: optical fiber, polarization mode dispersion, harsh environment, aging

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Authors: Zainab Dahrouch, Beatrix Petrovičová, Claudia Triolo, Fabiola Pantò, Angela Malara, Salvatore Patanè, Maria Allegrini, Saveria Santangelo

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Synthetic dyes dispersed in water cause environmental damage and have harmful effects on human health. Methylene blue (MB) is broadly used as a dye in the textile, pharmaceutical, printing, cosmetics, leather, and food industries. The complete removal of MB is difficult due to the presence of aromatic rings in its structure. The present study is focused on electrospun nanofibers (NFs) with engineered architecture and surface to be used as catalysts for the photodegradation of MB. Ti and/or Zn oxide NFs are produced by electrospinning precursor solutions with different Ti: Zn molar ratios (from 0:1 to 1:0). Subsequent calcination and cooling steps are operated at fast rates to generate porous NFs with capture centers to reduce the recombination rate of the photogenerated charges. The comparative evaluation of the NFs as photocatalysts for the removal of MB from an aqueous solution with a dye concentration of 15 µM under UV irradiation shows that the binary (wurtzite ZnO and anatase TiO₂) oxides exhibit higher catalytic activity compared to ternary (ZnTiO₃ and Zn₂TiO₄) oxides. The higher band gap and lower crystallinity of the ternary oxides are responsible for their lower photocatalytic activity. It has been found that the optimal load for the wurtzite ZnO is 0.66 mg mL⁻¹, obtaining a degradation rate of 7.94.10⁻² min⁻¹. The optimal load for anatase TiO₂ is lower (0.33 mg mL⁻¹) and the corresponding rate constant (1.12×10⁻¹ min⁻¹) is higher. This finding (higher activity with lower load) is of crucial importance for the scaling up of the process on an industrial scale. Indeed, the anatase NFs outperform even the commonly used P25-TiO₂ benchmark. Besides, they can be reused twice without any regeneration treatment, with 5.2% and 18.7% activity decrease after second and third use, respectively. Thanks to the scalability of the electrospinning technique, this laboratory-scale study provides a perspective towards the sustainable large-scale manufacture of photocatalysts for the treatment of industry effluents.

Keywords: anatase, capture centers, methylene blue dye, nanofibers, photodegradation, zinc oxide

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Authors: Abdul Matin, Muhammad Ajmal, Uzma Yunus, Noaman-ul Haq, Hafiz M. Shohaib, Ambreen G. Muazzam

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Carbon nanoparticles (CNPs) have unique properties that are useful for the diagnosis and treatment of cancer due to their precise properties like small size (ideal for delivery within the body) stability in solvent and tunable surface chemistry for targeted delivery. Here, highly fluorescent, monodispersed and water-soluble CNPs were synthesized directly from a suitable carbohydrate source (glucose and sucrose) by one-step acid assisted ultrasonic treatment at 35 KHz for 4 hours. This method is green, simple, rapid and economical and can be used for large scale production and applications. The average particle sizes of CNPs are less than 10nm and they emit bright and colorful green-blue fluorescence under the irradiation of UV-light at 365nm. The CNPs were characterized by scanning electron microscopy, fluorescent spectrophotometry, Fourier transform infrared spectrophotometry, ultraviolet-visible spectrophotometry and TGA analysis. Fluorescent CNPs were used as fluorescent probe and nano-carriers for anticancer drug. Functionalized CNPs (with ethylene diamine) were attached with anticancer drug-Methotrexate. In vitro bioactivity and biocompatibility of CNPs-drug conjugates was evaluated by LDH assay and Sulforhodamine B assay using human lung carcinoma cell lines (H157). Our results reveled that CNPs showed biocompatibility and CNPs-anticancer drug conjugates have shown potent cytotoxic effects and high antitumor activities in lung cancer cell lines. CNPs are proved to be excellent substitute for conventional drug delivery cargo systems and anticancer therapeutics in vitro. Our future studies will be more focused on using the same nanoparticles in vivo model system.

Keywords: carbon nanoparticles, carbon nanoparticles-methotrexate conjugates, human lung carcinoma cell lines, lactate dehydrogenase, methotrexate

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Authors: Ahmad Rasyadan Arshad, A. Rahman A. Jamal, N. Mohamed Ibrahim, Nor Azian Abdul Murad

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Introduction: Parkinson’s disease (PD) is a complex and asymptomatic disease where patients are usually diagnosed at late stage where about 70% of the dopaminergic neurons are lost. Therefore, identification of molecular biomarkers is crucial for early diagnosis of PD. MicroRNA (miRNA) is a short nucleotide non-coding small RNA which regulates the gene expression in post-translational process. The involvement of these miRNAs in neurodegenerative diseases includes maintenance of neuronal development, necrosis, mitochondrial dysfunction and oxidative stress. Thus, miRNA could be a potential biomarkers for diagnosis of PD. Objective: This study aim to identify the miRNA involved in Late Onset PD (LOPD) and Early Onset PD (EOPD) compared to the controls. Methods: This is a case-control study involved PD patients in the Chancellor Tunku Muhriz Hospital at the UKM Medical Centre. miRNA samples were extracted using miRNeasy serum/plasma kit from Qiagen. The quality of miRNA extracted was determined using Agilent RNA 6000 Nano kit in the Bioanalyzer. miRNA expression was performed using GeneChip miRNA 4.0 chip from Affymetrix. Microarray was performed in EOPD (n= 7), LOPD (n=9) and healthy control (n=11). Expression Console and Transcriptomic Analyses Console were used to analyze the microarray data. Result: miR-129-5p was significantly downregulated in EOPD compared to LOPD with -4.2 fold change (p = <0.050. miR-301a-3p was upregulated in EOPD compared to healthy control (fold = 10.3, p = <0.05). In LOPD versus healthy control, miR-486-3p (fold = 15.28, p = <0.05), miR-29c-3p (fold = 12.21, p = <0.05) and miR-301a-3p (fold = 10.01, p =< 0.05) were upregulated. Conclusion: Several miRNA have been identified to be differentially expressed in EOPD compared to LOPD and PD versus control. These miRNAs could serve as the potential biomarkers for early diagnosis of PD. However, these miRNAs need to be validated in a larger sample size.

Keywords: early onset PD, late onset PD, microRNA (miRNA), microarray

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Authors: Prakash Parasivamurthy, Vivek Rama Das, Ravikant Talluri, Veena Jawali

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India ranks among third in the production of coconut besides Philippines and Indonesia. About 92% of the total production in the country is contributed from four southern states especially, Kerala (45.22%), Tamil Nadu (26.56%), Karnataka (10.85%), and Andhra Pradesh (8.93%). Other states, such as Goa, Maharashtra, Odisha, West Bengal, and those in the northeast (Tripura and Assam) account for the remaining 8.44%. The use of coconut shell as coarse aggregate in concrete has never been a usual practice in the industry, particularly in areas where light weight concrete is required for non-load bearing walls, non-structural floors, and strip footings. The high cost of conventional building materials is a major factor affecting construction delivery in India. In India, where abundant agricultural and industrial wastes are discharged, these wastes can be used as potential material or replacement material in the construction industry. This will have double the advantages viz., reduction in the cost of construction material and also as a means of disposal of wastes. Therefore, an attempt has been made in this study to utilize the coconut shell (CS) as coarse aggregate in rigid pavement. The present study was initiated with the characterization of materials by the basic material testing. The casted moulds are cured and tests are conducted for hardened concrete. The procedure is continued with determination of fck (Characteristic strength), E (Modulus of Elasticity) and µ (Poisson Value) by the test results obtained. For the analytical studies, rigid pavement was modeled by the KEN PAVE software, finite element software developed specially for road pavements and simultaneously design of rigid pavement was carried out with Indian standards. Results show that physical properties of CSAC (Coconut Shell Aggregate Concrete) with 10% replacement gives better results. The flexural strength of CSAC is found to increase by 4.25% as compared to control concrete. About 13 % reduction in pavement thickness is observed using optimum coconut shell.

Keywords: coconut shell, rigid pavement, modulus of elasticity, poison ratio

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Authors: ZhenlinJu, Christopher P. Vellano, RehanAkbani, Yiling Lu, Gordon B. Mills

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The epithelial–mesenchymal transition (EMT) is a process by which epithelial cells acquire mesenchymal characteristics, such as profound disruption of cell-cell junctions, loss of apical-basolateral polarity, and extensive reorganization of the actin cytoskeleton to induce cell motility and invasion. A hallmark of EMT is its capacity to promote metastasis, which is due in part to activation of several transcription factors and subsequent downregulation of E-cadherin. Unfortunately, current approaches have yet to uncover robust protein marker sets that can classify tumors as possessing strong EMT signatures. In this study, we utilize reverse phase protein array (RPPA) data and consensus clustering methods to successfully classify a subset of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tumors into an EMT protein signaling group (EMT group). The overall survival (OS) of patients in the EMT group is significantly worse than those in the other Hormone and PI3K/AKT signaling groups. In addition to a shrinkage and selection method for linear regression (LASSO), we applied training/test set and Monte Carlo resampling approaches to identify a set of protein markers that predicts the EMT status of CESC tumors. We fit a logistic model to these protein markers and developed a classifier, which was fixed in the training set and validated in the testing set. The classifier robustly predicted the EMT status of the testing set with an area under the curve (AUC) of 0.975 by Receiver Operating Characteristic (ROC) analysis. This method not only identifies a core set of proteins underlying an EMT signature in cervical cancer patients, but also provides a tool to examine protein predictors that drive molecular subtypes in other diseases.

Keywords: consensus clustering, TCGA CESC, Silhouette, Monte Carlo LASSO

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Authors: Salma H. Abu Hafsa, A. Mendonca, B. Brehm-Stecher, A. A. Hassan, S. A. Ibrahim

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Enterococci are important inhabitants of the animal intestine and are widely used in probiotic products. A probiotic strain is expected to possess several desirable properties in order to exert beneficial effects. Therefore, the objective of this study was to isolate and characterize strains of Enterococcus sp. from chicken cecal and fecal samples to determine potential probiotic properties. Enterococci were isolated from thirty one chicken cecal and fecal samples collected from a local farm. In vitro studies were performed to assess antibacterial activity (using agar well diffusion and cell free supernatant broth technique against Salmonella enterica serotype Enteritidis), susceptibility to antibiotics (amoxycillin, cotrimoxazole, chloramphenicol, cefuroxime, ceftriaxone, ciprofloxacin, and nalidixic acid), survival in acidic conditions, resistance to bile salts, and their survival during simulated gastric juice conditions at pH 2.5. Isolates were identified using biochemical and molecular assays (API 50 CHL, and API ZYM kits followed by 16S rDNA gene sequence analysis). Two strains were identified, of which, Enteroccocus faecium was capable of inhibiting the growth of S. enteritidis and was susceptible to a wide range of antibiotics. In addition, the isolated strain exhibited significant resistance under highly acidic conditions (pH=2.5) for 8 hours and survived well in bile salt at 0.2% for 24 hours and showing ability to survive in the presence of simulated gastric juice at pH 2.5. Based on these results, the E. faecium isolate fulfills some of the criteria to be considered as a probiotic strain and therefore, could be used as a feed additive with good potential for controlling S. enteritidis in chickens. However, in vivo studies are needed to determine the safety of the strain.

Keywords: acid tolerance, antimicrobial activity, Enterococcus faecium, probiotic

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Authors: Talita Kato, Moises Grespan, Elza I. Ida, Massami Shimokomaki, Adriana L. Soares

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White Striping (WS) is becoming a concern for the poultry industry, as it affects the look of breast broiler chicken meat leading it to rejection by the consumers. It is characterized by the appearance of varying degrees of white striations on the Pectoralis major muscle surface following the direction of the muscle fiber. The etiology of this myopathy is still unknown, however it is suggested to be associated with increased weight gain rate and age of the bird, attributing the phenomenon to the genetically bird’s selection for efficiently higher meat production. The aim of this study was to evaluate the occurrence of Pectoralis major WS in a commercial plant in southern Brazil and its chemical characterization. The breast meat samples (n=660) from birds of 47 days of age, were classified as: Normal NG (no apparent white striations), Moderate MG (when the fillets present thin lines <1 mm) and Severe SG (white striations present ˃1 mm thick covering a large part of the fillet surface). Thirty samples (n = 10 for each level of severity) were analyzed for pH, color (L*, a*, b*), proximate chemical composition (moisture, protein, ash and lipids contents) and hydroxyproline in order to determine the collagen content. The results revealed the occurrence for NG group was 16.97%, 51.67% for MG group and 31.36% for SG group. Although the total protein content did not differ significantly, the collagen index was 42% higher in favor to SG in relation to NG. Also the lipid fraction was 27% higher for SG group. The NG presented the lowest values of the parameters L* and a* (P ≤ 0.05), as there was no white striations on its surface and highest b* value in SG, because of the maximum lipid contents. These results indicate there was a contribution of the SG muscle cells to oversynthesize connective tissue components on the muscle fascia. In conclusion, this study revealed a high incidence of White Striping on broiler commercial line in Brazil thus, there is a need to identify the causes of this abnormality in order to diminish or to eliminate it.

Keywords: collagen content, commercial line, pectoralis major muscle, proximate composition

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Authors: Naima Bouslah, Leila Bounabi, Farid Ouazib, Nabila Haddadine

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Conventional release dosage forms are known to provide an immediate release of the drug. Controlling the rate of drug release from polymeric matrices is very important for a number of applications, particularly in the pharmaceutical area. Hydrogels are polymers in three-dimensional network arrangement, which can absorb and retain large amounts of water without dissolution. They have been frequently used to develop controlled released formulations for oral administration because they can extend the duration of drug release and thus reduce dose to be administrated improving patient compliance. Tramadol is an opioid pain medication used to treat moderate to moderately severe pain. When taken as an immediate-release oral formulation, the onset of pain relief usually occurs within about an hour. In the present work, we synthesized pH-responsive hydrogels of (hydroxyl ethyl methacrylate-co-acrylic acid), (HEMA-AA) for control drug delivery of tramadol in the gastro-intestinal tractus. The hydrogels with different acrylic acid content, were synthesized by free radical polymerization and characterized by FTIR spectroscopy, X ray diffraction analysis (XRD), differential scanning calorimetry (DSC) and thermo gravimetric analysis (TGA). FTIR spectroscopy has shown specific hydrogen bonding interactions between the carbonyl groups of the hydrogels and hydroxyl groups of tramadol. Both the XRD and DSC studies revealed that the introduction of tramadol in the hydrogel network induced the amorphization of the drug. The swelling behaviour, absorptive kinetics and the release kinetics of tramadol in simulated gastric fluid (pH 1.2) and in simulated intestinal fluid (pH 7.4) were also investigated. The hydrogels exhibited pH-responsive behavior in the swelling study. The (HEMA-AA) hydrogel swelling was much higher in pH =7.4 medium. The tramadol release was significantly increased when pH of the medium was changed from simulated gastric fluid (pH 1.2) to simulated intestinal fluid (pH 7.4). Using suitable mathematical models, the apparent diffusional coefficients and the corresponding kinetic parameters have been calculated.

Keywords: biopolymres, drug delivery, hydrogels, tramadol

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Authors: Mohanapriya Subramanian, V. Raj

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Direct methanol fuel cells (DMFCs) are considered to be one of the most promising candidates for portable and stationary applications in the view of their advantages such as high energy density, easy manipulation, high efficiency and they operate with liquid fuel which could be used without requiring any fuel-processing units. Electrolyte membrane of DMFC plays a key role as a proton conductor as well as a separator between electrodes. Increasing concern over environmental protection, biopolymers gain tremendous interest owing to their eco-friendly bio-degradable nature. Pectin is a natural anionic polysaccharide which plays an essential part in regulating mechanical behavior of plant cell wall and it is extracted from outer cells of most of the plants. The aim of this study is to develop and demonstrate pectin based polymer composite membranes as methanol impermeable polymer electrolyte membranes for DMFCs. Pectin based nanocomposites membranes are prepared by solution-casting technique wherein pectin is blended with chitosan followed by the addition of optimal amount of sulphonic acid modified Titanium dioxide nanoparticle (S-TiO2). Nanocomposite membranes are characterized by Fourier Transform-Infra Red spectroscopy, Scanning electron microscopy, and Energy dispersive spectroscopy analyses. Proton conductivity and methanol permeability are determined into order to evaluate their suitability for DMFC application. Pectin-chitosan blends endow with a flexible polymeric network which is appropriate to disperse rigid S-TiO2 nanoparticles. Resulting nanocomposite membranes possess adequate thermo-mechanical stabilities as well as high charge-density per unit volume. Pectin-chitosan natural polymeric nanocomposite comprising optimal S-TiO2 exhibits good electrochemical selectivity and therefore desirable for DMFC application.

Keywords: biopolymers, fuel cells, nanocomposite, methanol crossover

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Authors: Neha Bhadauria, Indu Gaur, Shilpi Shilpi, Susmita Goswami, Prabir K. Paul

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The aerial surface of plants colonized by Human Enteric Pathogens ()has been implicated in outbreaks of enteric diseases in humans. Practice of organic farming primarily using animal dung as manure and sewage water for irrigation are the most significant source of enteric pathogens on the surface of leaves, fruits and vegetables. The present work aims to have an insight into the molecular mechanism of interaction of Human Enteric Pathogens or their metabolites with cell wall receptors in plants. Tomato plants grown under aseptic conditions at 12 hours L/D photoperiod, 25±1°C and 75% RH were inoculated individually with S. fonticola and K. pneumonia. The leaves from treated plants were sampled after 24 and 48 hours of incubation. The cell wall and cytoplasmic proteins were extracted and isocratically separated on 1D SDS-PAGE. The sampled leaves were also subjected to formaldehyde treatment prior to isolation of cytoplasmic proteins to study protein-protein interactions induced by Human Enteric Pathogens. Protein bands extracted from the gel were subjected to MALDI-TOF-TOF MS analysis. The foremost interaction of Human Enteric Pathogens on the plant surface was found to be cell wall bound receptors which possibly set ups a wave a critical protein-protein interaction in cytoplasm. The study revealed the expression and suppression of specific cytoplasmic and cell wall-bound proteins, some of them being important components of signaling pathways. The results also demonstrated HEP induced rearrangement of signaling pathways which possibly are crucial for adaptation of these pathogens to plant surface. At the end of the study, it can be concluded that controlling the over-expression or suppression of these specific proteins rearrange the signaling pathway thus reduces the outbreaks of food-borne illness.

Keywords: cytoplasmic protein, cell wall-bound protein, Human Enteric Pathogen (HEP), protein-protein interaction

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Authors: Pamphile Ndagijimana, Xuejiao Liu, Zhiwei Li, Yin Wang

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The valorization of plastic wastes, as a mitigation strategy, is attracting the researchers’ attention since these wastes have raised serious environmental concerns. Plastic wastes have been reported to adsorb the organic pollutants in the water environment and to be the main vector of those pollutants in the aquatic environment, especially dyes, as a serious water pollution concern. Recycling technologies of plastic wastes such as landfills, incineration, and energy recovery have been adopted to manage those wastes before getting exposed to the environment. However, they are far from being widely accepted due to their related environmental pollution, lack of space for the landfill as well as high cost. Therefore, modification is necessary for green plastic adsorbent in water applications. Current routes for plastic modification into adsorbents are based on the combustion method, but they have weaknesses of air pollution as well as high cost. Thus, the green strategy for plastic modification into adsorbents is highly required. Furthermore, recent researchers recommended that if plastic wastes are combined with other solid carbon materials, they could promote their application in water treatment. Herein, we present new insight into using plastic waste-based materials as future green adsorbents. Magnetic plastic-reduced graphene oxide (MPrGO) composite was synthesized by cross-linking method and applied in removing methylene blue (MB) from an aqueous solution. Furthermore, the following advantages have been achieved: (i) The density of plastic and reduced graphene oxide were enhanced, (ii) no second pollution of black color in solution, (iii) small amount of graphene oxide (1%) was linked on 10g of plastic waste, and the composite presented the high removal efficiency, (iv) easy recovery of adsorbent from water. The low concentration of MB (10-30mg/L) was all removed by 0.3g of MPrGO. Different characterization techniques such as XRD, SEM, FTIR, BET, XPS, and Raman spectroscopy were performed, and the results confirmed a conjugation between plastic waste and graphene oxide. This MPrGO composite presented a good prospect for the valorization of plastic waste, and it is a promising composite material in water treatment.

Keywords: plastic waste, graphene oxide, dye, adsorption

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Authors: Yuxi Liu, Boris Belousov, Mehrzad Esmaeili Charkhab, Oliver Tessmann

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This paper presents a computational solution for designing reconfigurable interlocking structures that are fully assembled with SL Blocks. Formed by S-shaped and L-shaped tetracubes, SL Block is a specific type of interlocking puzzle. Analogous to molecular self-assembly, the aggregation of SL blocks will build a reversible hierarchical and discrete system where a single module can be numerously replicated to compose semi-interlocking components that further align, wrap, and braid around each other to form complex high-order aggregations. These aggregations can be disassembled and reassembled, responding dynamically to design inputs and changes with a unique capacity for reconfiguration. To use these aggregations as architectural structures, we developed computational tools that automate the configuration of SL blocks based on architectural design objectives. There are three critical phases in our work. First, we revisit the hierarchy of the SL block system and devise a top-down-type design strategy. From this, we propose two key questions: 1) How to translate 3D polyominoes into SL block assembly? 2) How to decompose the desired voxelized shapes into a set of 3D polyominoes with interlocking joints? These two questions can be considered the Hamiltonian path problem and the 3D polyomino tiling problem. Then, we derive our solution to each of them based on two methods. The first method is to construct the optimal closed path from an undirected graph built from the voxelized shape and translate the node sequence of the resulting path into the assembly sequence of SL blocks. The second approach describes interlocking relationships of 3D polyominoes as a joint connection graph. Lastly, we formulate the desired shapes and leverage our methods to achieve their reconfiguration within different levels. We show that our computational strategy will facilitate the efficient design of hierarchical interlocking structures with a self-replicating geometric module.

Keywords: computational design, SL-blocks, 3D polyomino puzzle, combinatorial problem

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Authors: Hercules Argyropoulos, Thomas F. Johnson, Nigel B Jackson, Kalliopi Zourna, Daniel G. Bracewell

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Lipid encapsulation has become essential in drug delivery, notably for mRNA vaccines during the COVID-19 pandemic. However, their sterile filtration poses challenges due to the risk of deformation, filter fouling and product loss from adsorption onto the membrane. Choosing the right filtration membrane is crucial to maintain sterility and integrity while minimizing product loss. The objective of this study is to develop a rigorous analytical framework utilizing confocal microscopy and filtration blocking models to elucidate the fouling mechanisms of liposomes as a model system for this class of delivery vehicle during sterile filtration, particularly in response to variations in transmembrane pressure (TMP) during the filtration process. Experiments were conducted using fluorescent Lipoid S100 PC liposomes formulated by micro fluidization and characterized by Multi-Angle Dynamic Light Scattering. Dual-layer PES/PES and PES/PVDF membranes with 0.2 μm pores were used for filtration under constant pressure, cycling from 30 psi to 5 psi and back to 30 psi, with 5, 6, and 5-minute intervals. Cross-sectional membrane samples were prepared by microtome slicing and analyzed with confocal microscopy. Liposome characterization revealed a particle size range of 100-140 nm and an average concentration of 2.93x10¹¹ particles/mL. Goodness-of-fit analysis of flux decline data at varying TMPs identified the intermediate blocking model as most accurate at 30 psi and the cake filtration model at 5 psi. Membrane resistance analysis showed atypical behavior compared to therapeutic proteins, with resistance remaining below 1.38×10¹¹ m⁻¹ at 30 psi, increasing over fourfold at 5 psi, and then decreasing to 1-1.3-fold when pressure was returned to 30 psi. This suggests that increased flow/shear deforms liposomes enabling them to more effectively navigate membrane pores. Confocal microscopy indicated that liposome fouling mainly occurred in the upper parts of the dual-layer membrane.

Keywords: sterile filtration, membrane resistance, microfluidization, confocal microscopy, liposomes, filtration blocking models

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Authors: Rupa Jeena, Pankaj Chetry, Pradeep Sarin

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The study of fundamental particles and the forces governing them has always remained an attractive field of theoretical study to pursue. With the advancement and development of new technologies and instruments, it is possible now to perform particle physics experiments on a large scale for the validation of theoretical predictions. These experiments are generally carried out in a highly intense beam environment. This, in turn, requires the development of a detector prototype possessing properties like radiation tolerance, thermal stability, and fast timing response. Semiconductors like Silicon, Germanium, Diamond, and Gallium Nitride (GaN) have been widely used for particle detection applications. Silicon and germanium being narrow bandgap semiconductors, require pre-cooling to suppress the effect of noise by thermally generated intrinsic charge carriers. The application of diamond in large-scale experiments is rare owing to its high cost of fabrication, while GaN is one of the most extensively explored potential candidates. But we are aiming to introduce another wide bandgap semiconductor in this active area of research by considering all the requirements. We have made an attempt by utilizing the wide bandgap of rutile Titanium dioxide (TiO2) and other properties to use it for particle detection purposes. The thermal evaporation-oxidation (in PID furnace) technique is used for the deposition of the film, and the Metal Semiconductor Metal (MSM) electrical contacts are made using Titanium+Gold (Ti+Au) (20/80nm). The characterization comprising X-Ray Diffraction (XRD), Atomic Force Microscopy (AFM), Ultraviolet (UV)-Visible spectroscopy, and Laser Raman Spectroscopy (LRS) has been performed on the film to get detailed information about surface morphology. On the other hand, electrical characterizations like Current Voltage (IV) measurement in dark and light and test with laser are performed to have a better understanding of the working of the detector prototype. All these preliminary tests of the detector will be presented.

Keywords: particle detector, rutile titanium dioxide, thermal evaporation, wide bandgap semiconductors

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Authors: Yahia Massinissa, Yahia Mouloud

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Cystic fibrosis (CF), the most common lethal genetic disease in the Europe population, is caused by mutations in the transmembrane conductance regulator gene (CFTR). It affects most organs including an epithelial tissue, base of hydroelectrolytic transepithelial transport, notably that aerial ways, the pancreas, the biliary ways, the intestine, sweat glands and the genital tractus. The gene whose anomalies are responsible of the cystic fibrosis codes for a protein Cl channel named CFTR (cystic fibrosis transmembrane conductance regulator) that exercises multiple functions in the cell, one of the most important in control of sodium and chlorine through epithelia. The deficient function translates itself notably by an abnormal production of viscous secretion that obstructs the execrator channels of this target organ: one observes then a dilatation, an inflammation and an atrophy of these organs. It also translates itself by an increase of the concentration in sodium and in chloride in sweat, to the basis of the sweat test. In order to do a phenotypical and genotypical diagnosis at a part of the Algerian population, our survey has been carried on 16 patients with evocative symptoms of the cystic fibrosis at that the clinical context has been confirmed by a sweat test. However, anomalies of the CFTR gene have been determined by electrophoresis in gel of polyacrylamide of the PCR products (polymerase chain reaction), after enzymatic digestion, then visualized to the ultraviolet (UV) after action of the ethidium bromide. All mutations detected at the time of our survey have already been identified at patients attained by this pathology in other populations of the world. However, the important number of found mutation with regard to the one of the studied patients testifies that the origin of this big clinical variability that characterizes the illness in the consequences of an enormous diversity of molecular defects of the CFTR gene.

Keywords: cystic fibrosis, CFTR gene, polymorphism, algerian population, sweat test, genotypical diagnosis

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Authors: Maryam Monazzah, Ronak Samadpour, Mehdi Nasr-esfahani, Fatemeh Qalavand, Marziye Motamedi

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Bipolaris sorokiniana, and Heterodera filipjevi, are important wheat diseases that lead to yield losses worldwide. Identifying novel resistant sources helps us combat these devastating diseases. In this study, we studied the role of Cre3 gene and antioxidant enzymes in the immune responses of wheat genotypes to H. filipjevi and B. sorokiniana. Therefore, real-time PCR analysis using Cre3 gene marker, a resistant gene to cereal cyst nematodes, was conducted on leaves and roots, along with changes ‎in the activity of antioxidant enzymes, peroxidase, and catalase. Enzyme activity assay was performed on roots attacked by nematode and in leaves infected with Bipolaris. Wheat accessions including “Bam” (resistant), “Parsi” (moderately-resistant), “Azar2”, “Ohadi”, “Homa” (highly-susceptible) were previously screened against both stresses under greenhouse and field conditions. Results showed that Cre3 expression against cyst nematodes was significantly higher in resistant cultivars compared to susceptible cultivars. Cre3 was used in marker-assisted selection programs to identify genotypes carrying resistant genes to cyst nematodes. Interestingly, Cre3 was also up-regulated in both tissues of resistant cultivars to B. sorokiniana. Therefore, Cre3 in wheat similarly modulates immunity against B. sorokiniana and might be one of the central components of the induced immune system in wheat. The activity of antioxidant enzymes also indicated the highest increase in resistant genotypes upon both stresses that subsequently neutralize oxidative stress in tissues and decrease damage. Further studies on these resistance components may help us gain insight into the molecular basis of resistance and shed new light on the interaction and overlap between different forms of stress.

Keywords: Bipolaris sorokiniana, Heterodera filipjevi, resistant gene expression, wheat

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Authors: Manisha Choudhary, Sudarsan Neogi

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Malachite green (MG), an organic basic dye, has been widely used for the dyeing purpose, as well as a fungicide and antiseptic in aquaculture industry to control fish parasites and disease. However, MG has now turned out to be an extremely controversial compound due to its adverse impact on living beings. Due to high toxicity, proper treatment of wastewater containing MG is utmost important. Among different available technologies, adsorption process is one of the most efficient and cost-effective treatment method due to its simplicity of design, ease of operation and regeneration of used materials. Nonetheless, commercial activated carbon is expensive leading the researchers to focus on utilizing natural resources. In the present work, a species of cactus, Opuntia ficus-indica (OFI), was used to develop a highly efficient, low-cost powdered activated carbon by chemical activation using NaOH. The biosorbent was characterized by Fourier-transform infrared spectroscopy, field emission scanning electron microscope, energy-dispersive X-ray spectroscopy, Brunauer–Emmett–Teller (BET) and X-ray diffraction analysis. Batch adsorption studies were performed to remove MG from an aqueous solution as a function of contact time, initial solution pH, initial dye concentration, biosorbent dosages, the presence of salt and temperature. By increasing the initial dye concentration from 100 to 500 mg/l, adsorption capacity increased from 165.45 to 831.58 mg/g. The adsorption kinetics followed the pseudo-second-order model and the chemisorption mechanisms were revealed. The electrostatic attractions and chemical interactions were observed between amino and hydroxyl groups of the biosorbent and amine groups of the dye. The adsorption was solely controlled by film diffusion. Different isotherm models were used to fit the adsorption data. The excellent recovery of adsorption efficiency after the regeneration of biosorbent indicated the high potential of this adsorbent to remove MG from aqueous solution and an excellent cost-effective biosorbent for wide application in wastewater treatment.

Keywords: adsorption, biosorbent, cactus, malachite green

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Authors: Akhil Raj Pushparajan, Ranjit Ramachandran, Jijimole Gopi Reji, Ajay Kumar Ramakrishnan

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Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is one of the leading causes of death by an infectious disease. In spite of the availability of effective drugs and a vaccine, TB is a major health concern and was declared a global emergency by the World Health Organization (WHO). The success of intracellular pathogens like Mtb depends on its ability to overcome the challenging environment in the host. Gene regulation controlled by transcriptional regulators (TRs) plays a crucial role for the bacteria to adapt to the host environment. In vitro studies on gene regulatory mechanisms during dormancy and reactivation have provided insights into the adaptations employed by Mtb to survive in the host. Here we present our efforts to functionally characterize Rv1019, a putative TR of Mtb H37Rv which was found to be present at significantly varying levels during dormancy and reactivation in vitro. The expression of this protein in the dormancy-reactivation model was validated by qRT-PCR and western blot. By DNA- protein interaction studies and reporter assays we found that under normal laboratory conditions of growth this protein behaves as an auto-repressor and tetracycline was found to abrogate this repression by interfering with its ability to bind DNA. Further, by cDNA analysis, we found that this TR is co-transcribed with its downstream genes Rv1020 (mfd) and Rv1021 (mazG) which are involved in DNA damage response in Mtb. Constitutive expression of this regulator in the surrogate host M. smegmatis showed downregulation of the orthologues of downstream genes suggested that Rv1019 could negatively regulate these genes. Our finds also show that M. smegmatis expressing Rv1019 is sensitive to DNA damage suggests the role of this protein in regulating DNA damage response induced by oxidative stress. Because of its role in regulating DNA damage response which may help in the persistence of Mtb, Rv1019 could be used as a prospective target for therapeutic intervention to fight TB.

Keywords: auto-repressor, DNA repair, mycobacterium smegmatis, mycobacterium tuberculosis, tuberculosis

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Authors: Medhanie Gebremedhin Gebru, Alex Schechter

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Dimethyl ether (DME) possesses several advantages over other small organic molecules such as methanol, ethanol, and ammonia in terms of providing higher energy density, being less toxic, and having lower Nafion membrane crossover. However, the absence of an active and stable catalyst has been the bottleneck that hindered the commercialization of direct DME fuel cells. A Vulcan XC72 carbon-supported ternary metal catalyst, Pt₃Pd₃Sn₂/C is reported to have yielded the highest specific power density (90 mW mg-¹PGM) as compared to other catalysts tested fordirect DME fuel cell (DDMEFC). However, the micropores and sulfur groups present in Vulcan XC72 hinder the fuel utilization by causing Pt agglomeration and sulfur poisoning. Vulcan XC72 having a high carbon sp³ hybridization content, is also prone to corrosion. Therefore, carbon supports such as multi-walled carbon nanotube (MWCNT), black pearl 2000 (BP2000), and their cold N2 plasma-treated counterpartswere tested to further enhance the activity of the catalyst, and the outputs with these carbons were compared with the originally used support. Detailed characterization of the pristine and carbon supports was conducted. Electrochemical measurements in three-electrode cells and laboratory prototype fuel cells were conducted.Pt₃Pd₃Sn₂/BP2000 exhibited excellent performance in terms of electrochemical active surface area (ECSA), peak current density (jp), and DME oxidation charge (Qoxi). The effect of the plasma activation on the activity improvement was observed only in the case of MWCNT while having little or no effect on the other carbons. A Pt₃Pd₃Sn₂ supported on the optimized mixture of carbons containing 75% plasma-activated MWCNT and 25% BP2000 (Pt₃Pd₃Sn₂/75M25B) provided the highest reported power density of 117 mW mg-1PGM using an anode loading of1.55 mgPGMcm⁻².

Keywords: DME, DDMEFC, ternary metal catalyst, carbon support, plasma activation

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Authors: Mahfouz Saeed

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Cu₂(ZnSn)(S)₄ (CTZS) offers potential advantages over CuInGaSe₂ (CIGS) as solar thin film because to its higher band gap. Preparing such photovoltaic materials by electrochemical techniques is particularly attractive due to the lower processing cost and the high throughput of such techniques. Several recent publications report CTZS electroplating; however, the electrochemical process still facing serious challenges such as a sulfur atomic ration which is about 50% of the total alloy. We introduce in this work an improved electrolyte composition which enables the direct electrodeposition of CTZS from a single bath. The electrolyte is significantly more dilute in comparison to common baths described in the literature. The bath composition we introduce is: 0.0032 M CuSO₄, 0.0021 M ZnSO₄, 0.0303 M SnCl₂, 0.0038 M Na₂S₂O₃, and 0.3 mM Na₂S₂O3. PHydrion is applied to buffer the electrolyte to pH=2, and 0.7 M LiCl is applied as supporting electrolyte. Electrochemical process was carried at a rotating disk electrode which provides quantitative characterization of the flow (room temperature). Comprehensive electrochemical behavior study at different electrode rotation rates are provided. The effects of agitation on atomic composition of the deposit and its adhesion to the molybdenum back contact are discussed. The post treatment annealing was conducted under sulfur atmosphere with no need for metals addition from the gas phase during annealing. The potential which produced the desired atomic ratio of CTZS at -0.82 V/NHE. Smooth deposit, with uniform composition across the sample surface and depth was obtained at 500 rpm rotation speed. Final sulfur atomic ratio was adjusted to 50.2% in order to have the desired atomic ration. The final composition was investigated using Energy-dispersive X-ray spectroscopy technique (EDS). XRD technique used to analyze CTZS crystallography and thickness. Complete and functional CTZS PV devices were fabricated by depositing all the required layers in the correct order and the desired optical properties. Acknowledgments: Case Western Reserve University for the technical help and for using their instruments.

Keywords: photovoltaic, CTZS, thin film, electrochemical

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Authors: Sungmin Park, Gyungmok Nam, Seungpyo Woo, Young Choi, Sangheon Park, Sang-Hee Yoon

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Puncturing human skin with microneedles is critically important for microneedle-mediate drug delivery. Despite of extensive efforts in the past decades, the scale-up fabrication of sharp-tipped and high-aspect-ratio microneedles, especially made of biodegradable polymers, is still a long way off. Here, we present a UV dose insensitive and cost-effective microfabrication method for the biodegradable polymer microneedles with sharp tips and long lengths which can pierce human skin with low insertion force. The biodegradable polymer microneedles are fabricated with the polymer solution casting where a poly(lactic-co-glycolic acid) (PLGA, 50:50) solution is coated onto a SU-8 mold prepared with a reverse, ramped, and rotational (R3) UV exposure. The R3 UV exposure is modified from the multidirectional UV exposure both to suppress UV reflection from the bottom surface without anti-reflection layers and to optimize solvent concentration in the SU-8 photoresist, therefore achieving robust (i.e., highly insensitive to UV dose) and cost-effective fabrication of biodegradable polymer microneedles. An optical model for describing the spatial distribution of UV irradiation dose of the R3 UV exposure is also developed to theoretically predict the microneedle geometry fabricated with the R3 UV exposure and also to demonstrate the insensitiveness of microneedle geometry to UV dose. In the experimental characterization, the microneedles fabricated with the R3 UV exposure are compared with those fabricated with a conventional method (i.e., multidirectional UV exposure). The R3 UV exposure-based microfabrication reduces the end-tip radius by a factor of 5.8 and the deviation from ideal aspect ratio by 74.8%, compared with conventional method-based microfabrication. The PLGA microneedles fabricated with the R3 UV exposure pierce full-thickness porcine skins successfully and are demonstrated to completely dissolve in PBS (phosphate-buffered saline). The findings of this study will lead to an explosive growth of the microneedle-mediated drug delivery market.

Keywords: R³ UV exposure, optical model, UV dose, reflection, solvent concentration, biodegradable polymer microneedle

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Authors: Farha Mizana Shamsudin, Shahidan Radiman, Yusof Abdullah, Nasri Abdul Hamid

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Oxide dispersion strengthened (ODS) ferritic steels are amongst the most promising candidates for large scale structural materials to be applied in next generation fission and fusion nuclear power reactors. This kind of material is relatively stable at high temperature, possess remarkable mechanical properties and comparatively good resistance from neutron radiation damage. The superior performance of ODS ferritic steels over their conventional properties is attributed to the high number density of nano-sized dispersoids that act as nucleation sites and stable sinks for many small helium bubbles resulting from irradiation, and also as pinning points to dislocation movement and grain growth. ODS ferritic steels are usually produced by powder metallurgical routes involving mechanical alloying (MA) process of Y2O3 and pre-alloyed or elemental metallic powders, and then consolidated by hot isostatic pressing (HIP) or hot extrusion (HE) techniques. In this study, Fe-14Cr-3W-0.5Ti-0.3Y₂O₃ (designated as 14YWT) was produced by mechanical alloying process and followed by hot isostatic pressing (HIP) technique. Crystal structure and morphology of this sample were identified and characterized by using X-ray Diffraction (XRD) and field emission scanning electron microscope (FESEM) respectively. The magnetic measurement of this sample at room temperature was carried out by using a vibrating sample magnetometer (VSM). FESEM micrograph revealed a homogeneous microstructure constituted by fine grains of less than 650 nm in size. The ultra-fine dispersoids of size between 5 nm to 19 nm were observed homogeneously distributed within the BCC matrix. The EDS mapping reveals that the dispersoids contain Y-Ti-O nanoclusters and from the magnetization curve plotted by VSM, this sample approaches the behavior of soft ferromagnetic materials. In conclusion, ODS Fe-14Cr-3W-0.5Ti-0.3Y₂O₃ (14YWT) ferritic steel was successfully produced by HIP technique in this present study.

Keywords: hot isostatic pressing, magnetization, microstructure, ODS ferritic steel

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Authors: Evelyn Osehontue Uroro, Richard Bright, Jing Yang Quek, Krasimir Vasilev

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Bacterial infections have been a challenge both in the public and private sectors. The colonization of bacteria often occurs in medical devices such as catheters, heart valves, respirators, and orthopaedic implants. When biomedical devices are inserted into patients, the deposition of macromolecules such as fibrinogen and immunoglobin on their surfaces makes it easier for them to be prone to bacteria colonization leading to the formation of biofilms. The formation of biofilms on medical devices has led to a series of device-related infections which are usually difficult to eradicate and sometimes cause the death of patients. These infections require surgical replacements along with prolonged antibiotic therapy, which would incur additional health costs. It is, therefore, necessary to prevent device-related infections by inhibiting the formation of biofilms using intelligent technology. Antibiotic resistance of bacteria is also a major threat due to overuse. Different antimicrobial agents have been applied to microbial infections. They include conventional antibiotics like rifampicin. The use of conventional antibiotics like rifampicin has raised concerns as some have been found to have hepatic and nephrotoxic effects due to overuse. Hence, there is also a need for proper delivery of these antibiotics. Different techniques have been developed to encapsulate and slowly release antimicrobial agents, thus reducing host cytotoxicity. Examples of delivery systems are solid lipid nanoparticles, hydrogels, micelles, and polymeric nanoparticles. The different ways by which drugs are released from polymeric nanoparticles include diffusion-based release, elution-based release, and chemical/stimuli-responsive release. Polymeric nanoparticles have gained a lot of research interest as they are basically made from biodegradable polymers. An example of such a biodegradable polymer is polycaprolactone (PCL). PCL degrades slowly by hydrolysis but is often sensitive and responsive to stimuli like enzymes to release encapsulants for antimicrobial therapy. This study presents the synthesis of PCL nanoparticles loaded with rifampicin and the on-demand release of rifampicin for treating staphylococcus aureus infections.

Keywords: enzyme, Staphylococcus aureus, PCL, rifampicin

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Authors: Amin Ajabi, Chinchu Cherian, Sumi Siddiqua

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Rammed earth (RE) is a traditional soil-based building material made by compressing a mixture of natural earth and binder ingredients such as chalk or lime, in temporary formworks. However, the modern RE uses 5 to 10% cement as a binder in order to meet the strength and durability requirements as per the standard specifications and guidelines. RE construction is considered to be an energy-efficient and environmental-friendly approach when compared to conventional concrete systems, which use 20 to 30% cement. The present study aimed to develop RE mix designs by utilizing non-hazardous wood-based fly ash generated by pulp and paper mills as a partial replacement for cement. The pulp mill fly ash (PPFA)-stabilized RE is considered to be a sustainable approach keeping in view of the massive carbon footprints associated with cement production as well as the adverse environmental impacts due to disposal of PPFA in landfills. For the experimental study, as-received PPFA, as well as PPFA-based geopolymer (synthesized by alkaline activation method), were incorporated as cement substitutes in the RE mixtures. Initially, local soil was collected and characterized by index and engineering properties. The PPFA was procured from a pulp manufacturing mill, and its physicochemical, mineralogical and morphological characterization, as well as environmental impact assessment, was conducted. Further, the various mix designs of RE material incorporating local soil and different proportions of cement, PPFA, and alkaline activator (a mixture of sodium silicate and sodium hydroxide solutions) were developed. The compacted RE specimens were cured and tested for 7-day and 28-day unconfined compressive strength (UCS) variations. Based on UCS results, the optimum mix design was identified corresponding to maximum strength improvement. Further, the cured RE specimens were subjected to freeze-thaw cycle testing for evaluating its performance and durability as a sustainable construction technique under extreme climatic conditions.

Keywords: sustainability, rammed earth, stabilization, pulp mill fly ash, geopolymer, alkaline activation, strength, durability

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Authors: Hediyeh Talebi, Shokoofeh Ghiam, Changiz Eslahchi

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Traditionally, Alzheimer’s disease research has focused on genes with significant fold changes, potentially neglecting subtle but biologically important alterations. Our study introduces an integrative approach that highlights genes crucial to underlying biological processes, regardless of their fold change magnitude. Alzheimer's Single-cell RNA-seq data related to the peripheral blood mononuclear cells (PBMC) was extracted from the Gene Expression Omnibus (GEO). After quality control, normalization, scaling, batch effect correction, and clustering, differentially expressed genes (DEGs) were identified with adjusted p-values less than 0.05. These DEGs were categorized based on cell-type, resulting in four datasets, each corresponding to a distinct cell type. To distinguish between cells from healthy individuals and those with Alzheimer's, an adversarial autoencoder with a classifier was employed. This allowed for the separation of healthy and diseased samples. To identify the most influential genes in this classification, the weight matrices in the network, which includes the encoder and classifier components, were multiplied, and focused on the top 20 genes. The analysis revealed that while some of these genes exhibit a high fold change, others do not. These genes, which may be overlooked by previous methods due to their low fold change, were shown to be significant in our study. The findings highlight the critical role of genes with subtle alterations in diagnosing Alzheimer's disease, a facet frequently overlooked by conventional methods. These genes demonstrate remarkable discriminatory power, underscoring the need to integrate biological relevance with statistical measures in gene prioritization. This integrative approach enhances our understanding of the molecular mechanisms in Alzheimer’s disease and provides a promising direction for identifying potential therapeutic targets.

Keywords: alzheimer's disease, single-cell RNA-seq, neural networks, blood biomarkers

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Authors: Héctor González Espinosa, Ricardo Ivan Cordova Chávez, Alejandra Contreras Ramos, Itzia Irene Padilla Martínez, José Guadalupe Trujillo Ferrara, Marvin Antonio Soriano Ursúa

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Boronic acids are able to create diester bonds with carbohydrates because of their hydroxyl groups; in nature, there are some organoborates with these characteristics, such as the calcium fructoborate, formed by the union of two fructose molecules and a boron atom, synthesized by plants. In addition, it has been observed that, in animal cells only the compounds with cis-diol functional groups are capable of linking to boric or boronic acids. The formation of these organoboron compounds could impair the physical and chemical properties of the precursors, even their acute toxicity. In this project, two carbohydrate-derived boron-containing compounds from D-fructose and D-arabinose and phenylboronic acid are analyzed by different spectroscopy techniques such as Raman, Infrared with Fourier Transform Infrared (FT-IR), Nuclear Magnetic Resonance (NMR) and X-ray diffraction crystallography to describe their chemical characteristics. Also, an acute toxicity test was performed to determine their LD50 using the Lorke’s method. It was confirmed by multiple spectra the formation of the adducts by the generation of the diester bonds with a β-D-pyranose of fructose and arabinose. The most prominent findings were the presence of signals corresponding to the formation of new bonds, like the stretching of B-O bonds, or the absence of signals of functional groups like the hydroxyls presented in the reagents used for the synthesis of the adducts. The NMR spectra yielded information about the stereoselectivity in the synthesis reaction, observed by the interaction of the protons and their vicinal atoms in the anomeric and second position carbons; but also, the absence of a racemic mix by the finding of just one signal in the range for the anomeric carbon in the 13C NMR spectra of both adducts. The acute toxicity tests by the Lorke’s method showed that the LD50 value for both compounds is 1265 mg/kg. Those results let us to propose these adducts as highly safe agents for further biological evaluation with medical purposes.

Keywords: acute toxicity, adduct, boron, carbohydrate, diester bond

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Authors: Xianglu Tang, Zhenxue Jiang, Zhuo Li

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Characterization of shale multi scale heterogeneity is an important part to evaluate size and space distribution of shale gas reservoirs in sedimentary basins. The origin of shale heterogeneity has always been a hot research topic for it determines shale micro characteristics description and macro quality reservoir prediction. Shale multi scale heterogeneity was discussed based on thin section observation, FIB-SEM, QEMSCAN, TOC, XRD, mercury intrusion porosimetry (MIP), and nitrogen adsorption analysis from 30 core samples in Silurian Longmaxi formation. Results show that shale heterogeneity can be characterized by pore structure and mineral composition. The heterogeneity of shale pore is showed by different size pores at nm-μm scale. Macropores (pore diameter > 50 nm) have a large percentage of pore volume than mesopores (pore diameter between 2~ 50 nm) and micropores (pore diameter < 2nm). However, they have a low specific surface area than mesopores and micropores. Fractal dimensions of the pores from nitrogen adsorption data are higher than 2.7, what are higher than 2.8 from MIP data, showing extremely complex pore structure. This complexity in pore structure is mainly due to the organic matter and clay minerals with complex pore network structures, and diagenesis makes it more complicated. The heterogeneity of shale minerals is showed by mineral grains, lamina, and different lithology at nm-km scale under the continuous changing horizon. Through analyzing the change of mineral composition at each scale, random arrangement of mineral equal proportion, seasonal climate changes, large changes of sedimentary environment, and provenance supply are considered to be the main reasons that cause shale minerals heterogeneity from microcosmic to macroscopic. Due to scale effect, the change of shale multi scale heterogeneity is a discontinuous process, and there is a transformation boundary between homogeneous and in homogeneous. Therefore, a shale multi scale heterogeneity changing model is established by defining four types of homogeneous unit at different scales, which can be used to guide the prediction of shale gas distribution from micro scale to macro scale.

Keywords: heterogeneity, homogeneous unit, multiscale, shale

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Authors: Stephanie Boue, Nicolas Sierro, Julia Hoeng, Manuel C. Peitsch

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Systems biology relies on large numbers of data points and sophisticated methods to extract biologically meaningful signal and mechanistic understanding. For example, analyses of transcriptomics and proteomics data enable to gain insights into the molecular differences in tissues exposed to diverse stimuli or test items. Whereas the interpretation of endpoints specifically measuring a mechanism is relatively straightforward, the interpretation of big data is more complex and would benefit from comparing results obtained with diverse analysis methods. The sbv IMPROVER project was created to implement solutions to verify systems biology data, methods, and conclusions. Computational challenges leveraging the wisdom of the crowd allow benchmarking methods for specific tasks, such as signature extraction and/or samples classification. Four challenges have already been successfully conducted and confirmed that the aggregation of predictions often leads to better results than individual predictions and that methods perform best in specific contexts. Whenever the scientific question of interest does not have a gold standard, but may greatly benefit from the scientific community to come together and discuss their approaches and results, datathons are set up. The inaugural sbv IMPROVER datathon was held in Singapore on 23-24 September 2016. It allowed bioinformaticians and data scientists to consolidate their ideas and work on the most promising methods as teams, after having initially reflected on the problem on their own. The outcome is a set of visualization and analysis methods that will be shared with the scientific community via the Garuda platform, an open connectivity platform that provides a framework to navigate through different applications, databases and services in biology and medicine. We will present the results we obtained when analyzing data with our network-based method, and introduce a datathon that will take place in Japan to encourage the analysis of the same datasets with other methods to allow for the consolidation of conclusions.

Keywords: big data interpretation, datathon, systems toxicology, verification

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Authors: Lívia Pimentel Sant'ana Dourado, Raquel Das Neves Almeida, Luís Henrique Costa Corrêa Neto, Nayara Soares, Kelly Grace Magalhães

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Introduction: Obesity and high-fat diet intake have a crucial impact on immune cells and inflammatory profile, highlighting an emerging realization that obesity is an inflammatory disease. In the present work, we aimed to characterize the role of caspase-1/11 and NLRP3 inflammasome in the establishment of mice obesity and modulation of inflammatory lipid metabolism induced by high fat diet intake. Methods and results: Wild type, caspase-1/11 and NLRP3 knockout mice were fed with standard fat diet (SFD) or high fat diet (HFD) for 90 days. The weight of animals was measured weekly to monitor the weight gain. After 90 days, the blood, peritoneal lavage cells, heart and liver were collected from mice studied here. Cytokines were measured in serum by ELISA and analyzed in spectrophotometry. Lipid antigen presentation molecule CD1d expression, reactive oxygen species (ROS) generation and lipid droplets biogenesis were analyzed in cells from mice peritoneal cavity by flow cytometry. Liver histopathology was performed for morphological evaluation of the organ. The absence of caspase-1/11, but not NLRP3, in mice fed with HFD favored the mice weight gain, increased liver size, induced development of hepatic steatosis and IL-12 secretion in mice compared to mice fed with SFD. In addition, caspase-1/11 knockout mice fed with HFD presented an increased CD1d molecule expression, as well as higher levels of lipid droplets biogenesis and ROS generation compared to wild type mice also fed with HFD. Conclusion: Our data suggest that caspase-1/11 knockout mice have greater susceptibility to obesity as well as increased activation of lipid metabolism and inflammatory markers.

Keywords: caspase 1, caspase 11, inflamassome, obesity, lipids

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