Miracle-dz/UniFAR-FTUs huggingface dataset:
Review on Water Treatment Techniques Used for Riverbank Filtration

Water Treatment is defined as the selection of sampling sites and sampling frequency to determine physical, chemical, and biological properties of water. The main approaches to water treatment were identified as hydrogeologic and statistical. The various methods available in the hydrologic literature have been evaluated by considering the spatial scale of the monitoring program, the objective of sampling, data requirements, temporal effects, and range of applicability. Considerable advance has been made over the last two decades that now permit the application of methodical and testable approaches to water quality monitoring, design riverbank filtration, although they mostly serve for preliminary analysis and design. The main goal of these studies was to characterize the ability of riverbank filtration to provide a cost-effective, stand alone pretreatment for filtermedia technologies. Results indicate that the use of riverbank filtration can reduce membrane treatment costs by 10-20 percent. In addition, overall recommendations were developed to help other utilities evaluate this technology as a potential lower cost alternative for minimizing treatment costs. The opinion on Ground-Water Quality Monitoring Network Design is that as there continues to be advances in hydro geochemistry, ground-water hydrology, and risk and geo statistical analysis, methods for ground-water quality monitoring network design will be improved and refined, and they will become ever more useful in the important mission of water treatment.
Mining associative and comparative patterns for Thai sentiment analysis

The aspect-based sentiment analysis has been popularly applied for analyzing product reviews. The results from the analysis could help summarize the customer satisfaction towards the products. Previous aspect-based sentiment analysis only focuses on relating sentiment polarity with product aspect. In a competitive market, it is more important to gain some insight of the sentiment and aspect towards a product brand and in comparison with other brands. To enhance the existing aspect-based sentiment analysis, we propose the following extensions, (1) association of sentiment and aspect with the product brand, and (2) comparison between two product brands. Our proposed approach is based on the pattern analysis of simplified patterns with dynamic filler terms. The simplified patterns help increase the effectiveness of pattern extraction. To evaluate the proposed approach, we performed experiments using product reviews in the smartphone domain. The results show that the performance of product brand and aspect extraction is significantly improved with the simplified patterns for both associative and comparative pattern minings.
Effect on Aluminium Metal Matrix Composite Reinforced with Nano Sized Silica Particles

In recent times, it could be observed that metal matrix composites receive considerable importance on account of improved properties compared to unreinforced alloys which includes high specific strength, specific modulus, damping capacity and good wear resistance. Interest in composites containing low density and low cost reinforcements has been since growing. Among various discontinuous particulate, silica is one of the most inexpensive and low density reinforcement available in large quantities. Hence, composites with aluminium oxide as reinforcement after the in-situ reaction of aluminium and silica are likely to overcome the cost barrier for wide spread applications in automotive and small engine applications. It is therefore expected that the incorporation of aluminium oxide particles in aluminium alloy will improve the mechanical properties of base material that will see increased usage in aircraft application due to reduced weight. In this research an effect on aluminum matrix composite reinforced with nano sized silica particles with different weight percentage was carried out. From the results it was found that the composites with 4 to 6wt% particle volume fraction to be the best with good tensile strength, yield stress and percentage elongation.
Targeting Peptide Termini, a Novel Immunoaffinity Approach to Reduce Complexity in Mass Spectrometric Protein Identification

Mass spectrometry and peptide-centric approaches are powerful techniques for the identification of differentially expressed proteins. Despite enormous improvements in MS technologies, sample preparation and efficient fractionation of target analytes are still major bottlenecks in MS-based protein analysis. The complexity of tryptically digested whole proteomes needs to be considerably reduced before low abundance proteins can be effectively analyzed using MS/MS. Sample preparation strategies that use peptide-specific antibodies are able to reduce the complexity of tryptic digests and lead to a substantial increase in throughput and sensitivity; however, the number of peptide-specific capture reagents is low, and consequently immunoaffinity-based approaches are only capable of detecting small sets of protein-derived peptides. In this proof-of-principle study, special anti-peptide antibodies were used to enrich peptides from a complex mixture. These antibodies recognize short amino acid sequences that are found directly at the termini of the peptides. The recognized epitopes consist of three or four amino acids only and include the terminally charged group of the peptide. Because of its limited length, antibodies recognizing the epitope will enrich not only one peptide but a whole class of peptides that share this terminal epitope. In this study, β-catenin-derived peptides were used to demonstrate that it is possible (i) to effectively generate antibodies that recognize short C-terminal peptide epitopes and (ii) to enrich and identify peptide classes from a complex mixture using these antibodies in an immunoaffinity MS approach. The expected β-catenin peptides and a set of 38 epitope-containing peptides were identified from trypsin-digested cell lysates. This might be a first step in the development of proteomics applications that are based on the use of peptide class-specific antibodies.
Nonlinear Adaptive Control Design for Affine Systems

A nonlinear adaptive approach based on differential geometry and state space identification is presented for the control of affine systems. An affine system is transformed to an input/output linear process by internal state feedback. First the optimal controller that minimizes the given quadratic cost function is designed for the linearized system. Finally we design a nonlinear adaptive controller that identifies the process model online using state space identification. The system switches to the adaptive control strategy when the process dynamics change. The implementation of the proposed control strategy is simple and efficient with mature algebraic algorithms. The effectiveness and robustness of the proposed control design is demonstrated by a simulation example.
Evaluation of Neurogenic Potential of Human Umbilical Cord Mesenchymal Cells; a Time- and Concentration-Dependent Manner

Background: Retinoic acid as one of the most important regulators for cell differentiation was examined in this study for differentiation of human umbilical mesenchymal cells (hUCM). Methods: After isolation, hUCM were evaluated for mesenchymal stem cell properties by flow cytometry and alkaline phosphatase assay. Also, doubling time of the cells and their differentiation potential into adipogenic and osteogenic cells were tested. hUCM were then cultured with different concentrations of retinoic acid, and on days 1, 7, and 12, the percentage of differentiated cells was determined by immunostaining for nestin, anti-microtubule associated protein 2 (MAP2), glutamic acid decarboxylase (GAD), and gamma-aminobutyric acid (GABA) markers. Results: The isolated cells were negative for the hematopoietic markers and positive for the mesenchymal markers. They showed the population doubling time 60 ± 3 hours and differentiated into osteogenic and adipogenic cells. A descending trend in nestin and an ascending trend in MAP2, GAD, and GABA expression were observed from the first day until the last day between different concentrations of retinoic acid. Conclusion: hUCM cells may have the potential to differentiate into neural cells in the presence of different incubation period and concentration of retinoic acid.
Multi-leveled objects: color as a case study

The paper presents color as a case study for the analysis of phenomena that pertain to several levels of reality and are typically framed by different sciences and disciplines. Color, in fact, is studied by physics, biology, phenomenology, and esthetics, among others. Our thesis is that color is a different entity for each level of reality, and that for this reason color generates different observables in the epistemologies of the different sciences. By analyzing color as a paradigmatic case of an entity naturally spreading over different levels of reality, the paper raises the question as to whether making explicit the usually implicit ontological assumptions embedded within the different observables exploited by the different sciences may eventually clarify some of the difficulties of developing a comprehensive theory of color.
FINDSITE: a combined evolution/structure-based approach to protein function prediction

A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to protein function inference and ligand screening that can provide functional insights for a significant fraction of the approximately 50% of ORFs of unassigned function in an average proteome. We then describe FINDSITE, a recently developed algorithm for ligand binding site prediction, ligand screening and molecular function prediction, which is based on binding site conservation across evolutionary distant proteins identified by threading. Importantly, FINDSITE gives comparable results when high-resolution experimental structures as well as predicted protein models are used.
The Genetics of Pulmonary Arterial Hypertension

Pulmonary arterial hypertension (PAH) is a progressive and fatal disease for which there is an ever-expanding body of genetic and related pathophysiological information on disease pathogenesis. Many germline gene mutations have now been described, including mutations in the gene coding bone morphogenic protein receptor type 2 (BMPR2) and related genes. Recent advanced gene-sequencing methods have facilitated the discovery of additional genes with mutations among those with and those without familial forms of PAH (CAV1, KCNK3, EIF2AK4). The reduced penetrance, variable expressivity, and female predominance of PAH suggest that genetic, genomic, and other factors modify disease expression. These multi-faceted variations are an active area of investigation in the field, including but not limited to common genetic variants and epigenetic processes, and may provide novel opportunities for pharmacological intervention in the near future. They also highlight the need for a systems-oriented multi-level approach to incorporate the multitude of biological variations now associated with PAH. Ultimately, an in-depth understanding of the genetic factors relevant to PAH provides the opportunity for improved patient and family counseling about this devastating disease.
Compressed Sensing for Ultrawideband Impulse Radio

In this paper, ultrawideband (UWB) channel estimation based on the novel theory of compressive sensing (CS) is developed. The proposed approach relies on the fact that transmitting an ultra-short UWB pulse through a multipath channel leads to a received UWB signal that can be approximated by a linear combination of a few atoms from a pre-defined dictionary, yielding thus a sparse representation of the received signal. The CS reconstruction capabilities are exploited to recover the composite pulse-multipath channel from a reduced set of random projections using the matching pursuit algorithm. This reconstructed signal is subsequently used as a referent template in a correlator based detector. Extensive simulations show that for different propagation scenarios and UWB communication environments, the CS detector outperforms traditional correlators using just 1/3 of the sampling rate leading thus to a reduced use of analog-to-digital resources in the channel estimation stage.
Parameter Identifiability and Redundancy: Theoretical Considerations

Background Models for complex biological systems may involve a large number of parameters. It may well be that some of these parameters cannot be derived from observed data via regression techniques. Such parameters are said to be unidentifiable, the remaining parameters being identifiable. Closely related to this idea is that of redundancy, that a set of parameters can be expressed in terms of some smaller set. Before data is analysed it is critical to determine which model parameters are identifiable or redundant to avoid ill-defined and poorly convergent regression. Methodology/Principal Findings In this paper we outline general considerations on parameter identifiability, and introduce the notion of weak local identifiability and gradient weak local identifiability. These are based on local properties of the likelihood, in particular the rank of the Hessian matrix. We relate these to the notions of parameter identifiability and redundancy previously introduced by Rothenberg (Econometrica 39 (1971) 577–591) and Catchpole and Morgan (Biometrika 84 (1997) 187–196). Within the widely used exponential family, parameter irredundancy, local identifiability, gradient weak local identifiability and weak local identifiability are shown to be largely equivalent. We consider applications to a recently developed class of cancer models of Little and Wright (Math Biosciences 183 (2003) 111–134) and Little et al. (J Theoret Biol 254 (2008) 229–238) that generalize a large number of other recently used quasi-biological cancer models. Conclusions/Significance We have shown that the previously developed concepts of parameter local identifiability and redundancy are closely related to the apparently weaker properties of weak local identifiability and gradient weak local identifiability—within the widely used exponential family these concepts largely coincide.
Phenylmethanesulfonyl fluoride inactivates an archaeal superoxide dismutase by chemical modification of a specific tyrosine residue. Cloning, sequencing and expression of the gene coding for Sulfolobus solfataricus superoxide dismutase.

The gene encoding the superoxide dismutase from the hyperthermophilic archaeon Sulfolobus solfataricus (SsSOD) was cloned and sequenced and its expression in Escherichia coli obtained. The chemicophysical properties of the recombinant SsSOD were identical with those of the native enzyme. The recombinant SsSOD possessed a covalent modification of Tyr41, already observed in native SsSOD [Ursby, T. , Adinolfi, B.S., Al-Karadaghi, S. , De Vendittis, E. & Bocchini, V. (1999) J. Mol. Biol. 286, 189--205]. HPLC analysis of SsSOD samples prepared from cells treated or not with phenylmethanesulfonyl fluoride (PhCH(2)SO(2)F), a protease inhibitor routinely added during the preparation of cell-free extracts, showed that the modification was caused by PhCH(2)SO(2)F. Refinement of the crystal model of SsSOD confirmed that a phenylmethanesulfonyl moiety was attached to the hydroxy group of Tyr41. PhCH(2)SO(2)F behaved as an irreversible inactivator of SsSOD; in fact, the specific activity of both native and recombinant enzyme decreased as the percentage of modification increased. The covalent modification caused by PhCH2SO2F reinforced the heat stability of SsSOD. These results show that Tyr41 plays an important role in the enzyme activity and the maintenance of the structural architecture of SsSOD.
Overlapping functions of components of a bacterial Sec‐independent protein export pathway

We describe the identification of two Escherichia coli genes required for the export of cofactor‐containing periplasmic proteins, synthesized with signal peptides containing a twin arginine motif. Both gene products are homologous to the maize HCF106 protein required for the translocation of a subset of lumenal proteins across the thylakoid membrane. Disruption of either gene affects the export of a range of such proteins, and a complete block is observed when both genes are inactivated. The Sec protein export pathway was unaffected, indicating the involvement of the gene products in a novel export system. The accumulation of active cofactor‐containing proteins in the cytoplasm of the mutant strains suggests a role for the gene products in the translocation of folded proteins. One of the two HCF106 homologues is encoded by the first gene of a four cistron operon, tatABCD, and the second by an unlinked gene, tatE. A mutation previously assigned to the hcf106 homologue encoded at the tatABCD locus, mttA, lies instead in the tatB gene.
New Mass-Spring System Integrating Elasticity Parameters in 2D

Besides the finite element method, the mass- spring discrete modeling is widely used in computer gra- phics. This discrete model allows to perform very eas- ily interactive deformations and to handle quite complex interactions with only a few equations. Thus, it is per- fectly adapted to generate visually correct animations. However, a drawback of this simple formulation is the relative difficulty to control efficiently physically realis- tic behaviors. Indeed, none of the existing models has succeeded to deal satisfyingly with this. Moreover, we demonstrate that the mostly cited technique in the liter- ature, proposed by Van Gelder, is far to be exact in most real cases and its interest is limited to some specific non realistic animations. Here, we propose a new general 2D formulation that reconstructs the geometrical model as an assembly of elementary ”bricks”. Each brick (or el- ement) is then transformed into a mass-spring system, in which edges are springs connecting masses placed on the element vertices. The key point of our approach is the determination of the stiffness constant of each spring to reproduce the correct mechanical properties (Young’s modulus, Poisson’s ratio and shear modulus) of the re- constructed object. We validate our methodology with the help of some numerical experimentation of mechan- ics, like stretching, shearing and loading and then we evaluate the accuracy limits of our approach.
Concentration of enteroviruses from large volumes of tap water, treated sewage, and seawater

Methods are described for the efficient concentration of an enterovirus from large volumes of tap water, sewage, and seawater. Virus in acidified water (pH 3.5) in the presence of aluminum chloride was adsorbed to a 10-inch (ca. 25.4 cm) fiberglass depth cartridge and a 10-inch pleated epoxy-fiberglass filter in a series at flow rates of up to 37.8 liters (10 gallons) per min. Adsorbed viruses were eluted from the filters with glycine buffer (pH 10.5 to 11.5), and the eluate was reconcentrated by using a combination of aluminum flocculation followed by hydroextraction. With this procedure, poliovirus in large volumes of tap water, seawater, and sewage could be concentrated with an average efficiency of 52, 53, and 50%, respectively. It was demonstrated that this method is capable of detecting surface solid-associated viruses originating from sewage treatment plants. No difference in virus recovery between laboratory batch studies and a set-up with acid-salt injection was found. This unified scheme for the concentration of viruses has many advantages over previously described systems. These include: high operating flow rates, low weight and small size, effectiveness with a variety of waters with widely varying qualities, and filters with a high resistance to clogging.
Newly Discovered Antiterminator RNAs in Bacteriophage

ABSTRACT Antiterminator RNA directly modifies the transcription elongation complex so that it terminates less efficiently at intrinsic and factor-dependent terminators. These unusual RNAs were first discovered in bacteriophage HK022, where the nascent transcripts of the phage put sites promote full expression of phage genes during lytic infection. The activity of antiterminator RNA depends on specific structural elements that form as the transcript exits RNA polymerase. To further our understanding of the critical sequence features that permit RNA to serve as a transcriptional antiterminator, we have identified eight antiterminator RNA sequences in bacteriophages or prophages. There is strong sequence conservation among most of the put sequences, but sequence divergence is tolerated if critical structural elements are preserved. The most diverged antiterminator RNA is found in bacteriophage HK639. The HK639 putL transcript is an efficient antiterminator, and it has a novel structural feature that is critical for its activity. HK639 also displays a unique pattern of sensitivity to amino acid substitutions in the β′ subunit zinc binding domain of RNA polymerase, adding to existing evidence that this domain interacts specifically with antiterminator RNA.
Gas6 Downregulation Impaired Cytoplasmic Maturation and Pronuclear Formation Independent to the MPF Activity

Previously, we found that the growth arrest-specific gene 6 (Gas6) is more highly expressed in germinal vesicle (GV) oocytes than in metaphase II (MII) oocytes using annealing control primer (ACP)-PCR technology. The current study was undertaken to investigate the role of Gas6 in oocyte maturation and fertilization using RNA interference (RNAi). Interestingly, despite the specific and marked decrease in Gas6 mRNA and protein expression in GVs after Gas6 RNAi, nuclear maturation including spindle structures and chromosome segregation was not affected. The only discernible effect induced by Gas6 RNAi was a change in maturation promoting factor (MPF) activity. After parthenogenetic activation, Gas6 RNAi-treated oocytes at the MII stage had not developed further and arrested at MII (90.0%). After stimulation with Sr2+, Gas6-silenced MII oocytes had markedly reduced Ca2+ oscillation and exhibited no exocytosis of cortical granules. In these oocytes, sperm penetration occurred during fertilization but not pronucleus (PN) formation. By roscovitine and colcemid treatment, we found that the Gas6 knockdown affected cytoplasmic maturation directly, independent to the changed MPF activity. These results strongly suggest that 1) the Gas6 signaling itself is important to the cytoplasmic maturation, but not nuclear maturation, and 2) the decreased Gas6 expression and decreased MPF activity separately or mutually influence sperm head decondensation and PN formation.
Fabrication of PMMA/PANI/Fe3O4 as a Novel Conducting Hybrid Coating

ABSTRACT In this paper, an excellent new hybrid coating including poly(methyl methacrylate) (PMMA), polyaniline (PANI), and magnetite nanoparticles (Fe3O4) was obtained. Fe3O4 nanoparticles were synthesized using coprecipitation method, and then magnetite nanoparticles have been dispersed into the PANI to increase compatibility with PMMA. Also, PANI/Fe3O4 nanocomposites were synthesized through in situ emulsion polymerization, and then PMMA/PANI/Fe3O4 hybrid coating was successfully synthesized using batch emulsion polymerization method. Structure, morphology and thermal stability of the samples were characterized using Fourier transform infrared, X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and thermal gravimetric analysis (TGA). The synthesized samples were well distributed with an average diameter smaller than 20 nm. Microscopy and X-ray photoelectron spectroscopy results illustrated a great dispersion of magnetite nanoparticles in hybrid matrix. Moreover, the TGA results demonstrated that the PMMA/PANI/Fe3O4 hybrid coating nanoparticle is an excellent hybrid coating with high thermal resistance. GRAPHICAL ABSTRACT