Miracle-dz/UniFAR-FTUs huggingface dataset:
Arginase-1 and Treg Profile Appear to Modulate Inflammatory Process in Patients with Chronic Gastritis: IL-33 May Be the Alarm Cytokine in H. pylori-Positive Patients

Helicobacter pylori (H. pylori) is a highly prevalent bacterium in our environment, directly involved in various upper digestive tract diseases, such as gastritis, peptic ulcer, and gastric cancer. Several molecules activating the immune system have been reported to be involved in containing H. pylori infection. This study is aimed at analyzing the mRNA expression of the cytokines IFN-γ, IL-17, IL-10, TGF-β, IL-6, IL-22, IL-23, and IL-33; transcription factors T-bet, RORC, and FOXP3; enzymes ARG1, ARG2, and NOS2; and neuropeptides VIP and TAC and their respective receptors VIPR1 and TACR1 in the stomach lining of patients with severe digestive disorders. One hundred and twenty six patients have been evaluated, presenting with symptoms in the upper digestive tract, with the clinical indication for an Upper Digestive Endoscopy exam. Two fragments of the mucosa of the gastric body and antrum have been collected for anatomopathological examination and to analyze the expression of enzymes, cytokines, and transcription factors using qPCR. Expression of the ARG1 gene was seen as significantly higher in the group of patients with chronic inactive gastritis than in the control group. Expression of the TGF-β gene and its FOXP3 transcription factor was significantly higher in the group of chronic inactive gastritis patients than in the control. Expression of IFN-γ, IL-17, IL-10, and TGF-β and the transcription factors, T-bet and RORC, in the presence or absence of H. pylori showed no significant difference. However, the expression of FOXP3 was significantly lower in H. pylori-positive patients than that in H. pylori-negative patients. ARG1 and Treg profile appeared to be modulating the inflammatory process, protecting patients from the tissue lesions with chronic inactive gastritis. Furthermore, we suggest that IL-33 may be a crucial mediator of the immune response against an infection, after gastric mucosal damage.
Post-mining of Association Rules: Techniques for Effective Knowledge Extraction

There is often a large number of association rules discovered in data mining practice, making it difficult for users to identify those that are of particular interest to them. Therefore, it is important to remove insignificant rules and prune redundancy as well as summarize, visualize, and post-mine the discovered rules. Post-Mining of Association Rules: Techniques for Effective Knowledge Extraction provides a systematic collection of research on the summarization, presentation, and new forms of association rules for post-mining. This book presents researchers, practitioners, and academicians with tools to extract useful and actionable knowledge after discovering a large number of association rules.
A new DTAR (diversity–time–area relationship) model demonstrated with the indoor microbiome

The spatio‐temporal distribution of biodiversity is a core field of biogeography, and the so‐termed species–time–area relationship (STAR), together with its siblings, that is the SAR (species–area relationship) and STR (species–time relationship), has achieved the rare status of classic laws in ecology and biogeography. Traditionally, the STAR or its recent generalization DTAR (diversity–time–area relationship) has been described with the bivariate power law (BPL) model or more recently with Whittaker, Triantis, and Ladle (2008, Journal of Biography; 35: 18) general dynamic model (GDM). We propose to extend the classic BPL into a more flexible DTAR model, which offers new quantitative methods for estimating maximal global diversity and charactering the relationship between local and regional diversity.
Effect of different smoking processes on the nutritional and polycyclic aromatic hydrocarbons composition of smoked Clarias gariepinus and Cyprinus carpio

Abstract The effect of different smoking processes on the nutritional value and polycyclic aromatic hydrocarbon (PAHs) content of Clarias gariepinus and Cyprinus carpio has been assessed in this study. After smoking processes, the finish products were analyzed to determine the nutritional quality and the PAHs content. Different smoking processes significantly decreased (p < 0.05) lipids content of fish. The smoked fish with unfiltered Psidium guajava has revealed higher lipid contents of 14.17 ± 0.15% and 14.96 ± 0.05%, respectively, for SNE GSF and SE GSF. A significant reduction (p < 0.05) in protein content (% DM) has been observed in the two fish's species submitted to smoking processes. We found that evisceration of fish before smoking leads to increase the level of naphthalene, acenaphthene, and benzo (a) pyrene in smoked C. gariepinus and C. carpio. The use of metallic filter in the smoking of noneviscerated fish leads to the significant reduction (p < 0.05) of the PAHs content in smoked fishes. Higher levels of PAH such as naphthalene and acenaphthene with values of 1,451.54 ± 49.58 and 709.91 ± 8.12 ng/kg were found in smoked C. carpio and 1,841.1 ± 11.41 and 809.91 ± 1.10 ng/kg were found in smoked C. gariepinus obtained in the case of traditional smoking. The PAHs content was higher in fish smoked using traditional ovens. Therefore, the quality of smoked fish was improved using a metallic filter during different smoking processes.
Constrained H/sub 2/ design via convex optimization applied to precision pointing attitude control

A convex optimization controller design method is presented which minimizes the closed-loop H/sub 2/ norm, subject to constraints on the magnitude of closed-loop transfer functions and transient responses due to fixed inputs. This method is applied to the roll axis of the EOS-AM1 spacecraft attitude control system, with a set of performance and robustness specifications. This example serves as a good benchmark problem, because it has been used for previous model-based control studies. A controller is designed using constrained H/sub 2/ which successfully meets all of the design specifications of a previous study.
HPTLC pattern assessment of Avicennia marina stem and spectrometric analysis of the separated phyto-constituents

The scientifi c evaluation, validation and authentication of medicinal plants are highly essential and key steps to achieve effective phytochemicals and drugs for disease prevention. The checklist of medicinal plants especially mangroves along with their scientifi c validation is still biased. The traditional methods are poor, time consuming as well as less scientifi c, so there is a need to used emerging technological knowledge and sophisticated analytical methods to fulfi ll this knowledge gap. Therefore, present study is an attempt to study the phytochemistry and recognize HPTLC pattern of Avicennia marinastem and spectrum analysis of resolved compounds in three different extracts. As a result, presence of different class of phytochemicals were detected. HPTLC determination densitometry analysis of 10 μl sample size under UV258 nm of stem extract – 1 (5 % NH3) showed the presence of 2 components with Rf values ranging from 0.76– 0.90; the stem extract – 2 (methanol alone) revealed the presence of 4 components with Rf values in the range of 0.03 – 0.90; and the stem extract – 3 (5 % HCl) revealed presence of 7 components with Rf values in the range of 0.03 – 0.90. As result, extract – 3 (Slightly acidic) gave maximum number of separated compounds and characteristic fi ngerprinting pattern and may be useful as a biochemical integrity check marker for this plant as well as to assess the diversity and further characterization of phyto-compounds present in Avicennia marina stem.
Selective Automatic Focusing For Microscope Images

Several techniques have been proposed for automatic focusing. The methods employed in cyto-bacteriological image analysis sometimes appear to be ineffective due to the thickness of the preparation, the small depth of field of microscopes and the contrast inversion phenomenon. In this paper, we first propose a new global focusing method which is insensitive to the inversion contrast phenomenon. As a second step, to overcome the problems due to the different size of the elements of the preparation, a new selective focusing strategy is presented. It is based on focusing each element separately, such that the accuracy of the focusing procedure is improved.
Study of Shigella flexneri via traditional-bacterial isolation, PCR-sequencing identification, and phylogenetic tree analysis in Al-Diwaniyah City, Iraq

The current study intended to isolate and identify Shigella flexneri via traditional bacterial isolation (TBI), PCRsequencing identification (PSI), and phylogenetic tree analysis(PTA) from patients attended Al-Diwaniyah General Teaching Hospital, Al-Diwaniyah City, Iraq. A total of 25 stool samples were collected and subjected to the above mentioned techniques. The results of the TBI revealed the presence of S. flexneri in these samples. The PCR results confirmed the identification of these bacteria in these samples after a piece, 1256 bp, of the gyrB gene, encodes the subunit B protein of DNA gyrase, was targeted. For the sequencing of 2 samples, the results showed the complete confirmation revealing the correctness of the TBI and the PCR results in identifying these bacteria in the tested samples. The PTA revealed separate distinctive clustering of the sequenced samples in one branch of the phylogenetic tree. The current study enhances the documentation that S. flexneri is one of the infectious agents that causes GIT-related infections in the current tested city.
The surprising "B-side": description of a new foraging tactic for the pearl cichlid, Geophagus brasiliensis, in a coastal stream of the Atlantic Forest

Abstract: A new foraging tactic for the pearl cichlid, Geophagus brasiliensis, is described from underwater observations performed in a coastal stream of the Atlantic Forest, Southeastern Brazil. Named "shift picking", the foraging tactic involved the manoeuvering of leaves, wood twigs and tree bark present in the substrate, with fish using its mouth to turn objects and uncover macroinvertebrates adhered to the underside of the object being picked ("B-side"). The object-shifting behaviour is rarely reported for fish and the present description seems to be the first record for a freshwater species of South America.
Effect of essential and non-essential elements on cellular immune system of cotton bollworm, Helicoverpa armigera Hübner (Lepidoptera: Noctuidae)

Three concentrations of 12.5, 25 and 50 mg/kg of cadmium and 25, 50 and 100 mg/kg of copper were added to artificial diet and fed to larvae for 7 days. Total hemocytes count (THC) at 12.5 mg/kg concentration of cadmium significantly declined, but at 50 mg/ kg of cadmium and all treatments of copper, the THC was significantly enhanced. As for differential hemocytes count (DHC) prohemocytes were reduced at 12.5 mg/kg of cadmium treatment and all concentrations of copper, while granulocytes in all treatments of cadmium were increased. The phenoloxidase activity and nodulation were increased versus entomopathogenic fungi, Beauveria bassiana (Balsamo) Vuillemin and latex beads. The adverse influence of stresses on immune responses of pest can be an effective solution for insect pest control.
Tomato Yellow Leaf Curl Virus V2 Protein Plays a Critical Role in the Nuclear Export of V1 Protein and Viral Systemic Infection

Geminiviruses are an important group of circular, single-stranded DNA viruses that cause devastating diseases in crops. Geminiviruses replicate their genomic DNA in the nucleus. The newly-synthesized viral DNA is subsequently transported to the cytoplasm, moved to adjacent cells through plasmodesmata with the help of viral movement proteins, and, ultimately, moved long-distance to establish systemic infection. Thus, the nucleocytoplasmic transportation is crucial for a successful infection by geminiviruses. For Tomato yellow leaf curl virus (TYLCV), the V1 protein is known to bind and shuttle viral genomic DNA, but the role of V2 protein in this process is still unclear. Here, we report that the nucleus-localized V1 protein dramatically decreases when co-expressed with V2 protein, and that V2-facilitated nuclear export of V1 protein depends on host exportin-α and a specific V1-V2 interaction. Chemical inhibition of exportin-α or a substitutions at cysteine 85 of V2 protein, which abolishes the V1-V2 interaction, blocks the promoted redistribution of V1 protein to the perinuclear region and the cytoplasm. When the V2C85S mutation is incorporated into a TYLCV infectious clone, the TYLCV-C85S causes delayed onset of very mild symptoms compared to wild-type TYLCV, indicating that the V1-V2 interaction and, thus, V2-mediated nuclear export of V1 protein is crucial for viral spread and systemic infection. Our data point to a critical role of the V2 protein in promoting the nuclear export of the V1 protein, likely by promoting V1-mediated nucleocytoplasmic transportation of TYLCV genomic DNA, and in turn, promoting viral systemic infection. Author summary As both replication and the transcription of geminiviruses occur in the nucleus, transportation of the viral genomic DNA into and out of the nucleus of the infected cells is essential for a successful infection cycle. However, the nuclear export of geminiviruses is still little known and even less is known about the process for monopartite geminiviruses. We use TYLCV, a typical monopartite begomovirus in the family Geminiviridae, to examine the nucleocytoplasmic transportation. In this study, we found TYLCV V2 is able to redistribute the nucleus-localized V1 protein to the perinuclear region. Moreover, the nuclear export of V1 protein is dependent on the V1-V2 interaction and host exportin-α. Blocking the V1-V2 interaction impeded the V2-mediated V1 protein redistribution and decrease TYLCV infection efficiency with delayed and mild symptoms. This report shows us a new explanation for the role of V2 in the nuclear export of V1 protein and TYLCV viral systemic infection.
Edubot: a reconfigurable kit for control education. I. Mechanical design

This paper describes the mechanical design of a reconfigurable educational robotic kit, named the Edubot. This kit can be easily assembled to perform a wide range of both linear and nonlinear control system experiments. The modular design is described and a subset of the possible configurations shown. Two prototyped designs are detailed and critiqued. A Pendubot and an Acrobot are used as case studies to demonstrate the kit.
A nonlinear regression technique for the separation of kinetic compartments in dynamic SPECT imaging

The accuracy of SPECT images are compromised when the tracer distribution changes during image acquisition. Image analysis can be further complicated if there is an overlap between the kinetic compartments. For example, Tc-99m Teboroxime is an imaging agent with rapid washout from the myocardium and high liver uptake. The reconstructed myocardium in Tc-99m Teboroxime SPECT may be compromised with artifacts due to changing activity and contaminated by reconstruction artifacts due to the liver. This study proposes a nonlinear regression technique to separate the kinetic compartments, based on the knowledge of time-activity curves (TAC) coupled with dynamic SPECT scans. Dynamic scans (acquired with a rapid fanning acquisition) are reconstructed independently to generate dynamic short-axis images (representing the tracer distribution at different times), which are then transformed to allow each pixel to be evaluated over time independently. The objective function to be minimized is the deviation of the separated compartmental pixels scaled by the TAC plus a distance penalty. This minimization problem is solved subject to reference and nonnegative constraints. The reference constraint is produced from the reconstruction of the summed projections from the dynamic scans (with minimal artifacts due to changing activity). Patient studies of Tc-99m Teboroxime SPECT were used to evaluate this technique. Qualitatively, the kinetic compartments (the liver and heart) were separated producing images with reduced liver contamination in the myocardium. The quantitative accuracy of the separation depends on the accuracy of the tracer kinetics and can also be degraded by physical factors such as photon attenuation and Compton scatter.
Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity

Despite the transcription of noncoding RNAs in 75% of the human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained only from costly and inefficient 3D structure determination. Here, we performed deep mutational scanning of self-cleaving CPEB3 ribozyme by error-prone PCR and showed that a library of <5×104 single-to-triple mutants is sufficient to infer all 26 including nonhelical and noncanonical base pairs at the precision of a single false positive. The accurate inference, further confirmed by a twister ribozyme, is resulted from covariation analysis by utilizing both functional and nonfunctional variants for unsupervised learning, followed by restrained optimization. The result highlights the usefulness of deep mutational scanning for high-accuracy structural inference.
Biomechanical Analysis of Angular Motion in Association with Bilateral Semicircular Canal Function

The aim of this study was to develop a finite element (FE) model of bilateral human semicircular canals (SCCs) in order to simulate and analyze the complex fluid-structural interaction between the endolymph and cupulae by calculating the degree of cupular expansion and the cupular deflection. The results showed that cupular deflection responses were consistent with Ewald’s II law, whereas each pair of bilateral cupulae simultaneously expanded or compressed to the same degree. In addition, both the degree of cupular expansion and cupular deflection can be expressed as the solution of forced oscillation during head sinusoidal rotation, and the amplitude of cupular expansion was approximately two times greater than that of cupular deflection. Regarding the amplitude-frequency and phase-frequency characteristics, the amplitude ratios among the horizontal semicircular canal (HC) cupular expansion, the anterior semicircular canal (AC) cupular expansion, and the posterior semicircular canal (PC) cupular expansion was constant at 1:0.82:1.62, and the phase differences among them were constant at 0 or 180 degrees at the frequencies of 0.5 to 6 Hz. However, both the amplitude ratio and the phase differencies of the cupular deflection incresed nonlinearly with the increase of frequency and tended to be constant at the frequency band between 2 and 6 Hz. The results indicate that the responses of cupular expansion might only be related to the mass and rigidity of three cupulae and the endolymph, but the responses of cupular deflection are related to the mass, rigidity, or damping of them, and these physical properties would be affected by vestibular dysfunction. Therefore, both the degree of cupular expansion and cupular deflection should be considered important mechanical variables for induced neural signals. Such a numerical model can be further built to provide a useful theoretical approach for exploring the biomechanical nature underlying vestibular dysfunction. Statement of significance By taking the advantage of the torsional pendulum model and the FE model, a healthy human vestibular SCCs was developed to investigate the angular motion in association with SCC function. As a result, the responses of cupular expansion and deflection during head horizontal sinusoidal rotation were analyzed for the first time, showing quantitative correlation to the eye movement due to the vestibular ocular reflex (VOR) pathway. These responses play important roles in the cupular mechano-electrical transduction process. The significant outcome derived from this study provides a useful theoretical approach for further exploring the biomechanical nature underlying vestibular dysfunction.
Evaluating mechanisms of plant‐mediated effects on herbivore persistence and occupancy across an ecoregion

Contemporary climate change is rapidly creating one of the greatest challenges for management and conservation during the 21st century. Mountain ecosystems, which have a high degree of spatial heterogeneity and contain numerous habitat specialists, have been identified as particularly vulnerable. We used data from multiple years across sites spanning a >40 million ha ecoregion to test hypotheses regarding how community‐level characteristics of vegetation may affect a mammalian generalist herbivore, the American pika (Ochotona princeps). We examined patterns of pika persistence across sites in the hydrographic Great Basin, and occupancy within a subset of these sites. We used mixed‐effects logistic regression models to compare evidence in support of competing explanations for each pattern within an information–theoretic framework (using Akaike's information criterion). Models reflected four hypothesized classes of mechanisms related to nutritional ecology, ecosystem function, indirect indication of climatic effects, and (synergistic) combinations of these three classes. At the site level, models reflecting synergistic effects received the most support. At the within‐site level, support appeared to be split equally among hypotheses containing predictors related to either nutritional ecology or indirect climate effects. Well‐supported predictors included cover of invasive plant species, cover of more‐xeric plant species, species evenness, and proportion of graminoid species. Our results both (1) identify important aspects of vegetation communities that may influence herbivore distribution in mountainous areas across a large, diverse geographic region, and (2) contribute to an improved understanding of how mountain ecosystems may be affected by ongoing climate change, more broadly.
Morfometria da copa de povoamentos de Eucalyptus grandis Hill ex Maiden x E. urophylla S. T. Blake em diferentes espaçamentos de plantio

The canopy morphometry and its relationships with space and time subsidize decision-making on plant density and silvicultural interventions in forest stands. The aim of this work was to evaluate the effect of planting density and age on the canopy morphometry of Eucalyptus grandis x E. urophylla. The experiment was established in a randomized three blocks design, split plot scheme in time. The main treatments consisted of four planting spacing (T1: 3,0 × 0,5 m; T2: 3,0 × 1,0 m; T3: 3,0 × 1,5 m e T4: 3,0 × 2,0 m). at four ages (24, 37, 48 e 59 meses). The following morphometric indexes were calculated: Canopy Proportion (CP), Canopy Formal (CF), Slenderness Rate (SR), Range Index (RI) and Salience Index (SI). RI was the only morphometric attribute that interacted with spacing and age. CP, RI and SI tended to decrease over time. CF and SR remained statistically stable between 24 and 59 months of age. The trees of the spacing 3.0 × 2.0 m expressed lower SR, SI and, at the age of 59 months, RI, implying less intraspecific competition and more resistance to the weather. Planting spacing and age influenced the morphometry of the canopy of eucalyptus trees.