Miracle-dz/UniFAR-FTUs huggingface dataset:
Combinatorial Effects of Aromatic 1,3-Disubstituted Ureas and Fluoride on In vitro Inhibition of Streptococcus mutans Biofilm Formation

Dental caries occur as a result of disequilibrium between acid producing pathogenic bacteria and alkali generating commensal bacteria within a dental biofilm (dental plaque). Streptococcus mutans has been reported as a primary cariogenic pathogen associated with dental caries. Emergence of multidrug resistant as well as fluoride resistant strains of S. mutans due to over use of various antibiotics are a rising problem and prompted the researchers worldwide to search for alternative therapies. In this perspective, the present study was aimed to screen selective inhibitors against ComA, a bacteriocin associated ABC transporter, involved in the quorum sensing of S. mutans. In light of our present in silico findings, 1,3-disubstituted urea derivatives which had better affinity to ComA were chemically synthesized in the present study for in vitro evaluation of S. mutans biofilm inhibition. The results revealed that 1,3-disubstituted urea derivatives showed good biofilm inhibition. In addition, synthesized compounds exhibited potent synergy with a very low concentration of fluoride (31.25–62.5 ppm) in inhibiting the biofilm formation of S. mutans without affecting the bacterial growth. Further, the results were supported by confocal laser scanning microscopy. On the whole, from our experimental results we conclude that the combinatorial application of fluoride and disubstituted ureas has a potential synergistic effect which has a promising approach in combating multidrug resistant and fluoride resistant S. mutans in dental caries management.
Glomerular involvement in type II diabetes - is it all diabetic glomerulosclerosis?

1. Sprague SM, Popovtzer MM. Is /J2-microglobulin a mediator of bone disease? Kidney Int 1995; 47: 1-6 2. Ohashi K, Hara M, Kawai R et al. Cervical discs are most susceptible to beta2-microglobulin amyloid deposition in the vertebral column. Kidney Int 1992; 41: 1646-1652 3. Miyata T, Oda O, Inagi R et al. /? 2-Microglobulin modified with advanced glycation end products is a major component of hemodialysis-associated amyloidosis. J Clin Invest 1993; 92: 1243-1252 4. Miyata T, Taneda S, Kawai R et al. Identification of pentosidine as a native structure for advanced glycation end products in /? 2-microglobulin containing amyloid fibrils in patients with dialysis-related amyloidosis. Proc Natl Acad Sci USA (in press) 5. Brownlee M, Cerami A, Vlassara H. Advanced glycosylation end products in tissue and the biochemical basis of diabetic complications. N Engl J Med 1988; 318: 1315-1321 6. Schmidt AM, Yon SD, Brett J, Mora R, Nowygrod R, Stern D. Regulation of human mononuclear phagocyte migration by cell surface-binding proteins for advanced glycation end products. J Clin Invest 1993; 92: 2155-2168 7. Miyata T, Inagi R, Wada Y et al. Glycation of human /92-microglobulin in patients with hemodialysis-associated amyloidosis: identification of the glycated sites. Biochemistry 1994; 33: 12215-12221 Nephrol Dial Transplant (1996) 11: Editorial Comments
A 220-nucleotide deletion of the intronic enhancer reveals an epigenetic hierarchy in immunoglobulin heavy chain locus activation

A tissue-specific transcriptional enhancer, Eμ, has been implicated in developmentally regulated recombination and transcription of the immunoglobulin heavy chain (IgH) gene locus. We demonstrate that deleting 220 nucleotides that constitute the core Eμ results in partially active locus, characterized by reduced histone acetylation, chromatin remodeling, transcription, and recombination, whereas other hallmarks of tissue-specific locus activation, such as loss of H3K9 dimethylation or gain of H3K4 dimethylation, are less affected. These observations define Eμ-independent and Eμ-dependent phases of locus activation that reveal an unappreciated epigenetic hierarchy in tissue-specific gene expression.
Sedimentary Facies and Architecture of a Gigantic Gravelly Submarine Channel System in a Cretaceous Foredeep Trough (the Magallanes Basin, Southern Chile)

: The Lago Sofia conglomerate in southern Chile is a deep-marine gravelly deposit, which is hundreds of meters thick and kilometers wide and extends laterally for more than 100 km, filling the foredeep trough of the Cretaceous Magallanes Basin. For understanding the depositional processes and environments of this gigantic deep-sea conglomerate, detailed analyses on sedimentary facies, architecture and paleoflow patterns were carried out, highlighting the differences between the northern (Lago Pehoe and Lago Goic areas) and southern (Lago Sofia area) parts of the study area. The conglomerate bodies in the northern part occur as relatively thin (< 100 m thick), multiple units intervened by thick mudstone-dom-inated sequences. They show paleoflows toward ENE and S to SW, displaying a converging drainage pattern. In the southern part, the conglomerate bodies are vertically interconnected and form a thick (> 400 m thick) conglomerate sequence with rare intervening fine-grained deposits. Paleoflows are toward SW. The north-to-south variations are also distinct in sedimentary facies. The conglomerate bodies in the southern part are mainly composed of clast-supported conglomerate with sandy matrix, which is interpreted to be deposited from highly concentrated bedload layers under turbidity currents. Those in the northern part are dominated by matrix- to clast-supported conglomerate with muddy matrix, which is interpreted as the products of composite mass flows comprising a turbidity current, a gravelly hyperconcentrated flow and a mud-rich debris flow. All these characteristics suggest that the Lago Sofia conglomerate was formed in centripetally converging submarine channels, not in centrifugally diverging channels of submarine fans. The tributaries in the north were dominated by mass flows, probably affected by channel-bank failures or basin-marginal slope instability processes. In contrast, the trunk channel in the south was mostly filled by tractive processes, which resulted in the vertical and lateral accretion of gravel bars, deposition of gravel dunes and filling of scours and channels, similar to deposits of terrestrial gravel-bed rivers. The trunk channel developed along the axis of foredeep trough and its confinement within the trough is probably responsible for the thick, interconnected channel fills. The large-scale architecture of the trunk-channel fills shows an eastward offset stacking pattern, suggesting that the channel migrated eastwards most likely due to the uplift of the Andean Cordillera.
Characterization of insect galls from a vegetation area in Altinópolis, São Paulo State, Brazil

Herein, we studied the occurrence of insect galls from natural vegetation around the Itambé Cave, Altinópolis, SP, Brazil. A sampling effort of 7.5 hours resulted in 41 gall morphotypes on 21 host plant species from 14 families. The richest families of host plants in morphotypes were Fabaceae (N = 11), Euphorbiaceae (N = 7), and Malpighiaceae (N = 5). Copaifera langsdorffii Desf. (N = 8), Croton floribundus Spreng. (N = 7), Diplopterys pubipetala (A. Juss.) W.R. Anderson & C.C. Davis (N = 5), and Bauhinia holophylla (Bong.) Steud. (N = 4) were the super host plant species. Among the gall makers obtained, cecidomyiids were reared in 81% of cases and Hemiptera (Diaspididae), Hymenoptera (Eurytomidae), Coleoptera (Apion sp./Apionidae), and Lepidoptera in 4.5% of cases, each. The parasitoids belong to the Chalcidoidea superfamily (Hymenoptera). One new species of Camptoneuromyiia (Cecidomyiidae) was found in Smilax oblongifolia Pohl ex Griseb. (Smilacaceae) as inquiline and a new species of Lestodiplosis in Diplopterys pubipetala (Malpighiaceae) was a predator. We also present the first register of Bauhinia holophylla as host plants of Cecidomyiidae, and we expand the occurrence of Rochadiplosis tibouchinae Tavares and Couridiplosis vena to São Paulo State. The results of this paper are a continuation of the description of gall morphotypes from the vegetation in Northeastern São Paulo State, and they also increase knowledge about the diversity of host plant and gall-maker associations in the Neotropical region.
Bone marrow failure and myelofibrosis in a case of PVP storage disease

“PVP storage disease” is a disorder occurring in patients who have received high molecular weight polyvinylpyrrolidone (PVP), which cannot be excreted from the body. These large polymers deposit in the histiocytes and cause proliferation and infiltration of histiocytes in the reticuloendothelial system. There was usually no significant damage to these organs except that prolonged administration might cause bone destruction, skin lesions, arthritis, and polyneuropathy. We describe a patient who had received a large amount of PVP‐containing solution for years. Severe bone marrow failure with extensive infiltration of bone marrow by foamy histiocytes occurred later. In addition, she suffered from multiple pathological fractures with spinal cord compression and arthritis of bilateral knee joints. Am. J. Hematol. 57:68–71, 1998. © 1998 Wiley‐Liss, Inc.
ERP and fMRI correlates of retrieval cues in episodic memory.

EEG event-related potentials (ERPs) and fMRI blood oxygenation level dependent (BOLD) new item contrasts were employed in six experiments to investigate the neural correlates of retrieval orientations - cognitive states or 'sets' that align cue processing with the demands of a particular retrieval goal. It is proposed that the neural correlates of different retrieval orientations can be investigated by comparing the activity elicited by the same class of retrieval cues when these were used to probe memory for different kinds of information (Rugg & Wilding, 2000), preferably with new items in memory tests, so as to minimize the confound between cue processing and processes associated with successful retrieval. The reported results on new unstudied items replicate and extend recent findings (e.g. Robb & Rugg, 2002) by showing that retrieval orientation effects are robust ERP effects across different study and test materials and semantic encoding tasks. However, the occurrence of the same effect is sensitive to manipulations of the retrieval tasks employed, and further a one-to-one mapping of the reported scalp ERP effect onto the observed fMRI activations is difficult to make. In terms of a functional interpretation, the retrieval orientation effect seems to reflect differences in the need to constrain cue processing. Specifically, it is proposed that the more a cue representation must be constrained to the semantic/conceptual level, the more negative-going will be the associated ERPs.
An Iterative Learning Control of Nonlinear Systems Using Neural Network Design

In this paper, a feedforward neural network with sigmoid hidden units is used to design a neural network based iterative learning controller for nonlinear systems with state dependent input gains. No prior offline training phase is necessary, and only a single neural network is employed. All the weights of the neurons are tuned during the iteration process in order to achieve the desired learning performance. The adaptive laws for the weights of neurons and the analysis of learning performance are determined via Lyapunov‐like analysis. A projection learning algorithm is used to prevent drifting of weights. It is shown that the tracking error vector will asymptotically converges to zero as the iteration goes to infinity, and the all adjustable parameters as well as internal signals remain bounded.
Sediment Transportation Mechanics: H. Sediment Discharge Formulas

Thirteen well-known sediment discharge formulas are presented with a view to making them convenient to use. The basis for each formula is outlined and results of measured bed sediment discharge on two sand bed streams are compared with values calculated with each of the 13 formulas. This is done on a graph of sediment discharge against water discharge for the two streams. In these calculations the relation between water depth, velocity and discharge was calculated by the Einstein-Barbarossa method. These comparisons of results calculated by formulas with measurements and with each other are interesting in that they bring out the great variability of the calculated sediment discharges. However, they are of only limited value in determining the general reliability of each formula.
Prostate cancer antigen 3 (PCA3) RNA detection in blood and tissue samples for prostate cancer diagnosis

Abstract Background: The non-coding prostate cancer antigen 3 (PCA3) RNA is currently the most specific biomarker for prostate cancer (PCa) diagnosis. Although its clinical value has been validated in a urine assay after intensive prostatic massage, few studies have been conducted to establish its diagnostic value in the peripheral blood (PBL). The aim of the present study was to examine the PCA3 expression in blood as a diagnostic tool, and to provide an additional strategy to improve PCa diagnosis. Methods: PCA3 transcripts were detected by RT-PCR in PBL and prostatic tissues from patients. PBL sampling also included a group of young healthy volunteers. The relationship between the PCA3 RNA detection and clinical characteristics was analyzed. Results: PCA3 detection in blood presented 94% specificity and 32% sensitivity, and its combined detection in tissues significantly improved diagnostic parameters. However, PCA3 RNA detection in blood was also associated with PSA levels ≥10 ng/mL, and their combination provided a sensitivity of 60% and specificity of 93%. Conclusions: Detection of the PCA3 RNA in patients’ blood is an efficient tool for PCa diagnosis because it allows a routine collection procedure, which is also supported by the ongoing screening marker, prostate-specific antigen (PSA). We propose its combined use with PSA levels ≥10 ng/mL, which improves accuracy, and prevents overdiagnosis and overtreatment.
Stagewise Lasso

Many statistical machine learning algorithms minimize either an empirical loss function as in AdaBoost, or a penalized empirical loss as in Lasso or SVM. A single regularization tuning parameter controls the trade-off between fidelity to the data and generalizability, or equivalently between bias and variance. When this tuning parameter changes, a regularization "path" of solutions to the minimization problem is generated, and the whole path is needed to select a tuning parameter to optimize the prediction or interpretation performance. Algorithms such as homotopy-Lasso or LARS-Lasso and Forward Stagewise Fitting (FSF) (aka e-Boosting) are of great interest because of their resulted sparse models for interpretation in addition to prediction. In this paper, we propose the BLasso algorithm that ties the FSF (e-Boosting) algorithm with the Lasso method that minimizes the L1 penalized L2 loss. BLasso is derived as a coordinate descent method with a fixed stepsize applied to the general Lasso loss function (L1 penalized convex loss). It consists of both a forward step and a backward step. The forward step is similar to e-Boosting or FSF, but the backward step is new and revises the FSF (or e-Boosting) path to approximate the Lasso path. In the cases of a finite number of base learners and a bounded Hessian of the loss function, the BLasso path is shown to converge to the Lasso path when the stepsize goes to zero. For cases with a larger number of base learners than the sample size and when the true model is sparse, our simulations indicate that the BLasso model estimates are sparser than those from FSF with comparable or slightly better prediction performance, and that the the discrete stepsize of BLasso and FSF has an additional regularization effect in terms of prediction and sparsity. Moreover, we introduce the Generalized BLasso algorithm to minimize a general convex loss penalized by a general convex function. Since the (Generalized) BLasso relies only on differences not derivatives, we conclude that it provides a class of simple and easy-to-implement algorithms for tracing the regularization or solution paths of penalized minimization problems.
BOL-303242-X, a novel selective glucocorticoid receptor agonist, with full anti-inflammatory properties in human ocular cells

Purpose BOL-303242-X is a novel selective glucocorticoid receptor agonist under clinical evaluation for the treatment of inflammatory skin and eye diseases. Data from in vitro and in vivo studies suggest an improved side-effect profile of this compound compared to classical glucocorticoids. The aim of this study was to determine the anti-inflammatory effect of BOL-303242-X in ocular cells. Methods Four primary human ocular cell cultures, including human conjunctival fibroblasts (HConFs), human corneal epithelial cells (HCEpiCs), human optic nerve astrocytes (HONAs), and human retinal endothelial cells (HRECs), as well as a human monocytic cell line, THP-1, were challenged with either lipopolysacharide (LPS) or interleukin-1ß (IL-1ß). Luminex technology was used to determine the effect of BOL-303242-X on LPS- or IL-1ß-induced cytokine release and intercellular adhesion molecule-1 (ICAM-1) levels. Effects of BOL-303242-X on nuclear factor kappa B (NFκB) and mitogen-activated protein kinase (MAPK) in HCEpiCs were also assessed by measuring inhibitory kappa B protein-α (IκB-α), phosphorylated p65 NFκB, and MAPK levels by western blotting. Dexamethasone (DEX) or triamcinolone acetonide (TA) was used as the control. Results LPS or IL-1ß induced multiple cytokine release in all cell types studied. BOL-303242-X significantly reduced LPS- or IL-1ß-induced inflammatory cytokine release in a dose-dependent manner, including granulocyte colony-stimulating factor (G-CSF), IL-1ß, IL-6, IL-8, IL-12p40, monocyte chemotactic protein-1 (MCP-1), and tumor necrosis factor-α (TNF-α). BOL-303242-X showed activity and potency comparable to that observed for DEX or TA. A statistically significant inhibitory effect of BOL-303242-X was observed at doses ranging from 1 to 100 nM in HConFs, HCEpiCs, HONAs, and THP-1. The IC50 values for these effects were in the low nM range. BOL-303242-X also significantly reduced LPS-induced IL-1ß release and ICAM-1 levels in HRECs. Furthermore, BOL-303242-X inhibited IL-1ß-induced decreases in IκB-α levels, as well as IL-1ß-induced phosphorylation of NFκB, p38, and c-Jun-N-terminal kinase (JNK) MAPKs in HCEpiCs. Conclusions BOL-303242-X acts as a potent anti-inflammatory agent in various primary human ocular cells with similar activity and potency compared to classical steroids. Results also suggest that MAPK (p38 and JNK) and NFκB signaling pathways are involved in the anti-inflammatory properties of BOL-303242-X in HCEpiCs. An improved side effect profile of this novel SEGRA compound has been reported recently. Thus, BOL-303242-X may provide a new option for the treatment of ophthalmic conditions with an inflammatory component.
Very High Resolution & 3D Remote Sensing Data for Supporting Forestry in Wallonia. What Resolution? What Scale? What Purpose?

BONNET Stéphanie (2018). Very High Resolution & 3D Remote Sensing Data for Supporting Forestry in Wallonia. What Resolution? What Scale? What Purpose? PhD Thesis. Université de Liège Gembloux Agro-Bio Tech, Belgium. 152 p., 23 tabl. , 50 fig. The forest, which represents one-third of the Earth surface, has always been in close interaction with human societies. Forests provide many environmental services: soil and water resources protection, reduction of impact of gas emissions, biodiversity reservoir and conservation. Concerns about global changes add to social functions such as recreational activities or wood production and about forest management and silviculture practices. The need for information about the forest resource has never been greater to ensure a sustainable management. The description of the forest stands (location, extent, composition, structure .) and their dendrometric characterization (dominant height, number of trees per hectare, mean quadratic circumference, basal area and volume per hectare .) have become crucial prerequisites indispensable for planning. Remote sensing enables information acquisition over large areas and overcomes the capacity and accessibility limitations inherent in field data collection, which mobilizes significant human and financial resources. The Walloon forest is characterized by a great diversity of situations and preoccupations: type of owner, structure, composition, spatial distribution, stations, fragmentation, silvicultural practices. This diversity makes it particularly relevant to use remote sensing as an information acquisition tool. This thesis lies in this context. The main purpose was the implementation of different types of three-dimensional remote sensing data to determine how they could contribute properly to forest management in Wallonia. First, we considered the use of low-density and regional-scale Airborne Laser Scanning (ALS) data in combination with the data collected by the Walloon Regional Forest Inventory. This combination has shown its potential for quantifying coniferous forest attributes, coupled with regional allometry built on the inventory database. In parallel with the importance of coniferous forest, a major concern is the development of a close-to-nature forestry, promoting natural regeneration. The presence of gaps in the stands is therefore essential information. We focused on a robust mapping of gaps in broadleaved forests from high-density ALS data. To complete our progression in the use of three-dimensional data,
Sheep primary cells as in vitro models to investigate Mycoplasma agalactiae host cell interactions

Appropriate infection models are imperative for the understanding of pathogens like mycoplasmas that are known for their strict host and tissue specificity, and lack of suitable cell and small animal models has hindered pathogenicity studies. This is particularly true for the economically important group of ruminant mycoplasmas whose virulence factors need to be elucidated for designing effective intervention strategies. Mycoplasma agalactiae serves as a useful role model especially because it is phylogenetically very close to M. bovis and causes similar symptoms by as yet unknown mechanisms. Here, we successfully prepared and characterized four different primary sheep cell lines, namely the epithelial and stromal cells from the mammary gland and uterus, respectively. Using immunohistochemistry, we identified vimentin and cytokeratin as specific markers to confirm the typical cell phenotypes of these primary cells. Furthermore, M. agalactiae’s consistent adhesion and invasion into these primary cells proves the reliability of these cell models. Mimicking natural infections, mammary epithelial and stromal cells showed higher invasion and adhesion rates compared to the uterine cells as also seen via double immunofluorescence staining. Altogether, we have generated promising in vitro cell models to study host–pathogen interactions of M. agalactiae and related ruminant pathogens in a more authentic manner.