Miracle-dz/UniFAR-FTUs huggingface dataset:
The importance of red cell distribution width and neutrophil-lymphocyte ratio as a new biomarker in rheumatoid arthritis

Objectives: Rheumatoid arthritis (RA) is a long-lasting autoimmune disorder that primarily affects the joints . V arious biomarkers have been used for the prognosis and clinical follow-up. There are few studies that have investigated whether or not neutrophil-lymphocyte ratio (NLR) and red cell distribution width ( RDW) are good indicators of systemic inflammation. The present study aims to explore the prognostic value of RDW and NLR in rheumatoid arthritis (RA) as a new inflammatory marker. Methods: RA patients (n = 124) who presented to the Rheumatology outpatient clinic in our hospital between March 2015 and May 2015 were included in this study retrospectively. As a first group, 47 clinically active RA patients who had high acute phase proteins were included. In the second group, 73 clinically in-remission RA patients who had normal acute phase proteins were included. Fifty-five healthy volunteers constituted the control group. Results: The mean RDW was found to be 15.2 ± 2.9 in the active group; 14.6 ± 2 in the inactive group and 13.4 ± 1.4 in the control group ( p < 0.01). The mean NLR was found to be 3.7 ± 2.2 in the active group; 3.7 ± 1.6 in the inactive group and 3.2 ± 0.9 in the control group ( p = 0.190). There were statistically significant differences between the RDW values of the active-period RA patients with the control group ( p < 0.01). There was statistically significant difference between RDW values of active RA and inactive RA patients ( p < 0.01). The NLR results between the RA group and the control group ( p = 0.700); the active RA group, and the inactive RA group ( p = 0.169) were similar. There was not statistically difference between the NLR values of active RA patients with the control group ( p = 0.360). There was statistically difference between the NLR values of inactive RA patients with the control group ( p = 0.047). Conclusion: RDW was found higher in all RA group than control, additionally was also higher in active RA group than remission group. NLR values of remission group was higher than control.
Distributed under Creative Commons Cc-by 4.0 the Diversity of Membrane Transporters Encoded in Bacterial Arsenic-resistance Operons

Transporter-facilitated arsenite extrusion is the major pathway of arsenic resistance within bacteria. So far only two types of membrane-bound transporter proteins, ArsB and ArsY (ACR3), have been well studied, although the arsenic transporters in bacteria display considerable diversity. Utilizing accumulated genome sequence data, we searched arsenic resistance (ars) operons in about 2,500 bacterial strains and located over 700 membrane-bound transporters which are encoded in these operons. Sequence analysis revealed at least five distinct transporter families, with ArsY being the most dominant, followed by ArsB, ArsP (a recently reported permease family), Major Facilitator protein Superfamily (MFS) and Major Intrinsic Protein (MIP). In addition, other types of transporters encoded in the ars operons were found, but in much lower frequencies. The diversity and evolutionary relationships of these transporters with regard to arsenic resistance will be discussed.
Optimization of Laccase Production by Locally Isolated Trichoderma muroiana IS1037 Using Rubber Wood Dust as Substrate

Laccases have great biotechnological potential in various industries as they catalyze the oxidation of a broad variety of chemical compounds, diamines, and aromatic amines. The production of laccases by fungi has been broadly studied due to their secretion of enzymes and their growth using cheap substrates. In this study, five native fungi isolates (Dr1, Dr2, Dr4, K5, and K9) were screened for laccase enzyme production. The ability to produce laccase was evaluated based on light green to dark color formation on a potato dextrose agar using 2,2’-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) as an indicator. The highest laccase production was obtained by Dr4, which was identified as Trichoderma muroiana IS1037. Among the different carbon sources tested (rubber wood dust, rice straw, sugar cane bagasse, and oil palm empty fruit bunch), the highest laccase activity (5.84 U/mL) was obtained in submerged fermentation using rubber wood dust as substrate. Laccase production was further enhanced with the addition of 2 mM copper sulfate. In conclusion, the local fungus isolate Trichoderma muroiana IS1037 is a potential fungi-producing laccase that can use rubberwood dust as carbon source.
Comparison of two methods for computing action values in XCS with code-fragment actions

XCS is a learning classifier system that uses accuracy-based fitness to learn a problem. Commonly, a classifier rule in XCS is encoded using a ternary alphabet based condition and a numeric action. Previously, we implemented a code-fragment action based XCS, called XCSCFA, where the typically used numeric action was replaced by a genetic programming like tree-expression. In XCSCFA, the action value in a classifier was computed by loading the terminal symbols in the action-tree with the corresponding binary values in the condition of the classifier rule. This enabled accurate, general and compact rule sets to be simply produced. The main contribution of this work is to investigate an intuitive way, i.e. using the environmental instance, to compute the action value in XCSCFA, instead of the condition of the classifier rule. The methods will be compared in five different Boolean problem domains, i.e. multiplexer, even-parity, majority-on, design verification, and carry problems. The environmental instance based XCSCFA approach had better classification performance than standard XCS as well as classifier condition based XCSCFA and solved all the problems experimented here. In addition it produced more general and compact classifier rules in the final solution. However, classifier condition based XCSCFA has the advantage of producing the optimal classifiers such that they are clearly separated from the sub-optimal ones in certain domains.
Basic Study on Pretensioned Members with Ultra-High Strength Concrete

Ultra-high-strength concrete (UHSC) with compressive strength of 150N/mm2 makes it possible to reduce the weight of prestressed concrete structures. Particularly in case that UHSC is applied to pretensioned members, high bond strength can also be expected to reduce the transfer length. Considerable autogenous shrinkage of UHSC, however, reduces effective prestress and causes cracking due to the restraint of reinforcing steel. A new type UHSC with less autogenous shrinkage was developed, and its basic characteristics were investigated. Prestressing tests parameterizing the type of prestressing steel and the amount of introduced stress were also conducted to determine transfer length and to verify the effect of reduced autogenous shrinkage. Furthermore the predictability of effective prestress considering shrinkage and creep strain was studied.
Measuring CO2 and CH4 with a portable gas analyzer: Closed-loop operation, optimization and assessment

The use of cavity ring-down spectrometer (CRDS) based portable greenhouse gas analyzers (PGAs) in closed-loop configuration to measure small sample volumes (< 1 l) for CH4 and CO2 concentrations is increasing and offers certain advantages over conventional measurement methods in terms of speed as well as the ability to measure directly in field locations. This first systematic assessment of the uncertainties, problems and issues associated with achieving reliable and repeatable measurement with this technique presents the adaptation, measurement range, calibration and maintenance, accuracy and issues of efficient operation, for one example instrument. Regular open-loop calibration, a precise loop volume estimate, leak free system, and a high standard of injection practices are necessary for accurate results. For 100 μl injections, measured values ranging from 4.5 to 9 x104 ppm (CH4), and 1000 ppm to 1 x106 ppm (CO2) are possible with uncertainties ±5.9% and ±3.0%, respectively, beyond 100 ppm CH4 correction may be necessary. Uncertainty arising from variations water vapour content and atmospheric pressure are small (0.24% and -0.9% to +0.5%, respectively). With good practice, individual operator repeatability of 1.9% (CH4) and 2.48% (CO2) can be achieved. Between operator injection error was around 3% for both gases for four operators. Slow syringe plunger operation (> 1s) is recommended; generally delivered more (ca. 3–4%) sample into the closed instrument loop than did rapid operation. Automated value retrieval is recommended; we achieved a 3 to 5-fold time reduction for each injection cycle (ca. <2 min), and operator reading, recording, and digitization errors are eliminated.
Synthesis of a Novel Electrospun Polycaprolactone Scaffold Functionalized with Ibuprofen for Periodontal Regeneration: An In Vitro andIn Vivo Study

Ibuprofen (IBU) has been shown to improve periodontal treatment outcomes. The aim of this study was to develop a new anti-inflammatory scaffold by functionalizing an electrospun nanofibrous poly-ε-caprolactone membrane with IBU (IBU-PCL) and to evaluate its impact on periodontal inflammation, wound healing and regeneration in vitro and in vivo. IBU-PCL was synthesized through electrospinning. The effects of IBU-PCL on the proliferation and migration of epithelial cells (EC) and fibroblasts (FB) exposed to Porphyromonas gingivlais lipopolysaccharide (Pg-LPS) were evaluated through the AlamarBlue test and scratch assay, respectively. Anti-inflammatory and remodeling properties were investigated through Real time qPCR. Finally, the in vivo efficacy of the IBU-PCL membrane was assessed in an experimental periodontitis mouse model through histomorphometric analysis. The results showed that the anti-inflammatory effects of IBU on gingival cells were effectively amplified using the functionalized membrane. IBU-PCL reduced the proliferation and migration of cells challenged by Pg-LPS, as well as the expression of fibronectin-1, collagen-IV, integrin α3β1 and laminin-5. In vivo, the membranes significantly improved the clinical attachment and IBU-PCL also reduced inflammation-induced bone destruction. These data showed that the IBU-PCL membrane could efficiently and differentially control inflammatory and migratory gingival cell responses and potentially promote periodontal regeneration.
Effects of Long-Term Feeding of the Polyphenols Resveratrol and Kaempferol in Obese Mice

The effect of the intake of antioxidant polyphenols such as resveratrol and others on survival and different parameters of life quality has been a matter of debate in the last years. We have studied here the effects of the polyphenols resveratrol and kaempferol added to the diet in a murine model undergoing long-term hypercaloric diet. Using 50 mice for each condition, we have monitored weight, survival, biochemical parameters such as blood glucose, insulin, cholesterol, triglycerides and aspartate aminotransferase, neuromuscular coordination measured with the rotarod test and morphological aspect of stained sections of liver and heart histological samples. Our data show that mice fed since they are 3-months-old with hypercaloric diet supplemented with any of these polyphenols reduced their weight by about 5–7% with respect to the controls fed only with hypercaloric diet. We also observed that mice fed with any of the polyphenols had reduced levels of glucose, insulin and cholesterol, and better marks in the rotarod test, but only after 1 year of treatment, that is, during senescence. No effect was observed in the rest of the parameters studied. Furthermore, although treatment with hypercaloric diets induced large changes in the pattern of gene expression in liver, we found no significant changes in gene expression induced by the presence of any of the polyphenols. Thus, our data indicate that addition of resveratrol or kaempferol to mice food produces an initial decrease in weight in mice subjected to hypercaloric diet, but beneficial effects in other parameters such as blood glucose, insulin and cholesterol, and neuromuscular coordination, only appear after prolonged treatments.
Sexual and social competition: broadening perspectives by defining female roles

Males figured more prominently than females in Darwin's view of sexual selection. He considered female choice of secondary importance to male–male competition as a mechanism to explain the evolution of male ornaments and armaments. Fisher later demonstrated the importance of female choice in driving male trait evolution, but his ideas were largely ignored for decades. As sexual selection came to embrace the notions of parent–offspring and sexual conflict, and experimental tests of female choice showed promise, females began to feature more prominently in the framework of sexual selection theory. Recent debate over this theory has centred around the role of females, not only over the question of choice, but also over female–female competition. Whereas some have called for expanding the sexual selection framework to encompass all forms of female–female competition, others have called for subsuming sexual selection within a broader framework of social selection, or replacing it altogether. Still others have argued for linking sexual selection more clearly to other evolutionary theories such as kin selection. Rather than simply debating terminology, we must take a broader view of the general processes that lead to trait evolution in both sexes by clearly defining the roles that females play in the process, and by focusing on intra- and inter-sexual interactions in males and females.
Measuring 3D Droplet Shape and local Slope using Interferometry and Continuous Wavelet Transforms

Using Mach-Zehnder interferometry, sufficiently flat transparent objects can be measured with micrometric precision. In the present article, we will detail a novel image processing procedure capable of yielding precise height and local slope information in each pixel, even in the presence of substantial noise. This technique is based on the use of the continuous wavelet transform. A detailed overview of the algorithm will be given and sample results will be discussed.
Verbesserte tribologische Eigenschaften von Elastomeren durch PTFE Pulver

One way of improving the tribological properties ofelastomers is to incorporate solid lubricants in the rubber compound. This paper discusses the development of a new mixing process for the production of rubber compounds which are modified with PTFE micropowder. Working on the basis of the functionalisation of commercial PTFE micropowders, mixing process profiles are presented which make it possible to achieve a chemical coupling between the PTFE micropowder and the rubber matrix during either the mixing process or the moulding process.
Allometric Equations for Estimating Compartment Biomass and Stem Volume in Mature Hybrid Poplars: General or Site-Specific?

We evaluated the extent to which general or site-specific allometric equations, using diameter at breast height (DBH) as a predictor, are more accurate for estimating stem volume, stem biomass, branch biomass, aboveground woody biomass, and coarse root biomass in 14 year-old plantations of Populus canadensis × Populus maximowiczii (clone DN × M-915508) located along an environmental gradient in southern Quebec (eastern Canada). The effect of tree size and site on stem wood basic density, moisture content, and proportion of branch biomass was also evaluated. For stem volume, stem biomass, and aboveground biomass, site-specific and general models had comparable fit and accuracy, but lower Akaike’s Information Criterion (AICc) values were observed for the general models. For the branch and coarse root biomass, higher fit and accuracy and lower AICc values were observed for the site-specific models. Allometric trajectory changes (plastic allometry) across sites were mainly observed for coarse root biomass, branch biomass, and stem volume. On the low fertility site, allocation was increased to coarse roots and decreased to stem volume. Site-specific tradeoffs between tree architecture and stem wood density explained the relatively invariant allometry for the whole aboveground woody biomass across the plantation sites. On the high fertility sites, basic wood density was the lowest and declined as tree DBH increased. At all sites, stem wood moisture content and the proportion of branch biomass increased with DBH. Overall, this study showed that biomass allometry, tree architecture, and biomass quality are a function of both tree size and plantation environment in hybrid poplar. Allometric model selection (site-specific or general) should depend on the objective pursued (evaluation of yield, nutrient budget, carbon stocks).
Bridging the Feature Gaps for Retrieval of Multi-Dimensional Images

Content-based image retrieval (CBIR) refers to the use of visual features for images retrieval, and has become an attractive approach to managing biomedical image achieves. However, existing CBIR systems are typically designed for 2D single-modality imaging, and are restricted when multi-dimensional images are considered. With the advances in imaging scanners, image complexity and magnitude have rapidly expanded in both the temporal (time) and spatial (space) dimensions, i.e., dynamic PET provides physiological functions of the human body acquired in 3D volumes over multiple time sequences, and dual-modality imaging scanners that sequentially acquires co-aligned functional (PET) and anatomical (CT) images. This manuscript summarizes research in CBIR of multi-dimensional biomedical images with focuses on the feature extraction and retrieval techniques that utilize the information available in the imageâ€™s multidimensional data spaces. Applications of multi-dimensional CBIR will be exemplified with our ongoing studies with 4D dynamic PET and dual-modal PET/CT images.
The Analysis of the High Speed Wire Drawing Process of High Carbon Steel Wires Under Hydrodynamic Lubrication Conditions

In this work the analysis of the wire drawing process in hydrodynamic dies has been done. The drawing process of ϕ 5.5 mm wire rod to the ﬁnal wire of ϕ 1.7 mm was conducted in 12 passes, in drawing speed range of 5-25 m/s. For ﬁnal wires of ϕ 1.7 mm the investigation of topography of wire surface, the amount of lubricant on the wire surface and the pressure of lubricant in hydrodynamic dies were determined. Additionally, in the work selected mechanical properties of the wires have been estimated. Ithasbeen shown that in the drawing process under hydrodynamic lubrication by drawing speed of 25 m/s the phenomena of uncontrolled formation of the surface and the diameter of the wire appears, and in the process the compressive stresses eliminating cracks on the wire surface occur, causing further smoothing. The wires drawn hydrodynamically in speed of 25 m/s, besides clearly worse properties compared to the wires drawn hydrodynamically at speeds in the range of 5 to 20 m/s, also exhibit large dimensional variations.
mRNA structure determines specificity of a polyQ-driven phase separation

RNA and membraneless organelles Membraneless compartments can form in cells through liquidliquid phase separation (see the Perspective by Polymenidou). But what prevents these cellular condensates from randomly fusing together? Using the RNA-binding protein (RBP) Whi3, Langdon et al. demonstrated that the secondary structure of different RNA components determines the distinct biophysical and biological properties of the two types of condensates that Whi3 forms. Several RBPs, such as FUS and TDP43, contain prion-like domains and are linked to neurodegenerative diseases. These RBPs are usually soluble in the nucleus but can form pathological aggregates in the cytoplasm. Maharana et al. showed that local RNA concentrations determine distinct phase separation behaviors in different subcellular locations. The higher RNA concentrations in the nucleus act as a buffer to prevent phase separation of RBPs; when mislocalized to the cytoplasm, lower RNA concentrations trigger aggregation. Science, this issue p. 922, p. 918; see also p. 859 Certain RNA sequences, via secondary structures, specify the molecular properties of phase-separated cellular condensates. RNA promotes liquid-liquid phase separation (LLPS) to build membraneless compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here, we report that secondary structure allows messenger RNAs (mRNAs) to self-associate and determines whether an mRNA is recruited to or excluded from liquid compartments. The polyQ-protein Whi3 induces conformational changes in RNA structure and generates distinct molecular fluctuations depending on the RNA sequence. These data support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity. Thus, the shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell.
Webometrics: Some Critical Issues of WWW Size Estimation Methods

The number of webpages in the Internet has increased tremendously over the last two decades however only a part of it is indexed by various search engines. This small portion is the indexable web of the Internet and can be usually reachable from a Search Engine. Search engines play a big role in making the World Wide Web accessible to the end user, and how much of the World Wide Web is accessible on the size of the search engine’s index. Researchers have proposed several ways to estimate this size of the indexable web using search engines with and without privileged access to the search engine’s database. Our report provides a summary of methods used in the last two decades to estimate the size of the World Wide Web, as well as describe how this knowledge can be used in other aspects/tasks concerning the World Wide Web.
A high content, high throughput cellular thermal stability assay for measuring drug-target engagement in living cells

Determining and understanding drug target engagement is critical for drug discovery. This can be challenging within living cells as selective readouts are often unavailable. Here we describe a novel method for measuring target engagement in living cells based on the principle of altered protein thermal stabilization / destabilization in response to ligand binding. This assay (HCIF-CETSA) utilizes high content, high throughput single cell immunofluorescent detection to determine target protein levels following heating of adherent cells in a 96 well plate format. We have used target engagement of Chk1 by potent small molecule inhibitors to validate the assay. Target engagement measured by this method was subsequently compared to target engagement measured by two alternative methods (autophosphorylation and CETSA). The HCIF-CETSA method appeared robust and a good correlation in target engagement measured by this method and CETSA for the selective Chk1 inhibitor V158411 was observed. However, these EC50 values were 23- and 12-fold greater than the autophosphorylation IC50. The described method is therefore a valuable advance in the CETSA method allowing the high throughput determination of target engagement in adherent cells.