Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot ...regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. HotRegion is accessible at http://prism.ccbb.ku.edu.tr/hotregion.
With increasing ecological awareness, researchers around the world seek to make composites reinforced with more eco-friendly natural fibers. In this study,
Centaurea solstitialis
(yellow star ...thistle) fibers were characterized as a potential natural fiber reinforcement for green composites. Generally,
Centaurea solstitialis
plants are undesirable because of their detrimental effect on other plants. In this respect, they are generally considered economically worthless in terms of the economical aspect. From this point of view, characterizing
Centaurea solstitialis
and using them as a natural fiber reinforcement material can be more appropriate in terms of waste management. To characterize the
Centaurea solstitialis
fibers, Scanning Electron Microscopy, Fourier Transform Infrared Spectroscopy, Thermogravimetric Analysis, X-ray Photoelectron Spectroscopy, X-Ray Diffraction Analysis, single fiber tensile test, determinations of density and chemical composition were performed.
Centaurea solstitialis
fibers have 11.2% hemicellulose and 57.20% cellulose content. The crystallinity index and density of fibers were determined as 71.43% and 1.37 g/cm
3
, respectively. Also, fibers exhibited relatively high tensile strength with 111.85 ± 24.97 MPa and Young’s modulus with 3.41 ± 0.62 GPa. The thermal resistance temperature of
Centaurea solstitialis
fibers was found as 273 °C. It is suggested that
Centaurea solstitialis
fiber is a suitable reinforcement candidate for composites with low density, low cost, abundancy and relatively high tensile strength.
The photonic crystal materials are new generation advanced materials with various application areas. One-dimensional (1-D) photonic crystals are one kind of that can be produced easily. High quality ...structural colored surfaces could be obtained by high dielectric contrast between stocked layers such as CuO and TiO2. In this study, five-layered CuO/TiO2 multilayers prepared by the sol-gel method grown on borosilicate glass substrates by spin coating. Nitrogen and Cerium ions were doped into the TiO2 structure. X-Ray Diffractometer (XRD), X-ray Photoelectron Spectroscopy (XPS), Scanning Electron Microscope (SEM), Photoluminescence Spectroscopy (PL), UV-Vis Spectrophotometer (UV–Vis) and Optic Microscope (OM) devices were used to characterize the effects of these non-metal and rare earth dopants on the phase, structural and optical properties of coatings. Violet, indigo, green, yellow and red structural colors were obtained from photonic crystal coatings consist of monoclinic tenorite and anatase layers. It was found that the size of the anatase crystal decreased with the doping of both N and Ce elements. Also, both dopants have positive effects on improving surface morphologies. The lower crystalline size, the better surface morphology, and the more vivid structural color properties were obtained by Ce doping while a higher degree of redshift obtained by the N doping.
•Five-layered multilayer photonic crystal structures were synthesized by sol-gel method.•Both dopants have affirmative effects on improving the surface morphology, whereas Ce doping is more effective than N doping.•Violet, indigo, green, yellow and red structural colors were obtained successfully from photonic crystal coatings.•Both Ce and N doping affect the optical properties of photonic crystals.•Ce doping is more effective at obtaining vivid color compared to N doping.
The unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these ...proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and no less important how to combine these for a particular goal since usually it is not one tool, but some combination of tool-modules that is needed. This is the goal of this review.
Summary
The aim of this study was to determine the long‐term efficacy of entecavir (ETV) and tenofovir disoproxil fumarate (TDF) on the natural course of disease in chronic hepatitis B patients (CHB) ...with/without cirrhosis in clinical practice. A total of 355 treatment‐naïve CHB patients were enrolled into the study. The primary outcome measure was viral suppression as defined by serum HBV DNA level <20 IU/mL. A secondary outcome measure was to determine the development of Hepatocellular carcinoma (HCC). Virological and biochemical responses were similar between the two treatment groups over time. The presence of cirrhosis and hepatitis B e antigen (HBeAg) positivity did not appear to impact viral suppression. The cumulative probability of HBeAg loss was 41% at 4 years of therapy. Hepatitis B surface antigen (HBsAg) loss occurred in four patients. Model for End‐Stage Liver Disease score was significantly improved from baseline to week 48 and 96 under antiviral therapy (P = 0.013, P = 0.01). HCC was diagnosed in 17 patients (4.8%). The cumulative probability of the development of HCC was 3.3% at 1 year and 7.3% at 4 years of therapy. The development of HCC was independently associated with older age (P = 0.031) and the presence of cirrhosis (P = 0.004). Serum creatinine levels and creatinine clearance remained stable over time. ETV and TDF effectively maintained virological and biochemical responses in long‐term follow‐up of CHB patients with/without cirrhosis. HCC may still develop, although at a lower rate, and is more likely to develop in patients with cirrhosis, especially in older patients.
Summary
Chronic hepatitis D is caused by coinfection of hepatitis B and hepatitis D virus. While HDV is the dominant virus over HBV in the majority of cases, mechanisms and consequences of viral ...dominance are largely unknown. We aimed to investigate associations between viral dominance patterns and patients’ characteristics and inflammatory features; 109 HDV‐infected patients treated with PEG‐IFNa‐2α within the international multicentre, prospective HIDIT‐2 trial were studied. Patients were classified as D‐ or B‐dominant if the viral load of one virus exceeded that of the other virus by more than 1log10. Otherwise, no viral dominance (ND) was described. We used Luminex‐based multiplex technology to study 50 soluble immune mediators (SIM) in pretreatment samples of 105 HDV RNA‐positive patients. Dominance of HDV was evident in the majority (75%) of cases. While only 7% displayed B‐dominance, 17% showed nondominance. D‐dominance was associated with downregulation of 4 interleukins (IL‐2ra, IL‐13, IL‐16 and IL‐18) and 5 chemokines/cytokines (CTACK (CCL27), MCP‐1 (CCL2), M‐CSF, TRAIL and ICAM‐1) while no analyte was increased. In addition, D‐dominance could be linked to a delayed HDV RNA response to pegylated interferon as patients with B‐dominance or nondominance showed higher early HDV RNA responses (61% at week 12) than D‐dominant patients (11%; P < .001). In conclusion, this study revealed unexpected effects of viral dominance on clinical and immunological features in chronic hepatitis delta patients. Individualizing PEG‐IFNa‐2α treatment duration should consider viral dominance. Overall, our findings suggest an activated but exhausted IFN system in D‐dominant patients.
Prism (http://gordion.hpc.eng.ku.edu.tr/prism) is a website for protein interface analysis and prediction of putative protein–protein interactions. It is composed of a database holding protein ...interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein–protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution (January 2004). Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.
Introduction The reliability and validity of Turkish version of Childhood Asthma Control Test (C-ACT). Purpose The management of asthma is an important as well as difficult issue of physician's daily ...practice particularly in busy clinical settings. C-ACT was created to identify asthma control levels in children aged 4-11 years. Our aim was to evaluate the reliability, validity and responsiveness of C-ACT in a Turkish sample of children with asthma. Method In this multicenter study, 368 children were enrolled. C-ACT was completed every month by parents and patients who were evaluated in 3 visits within 2 month intervals. At each visit, physicians interpret the control level and decided for the treatment step as established in GIN A guidelines. Results The internal consistency reliability of the Turkish version of C-ACT (C-ACT1 to C-ACT5) was found to be 0.82, 0.83, 0.82, 0.82 and 0.80, respectively (reliability statistics, Cronbach's alpha). Test-retest reliability was 0.71. There was significant correlation between C-ACT and physician's assessment of asthma control at visit 1 (r = 0.65, P < 0.001).
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