Miracle-dz/UniFAR-FTUs huggingface dataset:
Reply to Farr and Jarvis

tions. In: O' Grady NP, Pittet D, eds. Catheter-Related Infections in the Critically III. Boston: Kluwer Academic Publishers; 2004:87-98. 6. Huang SS, Yokoe DS, Hinrichsen VL, et al. Impact of routine intensive care unit surveillance cultures and resultant barrier precautions on hospital-wide methicillin-resistant Staphylococcus aureus bacteremia. Clin Infect Dis 2006; 43:971-978. 7. Karchmer TB, Durbin LJ, Simonton BM, Farr BM. Cost-effectiveness of active surveillance cultures and contact/droplet precautions for control of methicillin-resistant Staphylococcus aureus. J Hosp Infect 2002; 51:126132. 8. Wenzel RP, Edmond MB. The evolving technology of venous access. N Engl J Med 1999; 340:48-50. 9. Rello J. Impact of nosocomial infections on outcome: myths and evidence. Infect Control Hosp Epidemiol 1999; 20:392-394. 10. Klevens RM, Morrison MA, Nadle J, et al. Invasive methicillin-resistant Staphylococcus aureus infections in the United States. JAMA 2007; 298: 1763-1771. 11. Thompson RL, Cabezudo I, Wenzel RP. Epidemiology of nosocomial infections caused by methicillin-resistant Staphylococcus aureus. Ann Intern Med 1982;97:309-317. 12. Farr BM. Doing the right thing (and figuring out what that is). Infect Control Hosp Epidemiol 2006; 27:999-1003.
Physicochemical characterization of atorvastatin calcium/ezetimibe amorphous nano-solid dispersions prepared by electrospraying method

Abstract In the present study, electrospraying was applied as a novel method for the fabrication of amorphous nano-solid dispersions (N-SDs) of atorvastatin calcium (ATV), ezetimibe (EZT), and ATV/EZT combination as poorly water-soluble drugs. N-SDs were prepared using polyvinylpyrrolidone K30 as an amorphous carrier in 1:1 and 1:5 drug to polymer ratios and the total solid (including drug and polymer) concentrations of 10 and 20% (w/v). The prepared formulations were further investigated for their morphological, physicochemical, and dissolution properties. Scanning electron microscopy studies indicated that the morphology and diameter of the electrosprayed samples (ESs) were influenced by the solution concentration and drug:polymer ratio, so that an increase in the solution concentration resulted in fiber formation while an increase in the polymer ratio led to enhancement of the particle diameter. Differential scanning calorimetry and X-ray powder diffraction studies together with in vitro dissolution test revealed that the ESs were present in an amorphous form with improved dissolution properties. Infrared spectroscopic studies showed hydrogen-bonding interaction between the drug and polymer in ESs. Since the electrospraying method benefits from the both amorphization and nanosizing effect, this novel approach seems to be an efficient method for the fabrication of N-SDs of poorly water-soluble drugs.
mRNA‐Independent way to regulate translation elongation rate in eukaryotic cells

The question of what governs the translation elongation rate in eukaryotes has not yet been completely answered. Earlier, different availability of different tRNAs was considered as a main factor involved, however, recent data revealed that the elongation rate does not always depend on tRNA availability. Here, we offer another, codon‐independent approach to explain specific tRNA‐dependence of the elongation rate in eukaryotes. We hypothesize that the exit rate of eukaryotic translation elongation factor 1A (eEF1A)*GDP from the 80S ribosome depends on the protein affinity to specific aminoacyl‐tRNA remaining on the ribosome after GTP hydrolysis. Subsequently, a slower dissociation of eEF1A*GDP from certain aminoacyl‐tRNAs in the ribosome can negatively influence the ribosomal elongation rate in a tRNA‐dependent and mRNA‐independent way. The specific tRNA‐dependent departure rate of eEF1A*GDP from the ribosome is suggested to be a novel factor contributing to the overall translation elongation control in eukaryotic cells. © 2018 IUBMB Life, 70(3):192–196, 2018
Development of polymorphic microsatellite markers for the livebearing fish Poecilia parae

We developed 16 novel polymorphic tetranucleotide microsatellite markers for Poecilia parae, a livebearing fish used in evolutionary studies because of its Y‐linked colour and size polymorphism. A set of 199 clones was sequenced out of an enriched genomic library, and we achieved an enrichment efficiency of nearly 80%. Primers were designed for 16 pure repeats, and 59 P. parae were screened for polymorphism. Cross‐amplification was tested on Poecilia picta and Poecilia reticulata, the guppy. The new microsatellite markers showed an exceptionally high allelic diversity and low stutter formation, proving their suitability for a broad range of applications in these species.
A small variation in average particle size of PLGA nanoparticles prepared by nanoprecipitation leads to considerable change in nanoparticles’ characteristics and efficacy of intracellular delivery

Abstract In this study, it was aimed to investigate characteristics and intracellular delivery of two different-sized PLGA nanoparticles in ouzo region by considering number of nanoparticles. To determine the effect of formulation parameters on average particle size, Dil labeled nanoparticles were prepared using a three-factor, two-level full factorial statistical experimental design. PLGA230 (230.8 ± 4.32 nm) and PLGA160 (157.9 ± 6.16 nm) nanoparticles were obtained by altering polymer amount based on experimental design results and characterized. Same number of PLGA230 and PLGA160 nanoparticles per cell were applied onto HEK293 cells; then, cytotoxicity, uptake kinetics and mechanism were evaluated by flow cytometry and fluorescent microscopy. Also same weight of PLGA230 and PLGA160 nanoparticles were applied and cellular uptake of these nanoparticles was evaluated. It was found that PLGA230 nanoparticles had higher encapsulation efficiency and slower dye release compared to PLGA160 nanoparticles. When they were applied at same counts per cell, PLGA230 nanoparticles displayed faster and higher intracellular dye transfer than PLGA160 nanoparticles. On the other hand, PLGA160 appeared to be a more effective vehicle than PLGA230 when applied at the same weight concentration. It was also shown that for both nanoparticles, HEK293 cells employed macropinocytic, caveolae- and clathrin-mediated endocytic pathways.
Elucidating the role of (p)ppGpp in mycobacterial persistence against antibiotics

Bacterial persistence, the ability of bacteria to survive high concentrations of antibiotics for extended periods of time, is an important contributing factor to therapy failure and development of chronic and recurrent infections. Several recent studies have suggested that this persistence is mediated primarily by (p)ppGpp, through its interactions with toxin–antitoxin modules and polyphosphates. In this study, we address whether these key players play a role in mycobacterial persistence against antibiotics. We targeted these specific pathways in Mycobacterium smegmatis by constructing deletion strains of (p)ppGpp synthetase/hydrolase (relA), polyphosphate kinases (ppk1 and ppk2), exopolyphosphatases (ppx1 and ppx2), and the lon protease. None of these mutant strains exhibited altered levels of persisters against isoniazid and ciprofloxacin, when compared with wild‐type strain. Even under conditions in which the stringent response usually gets activated, these strains displayed wild‐type persister levels. Interestingly, we also found that unlike Escherichia coli, maintaining M. smegmatis in exponential phase by repeated passaging does not eliminate persisters suggesting that at least against the antibiotics tested, stationary‐phase dependent persisters (type I) are not the major contributors. Thus, our data demonstrate that multiple mechanisms of antibiotic persistence exist and that these vary widely among different bacterial species. © 2018 IUBMB Life, 70(9):836–844, 2018
Antimicrobial Activity of Clinically Used Antiseptics and Wound Irrigating Agents in Combination with Wound Dressings

Background: A primary strategy for preventing and treating wound infection in chronic wounds is the use of topical antiseptics and wound irrigating agents. However, their interaction with commonly used wound dressings has not yet been investigated. In this study, the authors analyzed the antimicrobial activity of antiseptics and wound irrigating agents used with commercially available wound dressings. Methods: Five clinically used antiseptics and wound irrigating agents (Prontosan, Lavasept, Braunol, Octenisept, and Betaisodona) were tested in the presence or absence of 42 wound dressings against Staphylococcus aureus. The determination of antibacterial activity was performed by disk diffusion assay. Results: Povidone-iodine–based products showed sufficient antimicrobial activity in 64 to 78 percent of the combinations assessed (p > 0.01). The octenidine derivate Octenisept showed sufficient antimicrobial activity in 54 percent of combinations. Polyhexamethylene biguanide derivatives demonstrated sufficient antimicrobial activity in 32 percent of the combinations. Conclusion: This study revealed that commonly used wound dressings dramatically reduce antibacterial activity of clinically used antiseptics and wound irrigating agents in vitro.
Development and characterization of microsatellite markers for lippia (Phyla canescens: Verbenaceae)

Lippia (Phyla canescens: Verbenaceae) is a serious weed of wetlands, riparian zones and floodplains, particularly in eastern Australia where many Ramsar wetlands are threatened by hydrological changes precipitated by soil‐accreting lippia mats. Enriched genomic DNA libraries were used to develop nine informative microsatellite markers. These markers will be valuable tools to understand the genetic structure of the lippia populations in different regions throughout the world.
Association of Plasma Homocysteine Level and Arterial Stiffness in Subjects with Type 2 Diabetes Mellitus

Objective: Plasma homocysteine (Hcy) is considered to be a marker of endothelial dysfunction and a predictor of cardiovascular disease (CVD). Arterial stiffness measured by brachial-ankle pulse wave velocity (baPWV) is not only a marker of vascular damage but a significant predictor of CVD. Previous studies about the effect of high plasma Hcy levels on arterial stiffness have yielded inconsistent results. We therefore assessed the association between Hcy and baPWV in a relatively large number of subjects with type 2 diabetes mellitus (DM). Methods: We retrospectively assessed plasma Hcy concentration and arterial stiffness in 1,477 Korean type 2 diabetic patients. Participants were also evaluated for plasma glucose, hemoglobin A1c (HbA1c), duration of DM, microvascular complications, lipid profile, and high sensitivity C-reactive protein (hsCRP). Arterial stiffness was measured noninvasively by baPWV. Results: Correlation analysis indicated a significant positive association between serum Hcy levels and baPWV (r=0.245, p<0.001). In a multiple linear regression analysis, the association between serum Hcy levels and baPWV was independent of traditional cardiovascular risk factors (standardized β=3.8, p=0.01). Conclusion: The results support the hypothesis that plasma Hcy levels are associated with arterial stiffness in patients with type 2 DM. Prospective studies are warranted to determine whether lowering serum Hcy level could reduce arterial stiffness and cardiovascular morbidity in type 2 DM.
Anisotropic Elastic Materials With a Parabolic or Hyperbolic Boundary: A Classical Problem Revisited

When an anisotropic elastic material is under a two-dimensional deformation that has a hole of given geometry Γ subjected to a prescribed boundary condition, the problem can be solved by mapping Γ to a circle of unit radius. It is important that (i) each point on Γ is mapped to the same point for the three Stroh eigenvalues p 1 , p 2 , p 3 and (ii) the mapping is one-to-one for the region outside Γ. In an earlier paper it was shown that conditions (i) and (ii) are satisfied when Γ is an ellipse. The paper did not address to the case when Γ is an open boundary, such as a parabola or hyperbola that was studied by Lekhnitskii. We examine the mappings employed by Lekhnitskii for a parabola and hyperbola, and show that while the mapping for a parabola satisfies conditions (i) and (ii), the mapping for a hyperbola does not satisfy condition (i). Nevertheless, a valid solution can be obtained for the problem with a hyperbolic boundary, although the prescription of the boundary condition is restricted. We generalize Lekhnitskii's solutions for general anisotropic elastic materials and for more general boundary conditions. Using known identities and new identities presented here, real form expressions are given for the displacement and hoop stress vector at the parabolic and hyperbolic boundary.
Small‐molecule protein–protein interaction inhibitors: Therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations

As the ultimate function of proteins depends to a great extent on their binding partners, protein–protein interactions (PPIs) represent a treasure trove of possible new therapeutic targets. Unfortunately, interfaces involved in PPIs are not well‐suited for effective small molecule binding. Nevertheless, successful examples of small‐molecule PPI inhibitors (PPIIs) are beginning to accumulate, and the sheer number of PPIs that form the human interactome implies that, despite the relative unsuitability of PPIs to serve as “druggable” targets, small‐molecule PPIIs can still provide novel pharmacological tools and new innovative drugs in at least some areas. Here, after some illustrative examples, accumulating information on the binding efficiency, molecular size, and chemical space requirements will be briefly reviewed. Therapeutic success can only be achieved if these considerations are incorporated into the search process and if careful medicinal chemistry approaches are used to address the absorption, distribution, metabolism, and excretion requirements of larger molecules that are often needed for this target class due to the lower efficiency of binding. © 2010 IUBMB IUBMB Life, 62(10): 724–731, 2010
Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations

Neuroglobin (Ngb) is a heme protein, highly conserved along evolution, predominantly found in the nervous system. It is upregulated by hypoxia and ischemia and may have a neuroprotective role under hypoxic stress. Although many other roles have been proposed, the physiological function is still unclear. Antarctic icefishes lack hemoglobin and some species also lack myoglobin, but all have Ngb and thus may help the elucidation of Ngb function. We present the first theoretically derived structure of fish Ngb and describe its behavior using molecular dynamics simulations. Specifically, we sequenced and analyzed Ngbs from a colorless‐blooded Antarctic icefish species Chaenocephalus aceratus and a related red‐blooded species (Dissostichus mawsoni). Both fish Ngbs are 6‐coordinated but have some peculiarities that differentiate them from mammalian counterparts: they have extensions in the N and C termini that can interact with the EF loop, and a gap in the alignment that changes the CD‐region structure/dynamics that has been found to play a key role in human neuroglobin. Our results suggest that a single mutation between both fish Ngbs is responsible for significant difference in the behavior of the proteins. The functional role of these characteristics is discussed. © 2011 IUBMB IUBMB Life, 63(3): 206–213, 2011
DNA barcoding discriminates the noxious invasive plant species, floating pennywort (Hydrocotyle ranunculoides L.f.), from non‐invasive relatives

Floating pennywort (Hydrocotyle ranunculoides L.f.), a member of the plant family Araliaceae originating from North America, is an example of an invasive aquatic species posing serious problems to the management of waterways outside of its original distribution area in Australia and Western Europe. As a consequence, its import was banned in the Netherlands. It can be difficult to distinguish H. ranunculoides from other species of the genus on a morphological basis. In this regard, DNA barcoding may become a good alternative once this could be performed on a routine basis. In this study, we show that it is possible to distinguish H. ranunculoides from a series of closely related congeners by using a single plastid DNA sequence, trnH‐psbA.
Management of paraureteral pseudocyst and ureteral avulsion using a subcutaneous ureteral bypass (SUB) system in a cat

A 1.6-year-old male neutered domestic shorthair cat was presented after a road traffic accident with lethargy, anorexia, abdominal pain and inability to jump. On physical examination, a space-occupying lesion in the left flank was detected. Investigations demonstrated a cavitated fluid-filled structure in the left retroperitoneal space consistent with a paraureteral pseudocyst (urinoma) secondary to left ureteral rupture. Ventral midline exploratory laparotomy was completed. The urinoma was drained, the damaged ureter ligated and a subcutaneous ureteral bypass (SUB) device was placed under fluoroscopy guidance. On re-examination at five and nine weeks postoperatively, investigations revealed patency of the device and normal renal function. The use of a SUB allowed ureteral bypass and preserved the injured kidney.
DNA barcoding Central Asian butterflies: increasing geographical dimension does not significantly reduce the success of species identification

DNA barcoding employs short, standardized gene regions (5’ segment of mitochondrial cytochrome oxidase subunit I for animals) as an internal tag to enable species identification. Prior studies have indicated that it performs this task well, because interspecific variation at cytochrome oxidase subunit I is typically much greater than intraspecific variation. However, most previous studies have focused on local faunas only, and critics have suggested two reasons why barcoding should be less effective in species identification when the geographical coverage is expanded. They suggested that many recently diverged taxa will be excluded from local analyses because they are allopatric. Second, intraspecific variation may be seriously underestimated by local studies, because geographical variation in the barcode region is not considered. In this paper, we analyse how adding a geographical dimension affects barcode resolution, examining 353 butterfly species from Central Asia. Despite predictions, we found that geographically separated and recently diverged allopatric species did not show, on average, less sequence differentiation than recently diverged sympatric taxa. Although expanded geographical coverage did substantially increase intraspecific variation reducing the barcoding gap between species, this did not decrease species identification using neighbour‐joining clustering. The inclusion of additional populations increased the number of paraphyletic entities, but did not impede species‐level identification, because paraphyletic species were separated from their monophyletic relatives by substantial sequence divergence. Thus, this study demonstrates that DNA barcoding remains an effective identification tool even when taxa are sampled from a large geographical area.
Magnetic Fe3O4@MCM-41 core–shell nanoparticles functionalized with thiol silane for efficient l-asparaginase immobilization

Abstract l-Asparaginase (l-ASNase) is a vital enzyme for medical treatment and food industry. Here, we assessed the use of Fe3O4@Mobil Composition of Matter No. 41 (MCM-41) magnetic nanoparticles as carrier matrix for l-ASNase immobilization. In addition, surface of Fe3O4@MCM-41 magnetic nanoparticles was functionalized with 3-mercaptopropyltrimethoxysilane (MPTMS) to enhance stability of l-ASNase. The chemical structure, thermal properties, magnetic profile and morphology of the thiol-functionalized Fe3O4@MCM-41 magnetic nanoparticles were characterized with Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), differential thermal analysis (DTA), differential scanning calorimetry (DSC), vibrating sample magnetometer (VSM), scanning electron microscope (SEM), energy dispersive X-ray (EDX) spectroscopy and zeta-potential measurement. l-ASNase was covalently immobilized onto the thiol-functionalized Fe3O4@MCM-41 magnetic nanoparticles. The properties of the immobilized enzyme, including optimum pH, temperature, kinetic parameters, thermal stability, reusability and storage stability were investigated and compared to free one. Immobilized enzyme was found to be stable over a wide range of pH and temperature range than free enzyme. The immobilized l-ASNase also showed higher thermal stability after 180 min incubation at 50 °C. The immobilized enzyme still retained 63% of its original activity after 16 times of reuse. The Km value for the immobilized enzyme was 1.15-fold lower than the free enzyme, which indicates increased affinity for the substrate. Additionally, the immobilized enzyme was active over 65% and 53% after 30 days of storage at 4 °C and room temperature (∼25 °C), respectively. Thereby, the results confirmed that thiol-functionalized Fe3O4@MCM-41 magnetic nanoparticles had high efficiency for l-ASNase immobilization and improved stability of L-ASNase.
Characterization of microsatellite loci for the pitcher plant midge, Metriocnemus knabi Coq. (Diptera: Chironomidae)

As a component of the inquiline community of the purple pitcher plant (Sarracenia purpurea), the pitcher plant midge Metriocneus knabi has been the subject of various ecological studies. However, very little is known about its characteristics beyond the larval stage, in particular the dispersal ability of adults. This study presents new molecular tools developed for testing of evolutionary and ecological questions in natural populations of this species. We describe a set of 12 microsatellite loci specific to M. knabi that are sufficiently polymorphic to provide insight into population genetic structure and dispersal patterns.
PARVO VIRUS B19 INCIDENCE AND CHILDHOOD IDIOPATHIC THROMBOCYTOPENIC PURPURA

In her letter, Dr. Sipahi questions the discrepancy between their and our results of parvo virus B19 (PVB19) incidence in children with ITP [1, 2]. Our results can be explained as follows. The PVB19 incidence in our study is compatible with the control group in her study (73 vs. 68%) [3]. It is also striking that the incidence in their ITP patients is much lower than that of both the control and the thalassemia groups (17 vs. 68 and 41%). Their results are also lower than the values in the literature [4]. ITP usually follows a viral infection or immunization and is caused by inappropriate immune response. Therefore, in ITP, a higher incidence rate of PVB19 is expected than that in thalassemia and the control group. They could not have confirmed their results by viral genome evaluation in either of the groups. The prevalance of blood group P antigen had been found in concordance with their serologic results in thalassemia and the control [5]. Additionally, our serologic results were also confirmed by the viral genome study, the results of which were also compatible with those in the literature. The PCR study of Murray et al. [4] displayed PVB19 DNA in 49% of 35 ITP patients. However, Heeganted et al. [6] detected PVB19 DNA in only 6 of 47 patients. We did not examine blood group P antigen in our patients as we had already demonstrated the viral genome itself. We agree with Dr. Sipahi that, PVB19 incidence is different in different disease groups. If we had included a control group in our study, we might have found ineffectivity of PVB19 on ITP. However, the PVB19 incidence in Dr. Sipahi’s control group gives information about the incidence in the