Miracle-dz/UniFAR-FTUs huggingface dataset:
Control of ligand specificity in cyclic nucleotide-gated channels from rod photoreceptors and olfactory epithelium.

Cyclic nucleotide-gated ionic channels in photoreceptors and olfactory sensory neurons are activated by binding of cGMP or cAMP to a receptor site on the channel polypeptide. By site-directed mutagenesis and functional expression of bovine wild-type and mutant channels in Xenopus oocytes, we have tested the hypothesis that an alanine/threonine difference in the cyclic nucleotide-binding site determines the specificity of ligand binding, as has been proposed for cyclic nucleotide-dependent protein kinases [Weber, I.T. , Shabb, J.B. & Corbin, J.D. (1989) Biochemistry 28, 6122-6127]. The wild-type olfactory channel is approximately 25-fold more sensitive to both cAMP and cGMP than the wild-type rod photoreceptor channel, and both channels are 30- to 40-fold more sensitive to cGMP than to cAMP. Substitution of the respective threonine by alanine in the rod photoreceptor and olfactory channels decreases the cGMP sensitivity of channel activation 30-fold but little affects activation by cAMP. Substitution of threonine by serine, an amino acid that also carries a hydroxyl group, even improves cGMP sensitivity of the wild-type channels 2- to 5-fold. We conclude that the hydroxyl group of Thr-560 (rod) and Thr-537 (olfactory) forms an additional hydrogen bond with cGMP, but not cAMP, and thereby provides the structural basis for ligand discrimination in cyclic nucleotide-gated channels.
Emmprin (basigin/CD147): Matrix metalloproteinase modulator and multifunctional cell recognition molecule that plays a critical role in cancer progression

Emmprin (basigin, CD147) is a cell surface glycoprotein that belongs to the immunoglobulin superfamily. It is highly expressed on the surface of tumor cells and stimulates adjacent fibroblasts or tumor cells to produce matrix metalloproteinases. Moreover, it has recently been shown that emmprin also stimulates expression of vascular endothelial growth factor and hyaluronan, which leads to angiogenesis and anchorage‐independent growth/multidrug resistance, respectively. These findings have made emmprin an important molecule in tumor progression and, thus, more attractive as a target for antitumor treatment. However, other functions of emmprin, including as an activator of T cells, a chaperone for monocarboxylate transporters, a receptor for cyclophilin A and a neural recognition molecule, are also being identified in physiological and pathological conditions. Therefore, it is essential to develop specific means to control particular functions of emmprin, for which elucidation of each mechanism is crucial. This review will discuss the role of emmprin in tumor progression and recent advances in the molecular mechanisms of diverse phenomena regulated by emmprin.
Role of Platelets Rich Plasma in Management of Osteoporotic Fractures

Management of osteoporotic fracture is challenging. In most clinical settings, skeletal regenerations are biologically optimized, but still many patients continue to experience delayed or impaired healing. Methods to enhance these healing processes, are needed to decrease patient’s agony, so that they can return to their work and regain their socioeconomic status in the community. Till this time, autologous bone grafting remain the standard procedure against which all new technologies are compared and analyzed.The success rate of union even after these grafts varies between 80-85% which further becomes decreased in case of repeated bone graft surgeries with donor site morbidities. Considering the concept that the healing of fracture started as soon as the formation of fracture clot, several investigators have suggested that degranulation of platelets at fracture clot elaborates the bioactive component, that aided the healing process. Because autologous platelet rich plasma products are safe and easy to prepare and administer, in this review, we reviewed the role of bioactive component released by activated platelet rich plasma in the fracture healing process and hypothesized that by combining the advantages of autologous bone grafts with autologous platelets concentrate, better and prompt results in orthopedic trauma managements can be obtained. We also observe that the use of these bioactive factors to enhance skeletal repair/healing represents the future of skeletal trauma management. Review Article Annual Research & Review in Biology, 4(8): 1187-1210, 2014 1188
"Heavy metals" a meaningless term? (IUPAC Technical Report)

Abstract Over the past two decades, the term "heavy metals" has been widely used. It is often used as a group name for metals and semimetals (metalloids) that have been associated with contamination and potential toxicity or ecotoxicity. At the same time, legal regulations often specify a list of "heavy metals" to which they apply. Such lists differ from one set of regulations to another and the term is sometimes used without even specifying which "heavy metals" are covered. However, there is no authoritative definition to be found in the relevant literature. There is a tendency, unsupported by the facts, to assume that all so-called "heavy metals" and their compounds have highly toxic or ecotoxic properties. This has no basis in chemical or toxicological data. Thus, the term "heavy metals" is both meaningless and misleading. Even the term "metal" is commonly misused in both toxicological literature and in legislation to mean the pure metal and all the chemical species in which it may exist. This usage implies that the pure metal and all its compounds have the same physicochemical, biological, and toxicological properties, which is untrue. In order to avoid the use of the term "heavy metal", a new classification based on the periodic table is needed. Such a classification should reflect our understanding of the chemical basis of toxicity and allow toxic effects to be predicted.
[Persistence in the treatment of overactive bladder (OAB) with Mirabegron in a multicentre clinical study].

OBJECTIVE The objective of this monitoring was to evaluate persistence in the treatment of patients with overactive bladder syndrome (OAB) using mirabegron. DESIGN Prospective clinical study. SETTING 10 gynecological and urological departments in CZE. MATERIALS AND METHODS This is an analysis of a prospective, multicenter monitoring which started in May 2014 and will continue for 1 year. This monitoring included patients 18 years old who have had symptoms of OAB for minimum 3 months. The patient check-up was performed 6 months (±2 weeks) after the first visit. The dosage of mirabegron was 50 mg per day. For the evaluation the treatment efficacy we employed the TS-VAS and PPBC. During the check-up it was ascertained how many patients discontinued the treatment with mirabegron, and reasons for this interruption were established. The statistics were calculated using the software SPSS 20.0. RESULTS A prospective monitoring was performed on 206 patients. Their mean age was 62.8 years (range 23-89); mean body mass index for the whole group of patients was 27.3. At the check-up 6 months post-initiation of treatment it emerged that 55/206 (27%) patiens had discontinued the treatment. The reasons for discontinuation of treatment were: 24/55 (43%) insufficient treatment efficacy, 29/55 (53%) other reasons (the main reasons here were hospitalisation, surgery, gravidity) and 2/55 discontinued therapy because of side effects. The side effects were tachycardia, eye irritation, lower abdominal pain and vasculitis, and they were mild in nature. The termination of the study was 7/28 (25%) in the group of patients without previous treatment before mirabegron. Discontinuation of the treatment in the group of patients with previous anticholinergic treatment was 48/178 (27%). At the evaluation of the efficacy of the treatment during the check-up 6 months after initiation of treatment the mean TS-VAS was 77.5, a decrease of the scale of bothers evaluated by PPBC before treatment from a mean value of 3.56 to a value of 1.77. CONCLUSIONS Our hypothesis, that persistence in treat-ment with mirabegron would be relatively high due to reduced side effects and better cure effect, was confirmed, and this is the reason for higher rates of persistence in the treatment at 6 months check-up (73%).
Emotional overeating and its associations with eating disorder psychopathology among overweight patients with binge eating disorder.

OBJECTIVE The current study examined emotional overeating in overweight patients with binge eating disorder (BED). A new measure--the Emotional Overeating Questionnaire (EOQ)--was developed to measure the frequency of overeating in response to emotions. The internal consistency, test-retest reliability, and factor structure of this measure were examined, and its associations with eating disorder psychopathology, depression, and gender were explored. METHOD Two hundred twenty consecutive overweight (body mass index [BMI] > or = 25) treatment-seeking BED patients (48 men and 172 women) were administered the EOQ, which assesses overeating frequency in response to six emotions (anxiety, sadness, loneliness, tiredness, anger, and happiness). A subset of patients (n = 83) completed the measure again approximately 1 week later. BMI was measured, and participants completed measures of eating disorder psychopathology. RESULTS The EOQ was internally consistent (alpha =.85), its items were significantly and moderately correlated (range .32 to .70) with each other, and principal components analysis revealed one factor accounting for 58% of the variance. The EOQ items and total score were characterized by good test-retest reliability (intraclass correlation coefficients [ICCs] ranged from .62 to .73). Significant correlations were found between the emotional overeating items and total score, and binge frequency, eating disorder features, and depressive symptomatology. Emotional overeating was unrelated to BMI, and men and women reported similar rates of emotional overeating. CONCLUSION Emotional overeating was significantly associated with binge frequency, eating disorder features, and depression, but was not related to BMI or gender.
Levels of some heavy metals in water and tissues of chub mackerel (Scomber japonicus) compared with physico-chemical parameters, seasons and size of the fish.

This study was carried out between October 2009 to July 2010 and heavy metals like Ba, As, Co, Cd, Cr, Cu, Fe, Mn, Ni and Zn were determined from water and 60 fish samples (60 in total) from Antalya Bay. Physic-chemical parameter values were also measured in the seawater from catchment area. Analysis of DORM-3 and DOLT-4, reference materials showed good accuracy with the present analytic system. The temperature varied between 17.77 - 27.76oC; pH between 7.79 - 10.52; dissolved oxygen between 7.28 - 12.83 mg l 1 and salinity between 21.05‰ - 33.84‰. The seasonal variations of heavy metal levels in some tissues of Scomber japonicus were determined. Significant differences (P<0.05) were found in tissues in relation to the seasons. Linear regression analysis and significant associations between the metal levels in tissues and fish size were also determined. The concentrations of heavy metals in water and fish were also compared with acceptable limits given by national and international water quality guidelines. The present study revealed that the metals level in water increased during spring and decreased in autumn. Both positive and negative correlations were observed between metal contents in water and physico-chemical parameters.
Thermal-based finite control set model predictive control for IGBT power electronic converters

Thermal cycling is one of the main sources of aging and failure in power electronics. A possibility to reduce the thermal stress of semiconductors is to control the losses occurring in the semiconductor devices with the target to reduce the thermal cycles. This approach is known as active thermal control. The hardest limit of the existing active thermal control approaches is that they do not offer a general framework where the optimal switching sequence is selected in order to fulfill the applications demand and reduce the thermal stress in specific semiconductors. The goal is to achieve the minimum thermal stress for the best possible overall performance. For this purpose finite control-set model predictive control (FCS-MPC) seems the optimal approach because it allows including of non-linear thermal and lifetime related models into the control law. A precise control of the thermal stress in the semiconductors can be achieved as the optimal switching vector is directly applied to the physical system. This allows to avoid overrating of the used module or to increase its lifetime. In the paper the approach is proven using simulation and experimental results.
Neck and back pain in bicycling

Neck and back pain are among the most common overuse injuries in cyclists. Bicycle fit, improper equipment, training errors, and individual anatomic factors are important evaluation considerations. By learning how to recognize and treat contributing factors, as well as learning a few simple bike-fitting techniques, physicians can treat and prevent many common problems of this popular activity.
Determination of the Time Course and Extent of Neurotoxicity at Defined Temperatures in Cultured Neurons Using a Modified Multiwell Plate Fluorescence Scanner

The cellular and molecular mechanisms of hypoxic/ischemic neurodegeneration are sensitive to numerous factors that modulate the time course and degree of neuronal death. Among such factors is hypothermia, which can dramatically protect neurons from injury. To examine and control for temperature-dependent effects, we developed a technique that provides for a high-throughput, accurate, and reproducible determination of the time course and degree of neurotoxicity in cultured cortical neurons at precisely defined temperatures. We used a fluorescence multiwell plate scanner, modified by us to permit the control of temperature, to perform serial quantitative measurements of propidium iodide (PI) fluorescence in cortical neuronal cultures exposed to excitotoxic insults. In validating this approach, we show that these time course measurements correlate highly with manual counts of PI-stained cells in the same cultures (r = 0.958, p < 0.0001) and with lactate dehydrogenase release (r = 0.964, p < 0.0001). This method represents an efficient approach to mechanistic and quantitative studies of cell death as well as a high-throughput technique for screening new neuroprotective therapies in vitro.
Evidence for rapid extraction of numeric information

The present study investigated the rapid processing of numeric meaning. Participants compared briefly presented displays of digits, letters, or shapes. Experiment lrevealed three main findings: i . Participants were faster and more accurate when deciding which side of a display had the larger average value (when viewing displays of digits) than when determining which side of a display had the greater occurrence of a target shape (when viewing displays of letters or shapes), suggesting that numeric information was extracted faster and more accurately than information about familiarity or shape; i i . While participants compared digits faster and more accurately than they compared letters or shapes, they compared sideways digits (shapes), letters, and sideways letters (shapes) with equal speed and accuracy, showing a negative effect of sideways rotation for digits but no effect of rotation for letters, suggesting that impairment in performance produced by rotating digits may be attributed to the loss of numeric meaning and not to the loss of familiarity or shape similarities; i i i . Participants compared homogeneous displays and single items faster and more accurately than they compared heterogeneous displays across all display types (digits, letters, and shapes), suggesting that the faster and more accurate comparisons of numeric information were not based on the mean value, as found for rapidly extracted geometric properties. Experiment 2 tested the effects of task instructions to compare the average value of digit displays on the rapid extraction of numeric information. It was found that even when participants were told to compare all displays based on the greater occurrence of a target shape, displays of digits were still compared faster and more accurately than displays of familiar letters or simple shapes, suggesting that numeric meaning, not task instructions to compare digits based on average value, was driving the rapid digit comparisons. In Experiment 3, participants were allowed to view the displays of digits, letters, and shapes for as long as they wished. When participants were not under any time constraints imposed by brief stimulus presentations, they compared all display types with similar speed and accuracy, suggesting that they no longer rapidly extracted numeric information when given sufficient time to identify individual stimuli. Taken together, these results support the proposal that the visual system can rapidly represent meaningful (numeric) information when assessing briefly presented visual displays. Table of
Characterization of the microbial community in indoor environments by chemical marker analysis: an update and critical evaluation.

UNLABELLED We published recently an integrated procedure for applying chemical marker analysis to characterize the microbiology of indoor environments comprising a scheme for extraction and analysis of markers of endotoxin, peptidoglycan/bacterial biomass, and fungal biomass. In the present paper, we report some significant improvements and also new possibilities of the described approach. We found that while 3-hydroxy fatty acids (3-OH FAs) of 10-14 carbon chain lengths are useful endotoxin markers, longer 3-OH FAs (i.e. with 16 carbon atoms and more) may rather serve as markers of Actinobacteria. We introduced 13C-labeled 3-hydroxytridecanoic acid, from labeled Pectinatus cerevisiiphilus, as an internal standard to improve quantification of the 3-OH FAs in the gas chromatography-mass spectrometry analysis. Finally, in experiments aiming to identify a suitable method for collection of house dust for chemical marker analysis, we found that the marker compositions of dusts sedimented on plexiglass plates that were spatially well-distributed in a studied room at different heights above floor level, were undistinguishable. This type of sampling thus appears to be well suited for use, e.g. in epidemiological studies. In summary, the presented work describes important new capabilities of chemical marker analysis in defining human exposure to microorganisms in indoor environments. PRACTICAL IMPLICATIONS We are developing an integrated methodology for characterizing the microbiology of indoor environments where specific microbial monomeric constituents in building materials and inhalable house dust particles are determined by using mass spectrometry-based methods. The methodology should represent a firm basis in research aiming to relate microbial exposure indoors to well-being and health.
A Hybrid Frequency-Space Approach for Shape Measurement by Shadow Moiré Technique with Carrier Fringe Pattern

In this paper, a novel methodology to process fringe pattern is presented. The core of the signal processing technique is the use of the direction information, a modulo 2pi quantity that locally informs about the direction along which fringes grow with maximum rate. By using this information, it was possible to perform adaptive, direction- and orientation-based operations on fringe images in order to remove unwanted effects, to enhance the contrast and to extract the phase information encoded. The method has been applied on shadow moire interferograms with carrier fringes in order to measure the surface of small objects. The developed algorithm allows to process fringes whose phase information is not monotonically increasing everywhere and to more accurately estimate the phase itself. Results from two experimental fringe patterns are presented. Results are compared with measurements performed by means of a conoscopic system used as a reference. Hence, it was possible to calculate the uncertainty of the performed measurements. Besides the possibility to decode fringe patterns presenting closed fringes, the proposed method provides measurements characterized by an uncertainty more than halved compared to Fourier-based methods
Fast detection of spurious DNA reads

The current DNA sequencing technology can produce reading errors with frequencies up to 1 error per 5 base pairs. Depending on the experiment and analysis pipeline there may be millions of short reads (30-40 letters), some of which will differ only by a few letters. Such reads are most likely misreads of the same sequence and therefore may distort the results of following analysis. We introduce a hash-based solution for quickly finding sets of sequences that differ from each other in only small number of places.
Streptomyces coelicolor Dps‐like proteins: differential dual roles in response to stress during vegetative growth and in nucleoid condensation during reproductive cell division

The Dps protein, a member of the ferritin family, contributes to DNA protection during oxidative stress and plays a central role in nucleoid condensation during stationary phase in unicellular eubacteria. Genome searches revealed the presence of three Dps‐like orthologues within the genome of the Gram‐positive bacterium Streptomyces coelicolor. Disruption of the S. coelicolor dpsA, dpsB and dpsC genes resulted in irregular condensation of spore nucleoids in a gene‐specific manner. These irregularities are correlated with changes to the spacing between sporulation septa. This is the first example of these proteins playing a role in bacterial cell division. Translational fusions provided evidence for both developmental control of DpsA and DpsC expression and their localization to sporogenic compartments of aerial hyphae. In addition, various stress conditions induced expression of the Dps proteins in a stimulus‐dependent manner in vegetative hyphae, suggesting stress‐induced, protein‐specific protective functions in addition to their role during reproductive cell division. Unlike in other bacteria, the S. coelicolor Dps proteins are not induced in response to oxidative stress.
Error-locating pairs for cyclic codes

A general decoding method for linear codes is investigated for cyclic codes. The decoding consists of solving two systems of linear equations. All but four binary cyclic codes of length less than 63 can so be decoded up to their actual distance. A new family of codes is given for which the decoding needs only O(n/sup 2/) operations. >
Occupational assessment of exposure to organic solvents in an adhesive producing company in Sfax, Tunisia.

S fax, the second largest city in Tunisia, is considered one of the main industrial and agricultural pillars of the country’s economy. At the industrial level, adhesive producing companies are known for their great consumption of organic solvents. Chemical risks caused by organic solvents encountered in this sector occupy, by far, first place in terms of health hazards. (1,2) In spite of the large quantity of solvents used, there is little information on exposure of workers to these chemical reagents and on their health effects. Prevention of occupational hazards, and more specifically of chemical risks, rests on regulatory procedures. (3,4) The Tunisian regulation on health impact,(5–7) however, does not require employers to carry out air concentration measurements or to assess biological exposure indexes (BEI) in working areas. This investigation on solvent exposure levels was conducted in an adhesive producing company with the participation of a group of volunteer workers. The main solvents used in the studied company are acetone, cyclohexane, n-hexane, methylethylketone, toluene, and trichloroethylene. Assessment of the occupational exposure to this mixture of solvents was based on atmospheric measurements and analysis of workers’ urine.