Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of the Actinomadura R39 DD-peptidase Reveals New Domains in Penicillin-binding Proteins*

Actinomadura sp. R39 produces an exocellular DD-peptidase/penicillin-binding protein (PBP) whose primary structure is similar to that of Escherichia coli PBP4. It is characterized by a high β-lactam-binding activity (second order rate constant for the acylation of the active site serine by benzylpenicillin: k/K = 300 mm-1s-1). The crystal structure of the DD-peptidase from Actinomadura R39 was solved at a resolution of 1.8 Å by single anomalous dispersion at the cobalt resonance wavelength. The structure is composed of three domains: a penicillin-binding domain similar to the penicillin-binding domain of E. coli PBP5 and two domains of unknown function. In most multimodular PBPs, additional domains are generally located at the C or N termini of the penicillin-binding domain. In R39, the other two domains are inserted in the penicillin-binding domain, between the SXXK and SXN motifs, in a manner similar to “Matryoshka dolls. ” One of these domains is composed of a five-stranded β-sheet with two helices on one side, and the other domain is a double three-stranded β-sheet inserted in the previous domain. Additionally, the 2.4-Å structure of the acyl-enzyme complex of R39 with nitrocefin reveals the absence of active site conformational change upon binding the β-lactams.
snoRNA and piRNA expression levels modified by tobacco use in women with lung adenocarcinoma

Lung cancer is one of the most frequent types of cancer worldwide. Most patients are diagnosed at advanced stage and thus have poor prognosis. Smoking is a risk factor for lung cancer, however most smokers do not develop lung cancer while 20% of women with lung adenocarcinoma are non-smokers. Therefore, it is possible that these two groups present differences besides the smoking status, including differences in their gene expression signature. The altered expression patterns of non-coding RNAs in complex diseases make them potential biomarkers for diagnosis and treatment. We analyzed data from differentially and constitutively expressed PIWI-interacting RNAs and small nucleolar RNAs from publicly available small RNA high-throughput sequencing data in search of an expression pattern of non-coding RNA that could differentiate these two groups. Here, we report two sets of differentially expressed small non-coding RNAs identified in normal and tumoral tissues of women with lung adenocarcinoma, that discriminate between smokers and non-smokers. Our findings may offer new insights on metabolic alterations caused by tobacco and may be used for early diagnosis of lung cancer.
Cointegration and Priority Relationships between Stock Market of Turkey, Brazil and Argentina

The aim of this study is to expose the relationships between Istanbul (Turkey), Merval (Argentina) and Bovespa (Brazil) stock exchange markets using monthly data covering the period 1997:03-2007:06. The long term co-movement of the stock exchanges has been tested by cointegration test developed by Johansen (1998) and Johansen Juselius (1990). Besides, the priority relationships and direction of the relation among the variables have been examined by impulse-response functions and variance decomposition. A long run relationship has been detected between the stock markets as a conclusion. According to the variance decomposition results, Bovespa has a major effect on ISE. In addition to this, even Bovespa has also an effect on Merval, it itself is not affected by the other two stock exchanges.
Risk factors associated with asthma phenotypes in dental healthcare workers.

BACKGROUND Exposure in the dental environment can increase the risk of respiratory disease in dental healthcare workers (HCWs). This study investigated the prevalence of asthma phenotypes in dental HCWs and associated risk factors. METHODS A cross-sectional study of 454 dental HCWs in five dental institutions in South Africa was conducted. A self-administered questionnaire elicited the health and employment history of subjects. Sera was analyzed for atopic status and latex sensitization. Pre- and post-bronchodilator spirometry was performed. RESULTS The prevalence of atopic asthma was 6.9%, non-atopic asthma 5.9% and work-exacerbated asthma (WEA) 4.0%. Atopy and work-related ocular-nasal symptoms were strong predictors of WEA (OR: 3.4; 95% CI: 1.07-10.8; OR: 6.7, 95% CI: 2.4-19.1), respectively. Regular use of personal protective equipment (PPE) was associated with a protective affect (OR: 0.23, 95% CI: 0.1-0.7) among non-atopic asthmatics, while glove use and respiratory protection was protective among atopic asthmatics (OR: 0.39, 95% CI: 0.17-0.89). CONCLUSION Identification of risk factors associated with specific asthma phenotypes in dental HCWs can be used to focus preventive strategies for asthmatics.
Computing non-negative tensor factorizations

Non-negative tensor factorization (NTF) is a technique for computing a parts-based representation of high-dimensional data. NTF excels at exposing latent structures in datasets, and at finding good low-rank approximations to the data. We describe an approach for computing the NTF of a dataset that relies only on iterative linear-algebra techniques and that is comparable in cost to the non-negative matrix factorization (NMF). (The better-known NMF is a special case of NTF and is also handled by our implementation.) Some important features of our implementation include mechanisms for encouraging sparse factors and for ensuring that they are equilibrated in norm. The complete MATLAB software package is available under the GPL license.
DINAS: A Lightweight and Efficient Distributed Naming Service for All-IP Wireless Sensor Networks

The Internet of Things (IoT) requires a compact naming scheme, which can also bring significant advantages to service registration and discovery. We propose a novel approach, denoted as distributed naming service, which provides a new naming scheme as well as an efficient service discovery protocol for wireless sensor networks. It is based on three pillars: 1) Bloom filters, to create compact names from node descriptions; 2) message propagation strategies, to publish and discover information—not only names—within the network; and 3) distributed caches, to store names within the network. In this paper, we assume ContikiMAC at layer 2, IPv6 and Routing Protocol for Low-Power and Lossy Networks (RPL) at layer 3, and we present two particular UDP-based message propagation strategies that take advantage of the RPL protocol at layer 3. We evaluate the performance of the proposed solutions through Contiki/Cooja simulations and on a real testbed, using the open and large scale FIT IoT-LAB.
Reduced-order root-MUSIC based on Schur spectral factorization

The root multiple signal classification (Root-MUSIC) has recently drawn a considerable attention, by using a polynomial rooting instead of spectral searching to reduce the complexity. The Root-MUSIC is computationally efficient in conjunction with a uniform linear array (ULA) composed of M sensors. Compared with traditional multiple signal classification (MUISC) algorithm, Root-MUSIC is more advantaged but also has a redundancy by solving a (2M-2) order polynomial. The polynomial is intensely complex when large number of sensors is used, and consequently, tremendous computations are required. A reduced-order Root-MUSIC based on the Schur spectral factorization is presented in this paper, which only need to calculate a (M-1) order polynomial. Simulations are conducted to support the validity of the algorithm. The results show that reduced-order Root-MUSIC has a similar root mean square error (RMSE) performance as Root-MUSIC with less computation.
Why Coverage of Influenza Vaccine Is Not Enough in Patients Receiving Chemotherapy?

Instead of strict recommendations of experts of doing vaccination in chemotherapy patients, they may not be aware of its necessity, except to be encouraged by their responsible healthcare workers. As it is clear that morbidity and mortality of influenza is high in immunocompromised patients. 1,2 According to some reports, mortality rate of influenza infection can reach 9% among oncology patients. 3 Vaccination against influenza is recommended in immunosuppressed patients, including those receive anticancer chemotherapy. 4 Absence of immunization commands, particularly against influenza, endangers the quality of life in patients with cancer. 3 Generally, although patients with cancer respond positively to vaccination, the utility of influenza vaccination is very low in this population. The purpose of this study is to evaluate if the influenza vaccine coverage in oncology patients under chemotherapy treatment is enough to guarantee prevention during the season. We also tried to investigate the factors influencing coverage rate. Between January and March 2010, we performed a prospective, monocentric study in 100 patients with median age of 47 years (range 16–79). A standardized form was given to all cancer patients receiving chemotherapy in our department. The median time to receive chemotherapy was 14 months (range out of 1–180) among the patients with colorectal (30%), sarcoma (6%), leukemia (18%), and breast and ovarian (11%) cancers. Only nine patients (9%) had received influenza shots. Chemotherapy was the reason for shot in only 44.4% of those who were vaccinated, while 55.6% of remaining people got the vaccine for some other reasons. No relationship was found between the vaccination rate and age. A similar study published on 2008 reported 30% of coverage which is pretty much more in our study. Although cancer patients often care about their own health, but health workers may neglect to recommend influenza vaccine that may be the leading cause of low vaccination rate. It is important to encourage patients with cancer to get a flu shot before the season is going off. In addition, fear of side effects is among the factors that crash coverage of vaccination in this group. According to the immunologic status of oncology patients, more attention is required to make their coverage full especially in those undergoing chemotherapy.
TID effects on retention of 0.13 μm SONOS memory cell: A device simulation approach

Flash memory cells used in space applications are under continuous impact of Total Ionizing Dose (TID) effects. It causes charge trapping in the oxide and in the oxide/substrate interface. In this work, we investigate the TID radiation response of 0. 13μm SONOS flash memory cell with different charge states upto 1 Mrad(Si). It is found that threshold voltage of programmed and virgin states of memory decreases with irradiation due to accumulation of holes. For erased state, accumulation of induced holes and loss of holes in nitride layer tends to cancel each other, causing no significant change. Further, we also proposed a device simulation approach to test data retention at room and high temperature as a function of TID irradiations received. We observed that retention is not much dependent on irradiation dose. TID exposure degrades the device retention and this effect enhances with increase in temperature due to thermally activated electron detrapping. All the analyses are accomplished using physical simulation models of charge trapping in Sentaurus TCAD suite, comparing results with established qualitative models.
DAG‐sensitive and Ca2+ permeable TRPC6 channels are expressed in dentate granule cells and interneurons in the hippocampal formation

Members of the transient receptor potential (TRP) cation channel family play important roles in several neuronal functions. To understand the precise role of these channels in information processing, their presence on neuronal elements must be revealed. In this study, we investigated the localization of TRPC6 channels in the adult hippocampal formation. Immunostainings with a specific antibody, which was validated in Trpc6 knockout mice, showed that in the dentate gyrus, TRPC6 channels are strongly expressed in granule cells. Immunogold staining revealing the subcellular localization of TRPC6 channels clarified that these proteins were predominantly present on the membrane surface of the dendritic shafts of dentate granule cells, and also in their axons, often associated with intracellular membrane cisternae. In addition, TRPC6 channels could be observed in the dendrites of some interneurons. Double immunofluorescent staining showed that TRPC6 channels were present in the dendrites of hilar interneurons and hippocampal interneurons with horizontal dendrites in the stratum oriens expressing mGlu1a receptors, whereas parvalbumin immunoreactivity was revealed in TRPC6‐expressing dendrites with radial appearance in the stratum radiatum. Electron microscopy showed that the immunogold particles depicting TRPC6 channels were located on the surface membranes of the interneuron dendrites. Our results suggest that TRPC6 channels are in a key position to alter the information entry into the trisynaptic loop of the hippocampal formation from the entorhinal cortex, and to control the function of both feed‐forward and feed‐back inhibitory circuits in this brain region. © 2012 Wiley Periodicals, Inc.
Character identification by maximizing the difference between target and non-target responses in EEG without sophisticated classifiers

We propose a simple character identification method demonstrated by using an electroencephalogram (EEG) with a stimulus presentation technique. The method assigns a code maximizing the minimum Hamming distance between character codes. Character identification is achieved by increasing the difference between target and non-target responses without sophisticated classifiers such as neural network or support vector machine. Here, we introduce two kinds of scores reflecting the existence of the P300 component from the point of time and frequency domains. We then applied this method to character identification using a 3×3 matrix and compared the results to that of a conventional P300 speller. The accuracy of character identification with our method indicated a performance of 100% character identification from five subjects. In contrast, the correct character was detected in two subjects and a wrong one was detected for one subject. For the remaining two subjects, no character was detected within ten trials. Our method required 4.8 trials on average to detect the correct character.
Iterative OFDM receiver with combined interference suppression and cancellation

For cellular networks, the increased cell density and decreased cell size will give rise to significant inter-cell interference. In this work, an adaptive antenna array and an iterative receiver are combined to facilitate inter-cell interference suppression and cancellation at the receiver end. Iterative receivers exchange soft information between different receiver modules, e.g., symbol detector and channel decoder. An adaptive antenna array is integrated within the iterative receiver, which performs interference suppression and successive interference cancellation. The beamforming weight vectors are updated in each iteration using interference rejection combing, which takes into account the soft information from the channel decoder and previously estimated interfering signals. The proposed algorithm can effectively suppress and cancel the interference signal with various signal-to-interference ratios under different channel models.
Pleiotropic Effects of Atorvastatin on Monocytes in Atherosclerotic Patients

The objective of this study was to investigate the gene expression signature of monocyte/macrophages and the pleiotropic effects of atorvastatin on monocytes in atherosclerotic patients. Forty patients with coronary heart diseases were randomly assigned to double‐blind therapy with either 20 or 80 mg per day of atorvastatin. Follow‐up visits occurred at weeks 6 and 12, including complete chemistry and lipid analyses and quantification of 14 target genes in monocytes. After 12 weeks of therapy, both groups gained beneficial alterations in lipid profiles. Both groups experienced significant reductions in gene expression of lipoprotein‐associated phospholipase A2, CD13, leptin receptor, matrix metalloproteases‐1, legumain, and prolyl oligopeptidase after 12 weeks of therapy. Only tumor protein 53 was increased in the atorvastatin 80‐mg group. Moreover, nonsignificant interactions between dosage and duration of therapy were found. The pleiotropic effects of statins in atherosclerotic patients include increased expression of genes involved in apoptosis of monocyte/macrophage, inhibition of inflammatory responses, antioxidant properties, prevention of foam cell formation, and stabilization of atherosclerotic plaques. This property fuels potential clinical significance.
Avian proteomics: advances, challenges and new technologies

Proteomics is defined as an analysis of the full complement of proteins of a cell or tissue under given conditions. Avian proteomics, or more specifically chicken proteomics, has focussed on the study of individual tissues and organs of interest to specific researchers. Researchers have looked at skeletal muscle and growth, and embryonic development and have performed initial studies in avian disease. Traditional proteomics involves identifying and cataloguing proteins in a cell and identifying relative changes in populations between two or more states, be that physiological or disease-induced states. Recent advances in proteomic technologies have included absolute quantification, proteome simplification and the ability to determine the turnover of individual proteins in a global context. This review discusses the current developments in this relatively new field, new technologies and how they may be applied to biological questions, and the challenges faced by researchers in this ever-expanding and exciting field.
A Posteriori Approach of Real-time Ridesharing Problem with Intermediate Locations

Ridesharing is a travel mode that provides several benefits and solutions, such as the reduction of travel cost, the reduction of the traffic congestion and the provision of travel options. In the classical ridesharing approach, the driver makes a detour to the rider’s origin in order to pick-up the rider, then drives him to his destination and finally the driver goes to his own destination. This implies that the driver endures the whole detour and may not accept such matching if the detour is too long. However, the matching could be accepted if the rider meets the driver at an intermediate location. In this paper, we present a general ridesharing approach in which a driver and a rider accept to meet each other at an intermediate pick-up location and to separate at an intermediate drop-off location not necessarily their origins and destinations locations, respectively. Thus, for a given rider, we propose an exact and heuristic methods to determine the best driver and the best meeting locations that minimize a total travel cost. Finally, we perform a numerical study using a real road network and a real dataset. Our experimental analysis shows that our heuristics provide efficient performance within short CPU times and improve participants cost-savings and matching rate compared to the classical
Assembly-induced folding regulates interleukin 12 biogenesis and secretion

Members of the IL-12 family perform essential functions in immunoregulation by connecting innate and adaptive immunity and are emerging therapeutic targets. They are unique among other interleukins in forming heterodimers that arise from extensive subunit sharing within the family, leading to the production of at least four functionally distinct heterodimers from only five subunits. This raises important questions about how the assembly of IL-12 family members is regulated and controlled in the cell. Here, using cell-biological approaches, we have dissected basic principles that underlie the biogenesis of the founding member of the family, IL-12. Within the native IL-12 heterodimer, composed of IL-12α and IL-12β, IL-12α possesses three intramolecular and one intermolecular disulfide bridges. We show that, in isolation, IL-12α fails to form its native structure but, instead, misfolds, forming incorrect disulfide bonds. Co-expression of its β subunit inhibits misfolding and thus allows secretion of biologically active heterodimeric IL-12. On the basis of these findings, we identified the disulfide bonds in IL-12α that are critical for assembly-induced secretion and biological activity of IL-12 versus misfolding and degradation of IL-12α. Surprisingly, two of the three disulfide bridges in IL-12α are dispensable for IL-12 secretion, stability, and biological activity. Extending our findings, we show that misfolding also occurs for IL-23α, another IL-12 family protein. Our results indicate that assembly-induced folding is key in IL-12 family biogenesis and secretion. The identification of essential disulfide bonds that underlie this process lays the basis for a simplified yet functional IL-12 cytokine.
An unstructured protein with destructive potential: TPPP/p25 in neurodegeneration

TPPP/p25 is a recently discovered, unstructured protein involved in brain function. It is found predominantly in oligodendrocytes in normal brain but is enriched in neuronal and glial inclusions of Parkinson's disease and other synucleinopathies. Its physiological function seems to be the dynamic stabilization of microtubular ultrastructures, as well as the projections of mature oligodendrocytes and ciliary structures. We reappraise the earlier belief that TPPP/p25 is a brain‐specific protein. We have identified and cloned two shorter (N‐terminal‐free) homologs of TPPP/p25 that behave differently from each other and from TPPP/p25. Two unique cell models have been established and used to study the effect of the unstructured protein on the energy metabolism and the formation of pathological aggregates. Our data suggest that the intracellular level of TPPP/p25 influences the cell differentiation, proliferation and the formation of protein aggregates, and consequently, the etiology of central nervous system diseases.
Enterprise education in initial teacher education in Ireland

Purpose – The purpose of this paper is to examine the impact of enterprise education on students’ understanding of and attitudes to entrepreneurship and enterprise education in initial teacher education. Design/methodology/approach – This paper builds on current literature by introducing student teachers to the theory and practice of entrepreneurship and enterprise education, with a particular focus on experience-based approaches. Quantitative and qualitative data are used to evaluate student understanding and attitudes. Findings – Findings indicate that exposing student teachers to entrepreneurship and enterprise education specifically targeted at their subject area greatly increases their understanding of its importance and relevance. Students developed their ability to think and act in enterprising ways while recognising the benefits of incorporating enterprise education into their classrooms of the future. Originality/value – While literature on the value of entrepreneurship and enterprise education o.
Multiband LTE/WWAN phone antennas

Our group works in the eara of phone antennas in recent years will be reviewed. Firstly, some multiband single phone antennas will be presented, especially where the narrow-frame antenna is firstly proposed for the large touch-screen phone applications. Then, some decoupled antennas for LTE MIMO phone applications will be demonstrated, where two different decoupled techniques including well-designed protruded ground and neutralization line are used. Finally, two multiband antennas for metal-ring phone applications are proposed.