165 research outputs found
Decentralized Approximate Bayesian Inference for Distributed Sensor Network
No full textBayesian models provide a framework for probabilistic modelling of complex datasets. Many such models are computationally demanding, especially in the presence of large datasets. In sensor network applications, statistical (Bayesian) parameter estimation usually relies on decentralized algorithms, in which both data and computation are distributed across the nodes of the network. In this paper we propose a framework for decentralized Bayesian learning using Bregman Alternating Direction Method of Multipliers (B-ADMM).We demonstrate the utility of our framework, with Mean Field Variational Bayes (MFVB) as the primitive for distributed affine structure from motion (SfM).Peer reviewe
TNF receptor I on human keratinocytes is a binding partner for staphylococcal protein A resulting in the activation of NF kappa B, AP-1, and downstream gene transcription.
No full textPrimary human keratinocytes and immortalized HaCaT cells were analysed for their capacity to bind purified staphylococcal protein A (SpA). Co-incubation with FITC-labelled SpA led to a dose-depending attachment. Pull-down experiments with cellular extracts revealed the TNFα receptor I (TNF RI) as binding partner on keratinocytes. Thus, we next looked for expression of this receptor in human epidermis and cultured keratinocytes. TNF RI is strongly expressed on all keratinocytes analysed, both at the mRNA and protein level and activation by SpA at optimal doses of 50-100 μg/ml resulted in the phosphorylation of the TNF RI downstream kinases MEK1/2, JNK1/2, and p38 subsequently leading to translocation of the p65 NF kappa B subunit and AP-1 into the nucleus. This translocation was then followed by increased expression of IL-8 and COX-2, two known NF kappa B-induced pro-inflammatory genes. To further test the relevance of our findings, we analysed in vitro production of over 100 strains isolated from atopic eczema showing that more than 85% of the tested strains produced extracellular SpA in substantial amounts. Thus, besides superantigens, haemolysins, and other cell wall components, Staphylococcus aureus exerts pro-inflammatory stimuli on human keratinocytes through the production of SpA signalling through TNF RI
Interaktion von primären humanen Keratinozyten mit Liganden der Toll Like Rezeptoren und die daraus folgenden pro-inflammatorischen Signale
Get PDFEmerging evidence suggests an important role for human epidermal keratinocytes (KC) in innate immune mechanisms against skin infections. A crucial part in this first-line immune defence is performed by the ‘‘pattern recognition receptors,’’ amongst which the group of Toll-like receptors (TLRs) has evolved as the most essential contributor. In this study, functional TLR expression in KC was analysed in detail. It is demonstrated that KC express all known dsRNA sensing receptors at a constitutive and inducible level. Thus, in addition to building a physical barrier against infection, KC are specially equipped with a full antiviral defense program which enables them to efficiently target viral infections of the skin.Neue Erkenntnisse weisen auf eine wichtige Rolle humaner epidermaler Keratinozyten (KC) bei der angeborenen Immunabwehr gegen Hautinfektionen hin. Ein entscheidender Teil dieser Erstantwort wird von “pattern recognition” Rezeptoren getragen. Unter diesen hat sich die Gruppe der Toll-like Rezeptoren (TLRs) als der tragende Teil herausgestellt. In dieser Arbeit wurde die funktionelle Expression von TLRs in KC untersucht. KC exprimieren alle bekannten dsRNA Rezeptoren konstitutiv und induzierbar. Folglich bilden KC nicht nur eine physikalische Barriere gegen Infektionen, sondern sind weiterhin mit einem kompletten antiviralen Abwehrprogramm ausgestattet, um virale Hautinfektionen effektiv anzugreifen
Estimating the branching fraction for decay
Get PDFI present estimates of the branching fractions in the non-leptonic charmonium
two-body decay rates for decay and the same
decays of , and
. These estimates are based on a generalized
factorization approach making use of leading order (LO) and next-to-leading
order (NLO) contributions. I find that when the large enhancements from the
known NLO contributions by using the QCD factorization approach are taken into
account, the branching ratios are the following: , , and , while the experimental results are
, , and respectively. All
estimates are in good agreement with the experimental results.Comment: Repeated topi
Development and applications of programmable DNA-guided Argonaute-based artificial restriction enzymes
Get PDFRestriction enzymes or formally known as restriction endonucleases are a class of nuclease enzymes which recognize short DNA sequences and cleave DNA molecules at or near their recognition site. Type II restriction enzymes are capable of cleavage of DNA at a fixed location with respect to their recognition sequence and some type II restriction enzymes are able to generate defined cohesive ends (a.k.a sticky ends) on DNA molecules after cleavage. Because of these two remarkable features, upon their discovery, type II restriction enzymes revolutionized molecular biology and helped give rise to the field of modern biotechnology. To date, type II restriction enzymes still play a major role in biological research with more than 600 enzymes with >235 distinct sequence specificities commercially available. While type II restriction enzymes are able to cleave DNA molecules specifically, they only recognize short DNA sequences (4-8 base pairs) which limits some of their applications. To address this challenge, artificial restriction enzymes (AREs) such as ZFNs, TALENs, or CRISPR-Cas nucleases were developed. While these AREs have longer recognition sequences compared to type II restriction enzymes, they are not able to produce defined sticky ends on DNA molecules or target all desired DNA sequences which significantly constrains their applications in vitro. In this dissertation, I describe the development and applications of a new class of artificial restriction enzymes capable of targeting virtually any DNA sequences with high specificities and generating defined sticky ends of varying length.
Argonaute proteins are a family of nucleic acid guide-dependent proteins which can be found in all domains of life. Some prokaryotic Argonaute proteins (pAgos) are able to use short single-stranded DNA molecules as guides to target complementary DNA sequences. I first utilized this capability of pAgos and developed a Pyrococcus furiosus Argonaute (PfAgo) based platform for generation of programmable DNA-guided artificial restriction enzymes. This platform was used to generate 18 AREs for DNA fingerprinting and molecular cloning of PCR-amplified or genomic DNAs. Next, I studied the potential of other pAgos for use as AREs. Through these studies, I was able to create an engineered version of PfAgo enzyme which demonstrates lower non-guided nuclease activity as well as higher specificity for cleavage of high GC-content DNA sequences compared to the wild-type PfAgo enzyme.
To demonstrate some of the applications of the newly developed AREs, I first created a method for rapid and highly accurate assembly of linear DNA molecules by PfAgo-based AREs. Using this method, plasmid DNA molecules up to 27 kb in size can be assembled from up to 10 DNA fragments with high efficiencies. This method also exhibits extremely low error rates and is able to assemble DNA molecules containing sequence repeats as well as DNA molecules with high GC-content. Next, I evaluated the capability and limitations of PfAgo-based AREs in direct cloning of microbial biosynthetic gene clusters (BGCs). Using PfAgo-based AREs, I was able to clone microbial BGCs ranging from 13-42 kb in size from both Bacillus and Streptomyces species with high efficiencies. However, PfAgo-based AREs did not exhibit 100% success rate for this application. As a result, I developed an alternative method for cloning microbial BGCs named Cas12a assisted precise targeted cloning using in vivo Cre-lox recombination (CAPTURE). This method which consists of Cas12a digestion, a newly developed DNA assembly approach termed T4 polymerase exo + fill-in DNA assembly, and Cre-lox in vivo DNA circularization, is capable of cloning microbial natural product BGCs ranging from 10-113 kb in size regardless of their GC-content or repetitive DNA sequence with ~100% cloning efficiency and success rate.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2022-12-01The student, Behnam Enghiad, accepted the attached license on 2020-11-27 at 15:43.The student, Behnam Enghiad, submitted this Dissertation for approval on 2020-11-27 at 16:00.This Dissertation was approved for publication on 2020-12-03 at 07:52.DSpace SAF Submission Ingestion Package generated from Vireo submission #15970 on 2022-01-12 at 13:02:47Made available in DSpace on 2022-01-12T22:51:32Z (GMT). No. of bitstreams: 2
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Corrigendum:Social smart city research: interconnections between participatory governance, data privacy, artificial intelligence and ethical sustainable development
No full textIn the published article, the second author's name was incorrectly written as “Behnaz Bababei Morad.” The correct spelling is “Behnaz Babaeimorad.” In the published article, there was an error in affiliation 3. This was incorrectly written as “Department of Urban Planning, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran.” It should be “Department of Urban Planning, Ahv.C., Islamic Azad University, Ahvaz, Iran.” In the published article, there was an error regarding the affiliations for the third author, Behnam Ghasemzadeh. As well as having affiliations 2, 4, and 5, they should also have “1Azarbaijan Shahid Madani University, Tabriz, Iran.” The authors apologize for these errors and state that they do not change the scientific conclusions of the article in any way. The original article has been updated.</p
Diagnosis of Helicobacter pylori: Changes towards the Future
No full textSince the first evidence demonstrating the dramatically high incidence of H. pylori infection and the subsequent medical challenges it incurs, health management of H. pylori infection has been a high priority for health authorities worldwide. Despite a decreasing rate of infection in western countries, prevalence of H. pylori infection in developing and in some industrial countries is still very high. Whereas treatment and vaccination against H. pylori is a contemporary issue in medical communities, selective treatment and prior high-throughput screening of the subject population is a major concern of health organizations. So far, diagnostic tests are either elaborative and require relatively advanced medical care infrastructure or they do not fulfill the criteria recommended by the Maastricht IV/Florence consensus report. In this review, in light of recent scientific studies, we highlight current and possible future approaches for the diagnosis of H. pylori. We point out that novel non-invasive tests may not only cover the requirements of gold standard methods in H. pylori detection but also offer the potential for risk stratification of infection in a high throughput manner
The Sox17CreERT2 knock-in mouse line displays spatiotemporal activation of Cre recombinase in distinct Sox17 lineage progenitors.
No full textThe HMG-box transcription factor Sox17 is essential for endoderm formation, vascular development, and definitive hematopoiesis. To investigate the fate of distinct Sox17-expressing progenitor cells in a spatiotemporal manner, we generated a hormone-inducible CreERT2 knock-in mouse line. By homologous recombination we fused a codon improved, ligand-dependent estrogen receptor Cre recombinase by an intervening viral T2A sequence for co-translational cleavage to the 3' coding region of Sox17. Induction of Cre activity by administration of tamoxifen at defined time points of early mouse development and subsequent genetic lineage tracing confirmed the inducibility and tissue specificity of Cre recombination. Furthermore, Cre activity could be selectively induced in extra-embryonic and embryonic endoderm lineages, the primitive gut tube, and in endothelial cells of the vascular system as well as in the hemogenic endothelium of the dorsal aorta. The Sox17CreERT2 mouse line therefore represents a new tool for genetic lineage tracing in a tissue-specific manner and in addition enables lineage-restricted functional analysis
H. pylori virulence factors: influence on immune system and pathology.
No full textHelicobacter pylori is the most widespread chronic bacterial agent in humans and is well recognized for its association with ulcer disease and gastric cancer, with both representing major global health and socioeconomic issues. Given the high level of adaptation and the coevolution of this bacterium with its human host, a thorough and multidirectional view of the specific microbiological characteristics of this infection as well as the host physiology is needed in order to develop novel means of prevention of therapy. This review aims to pinpoint some of these potentially important angles, which have to be considered mutually when studying H. pylori's pathogenicity. The host's biological changes due to the virulence factors are a valuable pillar of H. pylori research as are the mechanisms by which bacteria provoke these changes. In this context, necessary adhesion molecules and significant virulence factors of H. pylori are discussed. Moreover, metabolism of the bacteria, one of the most important aspects for a better understanding of bacterial physiology and consequently possible therapeutic and prophylactic strategies, is addressed. On the other hand, we discuss the recent experimental proofs of the "hygiene hypothesis" in correlation with Helicobacter's infection, which adds another aspect of complexity to this infection
On the efficiency of mitigation measures in reducing the amplified response at transition zones in railway tracks: tuned mass dampers, auxiliary rails, and under-sleeper pads
No full textIn transition zones, railway tracks experience significant inhomogeneity in their mechanical properties—more specifically in vertical stiffness. In such areas, conventional tracks (soft tracks) are typically encountered with other engineering structures with noticeably larger stiffness, such as bridges and culverts (stiff tracks). This inhomogeneity together with the passage of high-speed trains leads to amplification in dynamic response, which in turn results in faster degradation and higher cost of maintenance at transition zones. In practice, various mitigation measures have been adopted which have led to improvement in track performance to a certain degree.This thesis is mainly focused on the feasibility of using the tuned mass damper (TMD), as a novel mitigation measure, for improving the aforementioned undesired behavior. Additionally, the efficiency of two already existing corrective measures, namely auxiliary rail and under sleeper pad (USP), is investigated at transition zone.The track is modeled as an infinite one-dimensional Euler-Bernoulli beam resting on a piecewise-homogeneous and continuously distributed Kelvin foundation. For each mitigation measure, semi-analytical solutions are derived through the Fourier transform method. Regarding TMD analysis, mechanical parameters are optimized by an evolutionary algorithm (NSGA-II), in which the discrepancy between the soft and the stiff tracks’ wavenumbers is minimized. In regard to auxiliary rail, two configurations with multiple number of extra rails (ERs) are evaluated; ERs over soft track only, and ERs over all domains. Additionally, USPs with different stiffness are considered for their arrangement along the track. The efficiency corresponding to each mitigation measure is mainly evaluated through dynamic amplification factor (DAF) and power input.The system with TMD demonstrates a significant reduction in DAF amplitude corresponding to the load velocity for which the optimization is performed. This improvement is also evident for velocities close to the aforementioned load speed. In fact, the addition of TMD results in presence of a free propagating wave behind the load and decreasing the critical velocity in the corresponding system. The outcomes corresponding to power input suggest a significant reduction in potential damage to the foundation due to the employment of TMD.Furthermore, the application of ER leads to improvement in dynamic performance of the track by increasing the critical velocity to a larger value, at which the corresponding DAF indicates no reduction. In addition, considering more than one ER along the track does not lead to a noticeably better result compared to when only one ER is added. Moreover, applying ER over soft track leads to inhomogeneity in bending stiffness and mass corresponding to the beam element at transition point. Therefore, the system with ER over all domains indicates a better dynamic behavior. Potentially, less damage to the foundation can be signified in the system with ER according to the power input response.Finally, USP can significantly affect the equivalent stiffness of the track. It is concluded that the efficiency of USPs in mitigating the amplified response is strongly dependent on their stiffness and arrangement along the track, as well as the stiffness variation in the supporting structure; improper design of USPs alignment can adversely result in even more amplified responses.Civil Engineering | Structural Engineerin
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