Miracle-dz/UniFAR-FTUs huggingface dataset:
Dominating Role of an Unusual Magnetotactic Bacterium in the Microaerobic Zone of a Freshwater Sediment

A combination of polymerase chain reaction-assisted rRNA sequence retrieval and fluorescent oligonucleotide probing was used to identify in situ a hitherto unculturable, big, magnetotactic, rod-shaped organism in freshwater sediment samples collected from Lake Chiemsee. Tentatively named “Magnetobacterium bavaricum,” this bacterium is evolutionarily distant from all other phylogenetically characterized magnetotactic bacteria and contains unusually high numbers of magnetosomes (up to 1,000 magnetosomes per cell). The spatial distribution in the sediment was studied, and up to 7 × 105 active cells per cm3 were found in the microaerobic zone. Considering its average volume (25.8 ± 4.1 μm3) and relative abundance (0.64 ± 0.17%), “M. bavaricum” may account for approximately 30% of the microbial biovolume and may therefore be a dominant fraction of the microbial community in this layer. Its microhabitat and its high content of sulfur globules and magnetosomes suggest that this organism has an iron-dependent way of energy conservation which depends on balanced gradients of oxygen and sulfide.
Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate.

Advenella mimigardefordensis strain DPN7(T) is a remarkable betaproteobacterium because of its extraordinary ability to use the synthetic disulfide 3,3'-dithiodipropionic acid (DTDP) as the sole carbon source and electron donor for aerobic growth. One application of DTDP is as a precursor substrate for biotechnically synthesized polythioesters (PTEs), which are interesting non-degradable biopolymers applicable for plastics materials. Metabolic engineering for optimization of PTE production requires an understanding of DTDP conversion. The genome of A. mimigardefordensis strain DPN7(T) was sequenced and annotated. The circular chromosome was found to be composed of 4,740,516 bp and 4112 predicted ORFs, whereas the circular plasmid consisted of 23,610 bp and 24 predicted ORFs. The genes participating in DTDP catabolism had been characterized in detail previously, but knowing the complete genome sequence and with support of Tn5: :mob-induced mutants, putatively involved transporter proteins and a transcriptional regulator were also identified. Most probably, DTDP is transported into the cell by a specific tripartite tricarboxylate transport system and is then cleaved by the disulfide reductase LpdA, sulfoxygenated by the 3-mercaptopropionate dioxygenase Mdo, activated by the CoA ligase SucCD and desulfinated by the acyl-CoA dehydrogenase-like desulfinase AcdA. Regulation of this pathway is presumably performed by a transcriptional regulator of the xenobiotic response element family. The excessive sulfate that is inevitably produced is secreted by the cells by a unique sulfate exporter of the CPA (cation : proton antiporter) superfamily.
TGF-β type I receptor / ALK-5 and Smad proteins mediate epithelial to mesenchymal transdifferentiation in NMuMG breast epithelial cells

Transforming growth factor (TGF)-β, which is the prototypic member of the TGF-β superfamily, exerts a broad range of biological activities. It has an antiproliferative effect primarily on cells of epithelial origin, whereas it promotes growth of mesenchymal cell types. It plays pivotal roles during embryonic development where it is involved in patterning the embryo and inducing cell differentiation and organogenesis (reviewed by Roberts and Sporn, 1990; Whitman, 1998). Several members of the TGF-β superfamily can modulate mesenchymal cell fates, including development of myoblasts, chondrocytes, or osteoblasts (Roberts and Sporn, 1990; Kingsley, 1994). Furthermore, TGF-β superfamily members might be involved in epithelial-mesenchymal differentiation processes such as nephrogenesis (Rogers et al., 1993), branching morphogenesis of the lungs and mammary glands (Silberstein and Daniel, 1987; Heine et al., 1990; Robinson et al., 1991; Hogan and Yingling, 1998), and budding morphogenesis of limbs, feathers and genitalia (Hogan, 1999). Processes that are beneficial and required for proper embryonic development frequently form the basis for pathological conditions in adults. Improper TGF-β signalling is often correlated with pathogenesis, like tumourigenesis (reviewed by Hata et al., 1998). Although TGF-β acts as a tumor suppressor during early benign stages of skin tumourigenesis, it potently aggravates the malignancy at later stages. This is accompanied by an epithelial to mesenchymal cell transition, which occurs during transformation of squamous carcinoma to invasive spindle cell carcinoma (Cui et al., 1996; Portella et al., 1998). 4557 Journal of Cell Science 112, 4557-4568 (1999) Printed in Great Britain © The Company of Biologists Limited 1999 JCS0423
Toxicity of Polymeric-Based Non-Viral Vector Systems for Pulmonary siRNA Application

Nanomedicine has the potential of clinical benefit by combination of engineering technologies and materials (Schatzlein, 2006). Development of nanometre scaled therapeutics which provides new and improved properties by specifically targeting the site of action and causing low level of side effects would be a big challenge to treat patients with severe and live-threatening diseases like cancer. Gene therapy provides a new way to treat patients and a lot of effort is made to improve the clinical benefit. But current gene therapy is still experimental and has not proven success in the clinics. Nevertheless there is a need for new approaches to treat „undruggable“ disease sites and there are some clinical trials ongoing which using RNA inference (RNAi) as therapeutic mechanism (Table 1).
Maximum DC-link voltage utilization for optimal operation of IPMSM

In hybrid and electrical vehicles the electric components have to be optimized to their limits. The voltage which is delivered by a high-voltage battery should be used fully by the machine. This paper describes the influence of the dc-link voltage on the efficiency and the operating limits of the electric system. For the optimal usage of the dc-link voltage, the converter control has to be extended to the six-step mode. This paper starts with a short introduction describing the electrical components of the developed hybrid vehicle. Afterwards the restrictions due to the voltage limit of the high voltage battery are analyzed. A field oriented control (FOC) is chosen to achieve a high performance control system. However, the field oriented control is not capable to fully utilize the available dc-link voltage. As will be shown it is possible to improve the control strategy of the electrical machine. Especially in applications with limited dc-link voltage and high power density, the new control strategy leads to a better utilization and a higher efficiency of the electrical system.
Microscopic computed tomography imaging of the cerebral circulation in mice: Feasibility and pitfalls

This study evaluates the utility and practical limitations of microcomputerized X‐ray tomography (CT) as a research tool for examination of the cerebral circulation in mice. Six micro CT angiograms of the circle of Willis (COW) from six mice were obtained by scanning whole head and brain specimen perfused with a radio‐opaque silicone contrast agent. Two‐dimensional volume rendered images were postprocessed from three‐dimensional image datasets using a partially automated high‐throughput model that generated 10 surface projections for each specimen. The image processing model employed a straightforward global thresholding and computerized component labeling software algorithm. Postprocessed images were analyzed and results correlated with microdissection. Micro CT demonstration of COW vessels and their branch anatomy was assessed. 71% of COW vessels were completely demonstrated, 26% were partially demonstrated, and 3% were not demonstrated. All cases of nondemonstration and most cases of partial demonstration resulted from scan coverage or postprocessing clip error. Thresholding effect caused pseudostenosis of 8% of COW vessels and accounted for a minority of partial demonstration cases. No imaging artifacts were caused by contrast extravasation or ineffective contrast perfusion. Volume averaging caused minor angioarchitectural distortion of 58% of COW vessels. Ninety‐five percent of COW ≥50 μm and 52% of COW vessels <50 μm were correctly identified by micro CT. Micro CT of the murine COW using a high‐throughput image processing model is feasible. Angioarchitectural distortion due to volume averaging and thresholding effect can occur and pathological findings should be confirmed. Synapse 62:557–565, 2008. © 2008 Wiley‐Liss, Inc.
Sparsity-based image reconstruction techniques for ISAR imaging

We present novel techniques for ISAR imaging via a Sparsity-based image reconstruction methodology. The latter offer a distinct advantage of Fourier based reconstruction techniques by offering the flexibility of using different basis functions to represent the underlying scene structure being imaged. We derive our ISAR algorithm in detail and present experimental results on real ISAR data showing its superiority over traditional Fourier based image reconstruction. We also demonstrate how our formulation of the ISAR imaging problem overcomes some of limitations associated previous approaches to CS (Compressive Sensing) based ISAR imaging in the literature.
Impact of Prior Seasonal H3N2 Influenza Vaccination or Infection on Protection and Transmission of Emerging Variants of Influenza A(H3N2)v Virus in Ferrets

ABSTRACT Influenza H3N2 A viruses continue to circulate in swine and occasionally infect humans, resulting in outbreaks of variant influenza H3N2 [A(H3N2)v] virus. It has been previously demonstrated in ferrets that A(H3N2)v viruses transmit as efficiently as seasonal influenza viruses, raising concern over the pandemic potential of these viruses. However, A(H3N2)v viruses have not acquired the ability to transmit efficiently among humans, which may be due in part to existing cross-reactive immunity to A(H3N2)v viruses. Although current seasonal H3N2 and A(H3N2)v viruses are antigenically distinct from one another, historical H3N2 viruses have some antigenic similarity to A(H3N2)v viruses and previous exposure to these viruses may provide a measure of immune protection sufficient to dampen A(H3N2)v virus transmission. Here, we evaluated whether prior seasonal H3N2 influenza virus vaccination or infection affects virus replication and transmission of A(H3N2)v virus in the ferret animal model. We found that the seasonal trivalent inactivated influenza virus vaccine (TIV) or a monovalent vaccine prepared from an antigenically related 1992 seasonal influenza H3N2 (A/Beijing/32/1992) virus failed to substantially reduce A(H3N2)v (A/Indiana/08/2011) virus shedding and subsequent transmission to naive hosts. Conversely, ferrets primed by seasonal H3N2 virus infection displayed reduced A(H3N2)v virus shedding following challenge, which blunted transmission to naive ferrets. A higher level of specific IgG and IgA antibody titers detected among infected versus vaccinated ferrets was associated with the degree of protection offered by seasonal H3N2 virus infection. The data demonstrate in ferrets that the efficiency of A(H3N2)v transmission is disrupted by preexisting immunity induced by seasonal H3N2 virus infection.
Influence of Fly Ash Content on Compaction Characteristics of Fly Ash Clay Mixture

In the present paper, a series of compaction tests have been performed to investigate the effect of fly ash content on compaction characteristics of fly ash clay mixture. Three types of fly ash and three types of clay have been used in this investigation. From the test results, it is observed that with the increase in fly ash content (0 to 25%) in the fly ash clay mixture, the value of maximum dry density decreases irrespective of type of soil, type of fly ash and type of compaction method. Fly ash content also influences significantly the optimum moisture content of fly ash clay mixture. Based on the present experimental data, a number of linear regression models have been developed to estimate the values of optimum moisture content and maximum dry density of fly ash clay mixture.
Optimization of organic nutrients for ginseng hairy roots production in large-scale bioreactors

Macro and micro-elements, carbon sources and elicitors play a central role during Panax ginseng hairy root growth, biomass and ginsenoside production and also influence numerous root developmental stages in large scale bioreactor culture. Due to the lack of biosynthetic nutrients and signalling-inducing nutrients, the regulatory role of mineral elements is not well understood. We have genetically engineered Agrobacterium rhizogenes KCTC 2703 to have the rol C gene in T -DNA of ginseng calluses that produce hairy roots. A normal MS medium nutrient in the bioreactor gave low hairy roots growth, biomass and ginsenoside content, indicating that an optimal mineral element ratio is required to increase hairy root growth and biomass. In addition, elicitors also play an important role in increas ing ginsenoside production. These results suggest that mineral elements are an important regulatory factor in hairy root growth and biomass, while elicitors decrease biomass and increase ginsenoside content.
Organization of cGMP sensing structures on the rod photoreceptor outer segment plasma membrane

A diffusion barrier segregates the plasma membrane of the rod photoreceptor outer segment into 2 domains; one which is optimized for the conductance of ions in the phototransduction cascade and another for disk membrane synthesis. We propose the former to be named “phototransductive plasma membrane domain," and the latter to be named “disk morphogenic plasma membrane domain. " Within the phototransductive plasma membrane, cGMP-gated channels are concentrated in striated membrane features, which are proximally located to the sites of active cGMP production within the disk membranes. For proper localization of cGMP-gated channel to the phototransductive plasma membrane, the glutamic acid-rich protein domain encoded in the β subunit plays a critical role. Quantitative study suggests that the disk morphogenic domain likely plays an important role in enriching rhodopsin prior to its sequestration into closed disk membranes. Thus, this and our previous studies provide new insight into the mechanism that spatially organizes the vertebrate phototransduction cascade.
Peroxiredoxin 1 and its role in cell signaling

Peroxiredoxins (Prdxs) are a family of small (22-27kDa) non-seleno peroxidases currently known to possess six mammalian isoforms. Although their individual roles in cellular redox regulation and antioxidant protection are quite distinct, they all catalyze peroxide reduction of H2O2, organic hydroperoxides and peroxynitrite. They are found to be expressed ubiquitously and in high levels, suggesting that they are both an ancient and important enzyme family. Prdxs can be divided into three major subclasses: typical 2-cysteine (2-Cys) Prdxs (Prdx1-4), atypical 2-Cys Prdx (Prdx 5) and 1-Cys Prdx (Prdx 6). Recent evidence suggests that 2-Cys peroxiredoxins are more than “just simple peroxidases”. This hypothesis has been discussed elegantly in recent review articles, considering “over”-oxidation of the protonated thiolate peroxidatic cysteine and post-translational modification of Prdxs as processes initiating a mechanistic switch from peroxidase to chaperon function. The process of over-oxidation of the peroxidatic cysteine (CP) occurs during catalysis in the presence of thioredoxin (Trx), thus rendering the sulfenic moiety to sulfinic acid , which can be reduced by sulfiredoxin (Srx). However, further oxidation to sulfonic acid is believed to promote Prdx degradation or, as recently shown, the formation of oligomeric peroxidase-inactive chaperones10 with questionable H2O2-scavenging capacity. In the light of this and given that Prdx1 has recently been shown by us and by others to interact directly with signaling molecules, we will explore the possibility that H2O2 regulates signaling in the cell in a temporal and spatial fashion via oxidizing Prdx1. Therefore, this review will focus on H2O2 modulating cell signaling via Prdxs by discussing: a) the activity of Prdxs towards H2O2; b) sub cellular localization and availability of other peroxidases, such as catalase or glutathione peroxidases; c) the availability of Prdxs reducing systems such as thioredoxin and sulfiredoxin and lastly, d) Prdx1 interacting signaling molecules.
Design and characterization of curvature sensors based on plastic optical fibers for structural monitoring

Sensors able to measure curvature changes are emerging as an effective alternative to the more common strain gauges in structural health monitoring. Particularly interesting is the optical fiber implementation of such sensors and this paper discusses the design and characterization of a simple, cheap, and compact curvature sensor based on plastic optical fibers. A characterization setup is also proposed in order to test the sensor performances with dynamic deformations.
Discovering Novel Interactions at the Nuclear Pore Complex Using Bead Halo

A highly sensitive, equilibrium-based binding assay termed “Bead Halo” was used here to identify and characterize interactions involving components of the nucleocytoplasmic transport machinery in eukaryotes. Bead Halo uncovered novel interactions between the importin Kap95 and the nucleoporins (nups) Nic96, Pom34, Gle1, Ndc1, Nup84, and Seh1, which likely occur during nuclear pore complex biogenesis. Bead Halo was also used to characterize the molecular determinants for binding between Kap95 and the family of nups that feature multiple phenylalanine-glycine motifs (FG nups). Binding was sensitive to the number of FG motifs present and to amino acid (AA) residues immediately flanking the FG motifs. Also, binding was reduced but not abolished when phenylalanine residues in all FG motifs were replaced by tyrosine or tryptophan. These results suggest flexibility in the binding pockets of Kap95 and synergism in binding FG motifs. The hypothesis that Nup53 and Nup59 bind directly to membranes through a C-terminal amphipathic alpha helix and to DNA via an RNA recognition motif domain was also tested and validated using Bead Halo. The results support a role for these nups in nuclear pore membrane biogenesis and in gene expression. Finally, Bead Halo detected binding of the nups Gle1, Nup60, and Nsp1 to phospholipid bilayers. This may reflect the known interaction between Gle1 and phosphoinositides and suggests similar interactions for Nup60 and Nsp1. As the Bead Halo assay detected molecular interactions in cell lysates, as well as between purified components, it can be adapted for large-scale proteomic studies using automated robotics and microscopy.
A study of vector transform coding of subband-decomposed images

Studies vector transform coding (VTC), a new image coding scheme, on subband-decomposed images. It is shown that vector transformation (VT) reduces the inter-vector correlation, although not as much as the discrete cosine transform (DCT). However, it is also shown that VT preserves the intra-vector correlation much better than the DCT so that vector quantization (VQ) in the VT domain can be made more efficient. VTC of subband-decomposed images introduces another dimension of adaptivity, in which coding parameters, bit allocation, and VQ codebooks can be adapted to each level of the subband pyramid as well as to each vector in the VT domain. The new subband/VTC scheme is compared with VQ of original images, VQ of subband-decomposed images, DCT-based transform coding, and subband/DCT/VQ schemes. Simulation results indicate that the new scheme achieves 1 to 3dB improvement over the other schemes in terms of peak signal-to-noise ratio. This improvement is also supported by subjective evaluations. >
Automatic phase-shift method for islanding detection of grid-connected photovoltaic inverters

The traditional frequency-shift methods for islanding detection of grid connected PV inverters (the active frequency-drift method and the slip mode frequency-shift method) become ineffective under certain paralleled RLC loads. The automatic phase-shift method is proposed in this paper to alleviate this problem. The method is based on the phase shift of the sinusoidal inverter output current. When the utility malfunctions, the phase-shift algorithm keeps the frequency of the inverter terminal voltage deviating until the protection circuit is triggered. Simulation and experiments are performed for verification.
Shape-based Trajectory Clustering

Automatic trajectory classification has countless applications, ranging from the natural sciences, such as zoology and meteorology, to urban planning and sports analysis, and has generated great interest and investigation. The purpose of this work is to propose and test new methods for trajectory clustering, based on shape, rather than spatial position, as is the case with previous methods. The proposed approach starts by uniformly resampling the trajectories using splines, and then characterizes them using the angles of the tangents at the resampled points. Angular data introduces some challenges for analysis, due to its periodic nature, therefore preventing the direct application of common clustering techniques. To overcome this problem, three methods are proposed/adapted: a variant of the k-means algorithm, a mixture model using multivariate Von Mises distributions, which is fitted using the EM algorithm, and sparse nonnegative matrix factorization. Since the number of clusters is seldom known a priori, methods for automatic model selection are also introduced. Finally, these techniques are tested on both real and synthetic data, and the viability of this approach is demonstrated.
O abandono de ensino de geometria : uma visão historica

A analise historica do que aconteceu, no Brasil e no mundo, com o ensino em geral torna evidente que a luta pelo conhecimento pode ser vista corno urna luta pelo poder. As decisoes relativas ao ensino nao podem, pois, serem vistas corno desvinculadas do contexto historico, polItico e social. o ensino de certas disciplinas, importantes para a formacao dos individuos, foi negligenciado, e nao por acaso. Este trabalho mostra corno este fato se deu com re lacao ao ensino da geometria. Abstract
Determinants of Full Child Immunization; Evidence from Ethiopia

Background: Immunization is one of the main health interventions to prevent childhood morbidity and mortality. The health of under 5 children has been a major problem in developing countries like Ethiopia. Immunization will become more effective if the child receive the full course of recommended immunization doses. Objective: The main objective of this study is to statistically identify and analyze the various possible determinants of full immunization among children in rural and urban households of SNNPRS, Ethiopia. Design: The sampling technique employed was multistage stratified cluster sampling. Results: Analysis of the study revealed that only 18.3% of children under 5 years of age are fully immunized in the region. Results of the multiple binary logistic regression show that place of residence, age of the child, educational status of mothers, access to media and place of child delivery are the most important determinant factors affecting full child immunization (p-value<5%) in the region. It is observed that children living in rural parts of the region whose community is usually facing shortage of basic services like education, access to media and health services are at higher risk of complete immunization. Conclusion: Primary health care and education programs which would fit the features of the region should be designed and implemented to safeguard children from immunization deficiency.