gebhart/patrepeval huggingface dataset:
Deletion of the cyclic <scp>di‐AMP</scp> phosphodiesterase gene (<scp><i>cnpB</i></scp>) in <scp><i>M</i></scp><i>ycobacterium tuberculosis</i> leads to reduced virulence in a mouse model of infection (2014)

Summary Tuberculosis ( TB ) remains a major cause of morbidity and mortality worldwide. The pathogenesis by the causative agent, M ycobacterium tuberculosis , is still not fully understood. We have previously reported that M . tuberculosis Rv 3586 ( disA ) encodes a diadenylate cyclase, which converts ATP to cyclic di‐AMP ( c‐di‐AMP ). In this study, we demonstrated that a protein encoded by Rv 2837c ( cnpB ) possesses c‐di‐AMP phosphodiesterase activity and cleaves c‐di‐AMP exclusively to AMP . Our results showed that in M . tuberculosis , deletion of disA abolished bacterial c‐di‐AMP production, whereas deletion of cnpB significantly enhanced the bacterial c‐di‐AMP accumulation and secretion. The c‐di‐AMP levels in both mutants could be corrected by expressing the respective gene. We also found that macrophages infected with Δ cnpB secreted much higher levels of IFN ‐β than those infected with the wild type ( WT ) or the complemented mutant. Interestingly, mice infected with M . tuberculosis Δ cnpB displayed significantly reduced inflammation, less bacterial burden in the lungs and spleens, and extended survival compared with those infected with the WT or the complemented mutant. These results indicate that deletion of cnpB results in attenuated virulence, which is correlated with elevated c‐di‐AMP levels.
Agentenbasierte Computersimulationen als Schlüssel zur demographischen Struktur des bandkeramischen Massengrabs von Talheim (2018)

[nicht vorhanden / not available]
Determination of reaction variables for the starch xanthide encapsulation of pesticides (1983)

Abstract Optimization of reaction variables such as xanthation and oxidation conditions was determined for the encapsulation of EPTC ( S ‐ethyl dipropylthiocarbamate) and butylate ( S ‐ethyl diisobutylthiocarbamate) in a crosslinked starch xanthide matrix. Sonification of EPTC and butylate emulsifiable concentrates before encapsulation decreased the size of the cells within the matrix and increased pesticide retention. Pesticide release from the matrix as determined using a constant temperature‐humidity chamber showed that low‐xanthation and sonified encapsulated products gave the slowest pesticide release.
Chemically Modified Oligonucleotides: Synthesis, Physicochemical and Biochemical Properties of their Duplexes with DNA and RNA (2004)

This thesis is based on 9 papers dealing with the synthesis, physicochemical and biochemical properties of two types of chemically modified oligonucleotides which have the potential to down-regulate gene expression: (i) The first set is comprised of antisense oligonucleotides (AONs) conjugated with different chromophores of varying size, charge and π-electron density. Conjugation of the chromophores at the 3'- or 5'-end enhanced the target RNA binding affinity and RNase H recruitment capabilities compared to the native counterpart without changing the global helical conformation of their AON/RNA hybrid duplexes. The 3'-dipyridophenazine (DPPZ) has emerged as the most promising non-toxic chromophore in this series. (ii) The second set encompasses a new class of AONs containing North-East conformationally constrained 1',2'-oxetane-nucleosides. The introduction of oxetane-<b>T</b> and -<b>C</b> units imparts lowering of the Tm by ~ 6º and ~ 3 ºC/modification, respectively, of the AON/RNA hybrids, whereas the incorporation of the corresponding oxetane-<b>A</b> and-<b>G</b> units into AONs did not alter the thermostability in comparison with that of the native hybrid duplex. The oxetane-modified AONs have been found to possess enhanced serum stability compared to that of the native, whereas oxetane-<b>T</b> and -<b>C</b> containing AONs were more endonuclease-resistant than oxetane-<b>A</b> and-<b>G</b> modified AONs. All oxetane-modified mixmer AON/ RNA hybrid duplexes were, however, found to be excellent substrates for RNase H cleavage, which has been analyzed by Michaelis-Menten kinetics. The oxetane-modified mixmer AONs have shown effective down-regulation of the proto-oncogene c-myb mRNA in the K562 human leukemia cells, which was analyzed by QRT-PCR and Western Blot. Based on the amount of AON uptake after delivery, determined by slot blot, it was apparent that the oxetane-modified AONs are 5-6 times more effective antisense agents than the corresponding isosequential phosphorothioate analogues. The electrochemical assay based on sensitive nucleic acid mediated charge transport (CT) has revealed that the presence of oxetane-<b>T</b> unit causes more stacking perturbations in a DNA/DNA duplex than in a DNA/RNA duplex.
Probing the pharmacology of G protein-coupled receptors with fluorescent ligands (2015)

G protein-coupled receptors control a wide range of physiological processes and are the target for many clinically used drugs. Understanding the way in which receptors bind agonists and antagonists, their organisation in the membrane and their regulation after agonist binding are important properties which are key to developing new drugs. One way to achieve this knowledge is through the use of fluorescent ligands, which have been used to study the expression and function of receptors in endogenously expressing systems. Fluorescent ligands with appropriate imaging properties can be used in conjunction with confocal microscopy to investigate the regulation of receptors after activation. Alternatively, through the use of single molecule microscopy, they can probe the spatial organisation of receptors within the membrane. This review focuses on the techniques in which fluorescent ligands have been used and the novel aspects of G protein-coupled receptor pharmacology which have been uncovered. This article is part of the Special Issue entitled 'Fluorescent Tools in Neuropharmacology'.
Choice of costimulatory domains and of cytokines determines CAR T-cell activity in neuroblastoma (2018)

Chimeric antigen receptor (CAR) T-cell therapy has been shown to be dramatically effective in the treatment of B-cell malignancies. However, there are still substantial obstacles to overcome, before similar responses can be achieved in patients with solid tumors. We evaluated both <i>in vitro</i> and in a preclinical murine model the efficacy of different 2nd and 3rd generation CAR constructs targeting GD2, a disial-ganglioside expressed on the surface of neuroblastoma (NB) tumor cells. In order to address potential safety concerns regarding clinical application, an inducible safety switch, namely inducible Caspase-9 (iC9), was also included in the vector constructs. Our data indicate that a 3rd generation CAR incorporating CD28.4-1BB costimulatory domains is associated with improved anti-tumor efficacy as compared with a CAR incorporating the combination of CD28.OX40 domains. We demonstrate that the choice of 4-1BB signaling results into significant amelioration of several CAR T-cell characteristics, including: 1) T-cell exhaustion, 2) basal T-cell activation, 3) <i>in vivo</i> tumor control and 4) T-cell persistence. The fine-tuning of T-cell culture conditions obtained using IL7 and IL15 was found to be synergic with the CAR.GD2 design in increasing the anti-tumor activity of CAR T cells. We also demonstrate that activation of the suicide gene iC9, included in our construct without significantly impairing neither CAR expression nor anti-tumor activity, leads to a prompt induction of apoptosis of GD2.CAR T cells. Altogether, these findings are instrumental in optimizing the function of CAR T-cell products to be employed in the treatment of children with NB.
“Wormhole” Geometry for Entrapping Topologically Protected Qubits in Non-Abelian Quantum Hall States and Probing Them with Voltage and Noise Measurements (2006)

We study a tunneling geometry defined by a single point-contact constriction that brings to close vicinity two points sitting at the same edge of a quantum Hall liquid, shortening the trip between the otherwise spatially separated points along the normal chiral edge path. This wormhole-like geometry allows for entrapping bulk quasiparticles between the edge path and the tunnel junction, possibly realizing a topologically protected qubit if the quasiparticles have non-Abelian statistics. We show how either noise or simpler voltage measurements along the edge can probe the non-Abelian nature of the trapped quasiparticles.
Robust Delay Control for Audio Streaming over Wireless Link (2006)

The audio delay is becoming an important factor in audio streaming over short-range wireless network. In this study, we propose an efficient two-level delay control method, called frame sequence adaptation and audio sampling frequency compensation, for achieving stable audio delay with a small variation. To prove the effectiveness of our scheme, we implemented and evaluated the scheme on a Bluetooth network. Experimental results show that our scheme can control audio delay robustly and remove phase shift problem in multi-channel stereophonic audio broadcasting as well.
The Construction of a Remote Game Control System By the Power Line Communication (2007)

In this paper, a game control system was constructed, in which a game was controlled by a remote joystick connected with a power line by the power line communication (PLC) method. The structure of the system was that the connection line between the remote joystick and a PC, and the PC and an audio play device was the home power line. And, the communication data rate between them was 2400 bps. The Polling communication technique was used for the PC to read the joystick's control commands, and to send some acoustic informations to the receiver PLC device. A game was programmed, in which an aircraft was moved according to the joystick's left, right, up, and, down direction, and was shooting its missile after the joystick's shooting button was pushed. The communication delay of about 100 msec between them didn't cause any big problem in playing the game.
The effect of clicking by smiling on the accuracy of head-mounted gaze tracking (2012)

The effect of facial behaviour on gaze tracking accuracy was studied while using a prototype system that integrated head-mounted, video-based gaze tracking and a capacitive facial movement detection for respective pointing and selecting objects in a simple graphical user interface. Experiments were carried out to determine how voluntary smiling movements that were used to indicate clicks affect the accuracy of gaze tracking due to the combination of user eye movement behaviour and the operation of gaze tracking algorithms. The results showed no observable degradation of the gaze tracking accuracy when using voluntary smiling for object selections.
3640 Unique EST Clusters from the Medaka Testis and Their Potential Use for Identifying Conserved Testicular Gene Expression in Fish and Mammals (2008)

Medaka exhibits a considerable similarity in testicular gene expression to mammals. The medaka testicular EST collection we obtained has wide range coverage and will not only consolidate our knowledge on the comparative analysis of known genes' functions in the testis but also provide a rich resource to dissect molecular events and mechanism of spermatogenesis in vivo and in vitro in medaka as an excellent vertebrate model.
Microwave heating (1991)

The principles of microwave heating as applied to industrial processing are outlined and the basic design of applicators for material processing is described. Industrial applications range from food tempering to rubber vulcanisation and from vacuum drying to sintering of ceramics. The most promising applications to date are summarised
The gene amyE(TV1) codes for a nonglucogenic alpha-amylase from Thermoactinomyces vulgaris 94-2A in Bacillus subtilis (1994)

We isolated the gene amyE(TV1) from Thermoactinomyces vulgaris 94-2A encoding a nonglucogenic alpha-amylase (AmyTV1). A chromosomal DNA fragment of 2,247 bp contained an open reading frame of 483 codons, which was expressed in Escherichia coli and Bacillus subtilis. The deduced amino acid sequence of the AmyTV1 protein was confirmed by sequencing of several peptides derived from the enzyme isolated from a T. vulgaris 94-2A culture. The amino acid sequence was aligned with several known alpha-amylase sequences. We found 83% homology with the 48-kDa alpha-amylase part of the Bacillus polymyxa beta-alpha-amylase polyprotein and 50% homology with Taka amylase A of Aspergillus oryzae but only 45% homology with another T. vulgaris amylase (neopullulanase, TVA II) recently cloned from strain R-47. The putative promoter region was characterized with primer extension and deletion experiments and by expression studies with B. subtilis. Multiple promoter sites (P3, P2, and P1) were found; P1 alone drives about 1/10 of the AmyTV1 expression directed by the native tandem configuration P3P2P1. The expression levels in B. subtilis could be enhanced by fusion of the amyE(TV1) coding region to the promoter of the Bacillus amyloliquefaciens alpha-amylase gene.
Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration (2006)

Cancer cell motility and invasion are critical targets for anticancer therapeutics. Whereas in vitro models could be designed for rapid screening with a view to investigate these targets, careful consideration must be given to the construction of appropriate model systems. Most investigations focus on two-dimensional (2-D) assays despite the fact that increasing evidence suggests that migration across rigid and planar substrates fails to recapitulate in vivo behavior. In contrast, few systems enable three-dimensional (3-D) cell migration to be quantitatively analyzed. We previously developed a digital holographic microscope (DHM) working in transmission with a partially spatial coherence source. This configuration avoids the noise artifacts of laser illumination and makes possible the direct recording of information on the 3-D structure of samples consisting of multiple objects embedded in scattering media, such as cell cultures in matrix gels. The software driving our DHM system is equipped with a time-lapse ability that enables the 3-D trajectories of living cells to be reconstituted and quantitatively analyzed.
Scalability analysis and parallel execution of unstructured problems. (1996)

this paper we present a generic approach TGEX for analyzing and executing unstructured problems. It separates the specification of a computational problem from the control of the parallel execution. A computational problem is first partitioned in terms of a computation task graph which serves as a machine-independent representation of the parallel program. This allows fast and accurate performance simulation with the Pamela tool and efficient parallel execution. Experimental results of using Pamela and TGEX for scalability analysis and parallel execution of unstructured problems are reported.
Rapid and enzyme-free nucleic acid detection based on exponential hairpin assembly in complex biological fluids (2016)

Herein, we have developed a rapid and enzyme-free nucleic acid amplification detection method that combined the exponential self-assembly of four DNA hairpins and the FRET pair Cy3 and Cy5. This strategy was very ingenious and rapid, and could detect nucleic acids at concentrations as low as 10 pM in 15 min in biological fluids.
Flow Mapping and Multivariate Visualization of Large Spatial Interaction Data (2009)

Spatial interactions (or flows), such as population migration and disease spread, naturally form a weighted location-to-location network (graph). Such geographically embedded networks (graphs) are usually very large. For example, the county-to-county migration data in the U.S. has thousands of counties and about a million migration paths. Moreover, many variables are associated with each flow, such as the number of migrants for different age groups, income levels, and occupations. It is a challenging task to visualize such data and discover network structures, multivariate relations, and their geographic patterns simultaneously. This paper addresses these challenges by developing an integrated interactive visualization framework that consists three coupled components: (1) a spatially constrained graph partitioning method that can construct a hierarchy of geographical regions (communities), where there are more flows or connections within regions than across regions; (2) a multivariate clustering and visualization method to detect and present multivariate patterns in the aggregated region-to-region flows; and (3) a highly interactive flow mapping component to map both flow and multivariate patterns in the geographic space, at different hierarchical levels. The proposed approach can process relatively large data sets and effectively discover and visualize major flow structures and multivariate relations at the same time. User interactions are supported to facilitate the understanding of both an overview and detailed patterns.
Template synthesis of cyanine dye H-aggregates on nanostructured [6,6]-phenyl C61-butyric acid methyl ester substrates (2011)

A novel and general method for the synthesis of H-aggregates is presented. H-aggregates can be precipitated from solutions of cyanine dyes in nanostructured [6,6]-phenyl C(61)-butyric acid methyl ester (PCBM) template films. H-aggregates synthesized that way have a narrow line shape width comparable to the smallest H-bands reported for thin films so far. We demonstrate that H-aggregates can be induced in different cyanine dyes (trimethine-, pentamethine- and heptamethine dyes). Aggregation follows a universal pathway, the concentration dependence of aggregation for different dyes can be scaled to fall onto one master curve. According to our model, H-aggregates have the form of 3D-crystals that form within cavities of the template. The template substrate is fabricated by means of a phase separation process of PCBM with a specific cyanine dye and consecutive selective dissolution of the dye. The dimensions of the template cavities have a major influence on aggregation.
Boron Binding by a Siderophore Isolated from Marine Bacteria Associated with the Toxic Dinoflagellate <i>Gymnodinium </i><i>catenatum</i> (2007)

The known siderophore vibrioferrin has been isolated from species of Marinobacter required for the growth of the toxic, bloom forming dinoflagellate Gymnodinium catenatum. A number of unique attributes of this siderophore, including its ability to bind boron, may provide important clues as to the nature of this and related algal-bacterial relationships.
Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers (2012)

Population genetic studies provide insights into the evolutionary processes that influence the distribution of sequence variants within and among wild populations. F(ST) is among the most widely used measures for genetic differentiation and plays a central role in ecological and evolutionary genetic studies. It is commonly thought that large sample sizes are required in order to precisely infer F(ST) and that small sample sizes lead to overestimation of genetic differentiation. Until recently, studies in ecological model organisms incorporated a limited number of genetic markers, but since the emergence of next generation sequencing, the panel size of genetic markers available even in non-reference organisms has rapidly increased. In this study we examine whether a large number of genetic markers can substitute for small sample sizes when estimating F(ST). We tested the behavior of three different estimators that infer F(ST) and that are commonly used in population genetic studies. By simulating populations, we assessed the effects of sample size and the number of markers on the various estimates of genetic differentiation. Furthermore, we tested the effect of ascertainment bias on these estimates. We show that the population sample size can be significantly reduced (as small as n = 4-6) when using an appropriate estimator and a large number of bi-allelic genetic markers (k>1,000). Therefore, conservation genetic studies can now obtain almost the same statistical power as studies performed on model organisms using markers developed with next-generation sequencing.
Build your working knowledge of process compressors (1993)

The role of compressors in the chemical process industries (CPI) is critical since they are used to circulate gas through a process, enhance conditions for chemical reactions, provide inert gas for safety or control systems, recover and recompress process gas, and maintain correct pressure levels by either adding and removing gas or vapors from a process system. The chemical engineer involved with process design and equipment selection must have a working knowledge of compressors, since they are the most mechanically complex machinery used in the CPI. This working knowledge must now only be related to the thermodynamics of the gas being compressed, but also to the type of compressor to be used for a particular process. The latter has become more important as the result of the passage of the Clean Air Act Amendments of 1990, legislation which places limitations on emissions from process equipment. Fugitive emissions from such sources as compressors, pumps, valves, and piping systems and connections must be reduced over the coming years in order to comply with EPA Equipment Leak Regulations. This article well primarily deal with reciprocating, positive displacement compressors with emphasis placed on applications and machines having installed power of 200 kW or less.more » However, some comments with respect to larger compressors will be made due to their importance in process applications. Typical applications of the unit is in oil refinery processes.« less
Situation Assessment of an Autonomous Emergency Brake for Arbitrary Vehicle-to-Vehicle Collision Scenarios (2009)

The autonomous emergency brake (AEB) is an active safety function for vehicles which aims to reduce the severity of a collision. An AEB performs a full brake when an accident becomes unavoidable. Even if this system cannot, in general, avoid the accident, it reduces the energy of the crash impact and is therefore referred to as a collision mitigation system. A new approach for the calculation of the trigger time of an emergency brake will be presented. The algorithm simultaneously considers all physically possible trajectories of the object and host vehicle. It can be applied to all different scenarios including rear-end collisions, collisions at intersections, and collisions with oncoming vehicles. Thus, 63% of possible accidents are addressed. The approach accounts for the object and host vehicles' dimensions. Unlike previous work, the orientation of the vehicles is incorporated into the collision estimation.