Miracle-dz/UniFAR-FTUs huggingface dataset:
Addressing Fluorogenic Real-time Qpcr Inhibition Using the Novel Custom Excel File System 'focusfield2-6gallupqpcrset-uptool-001' to Attain Consistently High Fidelity Qpcr Reactions

The purpose of this manuscript is to discuss fluorogenic real-time quantitative polymerase chain reaction (qPCR) inhibition and to introduce/define a novel Microsoft Excel-based file system which provides a way to detect and avoid inhibition, and enables investigators to consistently design dynamically-sound, truly LOG-linear qPCR reactions very quickly. The qPCR problems this invention solves are universal to all qPCR reactions, and it performs all necessary qPCR setup calculations in about 52 seconds (using a pentium 4 processor) for up to seven qPCR targets and seventy-two samples at a time – calculations that commonly take capable investigators days to finish. We have named this custom Excel-based file system " FocusField2-6GallupqPCRSet-upTool-001 " (FF2-6-001 qPCR setup tool), and are in the process of transforming it into professional qPCR setup software to be made available in 2007. The current prototype is already fully functional. PREFACE Bearing in mind that it is not possible to state with absolute certainty the exact causes of qPCR inhibitory phenomena, and since more than one kind of inhibition may be present at the same time, we begin this communication by creating a list of the top five most likely sources of such inhibition – two of which (inhibition Types 2 and 3) are inherently a function of one another. We propose that all five affect either the activity of reverse transcriptase enzymes, Taq DNA polymerases, or both. In order to avoid using sample RNA (or cDNA) at dilutions permissive of or conducive to real-time qPCR inhibitory phenomena (regardless of the type of inhibition), we have created the FF2-6-001 qPCR setup tool which is used to analyze preliminary qPCR Test Plate data generated by up to seven qPCR targets from serial progressive dilutions of representative (Stock I) RNA or cDNA mixtures all used in fluorogenic hydrolysis probe-based qPCR. Once Test Plate threshold cycle (CT) values are obtained for each target on any given Test Plate, they are entered into the TestPlateResultsAnalysis2006.xls portions of the FF2-6-001 qPCR setup tool which the user interacts with in order to quickly and precisely identify the useful RNA dilution ranges for each qPCR target – within these ranges which each target can be expected to amplify without inhibition, with LOG-linearity and with high efficiency. The FF2-6-001 qPCR setup tool then applies these ranges to final qPCR reaction designs allowing the investigator to formulate high-fidelity qPCR reactions every time since the FF2-6-001 file system ensures that each …
Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing

DNA methyltransferases (MTases), which catalyze the methylation of adenine and cytosine bases in DNA, can occur in bacteria and archaea alongside cognate restriction endonucleases (REases) in restriction-modification (RM) systems or independently as orphan MTases. Although DNA methylation and MTases have been well-characterized in bacteria, research into archaeal MTases has been limited. A previous study examined the genomic DNA methylation patterns (methylome) of the halophilic archaeon Haloferax volcanii, a model archaeal system which can be easily manipulated in laboratory settings, via single-molecule real-time (SMRT) sequencing and deletion of a putative MTase gene (HVO_A0006). In this follow-up study, we deleted other putative MTase genes in H. volcanii and sequenced the methylomes of the resulting deletion mutants via SMRT sequencing to characterize the genes responsible for DNA methylation. The results indicate that deletion of putative RM genes HVO_0794, HVO_A0006, and HVO_A0237 in a single strain abolished methylation of the sole cytosine motif in the genome (Cm4TAG). Amino acid alignments demonstrated that HVO_0794 shares homology with characterized cytosine CTAG MTases in other organisms, indicating that this MTase is responsible for Cm4TAG methylation in H. volcanii. The CTAG motif has high density at only one of the origins of replication, and there is no relative increase in CTAG motif frequency in the genome of H. volcanii, indicating that CTAG methylation might not have effectively taken over the role of regulating DNA replication and mismatch repair in the organism as previously predicted. Deletion of the putative Type I RM operon rmeRMS (HVO_2269-2271) resulted in abolished methylation of the adenine motif in the genome (GCAm6BN6VTGC). Alignments of the MTase (HVO_2270) and site specificity subunit (HVO_2271) demonstrate homology with other characterized Type I MTases and site specificity subunits, indicating that the rmeRMS operon is responsible for adenine methylation in H. volcanii. Together with HVO_0794, these genes appear to be responsible for all detected methylation in H. volcanii, even though other putative MTases (HVO_C0040, HVO_A0079) share homology with characterized MTases in other organisms. We also report the construction of a multi-RM deletion mutant (ΔRM), with multiple RM genes deleted and with no methylation detected via SMRT sequencing, which we anticipate will be useful for future studies on DNA methylation in H. volcanii.
FlowPut

Tangible interaction has shown to be beneficial in a wide variety of scenarios since it provides more direct manipulation and haptic feedback. Further, inherently three-dimensional information is represented more naturally by a 3D object than by a flat picture on a screen. Yet, today's tangibles have often pre-defined form factors and limited input and output facilities. To overcome this issue, the combination of projection and depth cameras is used as a fast and flexible way of non-intrusively adding input and output to tangibles. However, tangibles are often quite small and hence the space for output and interaction on their surface is limited. Therefore, we propose FlowPut: an environment-aware framework that utilizes the space available on and around a tangible object for projected visual output. By means of an optimization-based layout approach, FlowPut considers the environment of the objects to avoid interference between projection and real-world objects. Moreover, we contribute an occlusion resilient object recognition and tracking for tangible objects based on their 3D model and a point-cloud based multi-touch detection, that allows sensing touches also on the side of a tangible. Flowput is validated through a series of technical experiments, a user study, and two example applications.
Effect of bath components on the properties of nickel-coated diamond

The effect of bath components on the properties of Ni-coated diamond is investigated.The impact toughness is tested by impact toughness test apparatus,and the compressive strength of single grain is tested by diamond single particle compressive strength tester.Results show that NaCl is the main factor influencing the electrical conductivity of plating solution,while NiSO4has no effect on the electrical conductivity.The impact toughness of diamond increases with the increase of NaCl concentration when the concentration is among 5~30g/L,but when it is greater than 30g/L,the impact toughness decreases with the increase of NaCl concentration.The impact toughness increases with the increase of NiSO4concentration when the concentration is among 100~250g/L.The weight rate has a great effect on the compressive strength of diamond,while NaCl and NiSO4concentrations have no effect on the compressive strength.
Cytosolic Ascorbate Peroxidase 1 Is a Central Component of the Reactive Oxygen Gene Network of Arabidopsisw⃞

Reactive oxygen species (ROS), such as O2− and H2O2, play a key role in plant metabolism, cellular signaling, and defense. In leaf cells, the chloroplast is considered to be a focal point of ROS metabolism. It is a major producer of O2− and H2O2 during photosynthesis, and it contains a large array of ROS-scavenging mechanisms that have been extensively studied. By contrast, the function of the cytosolic ROS-scavenging mechanisms of leaf cells is largely unknown. In this study, we demonstrate that in the absence of the cytosolic H2O2-scavenging enzyme ascorbate peroxidase 1 (APX1), the entire chloroplastic H2O2-scavenging system of Arabidopsis thaliana collapses, H2O2 levels increase, and protein oxidation occurs. We further identify specific proteins oxidized in APX1-deficient plants and characterize the signaling events that ensue in knockout-Apx1 plants in response to a moderate level of light stress. Using a dominant-negative approach, we demonstrate that heat shock transcription factors play a central role in the early sensing of H2O2 stress in plants. Using knockout plants for the NADPH oxidase D protein (knockout-RbohD), we demonstrate that RbohD might be required for ROS signal amplification during light stress. Our study points to a key role for the cytosol in protecting the chloroplast during light stress and provides evidence for cross-compartment protection of thylakoid and stromal/mitochondrial APXs by cytosolic APX1.
Self-monitoring and self-management: new interventions to improve blood pressure control

Purpose of reviewThis article reviews recent developments in self-monitoring and self-management of hypertension aimed at the improvement of blood pressure (BP) control. Recent findingsThere is an increasing body of evidence examining the effects of self-monitoring on BP control. Several landmark studies in recent years have demonstrated clinically relevant benefit from self-monitoring based interventions. Self-management of BP with self-titration has shown particular promise, as has self-monitoring combined with intensive health-care led support. There is a lack of evidence on the benefits of self-monitoring for those with important comorbidity such as coronary heart disease, chronic kidney disease, diabetes and previous stroke, and future research should be directed towards this. SummaryThere is a growing body of evidence supporting the use of self-monitoring along with additional intervention including telemonitoring and self-titration in improving BP control. Further research is needed to understand which patients are likely to benefit most and how this is best integrated with routine care.
Testican‐1, as a novel diagnosis of sepsis

The development of new sepsis‐specific biomarkers is mandatory to improve the detection and monitoring of the disease. Testican‐1 is a highly conserved, multidomain proteoglycan that is most prominently expressed in the thalamus of the brain, and is upregulated in activated astroglial cells of the cerebrum. The aim of this study was to evaluate blood levels of Testican‐1 in septic patients. A prospective study of 82 patients with sepsis was conducted. Furthermore, C57BL/6 mice were administrated with lipopolysaccharide (LPS), high mobility group box 1 (HMGB1) protein or subjected to cecal ligation and puncture (CLP) surgery. Alternatively, human umbilical vein endothelial cells (HUVECs) or C57BL/6 mice were exposed to LPS (100 ng/mL) or HMGB1 (1 μg/mL). LPS, HMGB1, or CLP enhanced the synthesis and secretion of Testican‐1 in HUVECs and mice. In patients admitted to the intensive care unit (ICU) with sepsis, circulating levels of Testican‐1 were significantly high (sepsis, 20.44‐63.37 ng/mL, n = 30; severe sepsis, 41.30‐98.69 ng/mL, n = 22; septic shock, 98.10‐151.85 ng/mL, n = 30) when compared to the levels of control donors (6.97‐8.77 ng/mL, n = 21), reflecting the severity of the disease. These results suggest that in septic patients, Testican‐1 blood level is related to the severity of sepsis and Testican‐1 could be used as a biomarker to determine the severity of sepsis.
Systematic Generation of Algorithms for Iterative Methods

The FLAME methodology makes it possible to derive provably correct algorithms from a formal description of a linear algebra problem. So far, the methodology has been successfully used to automate the derivation of direct algorithms such as the Cholesky decomposition and the solution of Sylvester equations. In this thesis, we present an extension of the FLAME methodology to tackle iterative methods such as Conjugate Gradient. As a starting point, we use a formal description of the iterative method in matrix form. The result is a family of provably correct pseudocode algorithms. We argue that all the intermediate steps are sufficiently systematic to be fully automated.
Polypyridyl Metallo‐Organic Assemblies for Electrochromic Applications

Electrochromic films undergo optical changes in response to a redox stimulus. This intriguing phenomenon can be used for a wide range of applications, including smart windows, sensors, color displays, and memory elements. Despite the rapid progress of late, designing suitable electrochromic materials that offer low‐cost production, appealing colors, and pronounced optical contrast with high efficiency, as well as long‐term stability remains an engineering challenge. Solid‐state metal oxides, liquid crystals, and organic polymers have been for many years the leading candidates, successfully making their way into commercial products. An alternative class of materials relies on metal complexes that can be processed from solution, offer a variety of colors, and have metal‐centered stable and reversible redox chemistry. These metallo‐organic materials possess a full range of electrochromic properties, including ultrahigh coloration efficiencies, and cyclic stability. Here, some of the recent scientific developments in this field are highlighted.
Modeling and simulation of JetQuad aerial robot

The robotic industry, particularly the aerial robot corporations, is constantly developing. Nowadays, the application of aerial robots in cases such as package delivery and fast medical response markets is noticeable. JetQuad is a type of aerial robot, powered by four small jet engines. This is basically the Quadcopter whose four electric motors are replaced by four jet engines. Accordingly, modeling the complicated mechatronic system of the JetQuad to improve its performance is of significant importance. In this paper, modeling and simulation of the JetQuad motion using the bond graph approach are studied. The bond graph approach is an effective method for modeling mechatronic systems. On this account, modeling the JetQuad propulsion system (small jet engine) is carried out foremost. Then, the results of engine model simulation are compared to those of the experimental test. This comparison shows the acceptable accuracy of the simulation results. Next, the JetQuad body is modelled. Finally, by combining the models of the jet engine and body, the final model of JetQuad is obtained. Furthermore, the simulation of JetQuad model is carried out for two controlled and uncontrolled cases, followed by analyzing the results. The developed JetQuad model in this paper can be considered as the basis for the development of advanced control systems and diagnostic tools.
An improved no-search fractal image coding method

In order to improve the performance of no-search fractal coding further, a two order fitting surface is proposed to approximate the range blocks and domain blocks. In our research, a novel gray-level transform with a fitting surface is introduced. On one hand, the fitting surface we propose can approximate the range and domain blocks better than the previous fitting planes, this can lead to smaller collage errors between the range blocks and best matching domain blocks. On the other hand, since the introduced fitting surface can be also used for both the range blocks and domain blocks, many bits can be saved to improve the compression ratio. Moreover, the no-search and quadtree techniques are also adopted, so the proposed method can be completed in a short time. Experiments show that compared with the previous similar method, the proposed method can provide higher PSNR with the same Bpp, higher PSNR while maintaining the same encoding time.
A Novel Biomarker of Coronary Atherosclerosis: Serum DKK1 Concentration Correlates with Coronary Artery Calcification and Atherosclerotic Plaques

DKK1 modulates Wnt signaling, which is involved in the atherosclerosis. However, no data exist regarding the usefulness of measuring serum DKK1 concentration in predicting coronary atherosclerosis. A total of 270 consecutive patients (62.8 ± 11.2 yr; 70% male) were included. A contrast-enhanced 64-slice coronary MDCT was performed to identify the presence of atherosclerotic plaques. Agatston calcium scores (CS) were calculated to quantify the coronary artery calcification (CAC). DKK1 concentrations were measured by enzyme-linked immunosorbent assay. For each subsequent DKK1 quartile, there was a significant increase in CAC (P = 0.004) and the number of segments with coronary atherosclerosis (P < 0.001). In addition, DKK1 concentration was significantly higher in patients with atherosclerotic plaques, regardless of plaque composition (P = 0.01). Multivariate analysis identified DKK1 as an independent risk factor for the presence of coronary atherosclerotic plaque. The adjusted odds ratio for coronary atherosclerotic plaque was 4.88 (95% CI, 1.67 to 14.25) for highest versus lowest quartile of the DKK1 levels. Furthermore, patients with DKK1 concentrations ≥ 68.6 pg/mL demonstrated coronary atherosclerotic plaques even when they had low CS. Serum DKK1 concentrations correlate with the coronary atherosclerosis and play an independent role in predicting the presence of coronary atherosclerosis.
FRACTALS IN FAILURE OF CORRODED REINFORCED CONCRETE MEMBERS

It is verified that the surface cracks on the corroded reinforced concrete members take on the fractal behavior in the analysis of crack propagation using the experimental data. Fractal geometry is employed to investigate the cracking and failure process of the corroded reinforced concrete members. The relationships between the fractal dimension of surface cracks and the influence factors, which include compressive strength of corroded concrete, corrosion ratio of reinforcement and the ductility of the corroded member, are discussed respectively. As a result, the fractal dimension is proposed as an index to evaluate mechanical property of the corrosion degree of the corroded reinforced concrete members. A new approach is put forward to evaluate residual life of the corroded reinforced concrete members, which lays down a theoretical foundation for evaluation of bearing capacity of the corroded reinforced concrete structure.
An EMAT System for Detecting Flaws in Steam Generator Tubes

The detection of flaws in steam generator tubing is often made difficult by environmental considerations. The small diameter, 7/8 inch (2.2 cm), long, 70 feet (21.3m), tubes occur in large bundles with access only being possible from the inside of the end of each tube. Furthermore, inspection must be fully automatic when the steam generator is part of a nuclear power plant because of radiation exposure limits. Consequently, a couplant free probe which can be operated remotely at the end of an automatic probe puller is needed. This paper SUillllarizes the development of an EMAT systan for this application. The device uses periodic permanent magnet probes to excite the fundamental torsional mode traveling along the axis of the tube. Included is a discussion of data obtained during a recently completed feasibility study and a description of a prototype system presently under construction.
Phosphorylation of the exocyst protein Exo84 by TBK1 promotes insulin-stimulated GLUT4 trafficking

An inflammation-associated kinase also stimulates glucose uptake through plasma membrane translocation of GLUT4 in response to insulin. Kinase for both inflammatory and insulin responses After a meal, insulin released from the pancreas triggers glucose uptake by cells in part by promoting the translocation of the glucose transporter GLUT4 from intracellular vesicles to the plasma membrane. GLUT4 translocation requires a protein complex called the exocyst, which tethers GLUT4-containing vesicles to the plasma membrane. Uhm et al. found that the kinase TBK1, which mediates inflammatory responses, also phosphorylated exocyst subunits. These phosphorylation events were required for the fusion of GLUT4-containing vesicles with the plasma membrane. Insulin increased glucose uptake in adipocytes from wild-type mice but not in those from TBK1-deficient mice. The authors speculate that the involvement of TBK1 in insulin responses may be a means to counter the catabolic effects of inflammation. Insulin stimulates glucose uptake through the translocation of the glucose transporter GLUT4 to the plasma membrane. The exocyst complex tethers GLUT4-containing vesicles to the plasma membrane, a process that requires the binding of the G protein (heterotrimeric guanine nucleotide–binding protein) RalA to the exocyst complex. We report that upon activation of RalA, the protein kinase TBK1 phosphorylated the exocyst subunit Exo84. Knockdown of TBK1 blocked insulin-stimulated glucose uptake and GLUT4 translocation; knockout of TBK1 in adipocytes blocked insulin-stimulated glucose uptake; and ectopic overexpression of a kinase-inactive mutant of TBK1 reduced insulin-stimulated glucose uptake in 3T3-L1 adipocytes. The phosphorylation of Exo84 by TBK1 reduced its affinity for RalA and enabled its release from the exocyst. Overexpression of a kinase-inactive mutant of TBK1 blocked the dissociation of the TBK1/RalA/exocyst complex, and treatment of 3T3-L1 adipocytes with specific inhibitors of TBK1 reduced the rate of complex dissociation. Introduction of phosphorylation-mimicking or nonphosphorylatable mutant forms of Exo84 blocked insulin-stimulated GLUT4 translocation. Thus, these data indicate that TBK1 controls GLUT4 vesicle engagement and disengagement from the exocyst, suggesting that exocyst components not only constitute a tethering complex for the GLUT4 vesicle but also act as “gatekeepers” controlling vesicle fusion at the plasma membrane.
Optimal margin and edge-enhanced intensity maps in the presence of motion and uncertainty

In radiation therapy, intensity maps involving margins have long been used to counteract the effects of dose blurring arising from motion. More recently, intensity maps with increased intensity near the edge of the tumour (edge enhancements) have been studied to evaluate their ability to offset similar effects that affect tumour coverage. In this paper, we present a mathematical methodology to derive margin and edge-enhanced intensity maps that aim to provide tumour coverage while delivering minimum total dose. We show that if the tumour is at most about twice as large as the standard deviation of the blurring distribution, the optimal intensity map is a pure scaling increase of the static intensity map without any margins or edge enhancements. Otherwise, if the tumour size is roughly twice (or more) the standard deviation of motion, then margins and edge enhancements are preferred, and we present formulae to calculate the exact dimensions of these intensity maps. Furthermore, we extend our analysis to include scenarios where the parameters of the motion distribution are not known with certainty, but rather can take any value in some range. In these cases, we derive a similar threshold to determine the structure of an optimal margin intensity map.