gebhart/patrepeval huggingface dataset:
Role of cell-surface lysines in plasminogen binding to cells: identification of .alpha.-enolase as a candidate plasminogen receptor (1991)

Plasminogen binding to cell surfaces results in enhanced plasminogen activation, localization of the proteolytic activity of plasmin on cell surfaces, and protection of plasmin from alpha 2-antiplasmin. We sought to characterize candidate plasminogen binding sites on nucleated cells, using the U937 monocytoid cell as a model, specifically focusing on the role of cell-surface proteins with appropriately placed lysine residues as candidate plasminogen receptors. Lysine derivatives with free alpha-carboxyl groups and peptides with carboxy-terminal lysyl residues were effective inhibitors of plasminogen binding to the cells. One of the peptides, representing the carboxy-terminal 19 amino acids of alpha 2-antiplasmin, was approximately 5-fold more effective than others with carboxy-terminal lysines. Thus, in addition to a carboxy-terminal lysyl residue, other structural features of the cell-surface proteins may influence their affinity for plasminogen. Affinity chromatography has been used to isolate candidate plasminogen receptors from U937 cells. A major protein of Mr 54,000 was recovered and identified as alpha-enolase by immunochemical and functional criteria. alpha-Enolase was present on the cell surface and was capable of binding plasminogen in ligand blotting analyses. Plasminogen binding activity of a molecular weight similar to alpha-enolase also was present in a variety of other cell types. Carboxypeptidase B treatment of alpha-enolase abolished its ability to bind plasminogen, consistent with the presence of a C-terminal lysyl residue. Thus, cell-surface proteins with carboxy-terminal lysyl residues appear to function as plasminogen binding sites, and alpha-enolase has been identified as a prominent representative of this class of receptors.
Reducing Tachometer Jitter to Improve Gear Fault Detection (2016)

Much research has been published on gear fault analysis techniques, almost all based on the time synchronous average (TSA). These include and are not limited to: residual analysis, energy operator, energy ratio, amplitude modulation, frequency modulation, sideband index, zeroorder figure of merit, etc. Because the TSA is based on tachometer zero cross times for a key phasor, the performance of these analyses is dependent on the quality of the tachometer data. The tachometer signal always has jitter, due to electrical noise, magnetic noise, or manufacturing spacing error of the tachometer target (e.g. gear tooth spacing). By implementing a novel zero phase filter to reduce tachometer jitter, large improvements in the fault detection were observed. For a known gear fault, the separability, related to fault detection, increased from 10 to 25%.
Andrographolide interferes with binding of nuclear factor‐κB to DNA in HL‐60‐derived neutrophilic cells (2005)

1. Andrographolide, the major active component from Andrographis paniculata, has shown to possess anti-inflammatory activity. Andrographolide inhibits the expression of several proinflammatory proteins that exhibit a nuclear factor kappa B (NF-kappaB) binding site in their gene. 2. In the present study, we analyzed the effect of andrographolide on the activation of NF-kappaB induced by platelet-activating factor (PAF) and N-formyl-methionyl-leucyl-phenylalanine (fMLP) in HL-60 cells differentiated to neutrophils. 3. PAF (100 nM) and fMLP (100 nM) induced activation of NF-kappaB as determined by degradation of inhibitory factor B alpha (IkappaB alpha) using Western blotting in cytosolic extracts and by binding to DNA using electrophoretic mobility shift assay (EMSA) in nuclear extracts. 4. Andrographolide (5 and 50 microM) inhibited the NF-kappaB-luciferase activity induced by PAF. However, andrographolide did not reduce phosphorylation of p38 MAPK or ERK1/2 and did not change IkappaB alpha degradation induced by PAF and fMLP. 5. Andrographolide reduced the DNA binding of NF-kappaB in whole cells and in nuclear extracts induced by PAF and fMLP. 6. Andrographolide reduced cyclooxygenase-2 (COX-2) expression induced by PAF and fMLP in HL-60/neutrophils. 7. It is concluded that andrographolide exerts its anti-inflammatory effects by inhibiting NF-kappaB binding to DNA, and thus reducing the expression of proinflammatory proteins, such as COX-2.
Size-exclusion chromatography using self-organized nanopores in anodic porous alumina (2003)

We have achieved the size separation of DNA molecules on a biochip using an anodic porous alumina as a separation matrix in electrophoresis. The bottom of the microfluid channel on the chip was made of a porous alumina membrane that has uniform nanoscale pores on its surface. Since smaller molecules are much more frequently trapped by nanopores than larger ones, larger molecules elute earlier than smaller molecules. This type of separation is the same process as that resulting from size-exclusion chromatography. When two kinds of DNA samples (3.2 and 0.3 kilobases) were applied to the biochip, they were clearly separated into two bands, with the larger molecules (3.2 kilobases) eluting earlier. Since nanopore formation does not require any nanolithography, the fabrication is easy and inexpensive. The matrix can be integrated with other biomicroelectromechanical systems reactors on a micro total analysis system chip.
DAP12/TREM2 Deficiency Results in Impaired Osteoclast Differentiation and Osteoporotic Features (2003)

Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL), Nasu-Hakola disease, is a globally distributed recessively inherited disease. PLOSL is characterized by cystic bone lesions, osteoporotic features, and loss of white matter in the brain leading to spontaneous bone fractures and profound presenile dementia. We have earlier characterized the molecular genetic background of PLOSL by identifying mutations in two genes, DAP12 and TREM2. DAP12 is a transmembrane adaptor protein that associates with the cell surface receptor TREM2. The DAP12-TREM2 complex is involved in the maturation of dendritic cells. To test a hypothesis that osteoclasts would be the cell type responsible for the bone pathogenesis in PLOSL, we analyzed the differentiation of peripheral blood mononuclear cells isolated from DAP12- and TREM2-deficient PLOSL patients into osteoclasts. Here we show that loss of function mutations in DAP12 and TREM2 result in an inefficient and delayed differentiation of osteoclasts with a remarkably reduced bone resorption capability in vitro. These results indicate an important role for DAP12-TREM2 signaling complex in the differentiation and function of osteoclasts.
An efficient Fault Localization Algorithm for IP/WDM Networks (2000)

We propose an algorithm for localizing multiple failures in an IP/WDM network. They can be either hard failures (unexpected events that interrupt suddenly the established channels) or soft failures (events that progressively degrade the quality of transmission). Hard failures are detected at the WDM layer, whereas soft failures can be detected at the optical layer if proper testing equipment is deployed, and/or by performance monitoring at a higher layer, which is here IP. The algorithm also tolerates missing and false alarms. Even without missing and false alarms, multiple fault localization is NP-hard. The diagnosis phase (i.e., the localization of the faulty components upon reception of the alarms) can however remain very fast, but at the expense of a very complex precomputation phase, carried out whenever the optical channels are set up or cleared down. We show how the algorithm performs on an example of an IP/WDM network.
A signal adaptive diffusion filter for video coding: Mathematical framework and complexity reductions (2020)

In this paper we combine video compression and modern image processing methods. We construct novel iterative filter methods for prediction signals based on Partial Differential Equation (PDE) based methods. The mathematical framework of the employed diffusion filter class is given and some desirable properties are stated. In particular, two types of diffusion filters are constructed: a uniform diffusion filter using a fixed filter mask and a signal adaptive diffusion filter that incorporates the structures of the underlying prediction signal. The latter has the advantage of not attenuating existing edges while the uniform filter is less complex. The filters are embedded into a software based on HEVC with additional QTBT (Quadtree plus Binary Tree) and MTT (Multi-Type-Tree) block structure. In this setting, several measures to reduce the coding complexity of the tool are introduced, discussed and tested thoroughly. The coding complexity is reduced by up to 70% while maintaining over 80% of the gain. Overall, the diffusion filter method achieves average bitrate savings of 2.27% for Random Access having an average encoder runtime complexity of 119% and 117% decoder runtime complexity. For individual test sequences, results of 7.36% for Random Access are accomplished.
Efficacy of short novel antimicrobial and anti-inflammatory peptides in a mouse model of methicillin-resistant Staphylococcus aureus (MRSA) skin infection (2014)

The therapeutic efficacy of two novel short antimicrobial and anti-inflammatory peptides (RR and RRIKA) was evaluated in a mouse model of staphylococcal skin infection. RR (2%) and RRIKA (2%) significantly reduced the bacterial counts and the levels of proinflammatory cytokines, tumor necrosis factor (TNF)-α, and interleukin (IL)-6, in methicillin-resistant Staphylococcus aureus USA 300-0114 skin lesions. Furthermore, the combined therapy of RRIKA (1%) and lysostaphin (0.5%) had significantly higher antistaphylococcal and anti-inflammatory activity compared to monotherapy. This study supports the potential use of these peptides for topical treatment of methicillin-resistant Staphylococcus aureus skin infections.
Mixed Confidence Estimation for Iterative CT Reconstruction. (2014)

We present a statistical analysis of our previously proposed Constrain-Static Target-Kinetic algorithm for 4D CT reconstruction. This method, where framed iterative reconstruction is only performed on the dynamic regions of each frame, while static regions are fixed across frames to a composite image, was proposed to reduce computation time. In this work, we generalize the previous method to describe any application where a portion of the image is known with higher confidence (static, composite, lower-frequency content, etc.) and a portion of the image is known with lower confidence (dynamic, targeted, etc). We show that by splitting the image space into higher and lower confidence components, CSTK can lower the estimator variance in both regions compared to conventional reconstruction. We present a theoretical argument for this reduction in estimator variance and verify this argument with proof-of-principle simulations. This method allows for reduced computation time and improved image quality for imaging scenarios where portions of the image are known with more certainty than others.
Subthreshold Mobility in AlGaN/GaN HEMTs (2016)

Electron mobility of AlGaN/GaN HEMTs is studied using a gate admittance-based technique. This analysis extends to electron densities as low as 4×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> with good accuracy. Zero lateral electric field is applied, in contrast to conventional methods. At these low electron densities, the mobility can be a factor of ~50 less than that in the ON-state. We reveal a regime at low electron densities where the screening of the two dimensional electron gas (2-DEG) becomes negligible causing the mobility to be independent of electron concentration, suggesting percolative transport. This region defines the rate at which the channel depletes and is a strong indicator of the epitaxial control of the impurities in the GaN channel.
Deployment and coverage of cognitive radio networks in TV white space (2012)

This article presents experimental and simulation results for the use of TV band devices (TVBDs) in TV white space, considering the presence of interference by incumbent services. Digital TV (DTV) services are major incumbent services currently operating in the TV bands. With DTV service, co-channel and adjacent channel deployment scenarios of TVBD networks are introduced. To safely protect the incumbent service, a minimum separation distance from the DTV protected contour, which is called the keep-out distance, is required. We estimate the keep-out distance for different ranges of TVBD transmit antenna height by using several propagation models and measurements of ultra-high-frequency signals in Korea. We also investigate the hidden node problem for the spectrum sensing operation mode of TVBDs. According to the results of these measurements, the hidden node margin should be at least 38 dB in order to protect DTV service. Finally, the service coverage reduction of TVBD networks caused by neighboring DTV service is discussed. It is shown that the service coverage of a wireless local area network system decreases about 50 percent by co-channel interference from neighboring DTV service when the field strength of the DTV received signal is 41 dBu.
CDK13 cooperates with CDK12 to control global RNA polymerase II processivity (2020)

The RNA polymerase II (POLII)-driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases (CDKs) and their cognate cyclins. The molecular events underpinning transcriptional elongation, processivity, and the CDK-cyclin pair(s) involved remain poorly understood. Using CRISPR-Cas9 homology-directed repair, we generated analog-sensitive kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with cellular growth signaling pathways and/or DNA damage, with minimal effects on cell viability. In contrast, dual kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including widespread use of alternative 3' polyadenylation sites. At the molecular level, dual kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define substantial redundancy between CDK12 and CDK13 and identify both as fundamental regulators of global POLII processivity and transcription elongation.
Event detection in NILM using Cepstrum smoothing (2016)

Event detection plays an important role in nonintrusive load monitoring to accurately detect the switching of appliances in a residential environment.Improving the detection ratios of those methods while keeping the computational cost under control is important.This paper presents a new event detection mechanism that works in the frequency domain and uses Cepstrum smoothing to eliminate noise.We explore the potential of our method by comparing with the 2 GOF method on the BLUED dataset.The results indicate that our method is competitive with the state-of-the-art having as advantage that the same feature can also be used for appliance detection.
Interference modeling and performance of bluetooth mac protocol (2003)

The emergence of Bluetooth as a default radio interface has allowed handheld electronic devices to be instantly interconnected as ad hoc networks. These short-range ad hoc wireless networks, called piconets, operate in the unlicensed 2.4-GHz ISM (Industrial-Scientific-Medical) band where devices may be used to configure single or overlapping piconets, known as scatternet. As all piconets operate in the same frequency band, the presence of multiple piconets in the vicinity may create interference on signal reception. This paper employs a signal capture model to study the piconet MAC performance, taking inter-piconet interference into consideration. This model leads to several important mathematical relationships for Bluetooth networks, including successful packet transmission probability. Furthermore, our model and anticipated throughput are validated using extensive simulation. These results indicate that Bluetooth throughput is affected by multiple piconet interference. Definitely, our model can be considered to provide a solid foundation for future interference aware Bluetooth protocols.
TU‐B‐I‐609‐01: Therapeutic Ultrasound (2005)

The use of ultrasound in medicine is now quite commonplace, especially with the recent introduction of small, portable and relatively inexpensive, hand‐held diagnostic imaging devices. Moreover, ultrasound has expanded beyond the imaging realm, with methods and applications extending to novel therapeutic and surgical uses. These applications broadly include: Tissue ablation, acoustocautery, lipoplasty, site‐specific and ultrasound mediated drug activity, extracorporeal lithotripsy, and the enhancement of natural physiological functions such as wound healing and tissue regeneration. A particularly attractive aspect of this technology is that diagnostic and therapeutic systems can be combined to produce totally non‐invasive, image‐guided therapy. This general lecture will review a number of these exciting new applications of ultrasound and address some of the basic scientific questions and future challenges in developing these methods and technologies for general use in our society. We shall particularly emphasize the use of High Intensity Focused Ultrasound (HIFU) in the treatment of benign and malignant tumors as well as the introduction of acoustic hemostasis, especially in organs which are difficult to treat using conventional medical and surgical techniques. [Supported in part by the NIH and the US Army]
Effects of triamcinolone acetonide on vessels of the posterior segment of the eye. (2009)

This study demonstrates for the first time that glucocorticoids exert direct toxic effect on endothelial cells through caspase-independent cell death mechanisms. The choroidal changes observed after TA intravitreous injection may have important implications regarding the safety profile of TA use in human eyes.
Sub-wavelength grating interdigitated combs as photonic waveguides (2019)

In this Letter, we demonstrate a new, to the best of our knowledge, kind of photonic waveguide, in which the light propagates in the overlap of sub-wavelength patterned interdigitated combs. We present the fabrication and characterization of this waveguide, along with an adiabatic taper ensuring lossless transition with classical photonic waveguides. Finally, we explore some practical applications of this waveguide, as a bio-photonic sensor or as an optomechanical transduction scheme.
Closed angle glaucoma detection in RetCam images (2010)

Closed/Open angle glaucoma classification is important for glaucoma diagnosis. RetCam is a new imaging modality that captures the image of iridocorneal angle for the classification. However, manual grading and analysis of the RetCam image is subjective and time consuming. In this paper, we propose a system for intelligent analysis of iridocorneal angle images, which can differentiate closed angle glaucoma from open angle glaucoma automatically. Two approaches are proposed for the classification and their performances are compared. The experimental results show promising results.
Approaches to optical neuromodulation from rodents to non-human primates by integrated optoelectronic devices (2011)

Methods on rendering neurons in the central nervous system to be light responsive has led to a boom in using optical neuromodulation as a new approach for controlling brain states and understanding neural circuits. In addition to the developing versatility to "optogenetically" labeling of neural cells and their subtypes by microbiological methods, parallel efforts are under way to design and implement optoelectronic devices to achieve simultaneous optical neuromodulation and electrophysiological recording with high spatial and temporal resolution. Such new device-based technologies need to be developed for full exploitation of the promise of optogenetics. In this paper we present single- and multi-element optoelectronic devices developed in our laboratories. The single-unit element, namely the coaxial optrode, was utilized to characterize the neural responses in optogenetically modified rodent and primate models. Furthermore, the multi-element device, integrating the optrode with a 6×6 microelectrode array, was used to characterize the spatiotemporal spread of neural activity in response to single-site optical stimulation in freely moving rats. We suggest that the particular approaches we employed can lead to the emergence of methods where spatio-temporal optical modulation is integrated with real-time read out from neural populations.
Present Status of Coronary Bifurcation Stenting (2007)

Percutaneous coronary intervention (PCI) for bifurcation lesions is technically limited by the risk of side branch occlusion. In comparison with nonbifurcation interventions, bifurcation interventions have a lower rate of procedural success, higher procedural costs and a higher rate of clinical and angiographic restenosis. The recent introduction of drug-eluting stents (DES) has resulted in reduced incidence of main vessel restenosis compared with historical controls. However, side-branch ostial residual stenosis and long-term restenosis still remain problematic. In the era of DES, techniques employing two stents have emerged that allow stenting of the large side branch in addition to the main artery. Stenting of the main vessel with provisional side branch stenting seems to be the prevailing approach. This paper reviews outcome data with different treatment modalities for this complex lesion with particular emphasis on the use of DES as well as potential new therapeutic approaches.
Enantioselective Synthesis of Cyclic Amides and Amines Through Mo‐Catalyzed Asymmetric Ring‐Closing Metathesis. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Treatment of severe esophageal Crohn's disease with thalidomide (2001)

Department of Gastroenterology, University of Chicago Hospitals, Chicago, Illinois, USA Reprint requests and correspondence: Eli D Ehrenpreis, MD, Department of Gastroenterology, University of Chicago Hospitals, 5841 South Maryland Avenue, MC 4076, Chicago, IL 60637. Received 14 November 2000; accepted 04 December 2000