gebhart/patrepeval huggingface dataset:
Mine Environment Monitoring System Based on Wireless Sensor Network (2013)

There are a large number of sensors to detect information in mine environment system, which provides the original data for the prevention and treatment of mine accidents. According to data flow of data acquisition, data transmission, data storage and data processing, this paper used CC2530 to design the wireless sensor nodes, analyzed the Zigbee network topology and designed an optimized PEGASIS protocol. The multi-sensor data fusion method was applied to the multi-parameter and large-scale mine data, solved the nonlinear problems in the multi-feature selection and extraction and also improved the performance of mine monitoring system. DOI:  http://dx.doi.org/10.11591/telkomnika.v11i7.2815 Full Text: PDF
A Modified Chondroitin Sulfate Aldehyde Adhesive for Sealing Corneal Incisions (2005)

A novel chondroitin sulfate-aldehyde adhesive was shown to be effective ex vivo for sealing corneal incisions in rabbit eyes and was superior to sutures for this purpose.
Virulent and Avirulent Strains ofFrancisella tularensisPrevent Acidification and Maturation of Their Phagosomes and Escape into the Cytoplasm in Human Macrophages (2004)

Francisella tularensis, the agent of tularemia, is an intracellular pathogen, but little is known about the compartment in which it resides in human macrophages. We have examined the interaction of a recent virulent clinical isolate of F. tularensis subsp. tularensis and the live vaccine strain with human macrophages by immunoelectron and confocal immunofluorescence microscopy. We assessed the maturation of the F. tularensis phagosome by examining its acquisition of the lysosome-associated membrane glycoproteins (LAMPs) CD63 and LAMP1 and the acid hydrolase cathepsin D. Two to four hours after infection, vacuoles containing live F. tularensis cells acquired abundant staining for LAMPs but little or no staining for cathepsin D. However, after 4 h, the colocalization of LAMPs with live F. tularensis organisms declined dramatically. In contrast, vacuoles containing formalin-killed bacteria exhibited intense staining for all of these late endosomal/lysosomal markers at all time points examined (1 to 16 h). We examined the pH of the vacuoles 3 to 4 h after infection by quantitative immunogold staining and by fluorescence staining for lysosomotropic agents. Whereas phagosomes containing killed bacteria stained intensely for these agents, indicating a marked acidification of the phagosomes (pH 5.5), phagosomes containing live F. tularensis did not concentrate these markers and thus were not appreciably acidified (pH 6.7). An ultrastructural analysis of the F. tularensis compartment revealed that during the first 4 h after uptake, the majority of F. tularensis bacteria reside within phagosomes with identifiable membranes. The cytoplasmic side of the membranes of approximately 50% of these phagosomes was coated with densely staining fibrils of approximately 30 nm in length. In many cases, these coated phagosomal membranes appeared to bud, vesiculate, and fragment. By 8 h after infection, the majority of live F. tularensis bacteria lacked any ultrastructurally discernible membrane separating them from the host cell cytoplasm. These results indicate that F. tularensis initially enters a nonacidified phagosome with LAMPs but without cathepsin D and that the phagosomal membrane subsequently becomes morphologically disrupted, allowing the bacteria to gain direct access to the macrophagic cytoplasm. The capacity of F. tularensis to alter the maturation of its phagosome and to enter the cytoplasm is likely an important element of its capacity to parasitize macrophages and has major implications for vaccine development.
Optimizing plane-to-plane positioning tasks by image-based visual servoing and structured light (2006)

This paper considers the problem of positioning an eye-in-hand system so that it becomes parallel to a planar object. Our approach to this problem is based on linking to the camera a structured light emitter designed to produce a suitable set of visual features. The aim of using structured light is not only for simplifying the image processing and allowing low-textured objects to be considered, but also for producing a control scheme with nice properties like decoupling, convergence, and adequate camera trajectory. This paper focuses on an image-based approach that achieves decoupling in all the workspace, and for which the global convergence is ensured in perfect conditions. The behavior of the image-based approach is shown to be partially equivalent to a 3-D visual servoing scheme, but with a better robustness with respect to image noise. Concerning the robustness of the approach against calibration errors, it is demonstrated both analytically and experimentally
Ethidium bromide as a marker of mtDNA replication in living cells (2012)

Mitochondrial DNA (mtDNA) in tumor cells was found to play an important role in maintaining the malignant phenotype. Using laser scanning confocal fluorescence microscopy (LSCFM) in a recent work, we reported a variable fluorescence intensity of ethidium bromide (EB) in mitochondria nucleoids of living carcinoma cells. Since when EB is bound to nucleic acids its fluorescence is intensified; a higher EB fluorescence intensity could reflect a higher DNA accessibility to EB, suggesting a higher mtDNA replication activity. To prove this hypothesis, in the present work we studied, by LSCFM, the EB fluorescence in mitochondria nucleoids of living neuroblastoma cells, a model system in which differentiation affects the level of mtDNA replication. A drastic decrease of fluorescence was observed after differentiation. To correlate EB fluorescence intensity to the mtDNA replication state, we evaluated the mtDNA nascent strands content by ligation-mediated real-time PCR, and we found a halved amount of replicating mtDNA molecules in differentiating cells. A similar result was obtained by BrdU incorporation. These results indicate that the low EB fluorescence of nucleoids in differentiated cells is correlated to a low content of replicating mtDNA, suggesting that EB may be used as a marker of mtDNA replication in living cells.
Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review (2020)

The novel coronavirus, SARS-CoV-2, or 2019-nCoV, which originated in Wuhan, Hubei province, China in December 2019, is a grave threat to public health worldwide. A total of 3,672,238 confirmed cases of coronavirus disease 2019 (COVID-19) and 254,045 deaths were reported globally up to May 7, 2020. However, approved antiviral agents for the treatment of patients with COVID-19 remain unavailable. Drug repurposing of approved antivirals against other viruses such as HIV or Ebola virus is one of the most practical strategies to develop effective antiviral agents against SARS-CoV-2. A combination of repurposed drugs can improve the efficacy of treatment, and structure-based drug design can be employed to specifically target SARS-CoV-2. This review discusses therapeutic strategies using promising antiviral agents against SARS-CoV-2. In addition, structural characterization of potentially therapeutic viral or host cellular targets associated with COVID-19 have been discussed to refine structure-based drug design strategies.
Highlight substitution in light fields (2003)

Highlights occur especially when recording medical (color) images during micro-invasive operations. They disturb the physicians who can sometimes only guess the tissue at the position of the highlights. We present a new technique of highlight removal. A so-called light field is generated from the recorded image sequence. Then a binary highlight mask is computed for each image and used as confidence map for the light field pixels. The result is a light field in which pixels at highlight positions are interpolated by pixels which were not over-imposed by highlights. This leads to light fields with better images. We demonstrate and evaluate the technique on medical and synthetic image sequences.
Cryogenic Semiconductor Amplifier for RSFQ-Circuits With High Data Rates at 4.2 K (2009)

The connection of RSFQ circuits with commercial room temperature electronics and amplifying SFQ pulses with high data rates require cryogenic interface amplifiers. Such amplifiers should provide extremely high bandwidth, low noise and low power consumption at the same time. Various hybrid amplifiers based on commercial p-HEMT transistors in an embedded microwave design were designed and characterized. Towards the p-HEMT transistor characterization at cryogenic temperature the biasing settings according to an optimum between voltage gain and low power consumption were determined. Thus a total power consumption of 2 mW and a voltage gain of 12 dB per single stage were achieved. For a preamplifier and an amplifier concept a multiple number of these stages were implemented in a microstrip and a coplanar transmission line design with a special matched interconnect taper towards the RSFQ components. Measurements of the amplifiers, the combination of an amplifier with a RSFQ circuit at 4.2 K showed their good performances without any disturbance of the RSFQ circuit. Due to the losses between the stages a total gain of 25 dB with a four stage amplifier was achieved; pulse rates went up to 3 Gb/s. The total power consumption was in the range of 8 mW. Further increase of data rates will be achieved by improving the matching between RSFQ output stage and amplifier.
EGFRvIII Antibody–Conjugated Iron Oxide Nanoparticles for Magnetic Resonance Imaging–Guided Convection-Enhanced Delivery and Targeted Therapy of Glioblastoma (2010)

The magnetic nanoparticle has emerged as a potential multifunctional clinical tool that can provide cancer cell detection by magnetic resonance imaging (MRI) contrast enhancement as well as targeted cancer cell therapy. A major barrier in the use of nanotechnology for brain tumor applications is the difficulty in delivering nanoparticles to intracranial tumors. Iron oxide nanoparticles (IONP; 10 nm in core size) conjugated to a purified antibody that selectively binds to the epidermal growth factor receptor (EGFR) deletion mutant (EGFRvIII) present on human glioblastoma multiforme (GBM) cells were used for therapeutic targeting and MRI contrast enhancement of experimental glioblastoma, both in vitro and in vivo, after convection-enhanced delivery (CED). A significant decrease in glioblastoma cell survival was observed after nanoparticle treatment and no toxicity was observed with treatment of human astrocytes (P < 0.001). Lower EGFR phosphorylation was found in glioblastoma cells after EGFRvIIIAb-IONP treatment. Apoptosis was determined to be the mode of cell death after treatment of GBM cells and glioblastoma stem cell-containing neurospheres with EGFRvIIIAb-IONPs. MRI-guided CED of EGFRvIIIAb-IONPs allowed for the initial distribution of magnetic nanoparticles within or adjacent to intracranial human xenograft tumors and continued dispersion days later. A significant increase in animal survival was found after CED of magnetic nanoparticles (P < 0.01) in mice implanted with highly tumorigenic glioblastoma xenografts (U87DeltaEGFRvIII). IONPs conjugated to an antibody specific to the EGFRvIII deletion mutant constitutively expressed by human glioblastoma tumors can provide selective MRI contrast enhancement of tumor cells and targeted therapy of infiltrative glioblastoma cells after CED.
Simple Direct Synthesis of [Bis(trifluoroacetoxy)iodo]arenes (2006)

A modified procedure for the direct synthesis of hypervalent [bis(trifluoroacetoxy)iodo]arenes is described. It avoids the use of hazardous reagents with the workup being only an aqueous extraction.
Electron-cyclotron-resonance plasma etching of the ZnO layers grown by molecular-beam epitaxy (2004)

Etching of high-quality ZnO layers grown by molecular-beam epitaxy was examined by using electron-cyclotron-resonance plasma etching. Etching rates of ZnO layers were larger using CH4 than CF4, and four times more enhanced by using a mixture of the two gases. For a ZnO surface covered with photoresist layers by the plasma-etching procedure, degradation was mostly recovered by thermal annealing in an O2 atmosphere at the proper temperatures. This was found to be effective for the recovery of the layers.
A Helicase Assay Based on the Displacement of Fluorescent, Nucleic Acid-Binding Ligands (1996)

We have developed a new helicase assay that overcomes many limitations of other assays used to measure this activity. This continuous, kinetic assay is based on the displacement of fluorescent dyes from dsDNA upon DNA unwinding. These ligands exhibit significant fluorescence enhancement when bound to duplex nucleic acids and serve as the reporter molecules of DNA unwinding. We evaluated the potential of several dyes [acridine orange, ethidium bromide, ethidium homodimer, bis-benzimide (DAPI), Hoechst 33258 and thiazole orange] to function as suitable reporter molecules and demonstrate that the latter three dyes can be used to monitor the helicase activity of Escherichia coli RecBCD enzyme. Both the binding stoichiometry of RecBCD enzyme for the ends of duplex DNA and the apparent rate of unwinding are not significantly perturbed by two of these dyes. The effects of temperature and salt concentration on the rate of unwinding were also examined. We propose that this dye displacement assay can be readily adapted for use with other DNA helicases, with RNA helicases, and with other enzymes that act on nucleic acids.
Multivesicular Liposomes for the Sustained Release of Angiotensin I-Converting Enzyme (ACE) Inhibitory Peptides from Peanuts: Design, Characterization, and In Vitro Evaluation (2019)

The multivesicular liposome (MVL) provides a potential delivery approach to avoid the destruction of the structure of drugs by digestive enzymes of the oral cavity and gastrointestinal system. It also serves as a sustained-release drug delivery system. In this study, we aimed to incorporate a water-soluble substance into MVLs to enhance sustained release, prevent the destruction of drugs, and to expound the function of different components and their mechanism. MVLs were prepared using the spherical packing model. The morphology, structure, size distribution, and zeta potential of MVLs were examined using an optical microscope (OM), confocal microscopy (CLSM), transmission electron cryomicroscope (cryo-EM) micrograph, a Master Sizer 2000, and a zeta sizer, respectively. The digestion experiment was conducted using a bionic mouse digestive system model in vitro. An in vitro release and releasing mechanism were investigated using a dialysis method. The average particle size, polydispersity index, zeta potential, and encapsulation efficiency are 47.6 nm, 1.880, -70.5 ± 2.88 mV, and 82.00 ± 0.25%, respectively. The studies on the controlled release in vitro shows that MVLs have excellent controlled release and outstanding thermal stability. The angiotensin I-converting enzyme (ACE) inhibitory activity of ACE-inhibitory peptide (AP)-MVLs decreased only 2.84% after oral administration, and ACE inhibitory activity decreased by 5.03% after passing through the stomach. Therefore, it could serve as a promising sustained-release drug delivery system.
Amino Acid Replacements that Compensate for a Large Polypeptide Deletion in an Enzyme (1985)

Deletion of more than 400 amino acids from the carboxyl terminus of an enzyme causes a severe reduction in catalytic activity. Selected point mutations within the residual protein partially reverse the effects of the missing segment. The selection can yield mutants with activities at least ten times as high as those of the starting polypeptides. One well-characterized mutation, a single amino acid replacement in the residual polypeptide, increases the catalytic activity of the polypeptide by a factor of 5. The results suggest substantial potential for design of protein elements to compensate for missing polypeptide sequences. They also may reflect that progenitors of large aminoacyl-tRNA (transfer RNA) synthetases--one of which was used in these studies--were themselves much smaller.
Speakeasy: the military software radio (1995)

The Speakeasy Phase II radio will use programmable processing to emulate more than 15 existing military radios. Speakeasy is a challenge, even with recent advancements in DSP technologies. The benefits, however, make the challenge highly worthwhile.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Harmonic generation with temporally focused ultrashort pulses (2005)

The properties of harmonic generation with temporally focused ultrashort pulses are explored both theoretically and experimentally. Analyzing the phase-matching conditions for harmonic generation we find a correspondence between temporal focusing and spatial focusing along one dimension. In particular, temporally focused pulses experience a π phase shift in passing through the temporal focus, similar to the Guoy phase shift experienced by spatially focused beams. This correspondence is confirmed by measurements of third-harmonic generation induced by temporally focused pulses.
Middleware (1996)

T he computing facilities of largescale enterprises are evolving into a utility, much like power and telecommunications. In the vision of an information utility, each knowledge worker has a desktop appliance that connects to the utility. The desktop appliance is a computer or computer-like device, such as a terminal, personal computer, workstation, word processor, or stock trader's station. The utility itself is an enterprise-wide network of information services, including applications and databases, on the localarea and wide-area networks.
Extracellular Signal-Regulated Kinase Activity Is Sustained Early during Human Cytomegalovirus Infection (1998)

Expression of many early viral genes during human cytomegalovirus (HCMV) infection is dependent on cellular transcription factors. Several immediate-early and early viral promoters contain DNA binding sites for cellular factors such as CREB, AP-1, serum response factor, and Elk-1, and these transcription factors can be activated by phosphorylation via the cellular mitogen-activated protein kinase (MAPK) signal transduction cascade. To determine if the extracellular signal-regulated MAPKs, ERK1 and ERK2, play a role in transcription factor activation during infection, we tested for ERK activity during viral infection. We found that HCMV infection resulted in the maintenance of previously activated ERK1 and ERK2 by a mechanism which appears to involve the inhibition of a cellular phosphatase activity. ERK phosphorylation and activity were sustained for at least 8 h after infection, whereas in mock-infected cells, ERK activity steadily declined by 1 h postinfection. The activity of at least one cellular substrate of the ERKs, the protein kinase RSK1, was also maintained during this period. UV inactivation experiments suggested that viral gene expression was required for sustained ERK activity. In turn, activation of the ERKs appeared to be important for viral gene expression, as evidenced by the observed decrease in the transcriptional activity of the HCMV UL112-113 promoter during infection in the presence of the MEK inhibitor PD98059. These data suggest that HCMV utilizes cellular signal transduction pathways to activate viral or cellular transcription factors involved in the control of early viral gene expression and DNA replication.
Recombinant DNA methodology II (1989)

Isolation, synthesis and detection of DNA and RNA enzymes and methods for cleaving and manipulating DNA reporter genes vectors for cloning genes vectors for expressing cloned genes mutagenesis and gene disruption screening libraries, identifying and mapping genes methods for transforming animal and plant cells methods for sequencing DNA polymerase chain reaction for amplifying and manipulating DNA methods for detecting DNA-protein interaction other methods.
Viral and Bacterial Infections Interfere with Peripheral Tolerance Induction and Activate CD8+ T Cells to Cause Immunopathology (1998)

We studied the impact of various infectious and proinflammatory agents on the induction of peripheral T cell tolerance. Adoptive transfer of CD8+ T cells from lymphocytic choriomeningitis virus (LCMV) T cell receptor transgenic mice into LCMV antigen transgenic mice expressing the LCMV glycoprotein epitope (gp) 33-41 under control of a major histocompatibility complex class I promoter led to efficient induction of peripheral tolerance after a period of transient activation. If, however, the recipient mice were challenged with viral or bacterial infections or proinflammatory agents (lipopolysaccharide or Poly:IC) early after cell transfer, tolerance induction was prevented and instead, CD8+ T cell activation leading to vigorous expansion and generation of cytolytic activity ensued. This became manifest in significant immunopathology mainly involving destruction of the splenic architecture and lysis of antigen-expressing lymphocyte and macrophage populations. Important parameters involved in the activation of host-reactive T cells by nonspecific infectious agents included the presence, localization, and quantity of the specific transgene-encoded self-antigen; in contrast, CD4+ T cells were not required. In mice surviving the acute phase, the transferred CD8+ T cells persisted at high levels in an anergic state; they were unable to generate cytolytic activity in vitro or to control LCMV infection in vivo. These results impinge on our understanding of the role of infectious agents in graft verus host reactions towards minor histocompatibility antigens.
Intrapericardial Paclitaxel Delivery Inhibits Neointimal Proliferation and Promotes Arterial Enlargement After Porcine Coronary Overstretch (2000)

IPC space delivery of a single dose of paclitaxel significantly reduces vessel narrowing in this balloon-overstretch model. This effect is mediated by reduction of neointimal mass as well as positive vascular remodeling.
Updates on treatment of irritable bowel syndrome (2008)

Irritable bowel syndrome (IBS) is a highly prevalent gastrointestinal disorder characterized by abdominal pain and discomfort in association with altered bowel habits. It is estimated to affect 10%-15% of the Western population, and has a large impact on quality of life and (in)direct healthcare costs. IBS is a multifactorial disorder involving dysregulation within the brain-gut axis, and it is frequently associated with gastrointestinal motor and sensory dysfunction, enteric and central nervous system irregularities, neuroimmune dysregulation, and post-infectious inflammation. As with other functional medical disorders, the treatment for IBS can be challenging. Conventional therapy for those with moderate to severe symptoms is largely unsatisfactory, and the development of new and effective drugs is made difficult by the complex pathogenesis, variety of symptoms, and lack of objective clinical findings that are the hallmark of this disorder. Fortunately, research advances over the past several decades have provided insight into potential mechanisms responsible for the pathogenesis of IBS, and have led to the development of several promising pharmaceutical agents. In recent years there has been much publicity over several of these new IBS medications (alosetron and tegaserod) because of their reported association with ischemic colitis and cardiovascular disease. While these agents remain available for use under restricted prescribing programs, this highlights the need for continued development of safe and effective medication for IBS. This article provides a physiologically-based overview of recently developed and frequently employed pharmaceutical agents used to treat IBS, and discusses some non-pharmaceutical options that may be beneficial in this disorder.