gebhart/patrepeval huggingface dataset:
Haptic virtual reality for blind computer users (1998)

This paper describes a series of studies involving a haptic device which can display virtual textures and 3-D objects. The device has potential for simulating real world objects and assisting in the navigation of virtual environments. Three experiments investigated: (a) whether previous results from experiments using real textures could be replicated using virtual textures; (b) whether participants perceived virtual objects to have the intended size and angle; and (c) whether simulated real objects could be recognised. In all the experiments differences in perception by blind and sighted people were also explored. The results have implications for the future design of VEs in that it cannot be assumed that virtual textures and objects will feel to the user as the designer intends. However, they do show that a haptic interface has considerable potential for blind computer users.
A Model-in-the-Loop Interface to Emulate Source Dynamics in a Zonal DC Distribution System (2005)

A model-in-the-loop capability (MIL) has been developed to emulate the dynamics of alternative power sources in a hardware-based dc zonal electrical distribution system. Using this tool, models of the power sources are simulated in real-time and interfaced with hardware components at the voltage and current levels of the power system. Coupling between simulation and hardware is established through a dc/dc power converter using model/wall-clock time synchronization. The MIL capability is illustrated in the emulation of a synchronous machine/converter power source. Results of time-domain and frequency-domain studies are provided to validate the approach.
Regulation of Ribosomal S6 Kinase 2 by Mammalian Target of Rapamycin (2002)

Phosphorylation of the ribosomal S6 subunit is tightly correlated with enhanced translation initiation of a subset of mRNAs that encodes components of the protein synthesis machinery, which is an important early event that controls mammalian cell growth and proliferation. The recently identified S6 kinase 2 (S6K2), together with its homologue S6K1, is likely responsible for the mitogen-stimulated phosphorylation of S6. Like S6K1, the activation of S6K2 requires signaling from both the phosphatidylinositol 3-kinase and the mammalian target of rapamycin (mTOR). Here we report the investigation of the mechanisms of S6K2 regulation by mTOR. We demonstrate that similar to S6K1 the serum activation of S6K2 in cells is dependent on mTOR kinase activity, amino acid sufficiency, and phosphatidic acid. Previously we have shown that mTOR is a cytoplasmic-nuclear shuttling protein. As a predominantly nuclear protein, S6K2 activation was facilitated by enhanced mTOR nuclear import with the tagging of an exogenous nuclear localization signal and diminished by enhanced mTOR nuclear export with the tagging of a nuclear export sequence. However, further increase of mTOR nuclear import by the tagging of four copies of nuclear localization signal resulted in its decreased ability to activate S6K2, suggesting that mTOR nuclear export may also be an integral part of the activation process. Consistently, the nuclear export inhibitor leptomycin B inhibited S6K2 activation. Taken together, our observations suggest a novel regulatory mechanism in which an optimal cytoplasmic-nuclear distribution or shuttling rate for mTOR is required for maximal activation of the nuclear S6K2.
Improved Anatomical Specificity of Non-invasive Neuro-stimulation by High Frequency (5 MHz) Ultrasound (2016)

Low frequency ultrasound (<1 MHz) has been demonstrated to be a promising approach for non-invasive neuro-stimulation. However, the focal width is limited to be half centimeter scale. Minimizing the stimulation region with higher frequency ultrasound will provide a great opportunity to expand its application. This study first time examines the feasibility of using high frequency (5 MHz) ultrasound to achieve neuro-stimulation in brain, and verifies the anatomical specificity of neuro-stimulation in vivo. 1 MHz and 5 MHz ultrasound stimulation were evaluated in the same group of mice. Electromyography (EMG) collected from tail muscles together with the motion response videos were analyzed for evaluating the stimulation effects. Our results indicate that 5 MHz ultrasound can successfully achieve neuro-stimulation. The equivalent diameter (ED) of the stimulation region with 5 MHz ultrasound (0.29 ± 0.08 mm) is significantly smaller than that with 1 MHz (0.83 ± 0.11 mm). The response latency of 5 MHz ultrasound (45 ± 31 ms) is also shorter than that of 1 MHz ultrasound (208 ± 111 ms). Consequently, high frequency (5 MHz) ultrasound can successfully activate the brain circuits in mice. It provides a smaller stimulation region, which offers improved anatomical specificity for neuro-stimulation in a non-invasive manner.
The leukocyte/neuron cell surface antigen OX2 binds to a ligand on macrophages (1997)

The OX2 membrane glycoprotein contains two immunoglobulin superfamily (IgSF) domains and seems likely to interact with other cell surface proteins. A soluble chimeric protein with the two IgSF domains of OX2 engineered onto domains 3 + 4 of rat CD4 antigen was expressed. To detect possible weak interactions, the chimeric protein was coupled to fluorescent covaspheres to provide a highly avid display of OX2. The OX2 covaspheres bound macrophages but not other cell types. The specificity of the interaction was demonstrated by blocking with Fab fragments of the OX2 monoclonal antibody (mAb). A new mAb, MRC OX88, was raised against macrophages which also blocked the interaction and presumably recognizes the ligand. The epitope for the MRC OX2 mAb and a site for ligand binding were mapped to domain 1 by site-directed mutagenesis. The OX2 antigen is present on thymocytes, some lymphocytes, neurons and endothelial cells; thus, it has the potential to mediate interactions between these cell types and macrophages.
Induction of apoptosis in oral cancer cells by an anti-bcl-2 ribozyme delivered by an adenovirus vector. (2000)

Human oral cancer cells may have any of several genetic changes, but the role of the bcl-2 oncogene is relatively unexplored. To find out if this gene plays a significant role and whether it could act as a target for gene therapy of oral cancer, we have examined the effects of an anti-bcl-2 ribozyme on the phenotype of oral cancer cells. A hammer-head ribozyme was designed to cleave the bcl-2 transcript after nucleotide 279 and was confirmed to be effective against a synthetic bcl-2 transcript. A gene encoding the ribozyme was cloned into an adenovirus vector and transferred to the human oral cancer cell lines 686LN, 1483, and Tu183. Over a 6-day period, the growth of each cancer cell line was reduced, whereas growth of the fibroblast cell line FS7 was less inhibited. Inhibition of the oral cancer cells could be attributed to apoptosis, as indicated by the detection of histone-associated DNA fragments in an immunoassay. Northern blots showed no detectable reduction in the level of bcl-2 mRNA of Tu183 cells, but Western blots showed a reduction of Bcl-2 protein at 24 h after infection with the ribozyme-expressing adenovirus vector. The results imply that (a) expression of the bcl-2 oncogene is necessary for the survival of oral cancer cells, (b) the bcl-2 gene transcript presents a target for gene therapy by ribozymes, and (c) an adenovirus vector is a suitable method for transfection of the ribozyme-expressing gene.
Immunocytochemical localization of glycolytic and fermentative enzymes in Zymomonas mobilis (1992)

Gold-labeled antibodies were used to examine the subcellular locations of 11 glycolytic and fermentative enzymes in Zymomonas mobilis. Glucose-fructose oxidoreductase was clearly localized in the periplasmic region. Phosphogluconate lactonase and alcohol dehydrogenase I were concentrated in the cytoplasm near the plasma membrane. The eight remaining enzymes were more evenly distributed within the cytoplasmic matrix. Selected enzyme pairs were labeled on opposite sides of the same thin section to examine the frequency of colocalization. Results from these experiments provide evidence that glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, and alcohol dehydrogenase I form an enzyme complex.
Efficient Magnesium Catalysts for the Copolymerization of Epoxides and CO2; Using Water to Synthesize Polycarbonate Polyols (2012)

The synthesis and characterization of three highly active dimagnesium catalysts for the copolymerization of cyclohexene oxide and carbon dioxide, active under just 1 atm of carbon dioxide pressure, are reported. The catalysts have turnover numbers up to 6000 and turnover frequencies of up to 750 h(-1). These values are, respectively, 75 and 20 times higher than those of the other three known magnesium catalysts. Furthermore, the catalysts operate at 1/500th the loading of the best reported magnesium catalyst. The catalyst selectivities are excellent, yielding polymers with 99% carbonate repeat units and >99% selectivity for copolymer. Using a dimagnesium bis(trifluoroacetate) catalyst, and water as a renewable chain transfer reagent, poly(cyclohexene carbonate) polyols are synthesized with high selectivity.
Programmable via Using Indirectly Heated Phase-Change Switch for Reconfigurable Logic Applications (2008)

A novel concept for a programmable via using an indirectly heated phase-change switch is proposed and fabricated successfully. In this device concept, circuits associated with the programmable via are decoupled from the configuration circuits by using an independently contacted heater electrode. We demonstrate the prototype device in a standard 180-nm CMOS copper back-end technology.
Physiological factors involved in the transformation of Mycobacterium smegmatis (1978)

Transfer of streptomycin resistance and changes from methionine and leucine auxotrophy to prototrophy were achieved in Mycobacterium smegmatis by transformation. Recipient cells were more resistant to mitomycin C and methyl methlanesulfonate treatments than were wild-type cells. A high level of calcium ions was essential for transformation, especially during DNA adsorption, whereas the presence of magnesium ions and the exposure of recipient cells to mild doses of UV light enhanced recombination frequencies. Transformants were not isolated when recipient cell-DNA mixtures were first treated with deoxyribonuclease. Recipient cells at various stages of growth showed similar transformabilities. Transformation was successful only when recipient cells were incubated on rich agar medium after mixture with DNA. Exposure of recipient cells to Pronase before treatment with donor DNA did not affect transformation, suggesting the absence of a protein competence factor. Throughout the present experiments, cotransformation frequencies were very low and unselected-marker segregation patterns were independent, indicating that the methionine, leucine, and streptomycin markers are not closely linked in M. smegmatis.
New Opportunities for the Drilling Industry Through Innovative Emulsifier Chemistry (2003)

Abstract As the drilling industry operates in more stringent environmental constraints and conservative economical environment, the industry is poised to take advantage of innovative emulsifiers for new opportunities in solving the environmental problems and offer economical advantages over conventional invert emulsion drilling fluids. We have developed various innovative invert emulsion drilling fluids using novel emulsifiers. These systems provide a quantum leap in new drilling fluid technology in solving environmental problems while offering economical advantages over conventional invert emulsion drilling fluids. Since, the inception of invert emulsion drilling fluids decades ago, emulsifier technology for these systems has not advanced much. The focal points in development in past history have been in base fluids, O/W ratios and some in weight materials, however very little has been changed in emulsifier chemistry. Only step-changes in technology have been achieved with changes in base-fluids and other parameters of invert emulsion drilling fluids. It is time to move on. Using innovative emulsifier chemistry has produced novel invert emulsion fluids, which address the environmental as well as performance and cost-related issues in drilling operations. This paper discusses the systematic design, development and testing of novel emulsifiers for innovative invert emulsion drilling fluids. The overall impact of manipulation of emulsifier chemistry in invert emulsion drilling fluids to meet the environmental and functional requirements of drilling operation is presented. The formulations and applications of lime-free high temperature invert emulsion drilling fluid, negative alkalinity ester-based fluid, and reversible invert emulsion drilling fluids in laboratory experiments as well as field trials are highlighted.
Structure—Function Relationships in Amylases (1991)

Chemical modification has been used in conjunction with site-directed mutagenesis to identify and assign specific functional roles to amino acid residues involved in substrate binding and catalysis in glucoamylase from Aspergillus niger and in barley α-amylase. Kinetic properties of selected mutant enzymes thus indicated that the Trp120 of glucoamylase stabilized the substrate transition state, while Glu179 and Asp176 behaved as the general acid and base catalyst, respectively. In barley α-amylase Glu205 was proposed as the general acid catalyst while Trp276 and Trp277 were influenced by binding of β-cyclodextrin, and hence starch granules, at a distance from the catalytic site. Structure comparison guided by functional residues suggested that most starch-degrading enzymes share key active site features. A few also contain homologous raw starch binding domains.
Human antibodies against spores of the genus Bacillus : A model study for detection of and protection against anthrax and the bioterrorist threat (2002)

A naive, human single-chain Fv (scFv) phage-display library was used in bio-panning against live, native spores of Bacillus subtilis IFO 3336 suspended in solution. A direct in vitro panning and enzyme-linked immunosorbent assay-based selection afforded a panel of nine scFv-phage clones of which two, 5B and 7E, were chosen for further study. These two clones differed in their relative specificity and affinity for spores of B. subtilis IFO 3336 vs. a panel of spores from 11 other Bacillus species/strains. A variety of enzyme-linked immunosorbent assay protocols indicated these scFv-phage clones recognized different spore epitopes. Notably, some spore epitopes markedly changed between the free and microtiter-plate immobilized state as revealed by antibody-phage binding. An additional library selection procedure also was examined by constructing a Fab chain-shuffled sublibrary from the nine positive clones and by using a subtractive panning strategy to remove crossreactivity with B. licheniformis 5A24. The Fab-phage clone 52 was improved compared with 5B and was comparable to 7E in binding B. subtilis IFO 3336 vs. B. licheniformis 5A24, yet showed a distinctive crossreactivity pattern with other spores. We also developed a method to directly detect individual spores by using fluorescently labeled antibody-phage. Finally, a variety of "powders" that might be used in deploying spores of B. anthracis were examined for antibody-phage binding. The strategies described provide a foundation to discover human antibodies specific for native spores of B. anthracis that can be developed as diagnostic and therapeutic reagents.
Chronic wound fluid—thinking outside the box (2011)

Chronic wounds are associated with an altered wound milieu that results from an imbalance in extracellular matrix (ECM) homeostasis. This alteration is characterized by an increased destruction and degradation of components of the ECM with a concomitant lack of synthesis of these elements. Traditionally wound fluid has been considered a reflection of the internal wound milieu. It has been used to monitor and reflect on the chronic status of a wound or to measure the efficacy of wound treatment. However, on closer inspection of chronic wound fluid, certain components of the fluid, particularly matrix metalloproteinases (MMPs) and their subcomponents (MMP-9) have been found to exist at higher levels in wound fluid than in the corresponding wound. There is mounting evidence that much of the destructive effects observed in chronic wounds may be compounded by components of the wound exudate which are corrosive in nature resulting in a continuum of ECM breakdown. Isolation of these components has identified MMPs, in particular MMP-9 as dominant in this destructive process. Additionally an association has been made between high bacterial levels and elevated MMP9 in chronic wounds. Agents that have efficacy against MMP-9 and significant antibacterial potency thus provide a dual defense against chronic wounds. It is likely that these agents cause a change in the chronic wound fluid components that more closely resemble the balance of proteases and growth factors seen acute wounds, thus triggering a positive wound healing process. Nanocrystalline silver appears to fulfill these criteria. A strategy is suggested whereby wound fluid is directly targeted to diminish the corrosive wound fluid elements in an attempt to break the ongoing destructive inflammatory cycle. This presents a relatively new treatment paradigm attempting to influence wound healing by working from without to initiate changes within.
One hundred patients with acute leukemia treated by chemotherapy, total body irradiation, and allogeneic marrow transplantation (1977)

One hundred patients, 54 with acute myelogenous leukemia (AML) and 46 with acute lymphoblastic leukemia (ALL), considered to be in the end stages of their disease, after combination chemotherapy were treated by marrow transplantation. All patients were given a marrow graft from an HLA-identical sibling after receiving 1000-rad total body irradiation (TBI). One group of 43 patients was given cyclophosphamide (CY), 60 mg/kg on each of 2 days, 5 and 4 days before TBI. In a second group of 31 patients, additional chemotherapy was given before CY and TBI. In a third group of 19 patients, BCNU was given before CY and TBI. A fourth group of 7 patients received other chemotherapy regimens before TBI. Six patients died 3–17 days after marrow infusion without evidence of engraftment. Ninety-four patients were engrafted and only one patient rejected the graft. Thirteen patients are alive with a marrow graft, on no maintenance antileukemic therapy, and without recurrent leukemia 1–4 1/2 yr after transplantation. Three have chronic graft-versus-host disease (GVHD). Four patients are alive 1 1/2 - 3 1/2 yr after grafting but have had a relapse of their leukemia. Of 93 evaluable patients, 19 did not develop GVHD and 24 developed very mild GVHD. Fifty patients developed moderate to severe GVHD, and 40 of these were treated with antithymocyte globulin. Interstitial pneumonia occurred in 54 patients and was the primary cause of death in 34. Interstitial pneumonia often occurred in association with GVHD and the most common etiologic agent was cytomegalovirus. A total of 31 patients have had a relapse of leukemia. There was no definite correlation between relapse of leukemia and the presence or absence of GVHD. The relapse rate appeared to be relatively constant over the first 2 yr and was extremely low after that time. Neither survival nor leukemic relapse appeared to be influenced by the type of leukemia nor by the preparative chemotherapy regimen given before TBI. Patients in fair clinical condition at the time of transplantation showed significantly longer survival times than patients in poor condition (p = 0.001). This observation, coupled with the observation that some patients may be cured of their disease, indicates that marrow transplantation should now be undertaken earlier in the management of patients with acute leukemia who have an HLA- matched sibling marrow donor.
A solution hybridization/RNase protection assay with riboprobes to determine absolute levels of apoB, A-I, and E mRNA in human hepatoma cell lines. (1990)

A solution hybridization/RNase protection assay with riboprobes was developed to quantitate apolipoprotein mRNA concentrations. Previously, radiolabeled DNA probes have been used in solution hybridization/S1 nuclease protection assays for this purpose. The new assay requires less time for probe preparation and hybridization compared to previous assays. In addition, the vector used for riboprobe preparation can also be used to conveniently produce cRNA required to generate the standard curve to quantitate absolute apolipoprotein mRNA levels. The solution hybridization RNase protection assay was used to quantitate apoB, A-I, and E mRNA levels in four human hepatoma cell lines, HepG2, Hep3B, WRL-68, SK-Hep2. HepG2 and Hep3B, but not WRL-68 and SK-Hep2 cells had concentrations of all three apolipoprotein mRNAs comparable to liver in vivo. These data suggest that HepG2 and Hep3B are suitable models to study liver specific apolipoprotein gene expression.
Basic mechanisms of itch (2011)

Chronic itch represents a burdensome clinical problem that can originate from a variety of aetiologies. Pruriceptive itch originates following the activation of peripheral sensory nerve endings following damage or exposure to inflammatory mediators and ascends to the brain through the spinal thalamic tract. Much insight has been gained into the understanding of the mechanisms underlying pruriceptive itch through studies using humans and experimental animals. More than one sensory nerve subtype is thought to subserve pruriceptive itch which includes both unmyelinated C-fibres and thinly myelinated Aδ nerve fibres. There are a myriad of mediators capable of stimulating these afferent nerves leading to itch, including biogenic amines, proteases, cytokines, and peptides. Some of these mediators can also evoke sensations of pain and the sensory processing underlying both sensations overlaps in complex ways. Studies have demonstrated that both peripheral and central sensitization to pruritogenic stimuli occur during chronic itch.
Structure and Biological Role of Vitronectin (1991)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
New Principles for Glycoside‐Bond Formation (2009)

Increased understanding of the important roles that oligosaccharides and glycoconjugates play in biological processes has led to a demand for significant amounts of these materials for biological, medicinal, and pharmacological studies. Therefore, tremendous effort has been made to develop new procedures for the synthesis of glycosides, whereby the main focus is often the formation of the glycosidic bonds. Accordingly, quite a few review articles have been published over the past few years on glycoside synthesis; however, most are confined to either a specific type of glycoside or a specific strategy for glycoside synthesis. In this Review, new principles for the formation of glycoside bonds are discussed. Developments, mainly in the last ten years, that have led to significant advances in oligosaccharide and glycoconjugate synthesis have been compiled and are evaluated.