gebhart/patrepeval huggingface dataset:
A Bipedal DNA Brownian Motor with Coordinated Legs (2009)

A substantial challenge in engineering molecular motors is designing mechanisms to coordinate the motion between multiple domains of the motor so as to bias random thermal motion. For bipedal motors, this challenge takes the form of coordinating the movement of the biped's legs so that they can move in a synchronized fashion. To address this problem, we have constructed an autonomous DNA bipedal walker that coordinates the action of its two legs by cyclically catalyzing the hybridization of metastable DNA fuel strands. This process leads to a chemically ratcheted walk along a directionally polar DNA track. By covalently cross-linking aliquots of the walker to its track in successive walking states, we demonstrate that this Brownian motor can complete a full walking cycle on a track whose length could be extended for longer walks. We believe that this study helps to uncover principles behind the design of unidirectional devices that can function without intervention. This device should be able to fulfill roles that entail the performance of useful mechanical work on the nanometer scale.
Synthesis of 1,5-Anhydro-D-Mannitol Nucleosides with a Purine Base Moeety (1998)

Abstract D-Mannitol nucleosides with a purine base moiety have been conveniently synthesized strating from 1,5-anhydro-4,6-O-benzylidene-D-glucitol. The 3-OH function of 1,5-anhydro-4,6-O-benzylidene-D-glucitol was selectively protected with t-butyldimethylsilyl group and subsequently converted to the corresponding 0-triflate derivative for the introduction of the nucleobase moietes. These nucleoside derivatives were transformed to 1,5-Anhydro-6-O-MMTr-2-(N6-benzoyladenin-9-yl)-2-deoxy-3-O-TBDMS-D-mannitol and 1,5-Anhydro-6-O-MMTr-2-(N2-isobutyryl-guanin-9-yl)-2-deoxy-3-O-TBDMS-D-mannitol, useful as the building blocks for oligonucleotide synthesis. Also, the synthesis of the corresponding fully deprotected anhydrohexitol nucleosides were achieved for evaluation of antiviral activity test.
100-W CW cladding-pumped Raman fiber laser at 1120 nm (2010)

We report a 100 W continuous-wave cladding-pumped fiber Raman laser operating at 1120 nm. The fiber Raman laser consists of an 85 m long germanium-doped double-clad fiber in a 4% - 100% linear cavity, which is end-pumped by a multimode ytterbium-doped fiber laser source at 1064 nm. The Raman laser has a slope efficiency of 71% with respect to launched pump power. The laser output M<sup>2</sup> is measured to be ~ 1.6 at 80 W of output power.
Temporospatial cell interactions regulating mandibular and maxillary arch patterning (2000)

The cellular origin of the instructive information for hard tissue patterning of the jaws has been the subject of a long-standing controversy. Are the cranial neural crest cells prepatterned or does the epithelium pattern a developmentally uncommitted population of ectomesenchymal cells? In order to understand more about how orofacial patterning is controlled we have investigated the temporal signalling interactions and responses between epithelium and mesenchymal cells in the mandibular and maxillary primordia. We show that within the mandibular arch, homeobox genes that are expressed in different proximodistal spatial domains corresponding to presumptive molar and incisor ectomesenchymal cells are induced by signals from the oral epithelium. In mouse, prior to E10, all ectomesenchyme cells in the mandibular arch are equally responsive to epithelial signals such as Fgf8, indicating that there is no pre-specification of these cells into different populations and suggesting that patterning of the hard tissues of the mandible is instructed by the epithelium. By E10.5, ectomesenchymal cell gene expression domains are still dependent on epithelial signals but have become fixed and ectopic expression cannot be induced. At E11 expression becomes independent of epithelial signals such that removal of the epithelium does not affect spatial ectomesenchymal expression. Significantly, however, the response of ectomesenchyme cells to epithelial regulatory signals was found to be different in the mandibular and maxillary primordium. Thus, whereas both mandibular and maxillary arch epithelia could induce Dlx2 and Dlx5 expression in the mandible and Dlx2 expression in the maxilla, neither could induce Dlx5 expression in the maxilla. Reciprocal cell transplantations between mandibular and maxillary arch ectomesenchymal cells revealed intrinsic differences between these populations of cranial neural crest-derived cells. Research in odontogenesis has shown that the oral epithelium of the mandibular and maxillary primordia has unique instructive signaling properties required to direct odontogenesis, which are not found in other branchial arch epithelia. As a consequence, development of jaw-specific skeletal structures may require some prespecification of maxillary ectomesenchyme to restrict the instructive influence of the epithelial signals and allow development of maxillary structures distinct from mandibular structures.
Fibroblast Growth Factor Receptor-1 Signaling in Pancreatic Islet β-Cells Is Modulated by the Extracellular Matrix (2007)

Maintenance of pancreatic beta-cell mass depends on extracellular stimuli that promote survival and proliferation. In the islet, these stimuli come from the beta-cell microenvironment and include extracellular matrix deposited by associated vascular endothelial cells. Fibroblast growth factor receptor-1 (FGFR1) has recently been implicated as a signaling pathway that is important for normal beta-cell function. We would like to understand how extracellular matrix and FGFR1 signaling interact to promote beta-cell survival and proliferation. To examine beta-cell-specific receptor responses, we created lentiviral vectors with rat insulin promoter-driven expression of Venus fluorescent protein-tagged full-length (R1betav) and kinase-deficient (KDR1betav) FGFR1. Significant FGF-1-dependent activation of ERK1/2 was observed in betaTC3 cells, dispersed beta-cells, and beta-cells in intact islets. This response was enhanced by R1betav expression and reduced by KDR1betav expression. Plating-dispersed beta-cells on collagen type IV resulted in enhanced expression of endogenous FGFR1 that was associated with sustained activation of ERK1/2. Conversely, plating cells on laminin reduced expression of FGFR1, and this reduction was associated with transient activation of ERK1/2. Addition of neutralizing antibodies to inhibit beta-cell attachment to laminin via alpha(6)-integrin increased high-affinity FGF-1-binding at the plasma membrane and resulted in sustained ERK1/2 activity similar to cells plated on collagen type IV. These data show that the FGF-stimulated beta-cell response is negatively affected by alpha(6)-integrin binding to laminin and suggest regulation associated with vascular endothelial cell remodeling.
Performance optimization by dynamic code transformation (2011)

Even parts of a program that are sequential or just inherently difficult to parallelize can be optimized for ILP. For instance, eliminating loop overheads and potential pipeline stalls from control flow can alleviate performance bottle-necks. Unfortunately, static compilation is limited in the extent to which it can identify opportunities to apply such optimizations. Generating code dynamically at run time, however, create much more efficient applications by usin information not available at compile time. We demonstrate our approach on a sparse-matrix PET scan code by aggressive unrolling loops and specializing code via dynamic code generation. We leverage task-level parallelism by having an auxiliary processor core concurrently generate code and feed it to the core executing the application. Our approach to fast code generation leverages patching and concatenating prepared code skeletons.
A critical assessment of new therapies in inflammatory bowel disease (2002)

The only therapy in inflammatory bowel disease (IBD), which up to the mid-1990s was disease modifying, was immunosuppression with azathioprine. Other 'standard' therapies in IBD were merely symptomatic. With the advent of biological therapies, especially the chimeric monoclonal anti-TNF antibody infliximab, we start to target specific pathogenic disease mechanisms, which allow thorough suppression of the disease process and healing of the bowel in the long term. Moreover, infliximab is the only drug up to the present that allows short-term healing of fistulizing Crohn's disease. This therapy is, however, associated with problems of immunogenicity. The formation of antibodies to infliximab jeopardizes the efficacy and is associated with infusion reactions. Optimization of anti-TNF strategies will occur in the coming years. Another promising therapy is antagonization of alpha4 integrins and hence, of migration of inflammatory cells to the intestine. It can be expected that more simple therapies using small molecules that inhibit the key cytokines or pro-inflammatory processes will take over in the next decade. In the current and future approach to IBD therapy immunosuppression with azathioprine or 6-MP and methotrexate play a central role. At the present time, the combination of infliximab with azathioprine or methotrexate can be regarded as the new standard for the therapy of refractory Crohn's disease. In ulcerative colitis (UC) much less progress has been made and the value of biological therapy as well as of long-term management with immunosuppression remains controversial. Probiotics are an attractive treatment option for IBD but studies so far are small and data are not yet convincing.
Active membrane masks for improved overlay performance in proximity lithography (2004)

Membrane masks are thin (2 micron x 35 mm x 35 mm) structures that carry the master exposure patterns in proximity (X-ray) lithography. With the continuous drive to the printing of ever-finer features in microelectronics, the reduction of mask-wafer overlay positioning errors by passive rigid body positioning and passive stress control in the mask becomes impractical due to nano and sub-micron scale elastic deformations in the membrane mask. This paper describes the design, mechanics and performance of a system for actively stretching a membrane mask in-plane to control overlay distortion. The method uses thermoelectric heating/cooling elements placed on the mask perimeter. The thermoelectric elements cause controlled thermoelastic deformations in the supporting wafer, which in turn corrects distortions in the membrane mask. Silicon carbide masks are the focus of this study, but the method is believed to be applicable to other mask materials, such as diamond. Experimental and numerical results will be presented, as well as a discussion of the design issues and related design decisions.
MO-A-213AB-03: Commissioning of a Clinical Chair for Patients Treated in the Seated Position Using an Inclined Beam Line Treatment Room (2012)

Using in-house developed optical tracking system, the overall maximum displacement of treatment chair system from isocenter is within 3.0 mm with known sagging characteristics. This characterization is essential to reduce the total treatment time and limited the number of X-rays required for accurate patient alignment in the seated position.
Expression and Characterization of the Naturally Occurring Mutation L394R in Human γ-Glutamyl Carboxylase (2000)

Patients with mutation L394R in gamma-glutamyl carboxylase have a severe bleeding disorder because of decreased biological activities of all vitamin K-dependent coagulation proteins. Vitamin K administration partially corrects this deficiency. To characterize L394R, we purified recombinant mutant L394R and wild-type carboxylase expressed in baculovirus-infected insect cells. By kinetic studies, we analyzed the catalytic activity of mutant L394R and its binding to factor IX's propeptide and vitamin KH(2). Mutant L394R differs from its wild-type counterpart as follows: 1) 110-fold higher K(i) for Boc-mEEV, an active site-specific, competitive inhibitor of FLEEL; 2) 30-fold lower V(max)/K(m) toward the substrate FLEEL in the presence of the propeptide; 3) severely reduced activity toward FLEEL carboxylation in the absence of the propeptide; 4) 7-fold decreased affinity for the propeptide; 5) 9-fold higher K(m) for FIXproGla, a substrate containing the propeptide and the Gla domain of human factor IX; and 6) 5-fold higher K(m) for vitamin KH(2). The primary defect in mutant L394R appears to be in its glutamate-binding site. To a lesser degree, the propeptide and KH(2) binding properties are altered in the L394R mutant. Compared with its wild-type counterpart, the L394R mutant shows an augmented activation of FLEEL carboxylation by the propeptide.
Purification and Crystallization of the Alkaline Phosphatase of Escherichia coli* (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurification and Crystallization of the Alkaline Phosphatase of Escherichia coli*Michael H. Malamy and Bernard L. HoreckerCite this: Biochemistry 1964, 3, 12, 1893–1897Publication Date (Print):December 1, 1964Publication History Published online1 May 2002Published inissue 1 December 1964https://pubs.acs.org/doi/10.1021/bi00900a018https://doi.org/10.1021/bi00900a018research-articleACS PublicationsRequest reuse permissionsArticle Views1607Altmetric-Citations147LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effectiveness of Trailing Edge Active Flow Control on Pitch Control of an Unmanned Aerial Vehicle (2009)

A low-speed wind-tunnel study has made to explore the possibility of Gurney flap and Jet Flap as proposed pitch control effectors of an unmanned aerial vehicle at 20 m/s, yielding a Reynolds number of 375,000. Conventional control surface on the elevator of a one-third scale Extra 330 airplane has been replaced with a 3% Gurney flap at the trailing edge. The measurement results from a 6-component force balance suggest that the jet flap is capable of generating significant lift and rolling moments with realistic jet momentum coefficients. The comparison of coefficients of lift, drag and pitching moments for different configurations of active and conventional elevators have been made.
Structure of Mycobacteria: Recent Developments in Defining Cell Wall Carbohydrates and Proteins (1989)

Work from this laboratory on the immunogens of Mycobacterium species has focused on those based on carbohydrates (with a view to the development of specific tools for the serodiagnosis of mycobacterioses) and on the cell-wall proteins, as a source of protective immunity and as a means of observing specific delayed-type hypersensitivity. Most mycobacteria are endowed with specific, highly antigenic glycolipids that are powerful for the serodiagnosis of individual mycobacterial infections: e.g., the phenolic glycolipids of Mycobacterium leprae and Mycobacterium bovis, the glycopeptidolipids of the Mycobacterium avium complex, and the acylated trehalose-containing lipooligosaccharides of species such as Mycobacterium kansasii, Mycobacterium szulgai, and Mycobacterium malmoense. A search for analogous structures in Mycobacterium tuberculosis has revealed an antigenic diglycosyl diacylglycerol and the immunogenic phosphomannoinositides. Others have reported on the presence of a novel phenolic glycolipid in the Canetti strain of M. tuberculosis. The dominant carbohydrate-containing antigen of M. tuberculosis (responsible for the high-titer anti-arabinofuranosyl activity in tuberculous sera) is lipoarabinomannan, which has been purified in the native state from M. tuberculosis and shown to contain both phosphatidylinositol and phosphoinositol side-branches. The cell wall of M. tuberculosis--more precisely, the peptidoglycan skeleton--is a source of a few distinct, highly immunogenic protein antigens. The recognition, isolation, and characterization of these antigens will also be described.
Thickness Dependence of Gate Dielectric and Active Semiconductor on InGaZnO[sub 4] TFT Fabricated on Plastic Substrates (2008)

We investigated the thickness dependence of a room-temperature grown composite gate dielectric and an active semiconductor on the electrical characteristics of thin-film transistors (TFTs) fabricated on a polyethylene terephthalate substrate. The optimum gate dielectric and active semiconductor thickness were 300 and , respectively. The TFT showed a high field-effect mobility of , an on/off ratio of , a threshold voltage of , and a subthreshold swing of .
Power efficient Viterbi decoder based on pre-computation technique for portable digital multimedia broadcasting receiver (2007)

Digital multimedia broadcasting (DMB) is a reliable multi-service system for mobile and portable receivers. DMB system allows interference-free reception under the conditions of multipath propagation and transmission errors using coded orthogonal frequency division multiplexing modulation (COFDM) and unequal error protection (UEP) scheme. For error correction of portable DMB receivers, punctured convolutional code and viterbi decoder is developed but it needs lots of computations for real-time operation. So, it is desired to design a high speed and low-power hardware scheme for viterbi decoder. This paper proposes a combined add-compare-select (ACS) and path metric normalization (PMN) unit using pre-computation technique for DMB system. The proposed PMN unit reduces the critical path by applying fixed value selection algorithm using the comparison tree properties. We also propose an ACS structure using the decomposition and pre-computation technique for reducing the complexity of the adder, comparator and multiplexer. Simulation results shows that area, gate delay and power consumption are reduced about 3.78%, 23.80%, and 12.22%, respectively.
The protective effects of omega-6 fatty acids in experimental autoimmune encephalomyelitis (EAE) in relation to transforming growth factor-beta 1 (TGF-β1) up-regulation and increased prostaglandin E2 (PGE2) production (2000)

Polyunsaturated fatty acids are known to affect the immune response and administration of the omega-6 fatty acid linoleic acid has been reported to be beneficial in multiple sclerosis (MS) and EAE. In this study we have investigated the effects of oral feeding of plant lipid rich in the omega-6 fatty acid gamma-linolenic acid from Borago officinalis on acute and relapse disease and the immune response in EAE using SJL mice. EAE was induced by an encephalitogenic peptide (92-106) of myelin oligodendrocyte glycoprotein (MOG), and mice were fed the plant lipid daily from 7 days after EAE induction to assess the effects on acute disease and from day 25 to assess the effects on disease relapse. The clinical incidence and histological manifestations of acute EAE, and the clinical relapse phase of chronic relapsing EAE (CREAE) were markedly inhibited by omega-6 fatty acid feeding. A significant increase in the production of TGF-beta1 in response to concanavalin A (Con A) at day 13 and a significant increase in TGF-beta1 and PGE2 to Con A, PPD and MOG peptide (92-106) at day 21 were detected in spleen mononuclear cells from fatty acid-fed mice. There was no difference in interferon-gamma, IL-4 and IL-2 production between the fatty acid-fed and control groups. Significantly higher TGF-beta mRNA expression was found in the spleens of omega-6 fatty acid-fed mice at day 21. There were no differences in spleen cell proliferative response to Con A, PPD and MOG peptide (92-106). Biochemical analysis of spleen cell membrane fatty acids revealed significant increases in the eicosanoid precursor fatty acids dihomo-gamma-linolenic acid and arachidonic acid in response to gamma-linolenic acid feeding, indicating rapid metabolism to longer chain omega-6 fatty acids. These results show that oral feeding of gamma-linolenic acid-rich plant lipid markedly affects the disease course of acute EAE and CREAE and is associated with an increase in cell membrane long chain omega-6 fatty acids, production of PGE2 and gene transcription and, on activation, secretion of TGF-beta1.
Mammalian Oxygen Sensing, Signalling and Gene Regulation (2000)

Oxygen is essential to the life of all aerobic organisms. Virtually every cell type is able to sense a limited oxygen supply (hypoxia) and specifically to induce a set of oxygen-regulated genes. This review summarizes current concepts of mammalian oxygen-sensing and signal-transduction pathways. Since the discovery of the hypoxia-inducible factors (HIFs), a great deal of progress has been made in our comprehension of how hypoxia induces the expression of oxygen-regulated genes. The alpha subunit of the heterodimeric transcription factors HIF-1, 2 and 3 is unstable under normoxia but is rapidly stabilized upon exposure to hypoxic conditions. Following heterodimerization with the constitutively expressed beta subunit, HIFs activate the transcription of an increasing number of genes involved in maintaining oxygen homeostasis at the cellular, local and systemic levels.
A novel physical model for partial discharge in narrow channels (1999)

In order to reveal the mechanism of partial discharge (PD) in electrical trees, an artificial single channel is studied as model for tree channels. In a long-narrow channel, the behaviour of PD is similar to that in an actual tree. When the length of the channel is decreased, the /spl phi/-q-n pattern of PD in the channel changes from wing to turtle or rabbit like, and the range of light emission in the channel increases when the applied voltage is increased. Considering the influence of a PD on the total field distribution and thus on a later PD, a physical model is put forward to describe the PD behaviour. It is assumed that PD is induced by the high field at the needle tip, then propagates along the channel, and stops propagating when the field in the channel becomes lower than a critical value due to field divergence. Mathematical analysis on an ideal needle-plane electrode system clearly explains the physical meaning of the model. And the computer simulation by using the superposition method agrees with the experimental results very well. This model is also valid to describe the behaviour of PD in electrical trees.