gebhart/patrepeval huggingface dataset:
Intra-operative measurement and real-time visualization of the articulation of replaced knee joint surfaces during total knee anthroplasty (2002)

This study aims at establishing a system capable of evaluating knee-joint kinematics during total knee arthroplasty (TKA). This enables one to optimize the implantation of the prosthesis and the level of the joint line, intraoperatively. To achieve this the authors combined two different types of data (6-DOF kinematic data of knee movement obtained by a photostereometric system and an accurate computer model of the joint surfaces) in order to compute the articulation of replaced joint surfaces. To visualize this time-varying intersurface relationship on a real-time basis, the authors employed a distance-map technique, capable of visualizing the proximity and contact of opposing surfaces. Through cadaveric experiments, the articulation was verified to be visualized by using a wireframe-based animation at a rate of 25 frames per second, and the distance map with a surface resolution of 1 mm was verified to be updated at a rate of 10 frames per second.
Activation of Exocytosis by the Heterotrimeric G Protein G i3 (1993)

Secretagogues of rat peritoneal mast cells, such as mastoparan and compound 48/80, induce mast cell exocytosis by activating directly the guanosine triphosphate-binding proteins that are required for exocytosis. The introduction of a synthetic peptide that corresponds to the carboxyl-terminal end sequence of G alpha i3 into the cells specifically blocked this secretion. Similar results were obtained when antibodies to this peptide were introduced. The G alpha i3 was located in both the Golgi and the plasma membrane, but only the latter source of G alpha i3 appeared to be essential for secretion. These results indicate that G alpha i3 functions to control regulated exocytosis in mast cells.
Smart microplates: integrated photodiodes for detecting bead-based chemiluminescent reactions (2006)

A photodiode, integrated into a micromachined silicon pyramidal cavity for the purpose of detecting bead-based chemiluminescent reactions has been devised and fabricated. A large amount of previous work on the optical detection of chemical/biological reactions has concentrated on either improving the signal processing capabilities of planar, imager-like, detectors or developing a dedicated detector for sensing one specific phenomenon at a time. In our platform photodiodes are designed to be directly integrated into micromachined cavities in an array, reminiscent of a microplate, which potentially enables multi-analyte capabilities. Additionally, a concept of accessing a photodiode using inductive coupling, i.e. using a non-contact wireless reading, is introduced and demonstrated.
Adaptive data rate using ARQ and nonuniform constellations (2002)

We introduce an automatic repeat request (ARQ) scheme that uses nonuniform signal constellations in order to adapt the data rate to the received signal-to-noise ratio (SNR) in a fading channel without using channel state feedback or incremental redundancy. We have defined nonuniform phase shift key (PSK) and quadrature amplitude modulation (QAM) constellations with an arbitrary number of classes of bits. These constellations may also be of interest for further research into unequal error protection. We present simulations of the throughput in Rayleigh fading and lognormal shadowing, and discuss the cases where our proposed scheme may improve the throughput compared to standard ARQ using uniform signal constellations.
Decision support system for dynamic production scheduling (2003)

This paper presents a system to support decision-making of the production manager when scheduling the manufacturing orders. This system is mainly appropriate for small and medium size enterprises with productive systems like batch or job-shop. The manufacturing orders are dynamically scheduled considering namely deadlines and resource allocation. The system combines three modules: pre-scheduling, dynamic scheduling and re-scheduling. Each module applies heuristics to select the best solutions depending on the scheduling policies defined by the production manager.
Fabrication of Complex Three-Dimensional Microchannel Systems in PDMS (2002)

This paper describes a method for fabricating three-dimensional (3D) microfluidic channel systems in poly(dimethylsiloxane) (PDMS) with complex topologies and geometries that include a knot, a spiral channel, a "basketweave" of channels, a chaotic advective mixer, a system with "braided" channels, and a 3D grid of channels. Pseudo-3D channels, which are topologically equivalent to planar channels, are generated by bending corresponding planar channels in PDMS out of the plane into 3D shapes. True 3D channel systems are formed on the basis of the strategy of decomposing these complex networks into substructures that are planar or pseudo-3D. A methodology is developed that connects these planar and/or pseudo-3D structures to generate PDMS channel systems with the original 3D geometry. This technique of joining separate channel structures can also be used to create channel systems in PDMS over large areas by connecting features on different substrates. The channels can be used as templates to form 3D structures in other materials.
The Role of CBP in Estrogen Receptor Cross-Talk with Nuclear Factor-κB in HepG2 Cells (2000)

Functional interactions or cross-talk between ligand-activated nuclear receptors and the proinflammatory transcription factor nuclear factor-kappaB (NF-kappaB) may play a major role in ligand-mediated modification of diseases processes. In particular, the cardioprotective effects of estrogen replacement therapy are thought to be due in part to the ability of ligand-bound estrogen receptor (ER) to inhibit NF-kappaB function. In the current study 17beta-estradiol-bound ERalpha interfered with cytokine-induced activation of a NF-kappaB reporter in HepG2 cells. The estrogen metabolite, 17alpha-ethinyl estradiol, and the phytoestrogen, genistein, were also effective inhibitors of NF-kappaB activation, whereas tamoxifen, 4-hydroxytamoxifen, and raloxifene were inactive. This inhibition was reciprocal, as NF-kappaB interfered with the trans-activation properties of ERalpha. Ligand-bound ERalpha did not inhibit NF-kappaB binding to DNA, but it did decrease the histone acetyltransferase activity required for NF-kappaB transcriptional activity. Coexpression of the transcription coactivator CREB binding protein (CBP), but not steroid receptor coactivator 1a, reversed the ERalpha-mediated inhibition of NF-kappaB activity. Mammalian two-hybrid experiments also revealed that ligand-bound ERalpha can interact functionally with CBP-NF-kappaB complexes. We suggest that CBP targeting by ERalpha results in the inhibition of NF-kappaB and may occur through formation of transcriptionally inert multimeric complexes that are dependent upon the nature of the ERalpha ligand.
Partial Rescue of the Vif-Negative Phenotype of Mutant Human Immunodeficiency Virus Type 1 Strains from Nonpermissive Cells by Intravirion Reverse Transcription (2000)

Virion infectivity factor (Vif) is a protein encoded by human immunodeficiency virus type I (HIV-1) and is essential for viral replication. It appears that Vif functions in the virus-producing cells and affects viral assembly. Viruses with defects in the vif gene (vif-) generated from the "nonpermissive cells" are not able to complete reverse transcription. In previous studies, it was demonstrated that defects in the vif gene also affect endogenous reverse transcription (ERT) when mild detergents were utilized to permeabilize the viral envelope. In this report, we demonstrate that defects in the vif gene have much less of an effect on ERT if detergent is not used. When ERT was driven by addition of deoxyribonucleoside triphosphates (dNTPs) at high concentrations, certain levels of plus-strand viral DNA could also be achieved. Interestingly, if vif- viruses, generated from nonpermissive cells and harboring large quantities of viral DNA generated by ERT, were allowed to infect permissive cells, they could partially bypass the block at intracellular reverse transcription, through which vif- viruses without dNTP treatment could not pass. Consequently, viral infectivity can be partially rescued from the vif- phenotype. Based on our observations, we suggest that vif defects may cause the reverse transcription complex (RT complex) to become sensitive to mild detergent treatments within HIV-1 virions and become unstable in the target cells, such that the process of reverse transcription cannot be efficiently supported. Further dissection of RT complexes of vif- viruses may be key to uncovering the molecular mechanism(s) of Vif in HIV-1 pathogenesis.
PDE4 inhibitors: current status (2008)

Phosphodiesterase4 inhibitors are currently under development for the treatment of respiratory diseases including asthma and chronic obstructive pulmonary disease. The rationale for the development of this drug class stems from our understanding of the role of PDE4 in suppressing the function of a range of inflammatory and resident cells thought to contribute toward the pathogenesis of these diseases. Similarly, numerous preclinical in vivo studies have shown that PDE4 inhibitors suppress characteristic features of these diseases, namely, cell recruitment, activation of inflammatory cells and physiological changes in lung function in response to a range of insults to the airways. These potentially beneficial actions of PDE4 inhibitors have been successfully translated in phase II and III clinical trials with roflumilast and cilomilast. However, dose limiting side effects of nausea, diarrhoea and headache have tempered the enthusiasm of this drug class for the treatment of these respiratory diseases. A number of strategies are currently being pursued in attempts to improve clinical efficacy and reduce side effects, including delivery via the inhaled route, and/or development of non-emetic PDE4 inhibitors and mixed PDE inhibitors.
Endonuclease V of Escherichia coli. (1977)

A small endodeoxyribonuclease )2.3 S) that is active on single-stranded DNA has been extensively purified from Escherichia coli so as to be free of other known DNases. It has an alkaline pH optimum (9.5), requires Mg2+, and makes 3'-hydroxy and 5'-phosphate termini. The nuclease nicks duplex DNA, particularly if treated with OsO4, irradiated with ultraviolet light, or exposed to pH 5. The uracil-containing duplex DNA from the Bacillus subtilis phage PBS-2 is an especially good substrate; it is made acid-soluble by levels of the enzyme which fail to produce any acid-soluble material in other single-stranded or duplex DNAs. Neither RNA nor RNA-DNA hybrid are degraded by the enzyme. The enzyme specificity suggests that it might act at abnormal regions in DNA, so that its in vivo function could be to initiate an excision repair sequence. Its high activity on uracil-containing DNA could imply that the enzyme provides an alternative mechanism for excising uracil residues from DNA to the pathway utilizing uracil-DNA N-glycosidase. We suggest that this enzyme be designated as endonuclease V of E. coli.
Murine macrophage heparanase: Inhibition and comparison with metastatic tumor cells (1987)

Circulating macrophages and metastatic tumor cells can penetrate the vascular endothelium and migrate from the circulatory system to extravascular compartments. Both activated murine macrophages and different metastatic tumor cells (B16-BL6 melanoma; ESb T-lymphoma) attach, invade, and penetrate confluent vascular endothelial cell monlayer in vitro, by degrading heparan sulfate proteoglycans in the subendothelial extracellular matrix. The sensitivity of the enzymes from the various sources degrading the heparan sulfate proteoglycan was challenged and compared by a series of inhibitors. Activated macrophages demonstrate a heparanase with an endoglycosidase activity that cleaves from the [35S]O4 = -labeled heparan sulfate proteoglycans of the extracellular matrix 10 kDa glycosaminoglycan fragments. The macrophages do not store the heparanase intracellularly but it is instead found pericellularly and requires a continuous cell-matrix contact at the optimal pH for maintaining cell growth. The degradation of [35S]O4 = -labeled extracellular matrix proteoglycans by the macrophages' heparanase is significantly inhibited in the presence of heparan sulfate (10 micrograms/ml), arteparon (10 micrograms/ml), and heparin at a concentration of 3 micrograms/ml. In contrast, other glycosaminoglycans such as hyaluronic acid, dermatan sulfate, and chondroitin sulfate as well as the specific inhibitor of exo-beta-glucuronidase D-saccharic acid 1,4-lactone failed to inhibit the degradation of sulfated proteoglycans in the subendothelial extracellular matrix. Degradation of this heparan sulfate proteoglycan is a two-step sequential process involving protease activity followed by heparanase activity. However, the following antiproteases--alpha 2-macroglobulin, antithrombin III, leupeptin, and phenylmethylsulfony fluoride (PMSF)--failed to inhibit this degradation process, and only alpha 1-antitrypsin inhibited the heparanase activity. B16-BL6 metastatic melanoma cell heparanase, which is also a cell-associated enzyme, was inhibited by heparin to the same extent as the macrophage heparanase. On the other hand, heparanase of the highly metastatic variant (ESb) of a methylcholanthrene-induced T lymphoma, which is an extracellular enzyme released by the cells to the incubation medium, was more sensitive to heparin and arteparon than the macrophages' heparanase, inhibited at concentrations of 1 and 3 micrograms/ml, respectively. These results may indicate the potential use of heparin or other glycosaminoglycans as specific and differential inhibitors for the formation in certain cases of blood-borne tumor metastasis.
Optics of the Human Eye (2017)

The first stage in the process of vision is the formation of images of the outside world on the retina at the back of the eye. This article describes the optical structure and optical properties of the human eye, how the retinal image is formed and the factors affecting its quality. Brief mention is given to neural factors that combine with the optics to determine how well we see. The article concentrates on the optics of healthy eyes.
Detection and mitigation of signaling storms in mobile networks (2016)

Mobile Networks are subject to "signaling storms" launched by malware or apps, which overload the the bandwidth at the cell, the backbone signaling servers, and Cloud servers, and may also deplete the battery power of mobile devices. This paper reviews the subject and discusses a novel technique to detect and mitigate such signaling storms. Through a mathematical analysis we introduce a technique based on tracking time-out transitions in the signaling system that can substantially reduce both the number of misbehaving mobiles and the signaling overload in the backbone.
Inhibitory Effects of a Chemically Standardized Extract from Scutellaria barbata in Human Colon Cancer Cell Lines, LoVo (2005)

Scutellaria barbata (SB) is a medicinal plant that contains flavonone compounds such as scutellarein, scutellarin, carthamidin, isocarthamidin, and wogonin. A functional proteomic approach was used to study the inhibitory effects of a chemically standardized extract from SB in human colon adrencarcinoma, LoVo. In this work, a stable isotope was not used in the proposed method developed. The whole cell lysates from the control and treated cells were digested with trypsin, and the peptides were separated by two-dimensional (cation-exchange and reversed-phase) liquid chromatography and tandem mass spectrometry. The differentially expressed proteins identified using the current approach supported the data obtained from cell-cycle analysis with flow cytometry. With flow-cytometry analysis, a significant increase in the sub G1 phase was observed with a higher dose of extract from SB. Our results suggest that the chemically standardized extract from SB can induce cell death in the human colon cancer cell line. Our current work showed that the proposed platform provided a rapid approach to study the molecular mechanism because of the inhibitory effects of different doses of the botanical extracts on LoVo cell lines. This included a network of proteins involved in metabolism, regulation of the cell cycle, and transcription-factor activity.
Intralymphatic immunization enhances DNA vaccination (2001)

Although DNA vaccines have been shown to elicit potent immune responses in animal models, initial clinical trials in humans have been disappointing, highlighting a need to optimize their immunogenicity. Naked DNA vaccines are usually administered either i.m. or intradermally. The current study shows that immunization with naked DNA by direct injection into a peripheral lymph node enhances immunogenicity by 100- to 1,000-fold, inducing strong and biologically relevant CD8(+) cytotoxic T lymphocyte responses. Because injection directly into a lymph node is a rapid and easy procedure in humans, these results have important clinical implications for DNA vaccination.
Sensitive fluorescence detection of polyphosphate in polyacrylamide gels using 4′,6‐diamidino‐2‐phenylindol (2007)

PAGE is commonly used to identify and resolve inorganic polyphosphates (polyP). We now report highly sensitive and specific staining methods for polyP in polyacrylamide gels based on the fluorescent dye, 4',6-diamidino-2-phenylindol (DAPI). DAPI bound to polyP in gels fluoresced yellow while DAPI bound to nucleic acids or glycosaminoglycans fluoresced blue. Inclusion of EDTA prevented staining of glycosaminoglycans by DAPI. We also identified conditions under which DAPI that was bound to polyP (but not nucleic acids or other anionic polymers) rapidly photobleached. This allowed us to develop an even more sensitive and specific negative staining method that distinguishes polyP from nucleic acids and glycosaminoglycans. The lower LOD using DAPI negative staining was 4 pmol (0.3 ng) phosphate per band, compared to conventional toluidine blue staining with a lower LOD of 250 pmol per band.
fairseq: A Fast, Extensible Toolkit for Sequence Modeling (2019)

Myle Ott, Sergey Edunov, Alexei Baevski, Angela Fan, Sam Gross, Nathan Ng, David Grangier, Michael Auli. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics (Demonstrations). 2019.
Effect of proANF-(31--67) on sodium excretion in conscious monkeys (1995)

The purpose of this study was to determine the effect of proANF-(31--67) on renal function in conscious, chronically instrumented monkeys (Macaca fascicularis). The experimental protocol consisted of a 30-min control period followed by 60 min of peptide infusion and a 30-min recovery period. Atrial natriuretic factor (ANF)-(99--126), proANF-(31--67), of a combination of ANF-(99--126) plus proANF-(31--67) was infused at 15 pmol.kg-1.min-1. ANF-(99--126) caused sodium excretion to increase from 12.5 +/- 3 to a peak of 37.9 +/- 10.4 mueq/min, whereas fractional sodium excretion (FENa) increased from 0.69 +/- 0.2 to 2.3 +/- 0.43%. ProANF-(31--67) increased sodium excretion from 12.7 +/- 5 to a peak of 23.3 +/- 9.0 mueq/min and FENa from 0.56 +/- 0.07 to a peak of 1.15 +/- 0.4%. When ANF-(99--126) and proANF-(31--67) were infused in combination, sodium excretion increased from 9.6 +/- 3 to a peak of 5.19 +/- 12.5 mueq/min, whereas FENa increased from 0.97 +/- 0.4 to 3.9 +/- 1.1%. Mean arterial pressure decreased by approximately 10 mmHg in all three groups. These findings indicate that intravenously administered proANF-(31--67) causes an increase in sodium excretion and that when proANF-(31--67) and ANF-(99--126) are given in combination, they act in an additive fashion to increase renal sodium excretion.
Point-to-Point Positioning of Flexible Structures Using a Time Domain LQ Smoothness Constraint (1992)

An analytical procedure to implement optimal smoothing of the finite-time control waveform for point-to-point control problem is presented, which minimizes an optimality constraint consisting of a linear combination of the quadratic norms of its time derivatives. It is shown that the resulting control input is essentially the minimum norm solution augmented to satisfy some additional continuity requirements in the time domain. Application of the proposed technique to finite-time maneuvering of flexible structures is experimentally demonstrated and performances are compared using control torques evaluated based on different order of the smoothness constraint and order of the truncated plant model.
Macrocyclic [N42-] Coordinated Nickel Complexes as Catalysts for the Formation of Oxalate by Electrochemical Reduction of Carbon Dioxide (2000)

The macrocyclic nickel complexes shown in Figure 1 are able to catalyze the electrochemical reduction of CO2 to oxalate. In the case of the complexes with R2 = COOEt or COMe, the overall reaction can be interpreted in terms of an outer-sphere electron-transfer reaction (6) followed by a dimerization of the CO2•- radical anions (7), but the variation of the electron-transfer rate constants with the standard potentials points to a coordinative interaction between the complexes and the CO2 molecule. Complexes without COOEt or COMe substitution in the R2 position undergo a fast deactivation reaction (first order with respect to [CO2]) that is even visible in the time scale of the cyclic voltammetric experiments. The results of the cyclic voltammetric investigations could be confirmed in preparative-scale electrolyses where the complex Ni−Etn(Me/COOEt)Etn proved to be the most active and persistent redox catalyst for the electrochemical reduction of CO2 to oxalate that has been described so far.
Comparative analysis of Brucella serotype A and M and Yersinia enterocolitica O:9 polysaccharides for serological diagnosis of brucellosis in cattle, sheep, and goats (1993)

Hapten polysaccharides of Brucella smooth M and A serotypes were prepared from Brucella sp. and Yersinia enterocolitica O:9 by previously described hydrolytic (O chain) or nonhydrolytic (native hapten [NH]) procedures. The purified polysaccharides differed only in the presence (O chain) or absence (NH) of lipopolysaccharide core sugars. The polysaccharides were compared by reverse radial immunodiffusion for the diagnosis of brucellosis in cattle (Brucella abortus biotype 1 [A serotype] and Brucella melitensis biotype 3 [AM serotype]), sheep (B. melitensis biotypes 1 [M serotype] and 3), and goats (B. melitensis biotype 1). The reverse radial immunodiffusion test with the NH from B. melitensis 16 M (serotype M) showed the highest sensitivity (89.6 to 97.3%), regardless of the host species and the serotype of the infecting Brucella sp. Y. enterocolitica O:9 NH (A serotype) was useful for diagnosing disease in cattle infected with B. abortus biotype 1, but not in cattle infected with B. melitensis biotype 3, sheep, or goats. The different results obtained with the serotype M and A polysaccharides and the sera from animals infected with M, A, and AM serotypes of Brucella spp. showed that in naturally infected animals, a large proportion of the antibodies are directed to or react with a previously defined common epitope(s) (J. T. Douglas and D. A. Palmer, J. Clin. Microbiol. 26:1353-1356, 1988) different from the A or M epitopes. By using the radial immunodiffusion test with B. melitensis 16M NH, it was possible to differentiate infected from vaccinated cattle, sheep, and goats with a sensitivity and specificity similar to that of the complement fixation test.