gebhart/patrepeval huggingface dataset:
The reactive site loop of the serpin SCCA1 is essential for cysteine proteinase inhibition (1998)

The high-molecular-weight serine proteinase inhibitors (serpins) are restricted, generally, to inhibiting proteinases of the serine mechanistic class. However, the viral serpin, cytokine response modifier A, and the human serpins, antichymotrypsin and squamous cell carcinoma antigen 1 (SCCA1), inhibit different members of the cysteine proteinase class. Although serpins employ a mobile reactive site loop (RSL) to bait and trap their target serine proteinases, the mechanism by which they inactivate cysteine proteinases is unknown. Our previous studies suggest that SCCA1 inhibits papain-like cysteine proteinases in a manner similar to that observed for serpin-serine proteinase interactions. However, we could not preclude the possibility of an inhibitory mechanism that did not require the serpin RSL. To test this possibility, we employed site-directed mutagenesis to alter the different residues within the RSL. Mutations to either the hinge or the variable region of the RSL abolished inhibitory activity. Moreover, RSL swaps between SCCA1 and the nearly identical serpin, SCCA2 (an inhibitor of chymotrypsin-like serine proteinases), reversed their target specificities. Thus, there were no unique motifs within the framework of SCCA1 that independently accounted for cysteine proteinase inhibitory activity. Collectively, these data suggested that the sequence and mobility of the RSL of SCCA1 are essential for cysteine proteinase inhibition and that serpins are likely to utilize a common RSL-dependent mechanism to inhibit both serine and cysteine proteinases.
Compact, Tunable Optical Devices in Silicon-Oxynitride Waveguide Technology (2000)

We present an optical waveguide technology for low-loss, compact and tunable planar integrated optical devices. Examples of devices realized in this technology include finite and infinite impulse response (FIR and HR) filters and optical switches.
The receptor for interleukin 3 is selectively induced in human endothelial cells by tumor necrosis factor alpha and potentiates interleukin 8 secretion and neutrophil transmigration. (1993)

Interleukin (IL)-3 stimulates hemopoiesis in vitro. However, IL-3 is not normally found in bone marrow, raising doubts as to the in vivo role of IL-3. We have found that human umbilical vein endothelial cells (HUVEC) express functional high-affinity receptors for IL-3 after stimulation with tumor necrosis factor alpha (TNF-alpha), IL-1 beta, or lipopolysaccharide, and that this receptor is involved in inflammatory phenomena. TNF-alpha caused time- and dose-dependent up-regulation of mRNA for the IL-3 receptor alpha and beta chains, with maximal effects occurring 16-36 h after stimulation with TNF-alpha at 100 units/ml. Induction of mRNA correlated with protein expression on the cell surface as judged by monoclonal antibody staining and by the ability of HUVEC to specifically bind 125I-labeled IL-3. Scatchard analysis under optimal conditions of TNF-alpha stimulation revealed approximately 1500 IL-3 receptors per cell, which were of a high-affinity class (Kd = 500 pM) only. In contrast to a previous report, receptors for granulocyte-macrophage colony-stimulating factor could not be detected. IL-3 binding to TNF-alpha-activated HUVEC enhanced IL-8 production, E-selection expression, and neutrophil transmigration. The selective induction of a functional IL-3 receptor on endothelial cells suggests that, beyond hemopoiesis, IL-3 may have an important role in chronic inflammation and in allergic diseases.
The crystal structure of coenzyme B12‐dependent glycerol dehydratase in complex with cobalamin and propane‐1,2‐diol (2002)

Recombinant glycerol dehydratase of Klebsiella pneumoniae was purified to homogeneity. The subunit composition of the enzyme was most probably alpha 2 beta 2 gamma 2. When (R)- and (S)-propane-1,2-diols were used independently as substrates, the rate with the (R)-enantiomer was 2.5 times faster than that with the (S)-isomer. In contrast to diol dehydratase, an isofunctional enzyme, the affinity of the enzyme for the (S)-isomer was essentially the same or only slightly higher than that for the (R)-isomer (Km(R)/Km(S) = 1.5). The crystal structure of glycerol dehydratase in complex with cyanocobalamin and propane-1,2-diol was determined at 2.1 A resolution. The enzyme exists as a dimer of the alpha beta gamma heterotrimer. Cobalamin is bound at the interface between the alpha and beta subunits in the so-called 'base-on' mode with 5,6-dimethylbenzimidazole of the nucleotide moiety coordinating to the cobalt atom. The electron density of the cyano group was almost unobservable, suggesting that the cyanocobalamin was reduced to cob(II)alamin by X-ray irradiation. The active site is in a (beta/alpha)8 barrel that was formed by a central region of the alpha subunit. The substrate propane-1,2-diol and essential cofactor K+ are bound inside the (beta/alpha)8 barrel above the corrin ring of cobalamin. K+ is hepta-coordinated by the two hydroxyls of the substrate and five oxygen atoms from the active-site residues. These structural features are quite similar to those of diol dehydratase. A closer contact between the alpha and beta subunits in glycerol dehydratase may be reminiscent of the higher affinity of the enzyme for adenosylcobalamin than that of diol dehydratase. Although racemic propane-1,2-diol was used for crystallization, the substrate bound to glycerol dehydratase was assigned to the (R)-isomer. This is in clear contrast to diol dehydratase and accounts for the difference between the two enzymes in the susceptibility of suicide inactivation by glycerol.
Review: Molecular mimicry of host structures by lipopolysaccharides of Campylobacter and Helicobacter spp.: implications in pathogenesis (1996)

Molecular mimicry of host structures by the saccharide portion of lipopolysaccharide (LPS) contributes to the virulence of certain strains of mucosal pathogens. Mimicry by the low molecular weight (low-M r ) LPSs of Neisseria and Haemophilus spp. have been the most extensively studied. However, studies within the last decade have revealed other types of mimicry within the saccharide moieties of LPSs of the enteric pathogen Campylobacter jejuni and the gastroduodenal pathogen Helicobacter pylori. The core oligosaccharides of low-M r LPSs of C. jejuni serotypes which are associated with the development of Guillain-Barré syndrome (GBS), a neurological disorder, exhibit mimicry of gangliosides. Cross-reactive antibodies between LPSs and gangliosides which are induced during antecedent C. jejuni infection are considered to play an important role in GBS pathogenesis. The O-polysaccharide chains of high-M r LPSs of a number of H. pylori strains mimic Lewis x and/or Lewis y blood group antigens. This mimicry may camouflage the bacterium in the gastric mucosa upon initial infection. With the progression of infection, the mimicry may play a role in immune response regulation and the induction of autoantibodies against the gastric proton pump, a glycoprotein that also expresses Lewis antigens.
Under the fold (2013)

As the unemployed Frank is sinking into depression, his son's naïve but optimistic twist on the situation could be Frank's way out.
Tracking Manikin Tracheal Intubation Using Motion Analysis (2011)

It is feasible to track laryngoscope motion during manikin intubation comparing expert versus novice technique. Experts had a greater success rate, but longer path length, and took longer to achieve manikin intubation. Motion-tracking technology may provide an analytic tool to improve techniques of intubation.
Short-Term Storage of Human Spermatozoa in Electrolyte-Free Medium Without Freezing Maintains Sperm Chromatin Integrity Better Than Cryopreservation (2011)

Previous attempts to maintain human spermatozoa without freezing were based on short-term storage in component-rich medium and led to fast decline in motility and increased incidence of chromosome breaks. Here we report a new method in which sperm are maintained without freezing in an electrolyte-free medium (EFM) composed of glucose and bovine serum albumin. Human sperm were stored in EFM or human tubal fluid medium (HTFM) or were cryopreserved, and their motility, viability, and DNA integrity were examined at different intervals. Cryopreservation led to significant decline in sperm motility and viability and induced DNA fragmentation. Sperm stored in EFM maintained motility and viability for up to 4 and 7 wk, respectively, much longer than sperm stored in HTFM (<2 and <4 wk, respectively). DNA integrity, assessed with comet assay, was also maintained significantly better in EFM than in HTFM. One-week storage in EFM yielded motility and viability similar to that of cryopreserved sperm, but DNA integrity was significantly higher, resembling that of fresh sperm. After several weeks of storage in EFM, sperm were able to activate oocytes, undergo chromatin remodeling, and form normal zygotic chromosomes after intracytoplasmic sperm injection. This study demonstrated that human spermatozoa can be stored in EFM without freezing for several weeks while maintaining motility, viability, and chromatin integrity and that 1-wk storage in EFM offers better protection of sperm DNA integrity than cryopreservation. Sperm storage in EFM may become a viable option for the physicians working in assisted reproduction technology clinics, which would avoid cryodamage.
Global positioning system : theory and applications (1996)

Differential GPS and Integrity Monitoring Differential GPS Pseudolites Wide Area Differential GPS Wide Area Augmentation System Receiver Autonomous Integrity Monitoring Integrated Navigation Systems Integration of GPS and Loran-C GPS and Inertial Integration Receiver Autonomous Integrity Monitoring Availability for GPS Augmented with Barometric Altimeter Aiding and Clock Coasting GPS and Global Navigation Satellite System (GLONASS) GPS Navigation Applications Land Vehicle Navigation and Tracking Marine Applications Applications of the GPS to Air Traffic Control GPS Applications in General Aviation Aircraft Automatic Approach and Landing Using GPS Precision Landing of Aircraft Using Integrity Beacons Spacecraft Attitude Control Using GPS Carrier Phase Special Applications GPS for Precise Time and Time Interval Measurement Surveying with the Global Position System Attitude Determination Geodesy Orbit Determination Test Range Instrumentation.
The Impact of Aging on Sexual Function and Sexual Dysfunction in Women: A Review of Population-Based Studies (2005)

Age-related changes in sexually related personal distress may help explain why the prevalence of sexual dysfunctions remains constant with age while sexual function declines. More research is needed to demonstrate this.
Structural rearrangements of tubulin and actin during the cell cycle of the yeast Saccharomyces. (1984)

The distribution of actin and tubulin during the cell cycle of the budding yeast Saccharomyces was mapped by immunofluorescence using fixed cells from which the walls had been removed by digestion. The intranuclear mitotic spindle was shown clearly by staining with a monoclonal antitubulin; the presence of extensive bundles of cytoplasmic microtubules is reported. In cells containing short spindles still entirely within the mother cells, one of the bundles of cytoplasmic microtubules nearly always extended to (or into) the bud. Two independent reagents (anti-yeast actin and fluorescent phalloidin) revealed an unusual distribution of actin: it was present as a set of cortical dots or patches and also as distinct fibers that were presumably bundles of actin filaments. Double labeling showed that at no stage in the cell cycle do the distributions of actin and tubulin coincide for any significant length, and, in particular, that the mitotic spindle did not stain detectably for actin. However, both microtubule and actin staining patterns change in a characteristic way during the cell cycle. In particular, the actin dots clustered in rings about the bases of very small buds and at the sites on unbudded cells at which bud emergence was apparently imminent. Later in the budding cycle, the actin dots were present largely in the buds and, in many strains, primarily at the tips of these buds. At about the time of cytokinesis the actin dots clustered in the neck region between the separating cells. These aspects of actin distribution suggest that it may have a role in the localized deposition of new cell wall material.
Imaging Atherosclerotic Plaque Inflammation With [ 18 F]-Fluorodeoxyglucose Positron Emission Tomography (2002)

This study demonstrates that atherosclerotic plaque inflammation can be imaged with 18FDG-PET, and that symptomatic, unstable plaques accumulate more 18FDG than asymptomatic lesions.
Expression of Interleukin-6, c-Fos, and zif268 mRNAs in Rat Ischemic Cortex (1995)

The expression of interleukin-6 (IL-6) mRNA in the focal ischemic rat cortex was studied by means of Northern hybridization. IL-6 mRNA was induced after permanent occlusion of the middle cerebral artery, reached a significant level at 3 h, and peaked at 12 h, i.e., approximately 10-fold increase in the ischemic zone compared with the nonischemic cortex or sham-operated controls. The increased IL-6 mRNA was elevated for at least 24 h. Low levels of IL-6 mRNA were detected in sham-operated rats or in the contralateral nonischemic cortex. The expression of c-fos and zif268 mRNAs, two early response genes, was rapid (increased by 1 h postischemia) and transient (returned to basal levels by 24 and 12 h, respectively), clearly having different kinetic patterns from that of IL-6 mRNA. The early response kinetic pattern of c-fos and zif268 mRNAs in focal ischemia suggests their transcriptional regulatory roles in response to ischemic insult, while the delayed induction pattern of IL-6 mRNA suggests a role for this pleiotropic cytokine in the inflammatory response to the focal ischemic damage of the brain.
A Review: Eulerian Video Motion Magnification (2015)

Thispaper reviews computational techniques to efficiently represent, analyse and visualise both shortterm and long-term temporal variation in video and image sequences. This paper reveals temporal variation in videos that are imperceptible to the naked eye. The method takes a standard video sequence as an input, and applies spatial decomposition, followed by temporal filtering to the frames which is called “Eulerian Video Magnification”. The resulting signal is then amplified to reveal the hidden information. Paper contains four techniques which are: 1.Linear approximation method, 2.Phase based video processing, 3. Riesz pyramid for fast phase based video processing and 4.Enhanced Eulerian video magnification. Using above methods, one is able to amplify and visualize small motions and temporal colour changes.
The development of immunomodulatory monoclonal antibodies as a new therapeutic modality for cancer: The Bristol-Myers Squibb experience (2014)

The discovery and increased understanding of the complex interactions regulating the immune system have contributed to the pharmacologic activation of antitumor immunity. The activity of effector cells, such as T and NK cells, is regulated by an array of activating and attenuating receptors and ligands. Agents that target these molecules can modulate immune responses by exerting antagonistic or agonistic effects. Several T- or NK-cell modulators have entered clinical trials, and two have been approved for use. Ipilimumab (Yervoy®, Bristol-Myers Squibb) and nivolumab (OPDIVO, Ono Pharmaceutical Co., Ltd./Bristol-Myers Squibb) were approved for the treatment of metastatic melanoma, in March 2011 in the United States, and in July 2014 in Japan, respectively. The clinical activity of these two antibodies has not been limited to tumor types considered sensitive to immunotherapy, and promising activity has been reported in other solid and hematologic tumors. Clinical development of ipilimumab and nivolumab has presented unique challenges in terms of safety and efficacy, requiring the establishment of new evaluation criteria for adverse events and antitumor effects. Guidelines intended to help oncologists properly manage treatment in view of these non-traditional features have been implemented. The introduction of this new modality of cancer treatment, which is meant to integrate with or replace the current standards of care, requires additional efforts in terms of optimization of treatment administration, identification of biomarkers and application of new clinical trial designs. The availability of immune modulators with different mechanisms of action offers the opportunity to establish immunological combinations as new standards of care.
Optical Properties of Metal Nanoshells (2004)

We present a combination of theory and experiment designed to elucidate the properties of gold nanoshells. Wet chemistry methods are used to prepare the nanoshells, and transmission electron microscopy (TEM) analysis is used to characterize the shell structure, demonstrating the presence of pinholes in the shells. Both Mie theory and the discrete dipole approximation (a numerical method) are used to characterize the electrodynamics of the shell structures, including both perfect and pinhole defected shells. The calculations show that 2−5 nm pinholes have only a small effect on the extinction spectra; however, they lead to local electric fields that are enhanced by a factor of 3−4 close to the plasmon maximum. This makes metal nanoshells (with holes) attractive materials for surface enhanced Raman spectroscopy applications.
BRCA1 is a 220-kDa nuclear phosphoprotein that is expressed and phosphorylated in a cell cycle-dependent manner. (1996)

Mouse polyclonal antibodies, raised against three regions of the human BRCA1 protein, were characterized and revealed BRCA1 as a 220-kDa nuclear phosphoprotein in normal cells. All three antisera recognize both in vitro-translated and recombinant, baculovirus-derived BRCA1, which co-migrate with BRCA1 from the human breast epithelia cell line, HBL100. BRCA1 expression and phosphorylation are shown to be cell cycle dependent, with greatest expression and phosphorylation occurring in S and M phases. Cyclin-dependent kinase 2 and other kinases associated with cyclins D and A are shown to bind to and phosphorylate BRCA1, suggesting that the biological activity of BRCA1 may be regulated by cyclin-dependent kinases.
15.3: Invited Paper: A LC Display for the TV Application (2004)

Abstract Super IPS (S‐IPS) technology has intrinsic superiority in several aspects required for the TV application. Particularly, the wide view property and fast gray to gray response time of S‐IPS LCD are the most necessary requirements for TV, not only for the family use but also even for the personal use of it. High performance S‐IPS LCD TV has been developed by LG.Philips LCD and its status in the market is now competitive to that of PDP and the other mode of LCD TV, not to mention the CRT. Why the S‐IPS LCD is the best choice for the TV application will be addressed.
Familial amyotrophic lateral sclerosis/motor neurone disease (FALS): a review of current developments. (1995)

Amyotrophic lateral sclerosis (ALS)/motor neurone disease (MND) is a relatively common neurodegenerative condition with a prevalence of approximately 5 per 100 000 and is char- acterised by loss of motor neurones in the spinal cord, brain stem, and motor cortex. Approximately 5 to 10% of ALS cases are familial. The familial form is indistinguishable from the sporadic form with a mean age of onset of 50 years and a rapid progression of approximately three years duration. Recently, mutations in Cu/Zn superoxide dismutase (SOD-1) have been identified in a sub- population of familial cases and this has stim- ulated an enormous amount of interest. This finding has opened the way to investigating potential pathogenic mechanisms and de- veloping treatment rationales. However, the picture is still incomplete as SOD-1 mutations have only been detected in a minority of cases (fig 1) and the value of identifying subjects at risk in the subgroup is debatable. The aim of this review is to provide a summary of the most recent developments in FALS research which give an insight into the possible mechanisms underlying the disease and their implications and expectations for affected subjects.
Adenosine 5′-triphosphate (ATP) supplements are not orally bioavailable: a randomized, placebo-controlled cross-over trial in healthy humans (2012)

A single dose of orally administered ATP is not bioavailable, and this may explain why several studies did not find ergogenic effects of oral ATP supplementation. On the other hand, increases in uric acid after release of ATP in the proximal part of the small intestine suggest that ATP or one of its metabolites is absorbed and metabolized. Uric acid itself may have ergogenic effects, but this needs further study. Also, more studies are needed to determine whether chronic administration of ATP will enhance its oral bioavailability.
Comparison of API Rapid STREP, Baxter MicroScan Rapid Pos ID Panel, BBL Minitek Differential Identification System, IDS RapID STR System, and Vitek GPI to Conventional Biochemical Tests for Identification of Viridans Streptococci (1991)

Viridans group streptococci (36 stock strains and 167 single patient blood culture isolates) were assessed using API Rapid Strep, Baxter MicroScan Rapid Pos ID Panel, BBL Minitek Differential Identification System, IDS RapID STR System, and Vitek GPI methods. Identification data obtained with these systems were compared with those indicated by conventional biochemical procedures. API, Baxter MicroScan, BBL, IDS, and Vitek corresponded with conventional biochemical identification in 74%, 66%, 65%, 50%, and 61% of the isolates, respectively; using recommended supplemental tests, agreement was augmented in 9%, 11%, 20%, 11%, and 21% of the isolates, respectively. Disagreement with conventional biochemical methods occurred in 14%, 17%, 14%, 32%, and 10% of the commercial techniques, respectively; no identification was possible in 2%, 5%, fewer than 1%, 6%, and 8% of specimens, respectively. BBL, API, and Baxter MicroScan systems provided the most reliable rapid identification, although supplemental testing often was required. Until a higher percentage of correct identification data can be obtained without supplemental procedures, conventional biochemical techniques will remain the methods of choice for identification of viridans streptococci.
Characterization of a 100-kilodalton binding protein for the six serotypes of coxsackie B viruses (1995)

Viral infection of host cells primarily depends on binding of the virus to a specific cell surface protein. In order to characterize the binding protein for group B coxsackieviruses (CVB), detergent-solubilized membrane proteins of different cell lines were tested in virus overlay protein-binding assays. A prominent virus-binding protein with a molecular mass of 100 kDa was detected in various CVB-permissive human and monkey cell lines but was not detected in nonpermissive cell lines. The specificity of CVB binding to the 100-kDa protein on permissive human cells was substantiated by binding of all six serotypes of CVB and by competition experiments. In contrast, poliovirus and Sendai virus did not bind to the 100-kDa CVB-specific protein. A fraction of HeLa membrane proteins enriched in the range of 100 kDa showed functional activity by transforming infectious CVB (160S) into A-particles (135S). In order to purify this CVB-binding protein, solubilized membrane proteins from HeLa cells were separated by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by elution of the 100-kDa protein. Amino acid sequence analysis of tryptic fragments of the CVB-binding protein indicated that this 100-kDa CVB-specific protein is a cell surface protein related to nucleolin. These results were confirmed by immunoprecipitations of the CVB-binding protein with nucleolin-specific antibodies, suggesting that a nucleolin-related membrane protein acts as a specific binding protein for the six serotypes of CVB.