gebhart/patrepeval huggingface dataset:
Synthesis of the organic ligand of the molybdenum cofactor, in protected form (2001)

The organic ligand of the cofactor of the oxomolybdoenzymes has been synthesised in the protected and masked form, 5. The key steps in the conversion of the previously prepared 3, a protected 5-(2-amino-4-oxopteridin-6-yl)-4-(1,2-dihydroxyethyl)-1,3-dithiol-2-one were: formation of the pyran ring by reaction with a chloroformate giving a protected 8-amino-4-hydroxymethyl-6-(alkyloxycarbonyl)-5a,6,9,10-tetrahydro-[1,3]dithiolo[4′,5′:4,5]pyrano[3,2-g]pteridine-2,10-dione, 10, cyanoborohydride reduction of the 11,11a-imine, protection at N-11, and finally conversion of the alcohol into a protected phosphate giving 5.
Tumor invasiveness and prognosis in resected hepatocellular carcinoma.Clinical and pathogenetic implications (1988)

In order to elucidate the biologic behavior of hepatocellular carcinoma (HCC), the long-term prognostic impact of the pathologic features of 143 surgically resected HCC were studied. Seventy-four were smaller than 5 cm in diameter (small HCC), and 69 were larger (large HCC). This study confirmed that tumor size was an important but not the only determining prognostic factor in HCC. Although cirrhosis could cause hepatic failure, patient mortality was mainly attributable to tumor recurrence, which, in turn, was strongly correlated with the invasive nature of HCC. Tumor invasion to the liver and the intraportal spread were very frequent and particularly extensive in large HCC. In both small and large HCC the noninvasive groups not only had high 4-year actuarial survival (84.6% and 90%, respectively), but there was also no patient mortality from intrahepatic tumor recurrence. Therefore, it was concluded that invasiveness of an HCC is the most crucial factor in determining the long-term outcome for the patient, and that the clinical course of resected HCC is predictable in a great majority of the cases. In our small HCC series only 2.4% of HCC were regarded as having true multicentric origin. These findings suggest that the majority of HCC occur unicentrically, and that multiplicity and tumor recurrence result mostly from intrahepatic dissemination. In both small and large HCCs invasive tumors were accompanied by high patient mortality from tumor recurrence even when the tumor was small, indicating that intrahepatic spread may start very early during the growth of HCC.
Chinese Hamster Ovary K2 Cell Lipid Droplets Appear to Be Metabolic Organelles Involved in Membrane Traffic (2004)

The principal lipids in animal cell lipid droplets are cholesterol, cholesterol ester, and triglyceride, but the protein composition of this compartment is largely unknown. Here we report on the proteomic analysis of lipid droplets. Using a combination of mass spectrometry and immunoblotting, we identify nearly 40 specifically associated proteins in droplets isolated from Chinese hamster ovary K2 cells grown in normal medium. The proteins fall in to five groups: structural molecules of the droplet-like adipose differentiation-related protein; multiple enzymes involved in the synthesis, storage, utilization, and degradation of cholesterol esters and triglycerides; multiple, different Rab GTPases known to be involved in regulating membrane traffic; signaling molecules such as p50RhoGAP; and a group of proteins that do not fit any classification but include proteins often found in caveolae/rafts such as caveolin-1 and 2 and flotillin-1. The proteome of droplets isolated from cells grown in the presence of oleate is largely the same except for an increase in the amount of adipose differentiation-related protein, caveolin-1, and a protein thought to be involved in phospholipid recycling called CGI-58. Based on the protein profile, the lipid droplet appears to be a complex, metabolically active organelle that is directly involved in membrane traffic and possibly phospholipid recycling. We propose the name adiposome for this organelle.
Endoleak as a Complication of Endoluminal Grafting of Abdominal Aortic Aneurysms: Classification, Incidence, Diagnosis,and Management (1997)

The inability to obtain or maintain a secure seal between a vessel wall and a transluminally implanted intra-aneurysmal graft is a complication unique to the evolving technique of endovascular aneurysm exclusion. Because the term "leak" has long been associated with aneurysm rupture, the term "endoleak" is proposed as a more definitive description of this phenomenon. Embracing both persistent blood flow into the aneurysmal sac from within or around the graft (graft related) and from patent collateral arteries (nongraft related), endoleak can be classified as primary or secondary depending on the time of occurrence (within 30 days of implantation or following apparent initial seal, respectively). Diagnostic techniques to detect endoleak include arteriography, intraprocedural pressure monitoring, contrast-enhanced computed tomography, abdominal X ray, and duplex scanning. Management strategies for endoleak range from observation with periodic imaging surveillance to correction by additional endoluminal or surgical procedures. Standardization of the terminology describing this important sequela to endovascular aneurysm exclusion should facilitate uniform reporting of clinical trial data vital to the evaluation of this emerging technique.
Design Studies for a Solar Reactor Based on a Simple Radiative Heat Exchange Model (2005)

A high-temperature solar chemical reactor for the processing of solids is scaled up from a laboratory scale (5kW concentrated solar power input) to a pilot scale (200kW). The chosen design features two cavities in series: An upper cavity has a small aperture to let in concentrated solar power coming from the top. It serves as the solar receiver, radiant absorber, and radiant emitter to a lower cavity. The lower cavity is a well-insulated enclosure. It is subjected to thermal radiation from the upper cavity and serves in our application as the reaction chamber for a mixture of ZnO and carbon. Important insight for the definition of the geometrical parameters of the pilot reactor has been generated by a radiation heat transfer analysis based on the radiosity enclosure theory. The steady-state model accounts for radiation heat transfer within the solar reactor including reradiation losses through the reactor aperture, wall losses due to thermal conduction and heat consumption by the endothermic chemical reaction. Key results include temperatures of the different reactor walls and the thermal efficiency of the reactor as a function of the major geometrical and physical parameters. The model, hence, allows for a fast estimate of the influence of these parameters on the reactor performance.
Association of Hepatitis C Virus–Specific CD8<sup>+</sup>T Cells with Viral Clearance in Acute Hepatitis C (2000)

CD8+ T lymphocytes play a major role in antiviral immune defense. Their significance for acute hepatitis C is unclear. Our aim was to correlate the CD8+ T cell response with the outcome of infection. Eighteen patients with acute hepatitis C and 19 normal donors were studied. Hepatitis C virus (HCV)-specific CD8+ T cells were identified in the enzyme-linked immunospot assay by their interferon-gamma (IFN-gamma) production after specific stimulation. The highest numbers of IFN-gamma-producing HCV-specific CD8+ T cells were found in patients with acute hepatitis C and a self-limited course of disease during the first 6 months after onset of disease, but these numbers dropped thereafter to undetectable levels. The differences in responsiveness between patients with self-limited disease versus patients with a chronic course were statistically significant (P<.001). Our data show that the number of IFN-gamma-producing HCV-specific CD8+ T cells during the first 6 months after onset of disease is associated with eradication of the HCV infection.
Interfaces in polymer, ceramic, and metal matrix composites; Proceedings of the Second International Conference on Composite Interfaces (ICCI-II), Cleveland, OH, June 13-17, 1988 (1988)

The present conference on interfacial factors in advanced composite materials discusses such topics in their development status and properties as silane coupling, the electrochemical and plasma-surface treatment of carbon fibers, fiber surface-analytical techniques, polymer molecular scale characterization by atom-probe field-ion microscopy, the study of carbon fiber-epoxy resin interface interactions by means of labeling techniques, and the surface tailoring of SiC by ion implantation. Also discussed are developments in laser light-scattered photoelasticity, microstructural evolutions under heat treatment and radiation damage, TEM for composites, the interfaces of carbon fiber-reinforced Al composites, the influence of the interface on macroscopic composite properties, and the status of the theoretical understanding of composite interfaces.
A New Multivariate Approach for Prognostics Based on Extreme Learning Machine and Fuzzy Clustering (2015)

Prognostics is a core process of prognostics and health management (PHM) discipline, that estimates the remaining useful life (RUL) of a degrading machinery to optimize its service delivery potential. However, machinery operates in a dynamic environment and the acquired condition monitoring data are usually noisy and subject to a high level of uncertainty/unpredictability, which complicates prognostics. The complexity further increases, when there is absence of prior knowledge about ground truth (or failure definition). For such issues, data-driven prognostics can be a valuable solution without deep understanding of system physics. This paper contributes a new data-driven prognostics approach namely, an "enhanced multivariate degradation modeling," which enables modeling degrading states of machinery without assuming a homogeneous pattern. In brief, a predictability scheme is introduced to reduce the dimensionality of the data. Following that, the proposed prognostics model is achieved by integrating two new algorithms namely, the summation wavelet-extreme learning machine and subtractive-maximum entropy fuzzy clustering to show evolution of machine degradation by simultaneous predictions and discrete state estimation. The prognostics model is equipped with a dynamic failure threshold assignment procedure to estimate RUL in a realistic manner. To validate the proposition, a case study is performed on turbofan engines data from PHM challenge 2008 (NASA), and results are compared with recent publications.
Cleavage of interleukin 1 beta (IL-1 beta) precursor to produce active IL-1 beta by a conserved extracellular cysteine protease from Streptococcus pyogenes. (1993)

Streptococcal pyrogenic exotoxin B (SPE B), a conserved extracellular cysteine protease expressed by the human pathogenic bacterium Streptococcus pyogenes, was purified and shown to cleave inactive human interleukin 1 beta precursor (pIL-1 beta) to produce biologically active IL-1 beta. SPE B cleaves pIL-1 beta one residue amino-terminal to the site where a recently characterized endogenous human cysteine protease acts. IL-1 beta resulting from cleavage of pIL-1 beta by SPE B induced nitric oxide synthase activity in vascular smooth muscle cells and killed of the human melanoma A375 line. Two additional naturally occurring SPE B variants cleaved pIL-1 beta in a similar fashion. By demonstrating that SPE B catalyzes the formation of biologically active IL-1 beta from inactive pIL-1 beta, our data add a further dimension to an emerging theme in microbial pathogenesis that bacterial and viral virulence factors act directly on host cytokine pathways. The data also contribute to an enlarging literature demonstrating that microbial extracellular cysteine proteases are important in host-parasite interactions.
Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3‐hydroxypropanoate (2010)

Sustainable microbial production of high-value organic compounds such as 3-hydroxypropanoate (3HP) is becoming an increasingly attractive alternative to organic syntheses that utilize petrochemical feedstocks. We applied the Biochemical Network Integrated Computational Explorer (BNICE) framework to the automated design and evaluation of novel biosynthetic routes for the production of 3HP from pyruvate. Among the pathways generated by the BNICE framework were all of the known pathways for the production of 3HP as well as numerous novel pathways. The pathways generated by BNICE were ranked based on four criteria: pathway length, thermodynamic feasibility, maximum achievable yield to 3HP from glucose, and maximum achievable activity at which 3HP can be produced. Four pathways emerged from this ranking as the most promising for the biosynthesis of 3HP, and three of these pathways, including the shortest pathways discovered, were novel. We also discovered novel routes for the biosynthesis of 28 commercially available compounds that are currently produced exclusively through organic synthesis. Examination of the optimal pathways for the biosynthesis of these 28 compounds in E. coli revealed pyruvate and succinate to be ideal intermediates for achieving high product yields from glucose.
Rapid Node Reallocation Between Virtual Clusters for Data Intensive Utility Computing (2006)

Utility computing achieves efficiencies by dynamically reallocating shared resources between services operating on virtual clusters. These efficiencies can be hard to realize for data intensive applications; newly allocated nodes must be populated with a large amount of data which impedes rapid node reallocation. We describe a data management architecture that uses disk caches on each node to reduce data copying and speed up node reallocation for data intensive applications. Cache consistency management is simplified by extensive use of copy-on-write techniques. A data-driven scheme is then used to select nodes for reallocation between virtual clusters based on the amount of relevant cached data. These nodes are identified using a novel technique of statistically sampling the contents of caches. We demonstrate the benefits of this architecture using our implementation of an efficient block level caching and copy-on-write target for the Linux device-mapper framework
Death ligand-mediated apoptosis in HIV infection (2005)

Apoptosis has been suggested to cause severe CD4+ T cell depletion in patients infected with HIV. This review focuses on the biological events involved in death ligand-induced apoptosis during HIV infection. Among these ligands, TRAIL appears critical in HIV-infection. Death ligand-induced apoptosis might be a major pathogenic event in many virus-induced diseases including AIDS and the clarification of its mechanism will aid in the development of therapeutic strategies.
Using Deep Eutectic Solvents Based on Methyl Triphenyl Phosphunium Bromide for the Removal of Glycerol from Palm-Oil-Based Biodiesel (2011)

Biodiesel is a remarkable alternative to the decreasing resources for fossil fuels. One of the critical steps in producing biodiesel is its purification from the byproduct glycerol. The content of glycerol permissible must pass the EN 14214 and ASTM D6751 international biodiesel standards. In this work, methyl triphenyl phosphunium bromide as salt and three different hydrogen-bond donors, namely, glycerol, ethylene glycol, and triethylene glycol, were selected to synthesize three deep eutectic solvents (DESs). These DESs were employed as the solvent for the removal of glycerol from palm-oil-based biodiesel. The effects of DES type on the removal of free glycerol, bound glycerol, and total glycerol were investigated. The results revealed that the ethylene glycol DESs and triethylene glycol DESs were successful in removing all free glycerol from the palm-oil-based biodiesel. All tested DESs were able to reduce the content of monoglycerides (MGs) and diglycerides (DGs). Moreover, all used DESs had the tendency to reduce the DGs more effectively than removing MGs. The maximum removal efficiency of MGs and DGs was attained by triethylene-glycol-based DESs at a molar ratio of 3:1 (DES8:biodiesel) and 0.75:1 (DES8:biodiesel), with 37.9 and 53.4% removal, respectively. The total glycerol was reduced below the ASTM standards using all tested DESs. The DES:biodiesel molar ratios of 3:1 for DES4 and 3:1 for DES8 were found to be the most effective solvents for reducing total glycerol content, with 40 and 50% removal efficiency, respectively.
A communication agreement framework for access/action control (1996)

We introduce a framework for access/action control which shifts the emphasis from the participants to their relationships. The framework is based on a model in which participants negotiate the mutually agreed-upon boundary conditions of their relationships, and create social reference points by encapsulating them in compact communication pacts, called commpacts. Commpacts are designed to provide a language enabling a social mechanism of coordinated expectation. We argue that in networked environments characterized by multiple authorities and trusted proxies, this model can deal with the complexities of general (user- and content-dependent) distributed access/action control and provides a clear user-conceptual metaphor. The frame work embeds naturally into the existing legal and institutional infrastructure; it generalizes work in electronic contracting. Commpacts can be seen as a third fundamental type next to access-control lists (ACLs) and capabilities.
Molecular dissection of tight junctions: occludin and ZO-1 (1998)

The establishment of compositionally distinct fluid compartments by various types of cell sheets is crucial for the development and function of most organs in multicellular organisms. Since these cell sheets consist of two-dimensionally arranged cells, some mechanism is required to seal cells to create a primary barrier to the diffusion of solutes through the paracellular pathway. This mechanism is thus essential for morphogenesis of the multicellular system, and the tight junction, an element of epithelial and endothelial junctional complexes, is now believed to be directly involved in this mechanism (Schneeberger and Lynch, 1992; Gumbiner, 1987, 1993). The brain is an important compartment that is protected by a barrier of endothelial cell sheets bearing well-developed tight junctions. This is referred as the blood-brain barrier.
Time-gating improves the spatial resolution of STED microscopy (2011)

Stimulated-emission depletion (STED) microscopy improves image resolution by encoding additional spatial information in a second stimulated-decay channel with a spatially-varying strength. Here we demonstrate that spatial information is also encoded in the fluorophore lifetime and that this information can be used to improve the spatial resolution of STED microscopy. By solving a kinetic model for emission in the presence of a time-varying STED pulse, we derive the effective resolution as a function of fluorophore lifetime and pulse duration. We find that the best resolution for a given pulse power is achieved with a pulse of infinitesimally short duration; however, the maximum resolution can be restored for pulses of finite duration by time-gating the fluorescence signal. In parallel, we consider time-gating in the presence of a continuous-wave (CW) STED beam and find that time-gating produces theoretically unbounded resolution with finite laser power. In both cases, the cost of this improved resolution is a reduction in the brightness of the final image. We conclude by discussing situations in which time-gated STED microscopy (T-STED) may provide improved microscope performance beyond an increase in resolution.
Social Change: Reactivating the System (1995)

The return to work in this autumn of 1993 is characterised by very strong negative signals and messages. Problems unarguably exist, growth is hesitant and hence there is much uncertainty.
A potent and selective p38 inhibitor protects against bone damage in murine collagen‐induced arthritis: a comparison with neutralization of mouse TNFα (2008)

Pharmacological targeting of p38 kinase provided good protection against joint tissue damage in CIA. In our experiments, neutralization of mTNFalpha produced less prominent suppression of bone damage. Our data suggest a therapeutic potential for selective and potent p38 inhibitors in RA.
Expanded <i>ATXN2</i> CAG repeat size in ALS identifies genetic overlap between ALS and SCA2 (2011)

Our data reveal a novel genetic overlap between ALS and SCA2.
Dynamic modulation of modal coupling in microelectromechanical gyroscopic ring resonators (2019)

Understanding and controlling modal coupling in micro/nanomechanical devices is integral to the design of high-accuracy timing references and inertial sensors. However, insight into specific physical mechanisms underlying modal coupling, and the ability to tune such interactions is limited. Here, we demonstrate that tuneable mode coupling can be achieved in capacitive microelectromechanical devices with dynamic electrostatic fields enabling strong coupling between otherwise uncoupled modes. A vacuum-sealed microelectromechanical silicon ring resonator is employed in this work, with relevance to the gyroscopic lateral modes of vibration. It is shown that a parametric pumping scheme can be implemented through capacitive electrodes surrounding the device that allows for the mode coupling strength to be dynamically tuned, as well as allowing greater flexibility in the control of the coupling stiffness. Electrostatic pump based sideband coupling is demonstrated, and compared to conventional strain-mediated sideband operations. Electrostatic coupling is shown to be very efficient, enabling strong, tunable dynamical coupling.