gebhart/patrepeval huggingface dataset:
Acute myocardial infarction and inter-hospital transfer (2015)

Receipt of timely and specialised care for the management of acute myocardial infarction (AMI) is associated with improved clinical outcomes. Yet, not all hospitals are equipped and/or enabled to provide specialised interventions, and as a result patients may be transferred between centres to access these services. Given that there may be shortfalls in local capacity to deliver a high-quality cardiovascular service for AMI that may drive the necessity for centralisation of services, there is also a large body of evidence that suggests that inter-hospital transfer for the treatment of AMI, particularly primary percutaneous coronary intervention (PCI) for ST-elevation myocardial infarction (STEMI), is strongly associated with reduced mortality. Overall, the evidence suggests that higher volume and PCI-capable centres have lower mortality rates and that transfer of patients to such centres, through coordinated networks of care, is safe and effective. Such a notion is supported by international guidelines.1

One of the earliest reports of inter-hospital transfer for AMI studied 104 patients with suspected AMI, between 1983 and 1984, who were transferred by an aeromedical team. There were no deaths during transfer, and 87% of patients survived to be discharged from hospital.2 In 2000, the PRimary Angioplasty in patients transferred from General community hospitals to specialised PTCA Units with or without Emergency thrombolysis (PRAGUE) study found that of the 300 study participants presenting to hospital within 6 h of symptom onset with AMI, those who were randomised to immediate transportation for primary angioplasty without pretreatment with thrombolysis less frequently had the primary composite endpoint of death, reinfarction or stroke at 30 days.3 Notably, these findings were upheld at 5 years from date of randomisation.4 Other studies have investigated the impact of inter-hospital transfer across a range …
Investigating Hologram‐Based Route Planning (2009)

Abstract It is often assumed that three‐dimensional topographic maps provide more effective route planning, navigation, orientation, and way‐finding results than traditional two‐dimensional representations. The research reported here investigates whether three‐dimensional spatial mappings provide better support for route planning than two‐dimensional representations. In a set of experiments performed as part of this research, human subjects were randomly shown either a two‐ or three‐dimensional hologram of San Francisco and were asked to plan a bicycling route between an origin and a destination point. In a second task, participants used these holograms to identify the highest elevation point in the displayed area. The eye‐movements of the participants, throughout the process of looking at the geospatial holograms and executing the tasks, were recorded. The eye‐tracking metrics analysis indicates with a high statistical level of confidence that three‐dimensional holographic maps enable more efficient route planning. In addition, the research group is developing a new algorithm to analyze the differences between participant‐selected routes and a set of “good routes.” The algorithm employs techniques used to represent the boundary of objects and methods for assessing the difference between objects in modern digital image recognition, image registration, and image alignment applications. The overall goal is to create a theoretical framework for investigating and quantifying route planning effectiveness.
Two-axis MEMS scanner with transfer-printed high-reflectivity, broadband monolithic silicon photonic crystal mirrors (2013)

We present a two-axis electrostatic MEMS scanner with high-reflectivity monolithic single-crystal-silicon photonic crystal (PC) mirrors suitable for applications in harsh environments. The reflective surfaces of the MEMS scanner are transfer-printed PC mirrors with low polarization dependence, low angular dependence, and reflectivity over 85% in the wavelength range of 1490nm~1505nm and above 90% over the wavelength band of 1550~1570nm. In static mode, the scanner has total scan range of 10.2° on one rotation axis and 7.8° on the other. Dynamic operation on resonance increase the scan range to 21° at 608Hz around the outer rotation axis and 9.5° at 1.73kHz about the inner rotation axis.
Managing the Evolution of Dataflows with VisTrails (2006)

Scientists are now faced with an incredible volume of data to analyze. To successfully analyze and validate various hypotheses, it is necessary to pose several queries, correlate disparate data, and create insightful visualizations of both the simulated processes and observed phenomena. Data exploration through visualization requires scientists to go through several steps. In essence, they need to assemble complex workflows that consist of dataset selection, specification of series of operations that need to be applied to the data, and the creation of appropriate visual representations, before they can finally view and analyze the results. Often, insight comes from comparing the results of multiple visualizations that are created during the data exploration process.
Studies on the mechanism of oxidative phosphorylation. Catalytic site cooperativity in ATP synthesis. (1985)

Oxidative phosphorylation catalyzed by bovine heart submitochondrial particles appears to exhibit negative cooperativity with respect to [ADP] and positive cooperativity in catalysis. Eadie-Hofstee plots (v/[S]versus v) of the kinetics of oxidative phosphorylation at the variable ADP concentration range of 1-1200 microM were curvilinear and could be analyzed for two apparent KmADP values differing by one order of magnitude, and two apparent Vmax values. The KmADP values with either NADH or succinate as the respiratory substrate were in the ranges of 10 and 100 microM, and the Vmax values in nmol of ATP formed X min-1 (mg of protein)-1 were, respectively, 500 and 1840 when NADH was the oxidizable substrate, and 550 and 100 when succinate was the energy source. Site-site cooperativity of the ATP synthase, which is a central feature of current theories for the mechanism of oxidative phosphorylation, has been well-documented for ATP hydrolysis by isolated F1-ATPase, but never before demonstrated for mitochondrial ATP synthesis.
Oxygen Reduction on Carbon-Supported Pt−Ni and Pt−Co Alloy Catalysts (2002)

We describe a comparative study of the oxygen reduction reaction on two carbon-supported Pt-based alloy catalysts in aqueous acidic electrolyte at low temperature. Both alloys have the bulk compositions of 50 and 75 at. % Pt, with the alloying elements being Ni and Co. Comparison is made to a pure Pt catalyst on the same carbon support, Vulcan XC-72, having the same metal loading (20 wt %) and nominally the same particle size (4 ± 2 nm). High-resolution electron microscopy was used to determine the size and shape of the particles as well as the particle size distribution on all catalysts. Electrochemical measurements were performed using the thin-film rotating ring−disk electrode method in 0.1 M HClO4 at 20−60 °C. Hydrogen adsorption pseudocapacitance was used to determine the number of Pt surface atoms and to estimate the surface composition of the alloy catalysts. Kinetic analysis in comparison to pure Pt revealed a small activity enhancement (per Pt surface atom) of ca. 1.5 for the 25 at. % Ni and Co catalysts, and a more significant enhancement of a factor of 2−3 for the 50 at. % Co. The 50 at. % Ni catalyst was less active than the Pt standard and unstable at oxygen electrode potentials. Ring-current collection measurements for peroxide indicated no significant differences between the Pt−Co catalysts or the 25 at. % Ni catalyst and pure Pt, while the 50 at. % Ni catalyst had a higher peroxide yield. Together with the observed Tafel slopes and activation energies, it was concluded that the kinetic enhancement is contained in the preexponential factor of the conventional transition state theory rate expression. It is, however, not clear why the alloying with Ni or Co produces this change in the preexponential factor.
The Fbx4 Tumor Suppressor Regulates Cyclin D1 Accumulation and Prevents Neoplastic Transformation (2011)

Skp1-Cul1-F-box (SCF) E3 ubiquitin ligase complexes modulate the accumulation of key cell cycle regulatory proteins. Following the G(1)/S transition, SCF(Fbx4) targets cyclin D1 for proteasomal degradation, a critical event necessary for DNA replication fidelity. Deregulated cyclin D1 drives tumorigenesis, and inactivating mutations in Fbx4 have been identified in human cancer, suggesting that Fbx4 may function as a tumor suppressor. Fbx4(+/-) and Fbx4(-/-) mice succumb to multiple tumor phenotypes, including lymphomas, histiocytic sarcomas and, less frequently, mammary and hepatocellular carcinomas. Tumors and premalignant tissue from Fbx4(+/-) and Fbx4(-/-) mice exhibit elevated cyclin D1, an observation consistent with cyclin D1 as a target of Fbx4. Molecular dissection of the Fbx4 regulatory network in murine embryonic fibroblasts (MEFs) revealed that loss of Fbx4 results in cyclin D1 stabilization and nuclear accumulation throughout cell division. Increased proliferation in early passage primary MEFs is antagonized by DNA damage checkpoint activation, consistent with nuclear cyclin D1-driven genomic instability. Furthermore, Fbx4(-/-) MEFs exhibited increased susceptibility to Ras-dependent transformation in vitro, analogous to tumorigenesis observed in mice. Collectively, these data reveal a requisite role for the SCF(Fbx4) E3 ubiquitin ligase in regulating cyclin D1 accumulation, consistent with tumor suppressive function in vivo.
Expression of the Epstein-Barr virus gp350/220 gene in rodent and primate cells (1987)

The gene encoding the Epstein-Barr virus envelope glycoproteins gp350 and gp220 was inserted downstream of the cytomegalovirus immediate-early, Moloney murine leukemia virus, mouse mammary tumor virus, or varicella-zoster virus gpI promoters in vectors containing selectable markers. Host cell and recombinant vector systems were defined which enabled the isolation of rodent or primate cell clones which expressed gp350/220 in substantial quantities. Continued expression of gp350/220 required maintenance of cells under positive selection for linked markers and periodic cloning. gp350/220 expressed in various host cells varied slightly in electrophoretic mobility, probably reflecting differences in glycosylation. Insertion of a stop codon into the gp350/220 open reading frame, upstream of the putative membrane anchor sequence, resulted in efficient secretion of truncated gp350 and gp220 from rat pituitary (GH3) cells. gp350/220 expressed in mammalian cells is highly immunogenic and elicits virus-neutralizing antibodies when administered to mice.
Examination of shape complementarity in docking of Unbound proteins (1999)

Here we carry out an examination of shape complementarity as a criterion in protein-protein docking and binding. Specifically, we examine the quality of shape complementarity as a critical determinant not only in the docking of 26 protein-protein “bound” complexed cases, but in particular, of 19 “unbound” protein-protein cases, where the structures have been determined separately. In all cases, entire molecular surfaces are utilized in the docking, with no consideration of the location of the active site, or of particular residues/atoms in either the receptor or the ligand that participate in the binding. To evaluate the goodness of the strictly geometry-based shape complementarity in the docking process as compared to the main favorable and unfavorable energy components, we study systematically a potential correlation between each of these components and the root mean square deviation (RMSD) of the “unbound” protein-protein cases. Specifically, we examine the non-polar buried surface area, polar buried surface area, buried surface area relating to groups bearing unsatisfied buried charges, and the number of hydrogen bonds in all docked protein-protein interfaces. For these cases, where the two proteins have been crystallized separately, and where entire molecular surfaces are considered without a predefinition of the binding site, no correlation is observed. None of these parameters appears to consistently improve on shape complementarity in the docking of unbound molecules. These findings argue that simplicity in the docking process, utilizing geometrical shape criteria may capture many of the essential features in protein-protein docking. In particular, they further reinforce the long held notion of the importance of molecular surface shape complementarity in the binding, and hence in docking. This is particularly interesting in light of the fact that the structures of the docked pairs have been determined separately, allowing side chains on the surface of the proteins to move relatively freely. This study has been enabled by our efficient, computer vision-based docking algorithms. The fast CPU matching times, on the order of minutes on a PC, allow such large-scale docking experiments of large molecules, which may not be feasible by other techniques. Proteins 1999;36:307–317. © 1999 Wiley-Liss, Inc.
Characterization of mitochondrial cytochromes P-450 from pig kidney and liver catalysing 26-hydroxylation of 25-hydroxyvitamin D3 and C27 steroids (1991)

The properties of cytochrome P-450 from pig kidney mitochondria, catalysing 26-hydroxylation of 25-hydroxyvitamin D3 and C27 steroids [Postlind & Wikvall (1989) Biochem. Biophys. Res. Commun. 159, 1135-1140; Postlind (1990) Biochem. Biophys. Res. Commun. 168, 261-266], were compared with those of a 26-hydroxylating cytochrome P-450 from pig liver mitochondria. The liver enzyme was purified to a cytochrome P-450 content of 7.4 nmol/mg of protein and showed only one protein band with an apparent Mr of 53,000 upon SDS/PAGE. The cytochrome P-450 catalysed 26-hydroxylation of 25-hydroxyvitamin D3, cholesterol and 5 beta-cholestane-3 alpha, 7 alpha-diol at rates of 361, 1090 and 2065 pmol/min per nmol of cytochrome P-450. A monoclonal antibody against the purified liver mitochondrial cytochrome P-450 26-hydroxylase (cytochrome P-450(26] was prepared. After coupling to Sepharose, the antibody was able to bind to cytochrome P-450(26) from liver as well as from kidney mitochondria and to immunoprecipitate the 26-hydroxylase activity towards 25-hydroxyvitamin D3 and cholesterol when assayed in a reconstituted system. After SDS/PAGE and immunoblotting with the antibody, the cytochrome P-450(26) was detected in the purified liver and kidney preparations. These results indicate that similar species of cytochrome P-450 catalyse 26-hydroxylation of 25-hydroxyvitamin D3 and C27 steroids in liver and kidney mitochondria. The results with the monoclonal antibody together with the finding that cholesterol competitively inhibits the 26-hydroxylation of 25-hydroxyvitamin D3 further indicate that 26-hydroxylation of 25-hydroxyvitamin D3 and cholesterol is catalysed by the same species of cytochrome P-450 in each tissue. The N-terminal amino acid sequence of cytochrome P-450(26) in kidney mitochondria resembled that of pig kidney microsomal 25-hydroxylase active in 25-hydroxylation of vitamin D3 and C27 steroids, whereas the sequence of pig liver mitochondrial cytochrome P-450(26) differed from those of rabbit and rat liver mitochondrial 26-hydroxylases as well as from those of other hitherto isolated mammalian cytochromes P-450.
Diagnostic value of serum erythropoietin level in patients with absolute erythrocytosis. (2004)

Based on these data, we propose that measurement of serum Epo level, a simple, reliable and inexpensive test, should be considered as a first intention diagnostic test for patients with absolute erythrocytosis.
Abstract 552: Biological Properties and Regenerative Potential, in vitro and in vivo, of Human Cardiac Stem Cells Isolated from Each of the Four Chambers of the Adult Human Heart (2006)

The two outbreaks of haemorrhagic colitis (HC) that were traced to ground beef in 1982 were the first foodborne cases known to be caused by Escherichia coli 0157:H7. The 1993 outbreak in the U.S. Pacific Northwest is the largest foodborne disease outbreak ever traced to ground beef. Why these events occurred continues to be a matter of speculation and debate. It is the thesis of this review that HC-causing strains of E. coli, which could have been in the meat supply as early as the mid-1950s, can persist in meats that contain too few of the background bacterial biota. The antagonistic effect of background organisms against pathogenic bacteria (microbial interference) is well established. Fresh ground meats that contain 10(5)-10(6)/g of background organisms are inherently safer than those that contain, say, 10(3)/g. Although the production of fresh ground meats with as few microorganisms as possible would seem to be the ideal, there is little or no evidence to support the superior safety of such products. It is suggested that when pathogen-reduction strategies are applied to animal carcasses, the carcasses should be 'protected' against subsequent colonization by pathogens by actually adding appropriate mixtures of harmless bacteria.
Targeted disruption of gp130, a common signal transducer for the interleukin 6 family of cytokines, leads to myocardial and hematological disorders. (1996)

gp130 is a ubiquitously expressed signal-transducing receptor component shared by interleukin 6, interleukin 11, leukemia inhibitory factor, oncostatin M, ciliary neurotrophic factor, and cardiotrophin 1. To investigate physiological roles of gp130 and to examine pathological consequences of a lack of gp130, mice deficient for gp130 have been prepared. Embryos homozygous for the gp130 mutation progressively die between 12.5 days postcoitum and term. On 16.5 days postcoitum and later, they show hypoplastic ventricular myocardium without septal and trabecular defect. The subcellular ultrastructures in gp130-/- cardiomyocytes appear normal. The mutant embryos have greatly reduced numbers of pluripotential and committed hematopoietic progenitors in the liver and differentiated lineages such as T cells in the thymus. Some gp130-/- embryos show anemia due to impaired development of erythroid lineage cells. These results indicate that gp130 plays a crucial role in myocardial development and hematopoiesis during embryogenesis.
Rate-coded Restricted Boltzmann Machines for Face Recognition (2000)

We describe a neurally-inspired, unsupervised learning algorithm that builds a non-linear generative model for pairs of face images from the same individual. Individuals are then recognized by finding the highest relative probability pair among all pairs that consist of a test image and an image whose identity is known. Our method compares favorably with other methods in the literature. The generative model consists of a single layer of rate-coded, non-linear feature detectors and it has the property that, given a data vector, the true posterior probability distribution over the feature detector activities can be inferred rapidly without iteration or approximation. The weights of the feature detectors are learned by comparing the correlations of pixel intensities and feature activations in two phases: When the network is observing real data and when it is observing reconstructions of real data generated from the feature activations. 1 Introduction Face recognition is diff...
Plant Cell Culture Using a Novel Bioreactor: The Magnetically Stabilized Fluidized Bed (1990)

A novel bioreactor using magnetically stabilized fluidized bed (MSFB) technology has been developed that has certain advantages for cultivating cells continuously. In this system, the cells are protected from shear and are constrained to move through the fermenter in lock-step fashion by being immobilized in calcium alginate beads. The MSFB permits good mass transfer, minimizes particle collisions, and allows for the production of cells while maintaining a controlled cell residence time. Details of the experimental system are described. In addition, the experimental performance of an MSFB used to grow plant cells in batch mode is compared to the results obtained in shake flask culture.
An Envelope Modification That Renders a Primary, Neutralization-Resistant Clade B Human Immunodeficiency Virus Type 1 Isolate Highly Susceptible to Neutralization by Sera from Other Clades (1998)

SF162 is a primary (PR), non-syncytium-inducing, macrophagetropic human immunodeficiency virus type 1 (HIV-1) clade B isolate which is resistant to antibody-mediated neutralization. Deletion of the first or second hypervariable envelope gp120 region (V1 or V2 loop, respectively) of this virus does not abrogate its ability to replicate in peripheral blood mononuclear cells and primary macrophages, nor does it alter its coreceptor usage profile. The mutant virus with the V1 loop deletion, SF162DeltaV1, remains as resistant to antibody-mediated neutralization as the wild-type virus SF162. In contrast, the mutant virus with the V2 loop deletion, SF162DeltaV2, exhibits enhanced susceptibility to neutralization by certain monoclonal antibodies whose epitopes are located within the CD4-binding site and conserved regions of gp120. More importantly, SF162DeltaV2 is now up to 170-fold more susceptible to neutralization than SF162 by sera collected from patients infected with clade B HIV-1 isolates. In addition, it becomes susceptible to neutralization by sera collected from patients infected with clade A, C, D, E, and F HIV-1 isolates. These findings suggest that the V2, but not the V1, loop of SF162 shields an as yet unidentified region of the HIV envelope rich in neutralization epitopes and that the overall structure of this region appears to be conserved among clade B, C, D, E, and F HIV-1 PR isolates.
Interaction between Ephrins and mGlu5 Metabotropic Glutamate Receptors in the Induction of Long-Term Synaptic Depression in the Hippocampus (2010)

We applied the group-I metabotropic glutamate (mGlu) receptor agonist, 3,5-dihydroxyphenylglycine (DHPG), to neonatal or adult rat hippocampal slices at concentrations (10 microM) that induced a short-term depression (STD) of excitatory synaptic transmission at the Schaffer collateral/CA1 synapses. DHPG-induced STD was entirely mediated by the activation of mGlu5 receptors because it was abrogated by the mGlu5 receptor antagonist, MPEP [2-methyl-6-(phenylethynyl)pyridine], but not by the mGlu1 receptor antagonist, CPCCOEt [7-(hydroxyimino)cyclopropa[b]chromen-1a-carboxylate ethyl ester]. Knowing that ephrin-Bs functionally interact with group-I mGlu receptors (Calò et al., 2005), we examined whether pharmacological activation of ephrin-Bs could affect DHPG-induced STD. We activated ephrin-Bs using their cognate receptor, EphB1, under the form of a preclustered EphB1/Fc chimera. Addition of clustered EphB1/Fc alone to the slices induced a small but nondecremental depression of excitatory synaptic transmission, which differed from the depression induced by 10 microM DHPG. Surprisingly, EphB1/Fc-induced synaptic depression was abolished by MPEP (but not by CPCCOEt) suggesting that it required the endogenous activation of mGlu5 receptors. In addition, coapplication of DHPG and EphB1/Fc, resulted in a large and nondecremental long-term depression. The effect of clustered EphB1/Fc was specific because it was not mimicked by unclustered EphB1/Fc or clustered EphA1/Fc. These findings raise the intriguing possibility that changes in synaptic efficacy mediated by mGlu5 receptors are under the control of the ephrin/Eph receptor system, and that the neuronal actions of ephrins can be targeted by drugs that attenuate mGlu5 receptor signaling.