gebhart/patrepeval huggingface dataset:
IS THERE MORE TO UNCERTAINTY THAN SOME PROBABILITY THEORISTS MIGHT HAVE US BELIEVE?* (1989)

Abstract The aim of the paper is to challenge the claims (as described by Lindley38). “that probability is the only sensible description of uncertainty and is adequate for all problems involving uncertainty. All other methods are inadequate”. The paper concentrates primarily on the codification of the concept of uncertainty and the discussion of adequate principles of maximum and minimum uncertainty.
Global Genomic Analysis of Intraductal Papillary Mucinous Neoplasms of the Pancreas Reveals Significant Molecular Differences Compared to Ductal Adenocarcinoma (2009)

This study is the first to use array CGH to characterize IPMNs. Recurrent cytogenetic alterations were identified and were different than those described in PDAC. Array CGH may help distinguish between these 2 entities and give insight into the differences in their biology and prognosis.
Efficacy Of A Quadrivalent Rhesus Rotavirus-Based Human Rotavirus Vaccine Aimed At Preventing Severe Rotavirus Diarrhea In Infants And Young Children (1996)

The most extensively explored strategy for rotavirus vaccination has been the Jennerian approach, which uses an antigenically related rotavirus strain from an animal host as the immunogen to induce protection against the 4 epidemiologically important group A rotavirus VP7 serotypes. Because this approach has shown limited efficacy, a modified Jennerian approach was developed with the goal of achieving broader antigenic coverage. Four VP7 serotypes were incorporated into a quadrivalent vaccine comprised of three rhesus-human rotavirus reassortants, each with 10 rhesus rotavirus genes and 1 human rotavirus gene that encodes VP7 serotype 1, 2, or 4 specificity; the rhesus rotavirus itself provides coverage for VP7 serotype 3. This approach appears quite promising for preventing severe rotavirus diarrhea, including those episodes that lead to dehydration. Additional strategies under development stress the role not only of human rotavirus VP7 but also of human rotavirus VP4, the other outer capsid protein that also induces neutralizing antibodies.
<title>Fiducial point localization in multisensor 3-D surface scanning</title> (1992)

The estimation of fiducial point locations on surfaces is important in many close range photogrammetric applications, including biostereometrics, non-contact stress analysis, industrial metrology, and others. We have developed various methods for estimation of surface fiducial points based on optically sensed range maps obtained with a multisensor 3-D scanner originally designed for portrait sculpture. We previously described an algorithm based on a Kalman filter, a recursive spatially variant optimal estimator. The results demonstrated that accurate localization of surface landmarks can be readily achieved. Two new methods for estimation of fiducial point locations on surfaces were devised for the 3-D scanner. This high- speed non-contact 3-D scanner uses 6 CID cameras and 6 pattern projectors. Each projector incorporates coded bar patterns which are projected onto the object to be scanned. These patterns are captured in the camera image, mensurated, and tagged to identify corresponding projector profiles for each profile observed in the camera. The set of points belonging to a profile on the image plane are entered into a 2-D to 3-D solution, an analytical procedure where each image point (2-D point) is mapped to a point in space (3-D point). Three- dimensional surface points from all views are resampled onto a global cylindrical grid. Both range and texture maps are computed and stored. The range and texture information from all views is averaged and displayed on a 3-D graphics workstation (Silicon Graphics 4-D/340). Fiducial point localization achieved via the two new methods employing variations of Kalman filtering.
Difference between the Magnetic Properties of the Magnetotactic Bacteria and Those of the Extracted Magnetosomes: Influence of the Distance between the Chains of Magnetosomes (2008)

We report structural characterization and magnetic properties of various assemblies of chains of magnetosomes. The same magnetic properties are observed for the magnetotactic bacteria and for the extracted chains of magnetosomes isolated in a polymer. When the extracted chains of magnetosomes form a denser structure than that observed in the bacteria, the magnetic properties change markedly. A decrease in the coercivity and reduced remanence is observed. This behavior is attributed to an enhancement of the dipolar interactions between the chains of magnetosomes in the limit of a weakly interacting system; that is, the magnetostatic energy is lower than the anisotropy energy. The effect of the dipolar interactions is more pronounced at 250 K than at 10 K. This behavior is attributed to the existence of a family of small magnetosomes, which undergo a transition from a ferromagnetic to a superparamagnetic state.
The Second Line (2013)

A political boundary divided the City of Shenzhen in 1978. The southern portion is designated as a Special Economic Zone (SEZ), while the northern region remains a part of hinterland China. The divide creates a geographical and psychological chasm in the administrative and ontological existence of Shenzhen. The locals dubbed this border “the Second Line”.

The Second Line and SEZ were a part of Chairman Deng Xiaoping’s open and reform economic policies in 1978. The SEZs were designated areas along the southeast coast of China for the socialist state’s experimentation with global capitalism. After years of wars, revolution and repression of the individual pursuit of capital, Shenzhen underwent extraordinary urban and economic development, growing from clusters of villages holding 300 000 residents to a megalopolis of more than a million in one decade.

The Second Line drove uneven urban and economic growth in the Shenzhen SEZ. The radical speed of development and opportunities brought workers from rural areas of China. They made up the economic and urban substructure of the city, but were excluded from urban social welfare. Shenzhen’s industries rooted in instability and disposability of labour discouraged the settlement of the floating population.

The thesis proposal conceptually commemorates the site of the Second Line, and pays homage to its crucial role in the urban and economic formation of Shenzhen. At the urban scale, it acts as a public infrastructure, providing a framework for interface between the segregated territories of the city. The social housing component of the proposal is an architectural response and challenge to policies that allow for the migration of rural workers without provisions for everyday life. The proposal subverts the divisive ideology of the boundary through inhabitation, and creates a space of dwelling on the Second Line.
The role of MIP-1α in Inflammation and hematopoiesis (1996)

Macrophage inflammatory protein 1 alpha (MIP-1 alpha) is a member of the C-C subfamily of chemokines, a large superfamily of low-molecular weight, inducible proteins that exhibit a variety of proinflammatory activities in vitro including leukocyte chemotaxis. MIP-1 alpha is a particularly interesting chemokine, because in addition to its proinflammatory activities, it inhibits the proliferation of hematopoietic stem cells in vitro and in vivo. Here, the biologic properties of MIP-1 alpha are reviewed in light of recent data on mice homozygous for a disruption of the MIP-1 alpha gene. The MIP-1 alpha null mice have no overt abnormalities of peripheral blood or bone marrow cells, indicating that MIP-1 alpha is not necessary for normal hematopoiesis. However, the MIP-1 alpha null mice have a mice have a reduced inflammatory reduced inflammatory response to influenza virus and are resistant to coxsackievirus-induced myocarditis. These data demonstrate that MIP-1 alpha is required for a normal inflammatory response to these viruses. Agent that inhibit the action of MIP-1 alpha may therefore prove useful for controlling inflammation in these and other settings.
Final Report of the Safety Assessment of Hyaluronic Acid, Potassium Hyaluronate, and Sodium Hyaluronate (2009)

Hyaluronic acid, sodium hyaluronate, and potassium hyaluronate function in cosmetics as skin conditioning agents at concentrations up to 2%. Hyaluronic acid, primarily obtained from bacterial fermentation and rooster combs, does penetrate to the dermis. Hyaluronic acid was not toxic in a wide range of acute animal toxicity studies, over several species and with different exposure routes. Hyaluronic acid was not immunogenic, nor was it a sensitizer in animal studies. Hyaluronic acid was not a reproductive or developmental toxicant. Hyaluronic acid was not genotoxic. Hyaluronic acid likely does not play a causal role in cancer metastasis; rather, increased expression of hyaluronic acid genes may be a consequence of metastatic growth. Widespread clinical use of hyaluronic acid, primarily by injection, has been free of significant adverse reactions. Hyaluronic acid and its sodium and potassium salts are considered safe for use in cosmetics as described in the safety assessment.
Structural basis for differential binding of staphylococcal enterotoxin A and toxic shock syndrome toxin 1 to class II major histocompatibility molecules. (1991)

The related staphylococcal toxins staphylococcal enterotoxin A (SEA) and toxic shock syndrome toxin 1 (TSST-1) are microbial superantigens. They require interaction with class II major histocompatibility complex (MHC) molecules to activate T cells. We have previously identified a binding site on SEA, the N-terminal 45 amino acids, as well as its corresponding receptor on the MHC antigen, residues 65-85 of the beta chain. To further characterize the structural basis for SEA binding to class II MHC molecules we have examined its relationship to TSST-1 binding. Both toxins bound similarly to murine A20 cells, but blockage of binding was observed only with the homologous toxin, which suggests that the binding sites for the two toxins on A20 cells are distinct. In contrast, specific binding of SEA was greater than that of TSST-1 on human Raji cells. Further, SEA was a better inhibitor of TSST-1 binding than was TSST-1 itself at low concentrations, but TSST-1 only minimally inhibited SEA binding. The data suggest that TSST-1 interacts with Raji cells at an SEA binding site, but with a lower affinity. The peptides SEA-(1-45) and I-A beta b-(65-85) were capable of blocking SEA binding on both A20 and Raji cells, but blockage was more effective on A20 cells. Neither peptide was capable of blocking TSST-1 binding on either cell line. The data are compatible with a model in which SEA has a binding site on A20 cells involving SEA-(1-45) and I-A beta b-(65-85) which is distinct from that which binds TSST-1, while at least two binding sites are present on Raji cells. One site involves predominantly the residue 1-45 region on SEA and the 65-85 region of the MHC beta chain, while the other site involves both a different region on the SEA molecule and a different site on the class II MHC molecule to which it binds. This latter site also binds TSST-1.
CART-based duration modeling using a novel method of extracting prosodic features (1999)

This paper describes a robust parsing algorithm for spoken language understanding. Comparing with the other work in robust parsing, we focus on building a parser that is robust to not only ill-formed spontaneous spoken language inputs but also under-specified grammars. Preliminary experiment results show that the parsing performance deteriorates more gracefully than another parser we have used when the grammar is more underspecified.
Bone Morphogenetic Protein and Bone Morphogenetic Protein Gene Family in Bone Formation and Repair (1998)

The bone morphogenetic proteins are secreted signalling molecules that belong to the transforming growth factor beta family of growth and differentiation factors. Individual bone morphogenetic proteins are prominent at many sites during embryogenesis and are likely to be key regulators of early development and organogenesis. In vertebrates, one of the functions of bone morphogenetic like proteins is to induce formation of bone, cartilage, and connective tissues associated with the skeleton. This osteoinductive ability has led to the use of bone morphogenetic proteins as therapeutic agents for creation of new bone useful in treatment of skeletal injuries and diseases, and in oral and maxillofacial applications.
Method for Fabricating Supported Bilayer Lipid Membranes on Gold (2000)

The paper describes the synthesis of surfaces based on self-assembled monolayers (SAMs) of alkanethiolates on gold that were designed to support the adsorption of bilayer lipid membranes, and the feasibility of using these surfaces for making high-density arrays (HDAs) of membranes. The synthesis involved (i) the formation of SAMs of 16-mercaptohexadecanoic acid (MHA) on gold; (ii) the activation of the carboxylic acid groups to interchain anhydrides; (iii) the treatment of the reactive surfaces with Brij-76 (C18H37(OCH2CH2)n-10OH) (1) or Brij-76-amine (2) (C18H37(OCH2CH2)n-10NH2); and (iv) the formation of supported membranes by incubation or printing of the lipids. The oligo(ethylene glycol) moiety of the anchor lipid provides a hydrophilic spacer between the surface and the adsorbed lipid to enable the incorporation of membrane-spanning proteins with extramembrane domains. Data from infrared spectroscopy confirmed the coupling of 2 to the surface through the formation of peptide bonds. Ellipsometric measurements showed an increase of ∼15 Å in the thickness of the SAM after coupling to 2; this observation suggests that ∼25% of the carboxylic acid groups of the MHA-SAM are derivatized with Brij groups. The yields for coupling of 1 were ∼40% of that observed for 2. Experiments using surface plasmon resonance (SPR) were consistent with the binding of lipid bilayers to the Brij-derivatized surface, although alternative structures for the supported lipids cannot be ruled out; by contrast, SAMs of hexadecanethiolate on gold were observed to bind lipid monolayers. Biospecific binding of neutravidin was observed on supported membranes incorporating biotinylated lipids. HDAs of lipids were made by printing lipids onto the Brij-derivatized surfaces using a quill-pin printer. Fluorescence microscopy indicated that the printed lipids remained confined to the printed areas; these observations demonstrate the applicability of using commercial HDA printers for generating high-density membrane arrays on the Brij-modified surfaces.
X-ray Crystal Structure of C3d: A C3 Fragment and Ligand for Complement Receptor 2 (1998)

Activation and covalent attachment of complement component C3 to pathogens is the key step in complement-mediated host defense. Additionally, the antigen-bound C3d fragment interacts with complement receptor 2 (CR2; also known as CD21) on B cells and thereby contributes to the initiation of an acquired humoral response. The x-ray crystal structure of human C3d solved at 2.0 angstroms resolution reveals an alpha-alpha barrel with the residues responsible for thioester formation and covalent attachment at one end and an acidic pocket at the other. The structure supports a model whereby the transition of native C3 to its functionally active state involves the disruption of a complementary domain interface and provides insight into the basis for the interaction between C3d and CR2.
Generation of Human Osteoclasts from Peripheral Blood (2011)

Osteoclasts are multi-nucleated cells that have the unique ability to resorb calcified bone matrix. They derive from haematopoietic precursor cells, and can be generated in vitro by stimulation of peripheral blood mononuclear cells with the cytokines M-CSF and RANKL. In this chapter, we describe the method for generating human osteoclast from peripheral blood or buffy coats, as well as methods for studying both the differentiation and resorbing activity of these cells.
Interleukin-7 or Interleukin-15 Enhances Survival ofMycobacterium tuberculosis-Infected Mice (2000)

Both antigen-presenting cells and immune effector cells are required to effectively eradicate or contain Mycobacterium tuberculosis-infected cells. A variety of cytokines are involved to ensure productive "cross talk" between macrophages and T lymphocytes. For instance, infection of macrophages with mycobacteria leads to effective interleukin-7 (IL-7) and IL-15 secretion, and both cytokines are able to maintain strong cellular immune responses of alpha/beta and gamma/delta T cells. Here we show that either cytokine is able to enhance survival of M. tuberculosis-infected BALB/c mice significantly compared to application of IL-2, IL-4, or phosphate-buffered saline (as a control). Enhanced survival could be achieved only when IL-7 or IL-15 was delivered as a treatment (i.e., 3 weeks postinfection), not when it was administered at the time of infection. Increased survival of M. tuberculosis-infected animals was observed following passive transfer of spleen cells harvested from M. tuberculosis-infected, IL-7- or IL-15-treated animals, but not after transfer of spleen cells obtained from mice which received either cytokine alone. Histological examination revealed that IL-7 and IL-15 failed to significantly impact on the number and composition of granulomas formed or the bacterial load. Our data indicated that administration of IL-7 or IL-15 to M. tuberculosis-treated animals resulted in a qualitatively different cellular immune response in spleen cells as reflected by increased tumor necrosis factor alpha and decreased gamma interferon secretion in response to M. tuberculosis-infected antigen-presenting cells.
Porous‐Conductive Chitosan Scaffolds for Tissue Engineering, 1 (2004)

Novel porous-conductive chitosan scaffolds were fabricated by incorporating conductive polypyrrole (PPy) particles into a chitosan matrix and employing a phase separation technique to build pores inside the scaffolds. Conductive polypyrrole particles were prepared with a microemulsion method using FeCl3 as a dopant. The preparation conditions were optimized to obtain scaffolds with controlled pore size and porosity. The conductivity of the scaffolds was investigated using a standard four-point probe technique. It was found that several kinds of scaffolds showed a conductivity close to 10(-3) S.cm(-1) with a low polypyrrole loading of around 2 wt.-%. The main mechanical properties, such as tensile strength, breaking elongation and Young's modulus of the scaffolds, were examined both in the dry and in the hydrated states. The results indicated that a few different kinds of scaffolds exhibited the desired mechanical strength for some tissue engineering applications. The miscibility of polypyrrole and chitosan was also evaluated using a dynamic mechanical method. The presence of significant phase separation was detected in non-porous PPy/chitosan scaffolds but enhanced miscibility in porous PPy/chitosan scaffolds was observed.
The Nonstructural Protein 3 Protease/Helicase Requires an Intact Protease Domain to Unwind Duplex RNA Efficiently (2004)

The nonstructural 3 (NS3) protein encoded by the hepatitis C virus possesses both an N-terminal serine protease activity and a C-terminal 3'-5' helicase activity. This study examines the effects of the protease on the helicase by comparing the enzymatic properties of the full-length NS3 protein with truncated versions in which the protease is either deleted or replaced by a polyhistidine (His tag) or a glutathione S-transferase fusion protein (GST tag). When the NS3 protein lacks the protease domain it unwinds RNA more slowly and does not unwind RNA in the presence of excess nucleic acid that acts as an enzyme trap. Some but not all of the RNA helicase activity can be restored by adding a His tag or GST tag to the N terminus of the truncated helicase, suggesting that the effects of the protease are both specific and nonspecific. Similar but smaller effects are also seen in DNA helicase and translocation assays. While translocating on RNA (or DNA) the full-length protein hydrolyzes ATP more slowly than the truncated protein, suggesting that the protease allows for more efficient ATP usage. Binding assays reveal that the full-length protein assembles on single-stranded DNA as a higher order oligomer than the truncated fragment, and the binding appears to be more cooperative. The data suggest that hepatitis C virus RNA helicase, and therefore viral replication, could be influenced by the rotations of the protease domain which likely occur during polyprotein processing.
Applications, Properties and Synthesis of &#969;-Functionalized n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers (2004)

Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals are versatile constructs with which to study interfacial phenomena and reactions at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse environments, propensity to interact with or to resist adsorption of macromolecules -- depend on and can be controlled flexibly by the properties of the functional (head) groups in the w position of the alkyl chain. SAMs provide a basis for many important scientific and technological applications, ranging from micropatterning methods, through sensing, to biological recognition. Despite their importance, the literature on SAMs and the synthesis of molecules that constitute them remains scattered and often conflicting. The purpose of this Review is (i) to summarize the applications and physical properties of SAMs and (ii) to systematize the strategies of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme is developed that allows efficient synthetic planning. Issues related to the selection of appropriate protecting groups and the ways of introduction of the thiol functionality are discussed in detail, and illustrated with examples of syntheses of several complex alkane thiols.
Knowledge Management Impact Challenge case story overview (2012)

This article provides an overview of the key themes and lessons that emerged across the 47 case stories that were collected by the KM Impact Challenge. The paper starts by contextualizing the case stories and the diverse range of KM initiatives that were identified and explores the insights shared by the case story authors from their diverse experiences. Capturing evidence of use and uptake of new knowledge emerges as the key challenge faced by different types of KM initiatives. The article also explores our relationship with qualitative and quantitative data, with particular attention to our increasing use of webstats and agreement on the need to complement these with qualitative data to help tell our story. The case stories also highlighted the importance of using M&E systems to engage knowledge users through feedback mechanisms to enable them to contribute to shaping projects and technological solutions. The article concludes with an analysis of the common lessons that emerged across all case stories as well identifying the shared challenges that we face moving forward.
GPI-Anchored Cell-Surface Molecules Complexed to Protein Tyrosine Kinases (1991)

Binding of ligand or antibody to certain cell-surface proteins that are anchored to the membrane by glycophosphatidylinositol (GPI) can cause activation of leukocytes. However, it is not known how these molecules, which lack intracellular domains, can transduce signals. The GPI-linked human molecules CD59, CD55, CD48, CD24, and CD14 as well as the mouse molecules Thy-1 and Ly-6 were found to associate with protein tyrosine kinases, key regulators of cell activation and signal transduction. A protein tyrosine kinase associated with the GPI-linked proteins CD59, CD55, and CD48 in human T cells, and with Thy-1 in mouse T cells was identified as p56lck, a protein tyrosine kinase related to Src. This interaction of GPI-linked molecules with protein tyrosine kinases suggests a potential mechanism of signal transduction in cells.