gebhart/patrepeval huggingface dataset:
Fatty liver and drugs. (2006)

Drug-induced liver diseases (DILD) are clinico-pathologic patterns of liver injury caused by drugs or other foreign compounds. Steatohepatitis is a rare form of DILD, and drugs account for fewer than 2% of non-alcoholic steatohepatitis (NASH). Drugs known to be capable of inducing steatosis and steatohepatitis can be divided into three broad groups: those that cause steatosis and steatohepatitis independently (e.g., amiodarone, perhexiline maleate); drugs which can precipitate latent NASH (e.g., tamoxifen); drugs whic duce sporadic events of steatosis/steatohepatitis (e.g., carbamazepine). Clinical DILD syndromes include acute viral hepatitis-like injury, acute liver failure, cholestatic hepatitis,liver disease with signs of hypersensitivity, autoimmune hepatitis-like injury, acute venous-Outflow obstruction, chronic cholestasis, ciirrhosis, steatosis and steatohepatitis. The clinical picture is by no means dependent on the mechanism of injury (direct hepatotoxicity, idiosyncratic reactions, hypersensitivity reactions). Reliable diagnosis of drug-induced liver disease requires demonstration of close correlation between the patient history and clinical, laboratory, and histological data.
Scholarly Collections on the Web: Media Reconfigurations at Play (2004)

With the Internet a new medium has become available for communicating scholarly texts. This article focuses on the World Wide Web (the Web) as a global, hypertextual archive for scholarly texts and its significance in reconfiguring the corpus of scholarly texts. The first part addresses the Web in light of hypertext theory and a media theoretic perspective, concentrating on its roots in issues related to the flood of information and its qualities as a medium. The second part will zoom in on the actual use of the Web as a publication and archival medium for scholars, with a focus on two different scholarly archives. The article concludes with some general reflections on the Web as an archive of archives based on the concepts of network and complexity.
Microfluidic Western Blot (2010)

We develop a novel method for Western blot based on microfluidics, incorporating the internal molecular weight marker, loading control, and antibody titration in the same protocol. Compared with the conventional method which could detect only one protein, the microfluidic Western blot could analyze at least 10 proteins simultaneously from a single sample, and it requires only about 1% of the amount of antibody used in conventional Western blot.
Core–Shell Colloids and Hollow Polyelectrolyte Capsules Based on Diazoresins (2001)

Hollow polyelectrolyte microcapsules containing diazoresins (DZR) were fabricated by the layer-by-layer self-assembly of a polycation, DZR, in alternation with poly(styrenesulfonate) (PSS) onto polystyrene (PS) particles, followed by dissolution of the PS core by tetrahydrofuran (THF). The multilayer film buildup on the colloids was observed by UV-visible spectroscopy, single particle light scattering (SPLS), and transmission electron microscopy (TEM). The data confirmed regular and stepwise layer formation of DZR and PSS on the colloid particles, with a thickness of about 10 nm for each DZR/PSS bilayer when exposed to aqueous solution, and approximately 5 nm in the “dry state”. The photosensitive nature of the DZR layers was exploited to construct highly stable, covalently attached (polymerized) films by exposure of the ionic self-assembled DZR/PSS multilayer films to UV-irradiation. TEM and atomic force microscopy (AFM) confirmed the formation of hollow DZR/PSS multilayer capsules. Osmotic pressure experiments followed by confocal laser scanning microscopy revealed a high mechanical stability of the hollow DZR/PSS capsules. The mechanically robust polymerized multilayer films on the colloids and as free-standing three-dimensional hollow capsules are more stable in various chemical environments (i.e., resistant to etching by solvents) than their ionically linked counterparts.
Effects of quercetin and quercetin 3‐glucuronide on the expression of bone sialoprotein gene (2007)

Quercetin is a typical flavonol-type flavonoid and is present in a variety of vegetables, and their antioxidant effect implies their possible role in the prevention of oxidative stress related chronic diseases. Bone sialoprotein (BSP) is a noncollagenous protein of the extracellular matrix in the mineralized connective tissues that has been implicated in the nucleation of hydroxyapatite crystals. Previously, we reported that isoflavone (genistein) activated BSP gene transcription is mediated through an inverted CCAAT box in the proximal BSP gene promoter. The present study investigates the regulation of BSP transcription in a rat osteoblast-like cell line, ROS 17/2.8 cells, by quercetin and its conjugated metabolite quercetin 3-glucuronide. Quercetin and quercetin 3-glucuronide (5 microM) increased the BSP mRNA levels at 12 h and quercetin upregulated the Cbfa1/Runx2 mRNA expression at 12 h. From transient transfection assays using various sized BSP promoter-luciferase constructs, quercetin increased the luciferase activity of the construct (pLUC3), including the promoter sequence nucleotides -116 to -43. Transcriptional stimulations by quercetin were almost completely abrogated in the constructs that included 2 bp mutations in the inverted CCAAT and FRE elements whereas the CCAAT-protein complex did not change after stimulation by quercetin according to gel shift assays. Quercetin increased the nuclear protein binding to the FRE and 3'-FRE. These data suggest that quercetin and quercetin 3-glucuronide increased the BSP mRNA expression, and that the inverted CCAAT and FRE elements in the promoter of the BSP gene are required for quercetin induced BSP transcription.
Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality (2002)

Eight different polymerases, chosen from evolutionary families A (Taq, Tfl, HotTub and Tth) and B (Pfu, Pwo, Vent and Deep Vent), were examined for their ability to incorporate 5-position modified 2'-deoxyuridine derivatives that carry a protected thiol group appended via different linkers containing either three or four carbon atoms. This represents the first attempt to incorporate the thiol functionality into DNA via enzymatic synthesis. Each polymerase-substrate combination was evaluated using a hierarchy of increasingly more difficult challenges, starting with incorporation of a single derivative, proceeding to incorporation of two derivatives at adjacent sites and non-adjacent sites, then examining the ability of the polymerase to accept the derivative within the template, and concluding with a challenge involving PCR. The evaluation of thiol-bearing 2'-deoxyuridine derivatives was then extended to consider their chemical stabilities. Stability was found to be less than satisfactory when the thiol functionality has a 'propargylic' relationship to the unsaturation in the linker. The best polymerase-appendage combination used the polymerase from Pyrococcus woesei (Pwo) and the 5'-tBu-SS-CH2-CH2-C [triple bond] C-linker. This pair supported PCR amplification and therefore should have value in artificial in vitro selection experiments. Indeed, we discovered that Pwo and Pfu preferred the derivative triphosphate over TTP, the natural substrate, in competition studies. These studies confirm an earlier suggestion that membership of an evolutionary family of polymerases is a partial predictor of the ability of the polymerase to accept 5-modified 2'-deoxyuridines. Considerable differences are displayed by different members within a polymerase family, however. This remains curious, as the ability of the polymerase to replicate natural DNA with high fidelity and its propensity to exclude unnatural analogs are presumed to be correlated.
Interleaved asymmetric echo‐planar imaging (1995)

A version of interleaved echo-planar imaging (EPI) is presented in which only one polarity of the readout gradient is used for signal acquisition to avoid ghosting artifacts. Two possible forms of the phase encoding gradient, blipped and constant, are discussed. With the constant phase encoding, interleaving of partial trajectories in the Fourier domain (k-space) is controlled automatically by the echo train delay. The constant phase encoding gradient introduces a shear distortion of the k-space grid. A modification of the reconstruction procedure is given which corrects for this effect. The method provides a 128 x 128 image in 1 s on a clinical system with standard gradients.
Single Amino Acid Change in STING Leads to Constitutive Active Signaling (2015)

The production of cytokines by the immune system in response to cytosolic DNA plays an important role in host defense, autoimmune disease, and cancer immunogenicity. Recently a cytosolic DNA signaling pathway that is dependent on the endoplasmic reticulum adaptor and cyclic dinucleotide sensor protein STING has been identified. Association of cytosolic DNA with cyclic-GMP-AMP synthase (cGAS) activates its enzymatic activity to synthesize the cyclic dinucleotide second messenger cGAMP from GTP and ATP. Direct detection of cGAMP by STING triggers the activation of IRF3 and NF-kB, and the production of type I interferons and proinflammatory cytokines. The mechanism of how STING is able to mediate downstream signaling remains incompletely understood although it has been shown that dimerization is a prerequisite. Here, we identify a single amino acid change in STING that confers constitutive active signaling. This mutation appears to both enhance ability of STING to both dimerize and associate with its downstream target TBK1.
Enterprise messaging using JMS and IBM WebSphere (2004)

The real-world guide to JMS messaging with IBM WebSphere technologiesThis book offers start-to-finish guidance for building reliable, high-performance JMS-based messaging infrastructure with IBM WebSphere technologies.IBM expert Kareem Yusuf systematically introduces the latest versions of JMS-both 1.1 and 1.02b. Once you've thoroughly mastered JMS development on any platform, Yusuf turns to the exceptional JMS support found in IBM's WebSphere products. Using extensive code examples, he walks you step-by-step through WebSphere JMS development, configuration, deployment, and administration in several real-world scenarios. Coverage includes: Roles and goals of messaging infrastructure in the enterprise Key JMS concepts: messaging domains, messages, and Application Server Facilities Defining/structuring content, choosing message types, and manipulating messages The JMS API, explained through detailed code examples Using JMS with EJB, message-driven beans, servlets, and portlets Working with IBM WebSphere JMS providers, administered objects, and tools Hands-on tutorials: EJB message exchange, integration with non-JMS applications, and SSL security Resource location and physical topologies for maximizing availability and efficiencyWhether you're developing enterprise messaging infrastructure, architecting it, or managing it, this book delivers indispensable guidance-straight from the frontlines.On the WebDownload an extensive library of code samples for JMS 1.1 and 1.02b, including complete functional prototypes built for JMS 1.02b.
Synthesis of Unsymmetrical Tetrathiafulvalene Derivatives via Me<sub>3</sub>Al-Promoted Reactions of Organotin Compounds with Esters (1996)

Efficient synthetic methods for the construction of a wide variety of unsymmetrical tetrathiafulvalenes (TTFs) via the Me(3)Al-promoted reactions of organotin thiolates or selenolates with esters are described. Reaction of tin thiolates (3a-c and 10) and selenolates (3d, 5, and 7) with esters (11a,b) in the presence of Me(3)Al as a Lewis acid gave dihydrotetrathiafulvalene derivatives (12, 14, 15, and 17-20) and 1,3-dithiane derivatives (13 and 16). In addition, the synthesis of diselenadithiafulvalene derivatives (25-28) could be accomplished by Me(3)Al-mediated reaction of tin thiolate (2a) or selenolates (3d and 5) with esters (22a, 22d, and 24). Furthermore, the application of the Me(3)Al-promoted reaction of tin thiolate (34) with esters (11a-b, 22a-d, and 35a-b) for the synthesis of unsymmetrical TTFs-fused donors enabled us to obtain various TTFs-fused systems (29-33) in short steps.
A REVISION OF PHILIPPINE GARDENIA (RUBIACEAE) (2011)

A description of the defining characteristics of Gardenia (Rubiaceae) and a revision of the Philippine species distinguished mainly by calyx morphology are presented. A key to five species of Gardenia recognised for the Philippines, full descriptions and illustrations, and a list of names which should be excluded from Gardenia are given. Relevant Philippine names for which holotypes were not indicated or have been destroyed are lectotypified. Two new endemic species, Gardenia ornata K.M.Wong and G. vulcanica K.M.Wong, are described. Gardenia elata Ridl. and G. mutabilis Reinw. ex Blume are newly applied to Philippine species previously enumerated under other names. Gardenia pseudopsidium (Blanco) Fern.-Vill. is considered a doubtful name, to which some authors have referred the endemic G. barnesii Merr.
E2F5 status significantly improves malignancy diagnosis of epithelial ovarian cancer (2010)

Overall, our findings, in addition to opening a realistic possibility for improved OEC diagnosis, provide an indirect evidence that a cell-cycle regulatory protein E2F5 might play a significant role in OEC pathogenesis.
A Gigabit UDP/IP network stack in FPGA (2009)

This paper presents a proposal of a Gigabit UDP/IP network stack in FPGA, which is the stack of the widely used in VoIP and Video-conference applications. This network node implements the Network, Transport and Link Layer of a traditional stack. This architecture is integrated and developed using Xilinx ISE tool and synthesized to a Spartan-3E FPGA. We show architecture details, timing and area results of a practical prototyping. Also, we compare our prototype and results with other works in terms of area (Xilinx slices), speed (MHz), maximum Ethernet frame length (bytes) and maximum Ethernet speed (Mbps). Comparing to these works our architecture obtained a intermediate solution in area and is the best implementation in terms of speed (MHz).
Atomic steps on Si(100) surfaces (1987)

It is demonstrated that surface-sensitive electron diffraction measurements of steps on singular, but rough Si(100) surfaces are subject to a multiple-scattering effect that can be misinterpreted as double-atomic-height steps. It is shown that only single-height steps are present. This phenomenon can occur in any surface in which adjacent terraces have different terrace structure factors. Determination of terrace sizes can be influenced; however, they can be accurately made if the diffraction geometry is chosen appropriately. Possible terrace shape effects may also be inherent in the diffraction data.
Fluid Flow Modeling in Fractures (2004)

In this paper we study fluid flow in fractures using numerical simulation and address the challenging issue of hydraulic property characterization in fractures. The methodology is based on Computational Fluid Dynamics, using a finite-volume based discretization scheme. Steady-state, viscous, laminar flow simulations for a Newtonian fluid are carried out in both 2D and 3D fracture models. In 2D, flow is analyzed in single fractures, series and parallel combination of fractures, inclined fractures, intersecting fractures, mixed networks, and in real (rough-surface) fractures. In 3D, flow is simulated in both uniform and variable aperture fracture models. To characterize each fracture model with an equivalent hydraulic aperture, equations are derived for all possible scenarios followed by comparison and validation with results derived from flow simulation. Based on the fracture models analyzed, the following are some of the important findings: 1) For fractures connected in series, the equivalent hydraulic aperture is a weighted harmonic mean of cubed apertures of all fractures. 2) For fractures connected in parallel, the equivalent flow is simply the sum of all flows through individual fractures. 3) If a fracture is inclined with respect to the axis of pressure gradient, then the amount of flow will be reduced by a factor of cosine of the inclination angle. 4) Any network of randomly intersecting fractures can be replaced by a single fracture to give flow equivalence; the aperture of that equivalent fracture will roughly be close to the aperture of the fracture in the network that cuts across the boundaries (inlet and outlet) in the most continuous fashion and have the smallest inclination (with respect to the pressure gradient axis). 5) For hydraulic characterization purposes, fluid flow in fractures can be sufficiently modeled using both Stokes and Navier-Stokes equations for flow Reynolds number upto approximately 100.
A class of convex bodies (1969)

In this paper I show that the following four properties of a convex subset Z of Rn are equivalent:1. Z is the range of a vector measure.2. Z is a limit of sums of segments.3. The polar of Z is a central section of the unit ball of Lx. 4. The polar of Z is a projection body.A Z which enjoys one, and hence all, of the above properties is called a zonoid.Most of the results of this paper concern the class of zonoids and do not give simple geometric conditions characterizing membership in that class.Such conditions are known only for polytopes.Statements 1 through 4 above clearly imply that the study of zonoids belongs to several disciplines, among which are functional analysis, convexity and the geometry of polytopes.I have tried to make this paper self-contained enough to be accessible to any interested reader and have therefore restated some elementary definitions which would be unnecessary in a work directed at a specialist in one field.I have also tried to unify the study of zonoids, so many results known to some readers appear here with new-or sometimes old-proofs.I have been as accurate as I could in assigning priorities and giving references.1.The range of a measure.Let Sf be a a-field of subsets of the set X and a: Sf -^Än be countably additive.Such a <j will be called a vector measure; a is atom free if <r(£)^0 implies the existence of an £^£ with 0^a(F)^a(E).1.1.Definition.A zonoid is the range of an atom free vector measure.Write 2? for the set of zonoids.1.2.Theorem.The zonoid Z=a(£r°) 1.Is compact and convex.2. Contains 0. Is symmetric about \a(X).Proof.The first assertion is a well-known theorem of Liapounoff's : see [28] and [6], [22] and [30].The second is trivial: 0(0) = 0 eo(if).The third follows from o(E)-\o(X) = -("(X-E)-\o(X)).
Cutting Edge: Flt3 Ligand Mediates STAT3-Independent Expansion but STAT3-Dependent Activation of Myeloid-Derived Suppressor Cells (2014)

The Flt3-Flt3 ligand (Flt3L) pathway is critically involved in the differentiation and homeostasis of myeloid cells, including dendritic cells (DC); however, its role in the expansion and function of myeloid-derived suppressor cells (MDSC) has not been determined. In this article, we describe the ability of Flt3L to expand and activate murine MDSC capable of suppressing allograft rejection upon adoptive transfer. Although Flt3L expands and augments the stimulatory capacity of myeloid DC, MDSC expanded by Flt3L have increased suppressive activity. Although STAT3 is considered the central transcription factor for MDSC expansion, inhibition and genetic ablation of STAT3 did not block, but rather augmented, Flt3L-mediated MDSC expansion. MDSC suppressive function, preserved when STAT3 inhibition was removed, was reduced by genetic STAT3 deletion. Both STAT3 inhibition and deletion reduced Flt3L-mediated DC expansion, signifying that STAT3 had reciprocal effects on suppressive MDSC and immunostimulatory DC expansion. Together, these findings enhance our understanding of the immunomodulatory properties of Flt3L.
Use of the mouse for the isolation and investigation of stomach-associated, spiral-helical shaped bacteria from man and other animals (1989)

Summary Spiral-helical shaped bacteria other than Campylobacter pylori have been shown to infect the human stomach. The characteristic helical morphology of these bacteria appears to be similar to that of bacteria found in the stomachs of many other animal species. Early reports on gastric bacteria suggested that rodents may be useful for investigation and isolation of stomach-associated bacteria. Therefore, anaesthetised mice were given, through a stomach tube, a heavy suspension of a spiral-helical bacterium from a cat, scrapings of gastric mucus from primates, or a homogenised whole-antral biopsy from a human patient. At intervals after inoculation, gastric biopsies were examined by lightmicroscopy and electronmicroscopy for the presence of spiral-helical bacteria. Significant colonisation was observed in 40% of mice 1 week, and in 80% of mice 11 weeks, after inoculation with suspensions of the cat isolate. Mice were also successfully colonised by spiral bacteria present in homogenised human biopsy material and by other spiral bacteria from a monkey. These observations suggest that mice may prove to be useful animals for the study of gastric bacteria that are, as yet, non-cultivable and for analysis of some of the attributes commonly thought to be involved in colonisation.
Minimum delay path selection in multi-homed systems with path asymmetry (2006)

As mobile and fixed hosts are increasingly equipped with multiple network interfaces that enable multi-homing, there is significant current interest to seek appropriate method for access network selection. To address the presence of asymmetric forward-return path combinations in practice, we propose a simple but novel scheme to determine the one-way path with the lowest delay independently for both directions. This method provides delay sensitive multimedia applications with the lowest possible round-trip time in a multi-homed environment, compared to existing methods which assume path symmetry.
Quantifications of error propagation in slope-based wavefront estimations (2006)

We discuss error propagation in the slope-based and the difference-based wavefront estimations. The error propagation coefficient can be expressed as a function of the eigenvalues of the wavefront-estimation-related matrices, and we establish such functions for each of the basic geometries with the serial numbering scheme with which a square sampling grid array is sequentially indexed row by row. We first show that for the wavefront estimation with the wavefront piston value determined, the odd-number grid sizes yield better error propagators than the even-number grid sizes for all geometries. We further show that for both slope-based and difference-based wavefront estimations, the Southwell geometry offers the best error propagators with the minimum-norm least-squares solutions. Noll's theoretical result, which was extensively used as a reference in the previous literature for error propagation estimates, corresponds to the Southwell geometry with an odd-number grid size. Typically the Fried geometry is not preferred in slope-based optical testing because it either allows subsize wavefront estimations within the testing domain or yields a two-rank deficient estimations matrix, which usually suffers from high error propagation and the waffle mode problem. The Southwell geometry, with an odd-number grid size if a zero point is assigned for the wavefront, is usually recommended in optical testing because it provides the lowest-error propagation for both slope-based and difference-based wavefront estimations.