gebhart/patrepeval huggingface dataset:
Spray-dried plasma improves growth performance and reduces inflammatory status of weaned pigs challenged with enterotoxigenic Escherichia coli K881 (2004)

We investigated whether spray-dried plasma (SDP) improved growth and health of piglets challenged with enterotoxigenic Escherichia coli K88 (ETEC). Forty-eight pigs weaned at 21 d (BW = 4.88 +/- 0.43 kg) received one of four diets containing 6% SDP or fish proteins (as-fed basis) either nonmedicated (SDP-NM and FP-NM diets) or medicated with 0 or 250 mg/kg of colistine + 500 mg/kg of amoxycycline (SDP-M and FP-M diets), for 15 d. On d 4, pigs were orally challenged with ETEC. On d 15, eight pigs per dietary group were killed, blood and saliva were collected for analysis of K88 fimbriae-specific immunoglobulin (Ig)-A, and jejunum was removed for villi preparation, histological analysis, and cytokine expression. The presence or absence of K88 receptors (K88+ and K88- pigs respectively) was determined by villous adhesion assay. Effects of protein source on ADG (P = 0.04) and ADFI (P < 0.01), as well of medication on ADFI (P < 0.02), of all pigs were observed. In sacrified pigs, there was an effect of protein source on ADG (P = 0.03) and ADFI (P < 0.001), as well an interaction between medication and presence of K88 receptor (P = 0.02) for feed:gain ratio. Plasma K88 specific IgA were low in all K88 pigs and higher in K88+ pigs fed FP-NM compared with all the other groups (P < 0.05), except SDP-M. An interaction was found among protein source, medication, and presence of K88 receptors (P = 0.04). Saliva IgA concentrations were high in all pigs fed FP-NM and low in all other pigs. Jejunum of pigs fed FP-NM showed some ulcerations, edema, and mild inflammatory cell infiltration (ICI). In pigs fed FP-M, edema was reduced. Conversely, only a mild ICI was observed in pigs fed SDP-NM and SDP-M. Crypt depth was increased in K88+ pigs fed SDP-NM and an interaction between protein source and presence of K88 receptors was observed (P < 0.05). Expressions of tumor necrosis factor-alpha and interleukin (IL)-8 were lower in pigs fed SDP-NM and SDP-M than in those fed FP-NM and FP-M, either K88- or K88+ (P < 0.01). In pigs fed FP diets, expression of IL-8 tended to increase (P = 0.08) in K88+ compared with K88- subjects. Expression of interferon-gamma increased in K88 and K88+ pigs fed FP-M as compared with other pigs (P < 0.01). These results indicate that feeding with SDP improved growth performance and protected against E. coli-induced inflammatory status, and suggest that use of SDP-NM can be considered a valid antibiotic alternative.
Signal Transduction Pathways in Autoimmunity (2001)

An immensely complex network of interactions between multiple cell types and cytokines regulates the immune system. Ligand binding to antigen-specific, Fc, or cytokine receptors initiates differentiation, activation and proliferation of multiple immune system cell lineages. These activating pathways are counteracted by inhibitory receptors. In the
Profile of 513 patients with alopecia areata: associations of disease subtypes with atopy, autoimmune disease and positive family history (2006)

Our findings show marked associations between severity of AA, atopic dermatitis, thyroid disease and other autoimmune diseases, and extensive family history of AA, suggesting two clinically distinct subtypes of AA with the severe subtype possibly associated with greater familial autoimmunity. Further research exploring the possibility of a genetic basis to explain these clinical findings will be helpful in clarifying our understanding of AA, leading to improvements in diagnosis and treatment.
Accelerating SENSE using compressed sensing (2009)

Both parallel MRI and compressed sensing (CS) are emerging techniques to accelerate conventional MRI by reducing the number of acquired data. The combination of parallel MRI and CS for further acceleration is of great interest. In this paper, we propose a novel method to combine sensitivity encoding (SENSE), one of the standard methods for parallel MRI, and compressed sensing for rapid MR imaging (SparseMRI), a recently proposed method for applying CS in MR imaging with Cartesian trajectories. The proposed method, named CS-SENSE, sequentially reconstructs a set of aliased reduced-field-of-view images in each channel using SparseMRI and then reconstructs the final image from the aliased images using Cartesian SENSE. The results from simulations and phantom and in vivo experiments demonstrate that CS-SENSE can achieve a reduction factor higher than those achieved by SparseMRI and SENSE individually and outperform the existing method that combines parallel MRI and CS.
A 3D-printed, functionally graded soft robot powered by combustion (2015)

Roboticists have begun to design biologically inspired robots with soft or partially soft bodies, which have the potential to be more robust and adaptable, and safer for human interaction, than traditional rigid robots. However, key challenges in the design and manufacture of soft robots include the complex fabrication processes and the interfacing of soft and rigid components. We used multimaterial three-dimensional (3D) printing to manufacture a combustion-powered robot whose body transitions from a rigid core to a soft exterior. This stiffness gradient, spanning three orders of magnitude in modulus, enables reliable interfacing between rigid driving components (controller, battery, etc.) and the primarily soft body, and also enhances performance. Powered by the combustion of butane and oxygen, this robot is able to perform untethered jumping.
Enhanced efficacy of transcriptionally targeted suicide gene/prodrug therapy for thyroid carcinoma with the Cre-loxP system. (1999)

Our recent study demonstrates the feasibility of the thyroglobulin (TG) promoter in transcriptionally targeted gene therapy for thyroid carcinomas expressing TG, albeit less effectively than the constitutive viral promoter. The present study was, therefore, designed to enhance the activity of the TG promoter with the Cre-loxP system. Our data demonstrate that the in vitro cytotoxic effect of herpes simplex virus thymidine kinase/ganciclovir obtained with the TG promoter and the Cre-loxP system is approximately 5-10-fold higher than that with the TG promoter alone. Enhanced tumor growth inhibition was also observed in in vivo tumor models. These data indicate the usefulness of the Cre-loxP system to enhance the activity of a tissue (or tumor)-specific promoter in transcriptionally targeted cancer gene therapy.
Follicular Dendritic Cells Carry MHC Class II-Expressing Microvesicles at Their Surface (2000)

Follicular dendritic cells (FDCs) present in lymphoid follicles play a critical role in germinal center reactions. They trap native Ags in the form of immune complexes providing a source for continuous stimulation of specific B lymphocytes. FDCs have been reported to express MHC class II molecules, suggesting an additional role in the presentation of not only native, but also processed Ag in the form of peptide-loaded MHC class II. Adoptive bone marrow transfer experiments have shown that MHC class II molecules are only passively acquired. Up to now the origin of these MHC class II molecules was not clear. Here we show by cryoimmunogold electron microscopy that MHC class II molecules are not present at the plasma membrane of FDCs. In contrast, microvesicles attached to the FDC surface contain MHC class II and other surface proteins not expressed by FDCs themselves. The size and marker profiles of these microvesicles resemble exosomes. Exosomes, which are secreted internal vesicles from multivesicular endosomes, have been shown earlier to stimulate proliferation of specific T lymphocytes in vitro, but their target in vivo remained a matter of speculation. We demonstrate here that isolated exosomes in vitro bind specifically to FDCs and not to other cell types, suggesting that FDCs might be a physiological target for exosomes.
Universal Sentence Encoder (2018)

We present models for encoding sentences into embedding vectors that specifically target transfer learning to other NLP tasks. The models are efficient and result in accurate performance on diverse transfer tasks. Two variants of the encoding models allow for trade-offs between accuracy and compute resources. For both variants, we investigate and report the relationship between model complexity, resource consumption, the availability of transfer task training data, and task performance. Comparisons are made with baselines that use word level transfer learning via pretrained word embeddings as well as baselines do not use any transfer learning. We find that transfer learning using sentence embeddings tends to outperform word level transfer. With transfer learning via sentence embeddings, we observe surprisingly good performance with minimal amounts of supervised training data for a transfer task. We obtain encouraging results on Word Embedding Association Tests (WEAT) targeted at detecting model bias. Our pre-trained sentence encoding models are made freely available for download and on TF Hub.
Deterministic assembly of releasable single crystal silicon-metal oxide field-effect devices formed from bulk wafers (2013)

Deterministic assembly of ultrathin metal oxide-semiconductor field-effect transistors released from the surfaces of bulk wafers with (111) orientation provides a route to high quality electronics on nearly any type of substrate. Device parameters and bias stability characteristics from transistors on sheets of plastic confirm the effectiveness of the approach and the critical roles of thermally grown layers of silicon dioxide for the gate dielectrics and passivation layers. Systematic studies of the anisotropic etching processes used to release the devices illustrate capabilities into the sub-micron thickness regime, with beneficial effects on the bending stiffness and degree of bendability.
Rolling Circle Enzymatic Replication of a Complex Multi-Crossover DNA Nanostructure (2007)

Nature has evolved replicable biological molecules, such as DNA, as genetic information carriers. The replication process is tightly controlled by complicated cellular machinery. It is interesting to ask if artificial DNA nano-objects with a complex secondary structure can be replicated in the same way as simple DNA double helices. Here we demonstrate that paranemic crossover DNA, a structurally complicated multi-crossover DNA molecule, can be replicated successfully using Rolling Circle Amplification (RCA). The amplification efficiency is moderate with high fidelity, confirmed by native PAGE, thermal transition study, and Ferguson analysis. The structural details of the DNA structure after the full replication circle are verified by hydroxyl radical autofootprinting. We conclude that RCA can serve as a reliable method to replicate complex DNA structures. We also discuss the possibility of using viruses and bacteria to clone artificial DNA nano-objects. The findings that single stranded paranemic crossover DNA molecules can be replicated by DNA polymerase will not only be useful in nanotechnology but also may have implications for the possible existence of such complicated DNA structures in nature.
Adjunctive Therapy for Septic Shock: A Review of Experimental Approaches (1995)

Septic shock remains a major cause of morbidity and mortality, especially in the intensive care setting. A vast array of treatment strategies is under investigation; despite success in animal models, no effective adjunctive therapy has yet been approved for clinical use. This paper reviews the development of experimental therapies for sepsis and discusses those treatments that show promise for application in humans. Approaches to treatment fall into three broad categories: strategies directed against bacterial components, those directed against host-derived inflammatory mediators, and those designed to limit tissue damage. Because septic shock is a dynamic and evolving condition, different strategies may be needed at different stages in the pathogenesis of sepsis. Through carefully performed trials and thoughtful selection of combination therapy aimed at different points in the pathological process, it may be possible in the future to modify the course of this serious condition.
The Lithium–Oxygen Battery with Ether‐Based Electrolytes (2011)

Electrolyte puts up a fight: The electrolyte is one of the greatest challenges facing the development of the non-aqueous Li–O2 battery. Although ether-based electrolytes do from Li2O2 on the first discharge, it is shown by various techniques that they also decompose and that decomposition increases while Li2O2 decreases on cycling (see picture). Thus, these electrolytes are not suitable. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
HER2-positive breast cancer targeting and treatment by a peptide-conjugated mini nanodrug (2016)

HER2+ breast cancer is one of the most aggressive forms of breast cancer. The new polymalic acid-based mini nanodrug copolymers are synthesized and specifically characterized to inhibit growth of HER2+ breast cancer. These mini nanodrugs are highly effective and in the clinic may substitute for trastuzumab (the marketed therapeutic antibody) and antibody-targeted nanobioconjugates. Novel mini nanodrugs are designed to have slender shape and small size. HER2+ cells were recognized by the polymer-attached trastuzumab-mimetic 12-mer peptide. Synthesis of the nascent cell-transmembrane HER2/neu receptors by HER2+ cells was inhibited by antisense oligonucleotides that prevented cancer cell proliferation and significantly reduced tumor size by more than 15 times vs. untreated control or PBS-treated group. We emphasize that the shape and size of mini nanodrugs can enhance penetration of multiple bio-barriers to facilitate highly effective treatment. Replacement of trastuzumab by the mimetic peptide favors reduced production costs and technical efforts, and a negligible immune response.
Rock-physics templates for clay-rich source rocks (2015)

ABSTRACT Shale source rocks are composed of various minerals, mainly smectite and illite, depending on the burial depth, and they can be described as transversely isotropic media. The “pore space” may contain kerogen, water, oil, and gas determined by the in situ conditions. A petroelastic description is based on the following: Smectite-illite transformation as a function of depth is described by a fifth-order kinetic reaction. Backus averaging to “mix” isotropic smectite and anisotropic illite is then used to obtain the elasticity constants of the mineral composing the frame. Porosity is obtained from density, and water is part of the mineral, whose elasticity constants are obtained from Gassmann equations. Oil and gas generated from kerogen are assumed to saturate the kerogen phase. The bulk modulus of the oil-gas mixture is calculated by a mesoscopic-loss model, and the stiffnesses of the kerogen/fluid mixture are obtained with the Kuster and Toksöz model, assuming that the fluid is included in a kerogen matrix. Two models are considered to obtain the seismic velocities of the shale, namely, Backus averaging and the Gassmann equation generalized to the anisotropic case with a solid pore infill. We built rock-physics templates (RPTs) containing only kerogen (immature) and kerogen plus hydrocarbons (mature). Pore-pressure effects were modeled and used as templates. We considered the Kimmeridge Shale at different depths. To model kerogen-oil and oil-gas conversions, we assumed a basin-evolution model with a constant sedimentation rate, geothermal gradient, and a first-order kinetic (Arrhenius) reaction. The detection of the hydrocarbons was investigated from RPTs, built with wave velocities, impedances, Lamé constants, density, Poisson ratio, Young modulus, and anisotropy parameters for varying kerogen content, fluid saturations, and pore pressure. Moreover, the amplitude variation with offset intercept and gradients were computed, corresponding to the seismic response of a source rock layer for varying kerogen content and fluid saturation.
Nanoparticle-Based Delivery of RNAi Therapeutics: Progress and Challenges (2013)

RNA interference (RNAi) is an evolutionarily conserved, endogenous process for post-transcriptional regulation of gene expression. Although RNAi therapeutics have recently progressed through the pipeline toward clinical trials, the application of these as ideal, clinical therapeutics requires the development of safe and effective delivery systems. Inspired by the immense progress with nanotechnology in drug delivery, efforts have been dedicated to the development of nanoparticle-based RNAi delivery systems. For example, a precisely engineered, multifunctional nanocarrier with combined passive and active targeting capabilities may address the delivery challenges for the widespread use of RNAi as a therapy. Therefore, in this review, we introduce the major hurdles in achieving efficient RNAi delivery and discuss the current advances in applying nanotechnology-based delivery systems to overcome the delivery hurdles of RNAi therapeutics. In particular, some representative examples of nanoparticle-based delivery formulations for targeted RNAi therapeutics are highlighted.
A novel high-performance lateral bipolar on SOI (2002)

A novel lateral bipolar structure on SOI (silicon-on-insulator) is described. This device has a thin double-diffused base and a narrow emitter width, determined by the SOI thickness. It has minimal parasitic junction capacitance, as well as minimal emitter and collector resistances. Excellent device characteristics and an f/sub T/ of about 20 GHz were demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Regulation of NF-κB-Dependent Lymphocyte Activation and Development by Paracaspase (2003)

Paracaspase (MALT1), a member of an evolutionarily conserved superfamily of caspase-like proteins, has been shown to bind and colocalize with the protein Bcl10 in vitro and, because of this association, has been suggested to be involved in the CARMA1-Bcl10 pathway of antigen-induced nuclear factor kappaB (NF-kappaB) activation. We demonstrate that primary T and B lymphocytes from paracaspase-deficient mice are defective in antigen-receptor-induced NF-kappaB activation, cytokine production, and proliferation. Paracaspase acts downstream of Bcl10 to induce NF-kappaB activation and is required for the normal development of B cells, indicating that paracaspase provides the missing link between Bcl10 and activation of the IkappaB kinase complex.
α‐Synuclein mediates alterations in membrane conductance: a potential role for α‐synuclein oligomers in cell vulnerability (2010)

alpha-Synuclein has been linked to the pathogenesis of Parkinson's disease and other synucleinopathies through its propensity to form toxic oligomers. The exact mechanism for oligomeric synuclein-directed cell vulnerability has not been fully elucidated, but one hypothesis portends the formation of synuclein-containing pores within cell membranes leading to leak channel-mediated calcium influx and subsequent cell death. Here we demonstrate synuclein-induced formation of sodium dodecyl sulfate-stable oligomers, intracellular synuclein-positive aggregates, alterations in membrane conductance reminiscent of leak channels and subsequent cytotoxicity in a dopaminergic-like cell line. Furthermore we demonstrate that the synuclein-induced membrane conductance changes are blocked by direct extracellular application of an anti-synuclein antibody. The work presented here confirms that synuclein overexpression leads to membrane conductance changes and demonstrates for the first time through antibody-blocking studies that synuclein plays a direct role in the formation of leak channels.
Transdermal delivery of car vedilol in rats: probing the percutaneous permeation enhancement mechanism of soybean extract–chitosan mixture (2009)

The developed transdermal patches of CDL containing SS extract-CTN mixture exhibited better performance as compared to oral administration in controlling hypertension in rats.
An Efficient and Selective Enzymatic Oxidation System for the Synthesis of Enantiomerically Pured-tert-Leucine (2003)

[reaction: see text] d-tert-Leucine was prepared with an enantiomeric excess of >99% by an enzyme-catalyzed oxidative resolution of the racemic mixture of dl-tert-leucine with use of leucine dehydrogenase. The l-amino acid was oxidized completely due to coupling of the primary reaction with a highly efficient irreversible NAD(+)-regenerating step by NADH oxidase.
Retroviral reverse transcriptase: synthesis, structure, and function. (1990)

The virion particles of all retroviruses contain reverse transcriptase, a multifunctional enzyme required for the synthesis of a DNA copy of the viral RNA genome soon after entry into the infected cell. The enzyme is the target of the major antiviral drugs currently in use in the treatment of AIDS. This article reviews the strategies used by different retroviruses for the synthesis of the enzyme; the structure of the enzymes encoded by various viruses; the activities inherent in the enzyme; and the application of those activities to the process of reverse transcription of the viral RNA.
Prevention of endotoxin-induced monokine release by human low- and high-density lipoproteins and by apolipoprotein A-I (1993)

Interaction of endotoxin (lipopolysaccharide [LPS]) with human lipoproteins is known to prevent the LPS-induced activation of human monocytes and release of cytokines (monokines). LPS was exposed to lipoprotein classes separated by ultracentrifugation and to apolipoprotein A-I. Then monocytes were added, and the LPS activation of monocytes was determined by measuring the induced monokines. Failure of LPS to induce monokine release was called LPS inactivation caused by lipoproteins or apolipoproteins. The LPS inactivation is shown to be a function of low-density lipoproteins. High-density lipoproteins inactivate LPS to a much lesser extent. The very-low-density lipoproteins cannot inactivate LPS. Lipid components seemed not absolutely required for LPS inactivation, because purified human apolipoprotein A-I without its physiological lipid complement also inhibits LPS-induced monokine release.