gebhart/patrepeval huggingface dataset:
Vaccination with Brucella abortus Recombinant In Vivo-Induced Antigens Reduces Bacterial Load and Promotes Clearance in a Mouse Model for Infection (2011)

Current vaccines used for the prevention of brucellosis are ineffective in inducing protective immunity in animals that are chronically infected with Brucella abortus, such as elk. Using a gene discovery approach, in vivo-induced antigen technology (IVIAT) on B. abortus, we previously identified ten loci that encode products up-regulated during infection in elk and consequently may play a role in virulence. In our present study, five of the loci (D15, 0187, VirJ, Mdh, AfuA) were selected for further characterization and compared with three additional antigens with virulence potential (Hia, PrpA, MltA). All eight genes were PCR-amplified from B. abortus and cloned into E. coli. The recombinant products were then expressed, purified, adjuvanted, and delivered subcutaneously to BALB/c mice. After primary immunization and two boosts, mice were challenged i.p. with 5 x 10⁴ CFU of B. abortus strain 19. Spleens from challenged animals were harvested and bacterial loads determined by colony count at various time points. While vaccination with four of the eight individual proteins appeared to have some effect on clearance kinetics, mice vaccinated with recombinant Mdh displayed the most significant reduction in bacterial colonization. Furthermore, mice immunized with Mdh maintained higher levels of IFN-γ in spleens compared to other treatment groups. Collectively, our in vivo data gathered from the S19 murine colonization model suggest that vaccination with at least three of the IVIAT antigens conferred an enhanced ability of the host to respond to infection, reinforcing the utility of this methodology for the identification of potential vaccine candidates against brucellosis. Mechanisms for immunity to one protein, Mdh, require further in vitro exploration and evaluation against wild-type B. abortus challenge in mice, as well as other hosts. Additional studies are being undertaken to clarify the role of Mdh and other IVI antigens in B. abortus virulence and induction of protective immunity.
Dual Learning for Machine Translation (2016)

While neural machine translation (NMT) is making good progress in the past two years, tens of millions of bilingual sentence pairs are needed for its training. However, human labeling is very costly. To tackle this training data bottleneck, we develop a dual-learning mechanism, which can enable an NMT system to automatically learn from unlabeled data through a dual-learning game. This mechanism is inspired by the following observation: any machine translation task has a dual task, e.g., English-to-French translation (primal) versus French-to-English translation (dual); the primal and dual tasks can form a closed loop, and generate informative feedback signals to train the translation models, even if without the involvement of a human labeler. In the dual-learning mechanism, we use one agent to represent the model for the primal task and the other agent to represent the model for the dual task, then ask them to teach each other through a reinforcement learning process. Based on the feedback signals generated during this process (e.g., the language-model likelihood of the output of a model, and the reconstruction error of the original sentence after the primal and dual translations), we can iteratively update the two models until convergence (e.g., using the policy gradient methods). We call the corresponding approach to neural machine translation \emph{dual-NMT}. Experiments show that dual-NMT works very well on English$\leftrightarrow$French translation; especially, by learning from monolingual data (with 10% bilingual data for warm start), it achieves a comparable accuracy to NMT trained from the full bilingual data for the French-to-English translation task.
“Marker of Self” CD47 on lentiviral vectors decreases macrophage-mediated clearance and increases delivery to SIRPA-expressing lung carcinoma tumors (2016)

Lentiviruses infect many cell types and are now widely used for gene delivery <i>in vitro</i>, but <i>in vivo</i> uptake of these foreign vectors by macrophages is a limitation. Lentivectors are produced here from packaging cells that overexpress "Marker of Self" CD47, which inhibits macrophage uptake of cells when prophagocytic factors are also displayed. Single particle analyses show "hCD47-Lenti" display properly oriented human-CD47 for interactions with the macrophage's inhibitory receptor SIRPA. Macrophages derived from human and NOD/SCID/Il2rg<sup>-/-</sup> (NSG) mice show a SIRPA-dependent decrease in transduction, <i>i.e.</i>, transgene expression, by hCD47-Lenti compared to control Lenti. Consistent with known "Self" signaling pathways, macrophage transduction by control Lenti is decreased by drug inhibition of Myosin-II to the same levels as hCD47-Lenti. In contrast, human lung carcinoma cells express SIRPA and use it to enhance transduction by hCD47-Lenti- as illustrated by more efficient gene deletion using CRISPR/Cas9. Intravenous injection of hCD47-Lenti into NSG mice shows hCD47 prolongs circulation, unless a blocking anti-SIRPA is preinjected. <i>In vivo</i> transduction of spleen and liver macrophages also decreases for hCD47-Lenti while transduction of lung carcinoma xenografts increases. hCD47 could be useful when macrophage uptake is limiting on other viral vectors that are emerging in cancer treatments (<i>e.g.</i>, Measles glycoprotein-pseudotyped lentivectors) and also in targeting various SIRPA-expressing tumors such as glioblastomas.
Hybrid of Monkey and Human Adenoviruses (1968)

Following joint replication of monkey SA7 adenovirus (C8 strain) and human adenovirus type 2 in green monkey kidney tissue culture, a virus possessing the properties of a hybrid was obtained. It was designated Ad2C8. Ad2C8 preparations contained two types of viral particles: human adenovirus type 2, and hybrid particles. The hybrid virions multiplied in green monkey kidney cells in the presence of human adenovirus types 1, 2, and 3, but not 3 and 7, and acquired the capsid of the helper adenovirus. The hybrid can serve as a helper for human adenoviruses. It can apparently induce T antigen of the C8 virus but, in contrast to the latter, does not induce tumors in hamsters.
Fusion to an endoglucanase allows alkaline phosphatase to bind to cellulose (1989)

Endoglucanase CenA of Cellulomonas fimi comprises an N-terminal cellulose-binding domain and a C-terminal catalytic domain joined together by a sequence of 23 proline and threonine residues (the Pro-Thr box). The domains function independently when separated by proteolysis. TnphoA has been used to generate cenA'-'phoA fusions. CenA'-'PhoA fusion polypeptides which contain the entire cellulose-binding domain of CenA bind to cellulose, allowing their purification from periplasmic extracts in a single, facile step. This result has implications for purification or immobilisation of chimeric proteins on a cheap cellulose matrix.
CINEMA: Columbia InterNet Extensible Multimedia Architecture (2002)

We describe the architecture and implementation of our Internet telephony system (CINEMA: Columbia InterNet Extensible Multimedia Architecture) intended to replace the departmental PBX (telephone switch). It interworks with the traditional telephone networks via a PSTN/IP gateway. It also serves as a corporate or campus infrastructure for existing and future services like web, email, video and streaming media. Initially intended for a few users, it will eventually replace the plain old telephones from our offices, due to the cost benefit and new services it offers. We also discuss common inter-operability problems between the PBX and the gateway. This paper is intended as a design document of the overall system.
Clinical Inertia Contributes to Poor Diabetes Control in a Primary Care Setting (2005)

Medical Clinic patients had worse glycemic control, were less likely to be treated with insulin, and were less likely to have their therapy intensified if glucose levels were elevated. To improve diabetes management and glycemic control nationwide, physicians in training and generalists must learn to overcome clinical inertia, to intensify therapy when appropriate, and to use insulin when clinically indicated.
A network of redundant bHLH proteins functions in all TTG1-dependent pathways ofArabidopsis (2003)

GLABRA3 (GL3) encodes a bHLH protein that interacts with the WD repeat protein, TTG1. GL3 overexpression suppresses the trichome defect of the pleiotropic ttg1 mutations. However, single gl3 mutations only affect the trichome pathway with a modest trichome number reduction. A novel unlinked bHLH-encoding locus is described here, ENHANCER OF GLABRA3 (EGL3). When mutated, egl3 gives totally glabrous plants only in the gl3 mutant background. The double bHLH mutant, gl3 egl3, has a pleiotropic phenotype like ttg1 having defective anthocyanin production, seed coat mucilage production, and position-dependent root hair spacing. Furthermore, the triple bHLH mutant, gl3 egl3 tt8, phenocopies the ttg1 mutation. Yeast two-hybrid and plant overexpression studies show that EGL3, like GL3, interacts with TTG1, the myb proteins GL1, PAP1 and 2, CPC and TRY, and it will form heterodimers with GL3. These results suggest a combinatorial model for TTG1-dependent pathway regulation by this trio of partially functionally redundant bHLH proteins.
<title>Real-time 3D shape measurement with digital stripe projection by Texas Instruments Micro Mirror Devices DMD</title> (2000)

The fast, contact-free and highly precise shape measurement of technical objects is of key importance in the scientific- technological area as well as the area of practical measurement technology. The application areas of contact- free surface measurement extend across widely different areas, e.g., the automation of production processes, the measurement and inspection of components in microsystem technology or the fast 3D in-vivo measurement of human skin surfaces in cosmetics and medical technology. This paper describes methodological and technological possibilities as well as measurement technology applications for fast optical 3D shape measurements using micromirror-based high-velocity stripe projection. Depending on the available projector and camera facilities, it will be possible to shoot and evaluate compete 3D surface profiles within only a few milliseconds.
Probenecid as a Noninjurious Positive Inotrope in an Ischemic Heart Disease Murine Model (2012)

The current therapeutic options for acute decompensated heart failure are limited to afterload reducers and positive inotropes. The latter increases myocardial contractility through changes in myocyte calcium (Ca²⁺) handling (mostly through stimulation of the β-adrenergic pathways [β-ADR]) and is associated with paradoxical effects of arrhythmias, cell death, and subsequently increased mortality. We have previously demonstrated that probenecid can increase cytosolic Ca²⁺ levels in the cardiomyocyte resulting in an improved inotropic response in vitro and in vivo without activating the β-ADR system. We hypothesize that, in contrast to other commonly used inotropes, probenecid functions through a system separate from that of β-ADR and hence will increase contractility and improve function without damaging the heart. Furthermore, our goal was to evaluate the effect of probenecid on cell death in vitro and its use in vivo as a positive inotrope in a mouse model of ischemic cardiomyopathy. Herein, we demonstrate that probenecid induced an influx of Ca²⁺ similar to isoproterenol, but does not induce cell death in vitro. Through a series of in vivo experiments we also demonstrate that probenecid can be used at various time points and with various methods of administration in vivo in mice with myocardial ischemia, resulting in improved contractility and no significant difference in infarct size. In conclusion, we provide novel data that probenecid, through its activity on cellular Ca²⁺ levels, induces an inotropic effect without causing or exacerbating injury. This discovery may be translatable if this mechanism is preserved in man.
Dynamic Coattention Networks For Question Answering (2016)

Several deep learning models have been proposed for question answering. However, due to their single-pass nature, they have no way to recover from local maxima corresponding to incorrect answers. To address this problem, we introduce the Dynamic Coattention Network (DCN) for question answering. The DCN first fuses co-dependent representations of the question and the document in order to focus on relevant parts of both. Then a dynamic pointing decoder iterates over potential answer spans. This iterative procedure enables the model to recover from initial local maxima corresponding to incorrect answers. On the Stanford question answering dataset, a single DCN model improves the previous state of the art from 71.0% F1 to 75.9%, while a DCN ensemble obtains 80.4% F1.
Effects of Transforming Growth Factor-β on the Production of Immunoreactive Insulin-Like Growth Factor I and Progesterone and on [3H]Thymidine Incorporation in Porcine Granulosa Cell Cultures* (1988)

Transforming growth factor-beta (TGF beta) has been reported to enhance many FSH-stimulated functions in rat granulosa cell cultures. We therefore, investigated the actions of TGF beta on cultured porcine granulosa cells. We evaluated the production of immunoreactive insulin-like growth factor I (iIGF-I) and progesterone in short term (3-day) and in longer term (7-day) cultures using porcine TGF beta 1 (pTGF beta 1). TGF beta had a biphasic effect on epidermal growth factor (EGF)-stimulated iIGF-I production in short term cultures. A modest stimulatory effect was apparent at 10 pg/ml; however, this end point was completely inhibited by 1-10 ng/ml. TGF beta also had a slight stimulatory effect on basal iIGF-I production at 1 pg/ml, but not at higher levels. In longer term cultures TGF beta did not have a significant effect on either basal or FSH-stimulated iIGF-I production. In both short and longer term cultures TGF beta markedly inhibited basal and FSH-stimulated progesterone production. We also evaluated the effects of TGF beta on the incorporation of [3H]thymidine into DNA and found that basal and growth factor-stimulated [3H]thymidine incorporation were inhibited. No stimulatory effects of TGF beta on progesterone production or [3H]thymidine incorporation could be detected over the dose range tested (1 pg/ml to 10 ng/ml). The effects of human TGF beta 1 and pTGF beta 2 were compared with those of pTGF beta 1 on basal and EGF-stimulated [3H]thymidine incorporation. Effects of the peptides were qualitatively similar, but pTGF beta 2 was somewhat less inhibitory to EGF-stimulated [3H]thymidine incorporation than pTGF beta 1. The present studies show that in contrast to the well documented stimulatory actions of TGF beta in cultured rat granulosa cells, this growth factor is a predominantly negative regulator of porcine granulosa cells. With the exception of a modest stimulation of iIGF-I production at very low doses, the effects of TGF beta were to potently inhibit both growth and differentiated function. The inhibitory nature of TGF beta should not be overlooked when considering the possible role of this peptide in ovarian development and differentiation.
Efficient CRISPR-mediated gene targeting and transgene replacement in the beetleTribolium castaneum (2015)

Gene-editing techniques are revolutionizing the way we conduct genetics in many organisms. The CRISPR/Cas nuclease has emerged as a highly versatile, efficient and affordable tool for targeting chosen sites in the genome. Beyond its applications in established model organisms, CRISPR technology provides a platform for genetic intervention in a wide range of species, limited only by our ability to deliver it to cells and to select mutations efficiently. Here, we test the CRISPR technology in an emerging insect model and pest, the beetle Tribolium castaneum. We use simple assays to test CRISPR/Cas activity, we demonstrate efficient expression of guide RNAs and Cas9 from Tribolium U6 and hsp68 promoters and we test the efficiency of knockout and knock-in approaches in Tribolium. We find that 55-80% of injected individuals carry mutations (indels) generated by non-homologous end joining, including mosaic bi-allelic knockouts; 71-100% carry such mutations in their germ line and transmit them to the next generation. We show that CRISPR-mediated gene knockout of the Tribolium E-cadherin gene causes defects in dorsal closure, which is consistent with RNAi-induced phenotypes. Homology-directed knock-in of marker transgenes was observed in 14% of injected individuals and transmitted to the next generation by 6% of injected individuals. Previous work in Tribolium mapped a large number of transgene insertions associated with developmental phenotypes and enhancer traps. We present an efficient method for re-purposing these insertions, via CRISPR-mediated replacement of these transgenes by new constructs.
THE HIGH-AFFINITY IgE RECEPTOR (FcεRI): From Physiology to Pathology (1999)

The high affinity receptor for immunoglobulin E (designated Fc epsilon RI) is the member of the antigen (Ag) receptor superfamily responsible for linking pathogen-or allergen-specific IgEs with cellular immunologic effector functions. This review provides background information on Fc epsilon RI function combined with more detailed summaries of recent progress in understanding specific aspects of Fc epsilon RI biology and biochemistry. Topics covered include the coordination and function of the large multiprotein signaling complexes that are assembled when Fc epsilon RI and other Ag receptors are engaged, new information on human receptor structures and tissue distribution, and the role of the FcR beta chain in signaling and its potential contribution to atopic phenotypes.
The combined influence of mineralogical, hygric and thermal properties on the durability of porous building stones (2008)

It is a common practice to test building stones against an isolated decay factor when assessing the durability of building stones. Accordingly, the interpretation of results is often driven by the considerations of a limited number of properties thought as relevant to the action of that specific decay factor. In this way, the role of the synergies of decay processes and agents is often neglected. Contrarily, when different decay factors are included in the same experiment and the stone properties are examined conjunctly, the difficulties of isolating the effects of a specific decay factor or of isolating the contribution of “relevant” stone properties become apparent. The aim of this paper is to assess the combined contribution of mineralogical, hygric and thermal properties to the durability of different stones after exposure to laboratory-simulated cyclic decay combining wetness and temperature variations. For this purpose, 10 stone types were selected to emphasize the impact of the mineralogical heterogeneity on stone decay, in particular the coexistence of calcareous and siliceous grains and the occurrence of clays. The results emphasize the importance of considering the relations between decay factors and highlight how stone properties must be considered as a whole in order to assess and understand the durability of building stones.
Control of Barite Morphology by Double-Hydrophilic Block Copolymers (2000)

Barite particles with a rich variety of well-defined morphologies have been synthesized by using double-hydrophilic block copolymers (which consist of a hydrophilic solvating block and a hydrophilic binding block) as crystal growth modifiers to direct the controlled precipitation of barium sulfate from aqueous solution. The influences of variation in functional group and molecular structure of the copolymers as well as variation of pH condition on the particle size and morphology were investigated. It was revealed that in the presence of copolymers containing carboxylic acid groups at a pH above 5, the obtained BaSO4 particles always exhibit a nanocrystalline structure due to the large inhibition effect of the polyanionic chain on the barite crystallization. With decreasing pH, the particle size essentially increases, and the particle morphology generally varies from ovals through peanuts to peaches. In the presence of the phosphonated copolymer PEG-b-PMAA-PO3H2 at pH 5, large bundles of barite nanofilaments ranging from 20 to 30 nm in diameter, each of which is a single crystal elongated along the crystallographic [12̄0] axis, can be produced due to the strong and specific interaction between the phosphonate groups of the copolymer and the crystallizing BaSO4 particles. The obtained results demonstrate the tremendous potential of double-hydrophilic block copolymers as tools for the controlled synthesis of inorganic crystals with unusual, well defined morphologies.
Dissecting the Diverse Actions of Pro- and Mature Neurotrophins (2006)

The neurotrophins mediate diverse actions in the developing peripheral and central nervous systems. They are initially synthesized as precursor forms, or proneurotrophins, that are cleaved to release C-terminal mature forms that bind to Trk receptor tyrosine kinases to enhance synaptic plasticity and neuronal survival. Recent studies suggest that proneurotrophins are not inactive precursors, but signaling proteins that can activate the p75 receptor to mediate diverse responses. Proneurotrophins can activate a heteromeric receptor complex of p75 and sortilin to initiate cell death, or bind to p75 in hippocampal neurons to enhance long term depression. Thus, neurotrophin actions are regulated by the form of the neurotrophin (pro- or mature) secreted by cells, by extracellular proteolytic cleavage of proneurotrophins to generate mature forms, and by the expression of neurotrophin receptors Trk, or p75 and sortilin, that are selectively activated by mature or proneurotrophins, respectively. Here, recent studies are reviewed that reveal that pro- and mature neurotrophins have distinct and sometimes opposing actions in regulating cell death and survival in development and in pathophysiologic states, in regulating neurotrophin secretion, and in modulating synaptic plasticity.
A new modification method of exploded lignin for the preparation of a carbon fiber precursor (1993)

Abstract A lignin‐pitch for carbon fiber was prepared in a high yield from exploded lignin on phenolysis followed by heat treatment under a vacuum. The lignin‐pitch had an excellent spinnability in the melt state to form a fine filament. The green fibers were easily made infusible when heated in air at a relatively high heating rate (15‐60°C/h). The lignin‐based carbon fiber was produced in 43.7% of yield based on a starting material. The tensile strength was more than 400 MPa, indicating that the lignin‐based carbon fiber is classified into a general purpose grade. © 1993 John Wiley &amp; Sons, Inc.
Targeted synthesis of an electroactive organic framework (2011)

A new strategy for targeted design and synthesis of an electroactive microporous organic molecular sieve (JUC-Z2) is described. Experiment demonstrated that such a targeted synthesis approach to achieve phenyl–phenyl coupling was a controllable process and predominately generated two-dimensional polymer sheets, significantly different from the traditional chemical or electrochemical oxidation methods to prepare conducting polymers. Successive self-assembly leads to a lamellar organic framework comprised of stacked polymer sheets with an hcb topology. JUC-Z2 was found to have a well-defined uniform micropore distribution (∼1.2 nm), a large surface area (BET = 2081 m2 g−1) and high physicochemical stability (>440 °C). After doping with I2, JUC-Z2 exhibits typical p-type semiconductive properties. As the first example of an electroactive organic framework, JUC-Z2 possesses a unique ability of electrochemical ion recognition, arising from the synergistic function of the uniform micropores and the N-atom redox site.