gebhart/patrepeval huggingface dataset:
Activation of Canonical Wnt Pathway Promotes Proliferation of Retinal Stem Cells Derived from Adult Mouse Ciliary Margin (2005)

Adult retinal stem cells represent a possible cell source for the treatment of retinal degeneration. However, only a small number of stem cells reside in the ciliary margin. The present study aimed to promote the proliferation of adult retinal stem cells via the Wnt signaling pathway. Ciliary margin cells from 8-week-old mice were dissociated and cultured to allow sphere colony formation. Wnt3a, a glycogen synthase kinase (GSK) 3 inhibitor, fibroblast growth factor (FGF) 2, and a FGF receptor inhibitor were then applied in the culture media. The primary spheres were dissociated to prepare either monolayer or secondary sphere cultures. Wnt3a increased the size of the primary spheres and the number of Ki-67-positive proliferating cells in monolayer culture. The Wnt3a-treated primary sphere cells were capable of self-renewal and gave rise to fourfold the number of secondary spheres compared with nontreated sphere cells. These cells also retained their multilineage potential to express several retinal markers under differentiating culture conditions. The Wnt3a-treated cells showed nuclear accumulation of beta-catenin, and a GSK3 inhibitor, SB216763, mimicked the mitogenic activity of Wnt3a. The proliferative effect of SB216763 was attenuated by an FGF receptor inhibitor but was enhanced by FGF2, with Ki-67-positive cells reaching over 70% of the total cells. Wnt3a and SB216763 promoted the proliferation of retinal stem cells, and this was partly dependent on FGF2 signaling. A combination of Wnt and FGF signaling may provide a therapeutic strategy for in vitro expansion or in vivo activation of adult retinal stem cells.
Patterned superhydrophobic paper for microfluidic devices obtained by writing and printing (2013)

This work outlines inexpensive patterning methodologies to create open-air microfluidic paper-based devices. A phase-separation methodology was used to obtain biomimetic superhydrophobic paper, hierarchically composed by micro and nano topographies. Writing and printing are simple actions that can be used to pattern flat superhydrophobic paper with more wettable channels. In particular, inkjet printing permits controlling the wettability of the surface by changing the darkness of the printed regions. The difference between capillary forces provides the possibility to control and drive liquid flows through the open path lines, just by titling the piece of paper. Additionally, maintaining a continuous flow, it is possible to direct the liquid at different volumetric rates in a horizontal position along non-linear channel paths printed/written over the surface.
Plant response to irrigation with water enriched with carbon dioxide (1993)

The influence of irrigation with CO<sub>2</sub> -enriched water on plant development and yield is reviewed. The reason for irrigation with CO<sub>2</sub> -enriched water was - in most cases - to increase yield. The present evaluation considers results from over a hundred studies performed since the first experiment in 1866. Special emphasis is given to the comparison of 85 experiments made by Mitscherlich in 1910 with 358 irrigation experiments made in the last 80 years. In a statistical analysis of these experiments, the measured plant parameter (often growth and/or gas exchange rates) showed a highly significant mean increase of 2.9 % in plants irrigated with CO<sub>2</sub> -enriched water as compared with control. Evidence of five mechanisms was found. The subterranean carbon dioxide concentration influences: (a) the rate of nitrification and hence of nitrogen availability; (b) the rate of weathering and pH, and hence the availability of other plant nutrients; (c) the CO<sub>2</sub> uptake via roots into the transpiration stream, contributing to the rate of leaf photosynthesis; (d) the hormone levels in the plant; and (e) the rate of pesticide decomposition in soils. After examining the available evidence we found that (a) and (b) in some experiments are important to plant growth, since they change the physiochemical environment of the roots. On the other hand, while (c) could theoretically contribute up to 5% of plant carbon assimilation, it usually contributes less than 1 %, while (d) contributes most of the observed effects of CO<sub>2</sub> -enriched water on plants. In addition, pesticide decomposition in soils can be delayed by supra- or sub-optimal CO<sub>2</sub> concentrations. Contents Summary 249 I. Introduction 249 II. Historical background 250 III. Methods for comparing experimental data 251 IV. Analysis of yield ratios 251 V. Temporal and spatial changes in the soil atmosphere during and after irrigation with CO<sub>2</sub> -enriched water 252 VI. Mechanisms through which irrigation with CO<sub>2</sub> -enriched water influences yield 253 Acknowledgements 256 References 257.
Verrucae vulgares. II. Demonstration of a complement fixation reaction (1971)

No abstract available
Strategies for the Control of Viral Diseases of Shrimp in the Americas. (1998)

Viral diseases have severely impacted many of the penaeid shrimp farming industries of the world causing significant production and economic losses. Nearly 20 distinct viruses, or groups of viruses, are known to infect penaeid shrimp. Viruses belonging to the WSSV, MBV, BMN, HPV, IHHNV, and YHV groups have been important pathogens of cultured shrimp in Asia and the Indo-Pacific regions, while TSV, IHHNV, and BP have been the principal viruses of concern in the Americas. Numerous strategies have been attempted for the control of viral diseases in penaeid shrimp aquaculture. These strategies range from the use of improved culture practices (i.e. where sources of virus contamination are reduced or eliminated, sanitation practices are improved, stocking densities are reduced, etc.) to stocking “specific pathogen-free” (SPF) or “specific pathogen resistant” (SPR) species or stocks. In the Americas many strategies have been employed in efforts to reduce production losses due to the enzootic viruses IHHNV, BP, and TSV. Improved husbandry practices have been successfully employed for the control of BP, and for nearly a decade, this virus has seldomly been reported as an economic constraint to successful shrimp culture.Until recently, the popularity and use of the relatively IHHNV resistant species Penaeus vannamei, in preference to the culture of the more IHHNV susceptible P. stylirostris, was characteristic of the shrimp farming industries of the Americas. The popularity of P. vannamei began to decline when TSV emerged as a very serious pathogen of this species in 1992 and then spread to virtually all of the shrimp growing regions of the Americas during the ensuing four years. Because P. stylirostris was found to be innately TSV resistant, two domesticated, genetically selected SPR strains of this species, which are resistant to IHHN disease, are currently being developed and marketed in the Americas. In some regions, these SPR stocks of TSV and IHHNV resistant P. stylirostris are replacing P. vannamei stocks in culture. Other shrimp farming interests are using wild or domesticated stocks of P. vannamei that show improved resistance to TSV. While resistance to TSV was used as a selection criteria for the domesticated stocks of P. vannamei, natural selection for TSV resistance appears to be occurring in wild stocks where TSV has been enzootic for several years. The same selective process for IHHNV resistance seems to be occurring in some wild stocks of P. stylirostris.
Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway (2008)

General methods to engineer genetically encoded, reversible, light-mediated control over protein function would be useful in many areas of biomedical research and technology. We describe a system that yields such photo-control over actin assembly. We fused the Rho family GTPase Cdc42 in its GDP-bound form to the photosensory domain of phytochrome B (PhyB) and fused the Cdc42 effector, the Wiskott-Aldrich Syndrome Protein (WASP), to the light-dependent PhyB-binding domain of phytochrome interacting factor 3 (Pif3). Upon red light illumination, the fusion proteins bind each other, activating WASP, and consequently stimulating actin assembly by the WASP target, the Arp2/3 complex. Binding and WASP activation are reversed by far-red illumination. Our approach, in which the biochemical specificity of the nucleotide switch in Cdc42 is overridden by the light-dependent PhyB-Pif3 interaction, should be generally applicable to other GTPase-effector pairs.
Ba and Bb Fragments of Factor B Activation:Fragment Production, Biological Activities, Neoepitope Expression and Quantitation in Clinical Samples (1989)

Factor B is a centrally important component of the alternative complement pathway. Alternative pathway activation results in factor B cleavage and production of the amino-terminal Ba and the carboxyl-terminal Bb fragments which have molecular weights of approximately 30,000 and 63,000 daltons, respectively. Both Ba and Bb fragments have been reported to express a variety of biological activities in vitro. Thus, binding of Ba and Bb fragments to specific B lymphocyte surface receptors modulates proliferation of prestimulated B cells. In addition, the enzymatically active Bb fragment induces activation and spreading of human and murine macrophages and monocytes as well as regulates C5a des Arg chemotactic activity. The fractional catabolic rate and metabolism of factor B in vivo is similar to that of C3, C4 and C5 complement proteins, which are among the most metabolically active plasma proteins in the circulatory system. Factor B hyperconsumption and increased catabolism, concomitant with factor B fragment production, occurs in a wide variety of diseases, including gram-negative sepsis, autoimmune diseases and burns. Measurement of alternative pathway activation in vivo has been attempted utilized a number of different techniques to quantitate factor B fragments in biological fluids. However, the recent development of enzyme immunoassays (EIA) employing monoclonal antibodies (MoAbs) reactive with factor B fragment neoepitopes provides the best approach currently available for the quantitation of factor B activation fragments. Results obtained using these new MoAb-based EIAs have indicated that factor B fragment concentrations were elevated, as compared with normal donor levels, in EDTA plasma samples obtained from patients with rheumatoid arthritis and systemic lupus erythematosus (SLE). Plasma concentrations of factor B fragments, especially Ba fragment levels, in these patients showed a positive correlation with disease activity scores. One of the highest disease activity correlations was obtained with Ba fragment measurements in SLE plasma samples. In fact, the results strongly suggested that quantitation of Ba fragment levels in SLE plasma samples more accurately reflected disease activity and was a more sensitive predictor of impending flare in these patients than any other test(s) currently available.
Convolutional Neural Networks for Medical Image Analysis: Full Training or Fine Tuning? (2016)

Training a deep convolutional neural network (CNN) from scratch is difficult because it requires a large amount of labeled training data and a great deal of expertise to ensure proper convergence. A promising alternative is to fine-tune a CNN that has been pre-trained using, for instance, a large set of labeled natural images. However, the substantial differences between natural and medical images may advise against such knowledge transfer. In this paper, we seek to answer the following central question in the context of medical image analysis: Can the use of pre-trained deep CNNs with sufficient fine-tuning eliminate the need for training a deep CNN from scratch? To address this question, we considered four distinct medical imaging applications in three specialties (radiology, cardiology, and gastroenterology) involving classification, detection, and segmentation from three different imaging modalities, and investigated how the performance of deep CNNs trained from scratch compared with the pre-trained CNNs fine-tuned in a layer-wise manner. Our experiments consistently demonstrated that 1) the use of a pre-trained CNN with adequate fine-tuning outperformed or, in the worst case, performed as well as a CNN trained from scratch; 2) fine-tuned CNNs were more robust to the size of training sets than CNNs trained from scratch; 3) neither shallow tuning nor deep tuning was the optimal choice for a particular application; and 4) our layer-wise fine-tuning scheme could offer a practical way to reach the best performance for the application at hand based on the amount of available data.
Surface oxidation activates indium tin oxide for hole injection (2000)

Oxygen plasma treatment of indium tin oxide (ITO) results in a change in work function and electron affinity by ∼0.5 eV. This change correlates with the measured increase in injected current in simple “hole-only” organic devices with O-plasma treated ITO electrodes. Neither addition nor removal of surface hydroxyl functionality accounts for the observed work function and electron affinity changes. X-ray and ultraviolet photoelectron spectroscopies show a new type of oxygen species is formed. Oxidation of surface Sn-OH to surface Sn-O• units is proposed to account for the observed changes in O-plasma treated ITO; this proposal can explain a wide variety of previously described ITO surface activation results.
Signal transduction by Fc gamma RIII (CD16) is mediated through the gamma chain. (1992)

To determine the functional role of the two isoforms of Fc gamma RIII (CD16) (IIIA, IIIB), the signal transduction capabilities of wild-type and mutant forms of these receptors were analyzed in transfected lymphoid, myeloid, and fibroblastic cell lines. Functional reconstitution of receptor signalling was observed in hematopoietic T and mast cells, and was absent in nonhematopoietic (CHO) cells. Fc gamma RIIIA, a hetero-oligomeric receptor composed of a ligand-binding subunit alpha and dimeric gamma chains, generated both proximal and distal responses in Jurkat and P815 cells, typical of what is seen in natural killer cells and macrophages upon receptor activation. In contrast, Fc gamma RIIIB, which is normally attached to the cell surface via a glycosyl-phosphatidylinositol anchor, was incapable of transducing signals. After crosslinking, Fc gamma RIIIA signalling was dependent only upon the gamma chain. Fc gamma RIIIA chimeras in which the alpha subunit transmembrane and cytoplasmic domains were substituted with the corresponding gamma chain sequences functioned as well as wild-type hetero-oligomeric receptors. These data indicate that the ability of the Fc gamma RIIIA complex to activate the appropriate pathways for cell activation is cell-type restricted and independent of the transmembrane and cytoplasmic domains of the alpha subunit. The presence of the gamma chain is responsible for the assembly of, as well as the signal transduction by, the functional cell surface complex.
Breast cancer risk in ataxia telangiectasia (AT) heterozygotes: haplotype study in French AT families (1999)

Epidemiological studies in ataxia telangiectasia (AT) families have suggested that AT heterozygotes could have an increased cancer risk, especially breast cancer (BC) in women. It has also been suggested that an increased sensibility of AT heterozygotes to the effect of ionizing radiation could be responsible for the increased BC risk. BC relative risk (RR) estimation in AT heterozygotes within families ascertained through AT children is presented here. Family data collected included demographic characteristics, occurrence of cancers, past radiation exposures and blood samples. DNA samples were studied using seven ATM linked microsatellites markers allowing AT haplotypes reconstitution. The relative risk of BC was assessed using French estimated incidence rates. A significant increase risk of BC is found among obligate ATM heterozygotes with a point estimate of 3.32 (P = 0.002). BC relative risk calculated according to age is significantly increased among the obligate ATM heterozygotes female relatives with an age < or = 44 years (RR = 4.55, P = 0.005). The BC relative risk is statistically borderline among the obligate ATM heterozygote female relatives with an age > or = 45 years (RR = 2.48, P = 0.08). The estimated BC relative risk among ATM heterozygotes is consistent with previously published data. However, the increased risk is only a little higher than classical reproductive risk factors and similar to the risk associated with a first-degree relative affected by BC.
Optimization of wave packet coefficients in Li2 using an evolutionary algorithm: The role of resonant and nonresonant wavelengths (2002)

Using feedback and an evolutionary algorithm (EA), the weak field pump–probe photoionization signal at a single time delay is optimized in Li2. A single launch state is prepared via excitation with a cw laser, from which a pump pulse excites a superposition of two rotational states on an excited electronic potential energy curve: E 1Σg+(vE=9, JE=27 and 29). The EA modifies the phase pattern versus wavelength of the ultrafast pump pulses using a pulse shaper with a 128 pixel liquid crystal spatial light modulator. Limitations of frequency resolution for the pulse shaper create an effective temporal window in which pulses can be shaped. Optimization of the photoionization signal at pump–probe time delays outside of this temporal pulse shaping window involves phase shifts of only the two frequencies resonant with the transition of the wave packet states, effectively introducing a phase shift in the wave packet recurrences. For pump–probe time delays inside the pulse shaping window, optimization of the photoionization shows the influence of not only resonant but also nonresonant wavelengths. In this regime, the phase shift of wave packet recurrences as well as the time-dependent wave packet amplitude coefficients are optimized. First order time dependent perturbation theory is used to explain the mechanism by which the photoionization is maximized. These experiments are the first to use an optimization routine as a tool to identify a variety of simultaneous mechanisms that underlie the maximization of a process.
Multimaterial Fibers (2012)

Recent progress in combining multiple materials with disparate optical, electronic, and thermomechanical properties monolithically in the same fiber drawn from a preform is paving the way to a new generation of multimaterial fibers endowed with unique functionalities delivered at optical fiber length scales and costs. A wide range of unique devices have been developed to date in fiber form‐factor using this strategy, such as transversely emitting fiber lasers, fibers that detect light, heat, or sound impinging on their external surfaces, and fibers containing crystalline semiconductor cores. Incorporating such fibers in future fabrics will lead to textiles with sophisticated functionality. Additionally, long‐standing issues in traditional applications of optical fibers have been addressed by multimaterial fibers, such as photonic bandgap guidance in hollow‐core all‐solid‐cladding fibers and imparting mechanical robustness to soft‐glass mid‐infrared fibers. We review recent progress in this nascent but rapidly growing field and highlight areas where growth is anticipated. Furthermore, the insights emerging from this research are pointing to new ways that the fiber drawing process itself may be leveraged as a fabrication methodology. In particular, we describe recent efforts directed at appropriating multimaterial‐fiber drawing for chemical synthesis and the fabrication of nanostructures such as nanowire arrays and structured nanoparticles.
In Vivo Manipulation of Dendritic Cells Overcomes Tolerance to Unmodified Tumor-Associated Self Antigens and Induces Potent Antitumor Immunity (2005)

Most tumor-associated Ags are self proteins that fail to elicit a T cell response as a consequence of immune tolerance. Dendritic cells (DCs) generated ex vivo have been used to break tolerance against such self Ags; however, in vitro manipulation of DCs is cumbersome and difficult to control, resulting in vaccines of variable potency. To address this problem we developed a method for loading and activating DCs, in situ, by first directing sufficient numbers of DCs to peripheral tissues using Flt3 ligand and then delivering a tumor-associated Ag and oligonucleotide containing unmethylated CG motifs to these tissues. In this study, we show in three different tumor models that this method can overcome tolerance and induce effective antitumor immunity. Vaccination resulted in the generation of CD8(+) T and NK cell effectors that mediated durable tumor responses without attacking normal tissues. These findings demonstrate that unmodified tumor-associated self Ags can be targeted to DCs in vivo to induce potent systemic antitumor immunity.
Fullerene Bisadducts for Enhanced Open‐Circuit Voltages and Efficiencies in Polymer Solar Cells (2008)

A fullerene bisadduct can enhance the efficiency of polymer:fullerene bulk heterojunction solar cells. The bisadduct has a LUMO that is 100 meV higher compared to that of [6,6]-phenyl C61 butyric acid methyl ester (PCBM). This increases the open-circuit voltage of polymer:fullerene bulk heterojunction solar cells based on poly(3-hexylthio phene) and bisadduct PCBM to 0.73 V, while maintaining high fill factors and currents.
Creation with a stent of an unrestrictive lasting atrial communication (2002)

A new technique is presented to create percutaneously an unrestrictive and lasting atrial communication in small children. In 2 infants, a stent was deployed in a restrictive atrial communication and first inflated with an 8 mm balloon. The stent was then further expanded up to 10 or 12 mm. The gradient and turbulent flow between the two atriums disappeared completely. The stent retained a very stable position without embolisation. Other complications, such as formation of thrombus or arrhythmia, were not observed until elective explantation after 2 and 11 months. We conclude that, in infants, dilation of the atrial septum with a stent can provide a safe, lasting, and unrestrictive atrial communication.