gebhart/patrepeval huggingface dataset:
In-situ product recovery from fermentation broths (2010)

Life sciences will be one of the decisive factors in the 21st century. A major part of this field is the so-called white biotechnology, also known as industrial biotechnology. White biotechnology is an emerging field where bio-chemicals are produced using micro-organisms. However, the production of bio-chemicals is severely inhibited due to toxicity of the product towards the host-organism. Therefore, it is necessary to remove the products from the micro-organisms’ environment. One approach for achieving this is applying so-called in-situ product removal. In this thesis solvent impregnated resins are added to a fermentation broth as an in-situ product removal tool. These particles contain an organic phase able to selectively extract a certain product from an aqueous phase such as fermentation broths.
Effect of phosphate depletion on blood pressure and vascular reactivity to norepinephrine and angiotensin II in the rat (1985)

Phosphate depletion (PD) adversely affects myocardial function but its influence on blood pressure is not well elucidated. In this study we evaluated whether PD influences blood pressure and/or affects its hormonal regulation or the peripheral vascular response to pressor agonists. Mean arterial pressure (MAP) in PD rats was lower than in normal animals, whereas heart rate was not significantly different between the two groups. Cardiac index (CI) in PD rats was lower and systemic vascular resistance (SVR) was higher than in controls. Plasma norepinephrine (NE) in the resting state and during the stress of immobilization was significantly greater in PD rats than in controls. Base-line plasma renin activity was also significantly higher in PD rats and increased similarly in the two groups of rats after administration of isoproterenol. Bolus injections of NE or angiotensin II produced a smaller rise in MAP in PD rats than in controls. Reduced responsiveness to NE was also demonstrated in isolated hind-limb preparation from PD rats. When NE was infused to achieve a rise in MAP of 30 mmHg, the dose required in PD was higher than in controls. Treatment with indomethacin did not affect the response in MAP to NE. The content and affinity of both alpha- and beta-receptors in PD hearts were not different from those of control hearts. The contents of PiATP, and AMP in the mesenteric vessels of PD rats were significantly lower than in control animals. These data show that PD leads to reductions in MAP, arteriolar response to pressor agents, and CI with appropriate compensatory rise in NE but with inadequate compensatory increase in SVR.(ABSTRACT TRUNCATED AT 250 WORDS)
Rapid sex determination of chick embryos using the polymerase chain reaction1 (1995)

Abstract The sex of early chicken embryos was determined by DNA dot‐blot hybridization and the polymerase chain reaction (PCR). An oligonucleotide probe, specific to the XhoI family of repetitive DNA of the W chromosome, was hybridized to crude and purified preparations of DNA obtained from blood or cells from embryos and detected using chemiluminescence. Complete agreement was observed in sexing 100 embryos using the dot‐blot assay and visual inspection of embryonic gonadal tissue. Although the dot‐blot system was useful for determining the sex of embryos prior to and throughout incubation, the time required for hybridization and detection did not allow for the immediate manipulation of embryos. Therefore, a PCR assay was developed using primers specific to the XhoI repetitive element and rapid thermocycling with an air thermocycler. A female‐specific amplification product was observed using DNA from as few as two cells in the PCR. Furthermore, female DNA was detected in mixtures of male and female DNA at levels equivalent to one female cell in 5000 male cells. The high level of sensitivity permitted the sexing of unincubated embryos using a small biopsy of cells sampled in ovo. In general, the entire procedure, including sample preparation, the PCR, and electrophoresis could be completed within 2.5 hours thereby saving a considerable amount of time over techniques requiring hybridization. The ability to rapidly determine the sex of the unincubated chick embryo will facilitate studies on gonadal differentiation, the examination of sex differences during development, and assist current efforts to manipulate the avian genome using germline chimeras.
Statistical approaches and software for clustering islet cell functional heterogeneity (2016)

Worldwide efforts are underway to replace or repair lost or dysfunctional pancreatic β-cells to cure diabetes. However, it is unclear what the final product of these efforts should be, as β-cells are thought to be heterogeneous. To enable the analysis of β-cell heterogeneity in an unbiased and quantitative way, we developed model-free and model-based statistical clustering approaches, and created new software called TraceCluster. Using an example data set, we illustrate the utility of these approaches by clustering dynamic intracellular Ca(2+) responses to high glucose in ∼300 simultaneously imaged single islet cells. Using feature extraction from the Ca(2+) traces on this reference data set, we identified 2 distinct populations of cells with β-like responses to glucose. To the best of our knowledge, this report represents the first unbiased cluster-based analysis of human β-cell functional heterogeneity of simultaneous recordings. We hope that the approaches and tools described here will be helpful for those studying heterogeneity in primary islet cells, as well as excitable cells derived from embryonic stem cells or induced pluripotent cells.
The parallel implementation of N-body algorithms (1995)

Recent studies examining patterns and consequences of variation in maternally deposited steroids in avian egg yolk have demonstrated that these maternal hormones can have dramatic effects on chick phenotypes. However, maternal steroids are not the only source for avian embryos, which activate endocrine axes relatively early in development and are capable of producing substantial amounts of endogenous steroids. Although organizational effects of steroids have been demonstrated, the interactions between steroids from yolk and endogenous production have not been addressed. Steroids in the yolk are likely to alter development of the embryo's endocrine axes. The ability to assess total steroid exposure in ovo in a nonlethal fashion would improve our understanding of these interactions and help elucidate the mechanisms by which maternal steroids alter chick phenotype. Steroid levels in allantoic waste provide a cumulative measure of steroids excreted in ovo and may prove to be a useful tool. We present data from semiprecocial seabirds, common murres, demonstrating the presence of detectable steroids in allantoic waste and suggesting that some reflect differences in timing of hatching and may provide information about aspects of chick phenotype.
Réactions d'halocarbocyclisation par activation électrophile de fonctions carbonées insaturées (alcènes, alcynes, allènes). Etude des versions racémiques et chirales catalysées par des bases de Lewis (2016)

This manuscrit concerns the development of new reactivities, involving electrophilic halogen sources and their application in carbocyclization reactions of substrates bearing unsaturated carbon functions. The concept of Lewis base activation of the halogenation reagent was assessed in this type of reaction, first in a racemic version, then in an enantioselective fashion. In particular, the efficiency of phosphine and phosphite chalcogenides has been demonstrated in iodocarbocyclization reactions of 1,5-enynes and iodoarylation reactions of olefins. New chiral organocatalysts were afterwards synthesized by analogy with achiral Lewis bases previously employed. Thus, chiral molecules such as phosphoramidite and phosphite chalcogenides were prepared and their activity has been evaluated in the perspective of the development of an asymmetric version of these reactions. In parallel, new methodologies involving substrates bearing an allene function were developed. In particular, the iodocarbocyclization reaction of arylallenes was exploited to access polysubstituted 2-iodoindenes following a 5-endo process with yields up to 95%.
Prototyping Fast, Simple, Secure Switches for Etha (2007)

We recently published our proposal for Ethane: A clean- slate approach to managing and securing enterprise networks. The goal of Ethane is to make enterprise networks (e.g. networks in companies, universities, and home offices) much easier to manage. Ethane is built on the premise that the only way to manage and secure networks is to make sure we can identify the origin of all traffic, and hold someone (or some machine) accountable for it. So first, Ethane authenticates every human, computer and switch in the network, and tracks them at all times. Every packet can be immediately identified with its sender. Second, Ethane implements a network-wide policy language in terms of users, machines and services. Before a flow is allowed into the network, it is checked against the policy. Ethane requires two substantial changes to the network: Network switches and routers are replaced with much simpler switches, which are based on flow tables. The switch doesn't learn addresses, doesn't run spanning tree, routing protocols or any access control lists. All it does is permit or deny flows under the control of a central controller. The controller is the second big change. Each network contains a central controller that decides if a flow is to be allowed into the network. It makes its decisions based on a set of rules that make up a policy. One premise of Ethane is that although the network is much more powerful as a whole, the switches are much simpler than conventional switches and routers. To explore whether this is true, we built 4-port Ethane switches in dedicated hardware (on the NetFPGA platform), running at 1Gb/s per port. We have deployed the switches in our network at Stanford University, and demonstrated that despite the simplicity of the switches, Ethane can support a very feature-rich and easy-to-manage network.
An Autocrine/Paracrine Role of Human Decidual Relaxin. II. Stromelysin-1 (MMP-3) and Tissue Inhibitor of Matrix Metalloproteinase-1 (TIMP-1)1 (1997)

Interstitial collagen types I and III are the predominant collagens in the amniotic and chorionic connective tissues. However, this matrix also contains proteoglycans, fibronectin, laminin, and elastin, which together with the collagens may undergo partial degradation prior to fetal membrane rupture at term. In this study, stromelysin (MMP-3) and tissue inhibitor of metalloproteinases-1 (TIMP-1) were immunolocalized in fetal membranes obtained at term prior to labor. MMP-3 stained the cells of the amniotic epithelium, fibroblasts and macrophages of the amniotic and chorionic matrix, and those of the chorionic cytotrophoblast; there was no staining in the maternal decidua. TIMP-1 showed a similar staining pattern, except that the staining was darker in some amniotic epithelial cells and was present in the maternal decidua. The maternal decidua produces the two human relaxins H1 and H2; the latter, when incubated with explants of human fetal membranes, caused a dose-dependent and significant increase in expression of the MMP-3 gene and its secreted protein into the media. A significant effect of relaxin H2 on 92-kDa gelatinase (MMP-9) gene expression was also shown--an effect requiring poly(A)+ RNA rather than total RNA. Both relaxin H1 and H2 caused a significant increase in secretion of MMP-9 protein and its enzyme activity in the media. The magnitude of the effects of the two relaxins was similar, in contrast to findings from other biological studies in which relaxin H2 was shown to be more active. Neither of the relaxins had any effect on 72-kDa gelatinase (MMP-2) activity or on the TIMP-1 protein or its activity. This study suggests that local relaxins may be involved in the degradation of the complex fetal membrane extracellular matrix and may cause activation of an enzyme cascade resulting in fully activated MMP-9. Such effects could be important in the degradative pathways occurring in the amnion and chorion in the peripartal period.
Thermal Conductivity and Operating Temperature Effect on the Interline Region in a Micro/Miniature Heat Pipe (2008)

An analytical model describing thin film evaporation is developed that includes the effects of surface tension, frictional shear stress, wetting characteristics and disjoining pressure. The effects of thermal conductivity of working fluids and operating temperature on the evaporating thin film region are also studied. The results indicate that when the thermal conductivity of the working fluid increases, a high heat flux can be removed from the evaporating thin film region. The operating temperature affects the thin film evaporation. The higher the operating temperature, the more heat flux can be removed from the region. The information of thin film evaporation presented in the paper results in a better understanding of heat transfer mechanism occurring in micro heat pipes.
X-Ray Detection Using Superconducting Tunnel Junctions With Polyimide Insulation Layer (2005)

We have fabricated Nb-based superconducting tunnel junctions (STJs) with Al trapping layers using the photosensitive polyimide insulation layer for X-ray detector. It is possible to simplify the fabrication process of the STJs, because the photosensitive polyimide is used as the insulation layer instead of conventional inorganic insulation films without an etching process in a vacuum chamber. The polyimide insulation layer expects to be stable for thermal cycling between 0.3 K and room temperature. The preliminary experiments of 5.9 keV radiation shows the energy resolution of 86 eV.
Multiscale Vascular Surface Model Generation From Medical Imaging Data Using Hierarchical Features (2008)

Computational fluid dynamics (CFD) modeling of blood flow from image-based patient specific models can provide useful physiologic information for guiding clinical decision making. A novel method for the generation of image-based, 3-D, multiscale vascular surface models for CFD is presented. The method generates multiscale surfaces based on either a linear triangulated or a globally smooth nonuniform rational B-spline (NURB) representation. A robust local curvature analysis is combined with a novel global feature analysis to set mesh element size. The method is particularly useful for CFD modeling of complex vascular geometries that have a wide range of vasculature size scales, in conditions where 1) initial surface mesh density is an important consideration for balancing surface accuracy with manageable size volumetric meshes, 2) adaptive mesh refinement based on flow features makes an underlying explicit smooth surface representation desirable, and 3) semi-automated detection and trimming of a large number of inlet and outlet vessels expedites model construction.
Design, manufacturing and measurement of a PV miniconcentrator for front point-contact silicon solar cells (2005)

A novel photovoltaic concentrator has been developed in the framework of the European project "High efficiency silicon solar cells concentrator". In this project, front-contacted silicon solar cell have also been designed and manufactured by the project leader (the French LETI). This silicon cell concept is potentially capable to perform well (24% efficiency has been predicted) for much higher concentration levels than the back-contacted cells (and, of course, than the two-side contacted cells). The concentrator is formed by one lens of squared contour with flat entry surface and large-facet Fresnel exit surface, and a secondary that encapsulates the solar cell. On the contrary to the conventional Fresnel lens plus nonimaging secondary concentrators, the primary and secondary are designed simultaneously, leading to better concentration-acceptance angle product without compromise with the compactness. The grid lines in the front-contacted cells are aluminium prisms (which contact the p+ and n+ emitters, alternatively), acting as a linear cone concentrator that concentrates Cg =1.52× in the cross sectional dimension of the prisms. The secondary concentrator has a refractive rotational symmetric top surface that is crossed with two linear flow-line TIR mirror. Then, in the cross section normal to the aluminium prisms, the secondary provides a 2D concentration of Cg =12×, while in the cross section parallel to the prisms it provides a 2D concentration of Cg =24.16× as the grid lines in this dimension. Therefore, the cell is rectangular (1:2.08 aspect ratio), being the grid lines parallel to the shorter rectangle side. The total 3D geometrical concentration is 24.16×(12×1.52) = 455× for the square aperture and rectangular cell, and gets a design acceptance angle &#945;=±1.8 degrees. Injection moulded prototypes are have been manufactured and measured, proving an optical efficiency of 79%. Computer modelling of the concentrator performance will also be presented.
Recombinant AAV-Transduced Iris Pigment Epithelial Cell Transplantation May Transfer Vector to Native RPE but Suppress Systemic Dissemination (2006)

AAV-mediated LacZ was expressed in the transplanted cells after subretinal transplantation, and the transplanted IPE cells may transfer the rAAV to host tissues, such as RPE cells, long after the transplantation. This method of gene delivery did not lead to systemic dissemination of the vectors.
Spin-transfer torque in magnetic tunnel junctions (2009)

We present a theoretical study of the spin-transfer torque vector and the tunneling magnetoresistance (TMR) for symmetric magnetic tunnel junctions (MTJ) using the single-band tight-binding model and the nonequilibrium Keldysh formalism. We provide a comprehensive analysis of the effect of band filling and exchange splitting of the FM leads on the bias behavior of the spin-transfer component, ${T}_{\ensuremath{\parallel}}$, in the plane containing the magnetizations of the two magnetic layers, and the fieldlike component, ${T}_{\ensuremath{\perp}}$, perpendicular to this plane. We demonstrate that both components of the spin torque and the TMR can exhibit a wide range of interesting and unusual bias behavior. We show that ${T}_{\ensuremath{\parallel}}(V)$ satisfies an expression involving the difference in spin currents between the ferromagnetic (FM) and antiferromagnetic (AF) configurations, which is general and independent of the details of the electronic structure. The spin current for the FM (AF) alignment is shown to have a linear (quadratic) bias dependence, whose origin lies in the symmetric (asymmetric) nature of the barrier. On the other hand, the bias dependence of ${T}_{\ensuremath{\perp}}$ is quadratic with ${d}^{2}{T}_{\ensuremath{\perp}}/d{V}^{2}&lt;0$, and it can change sign at finite bias. Finally, we show that the exchange splitting and band filling have a large effect on the bias dependence of the TMR.
Extracting Valley-Ridge Lines from Point-Cloud-Based 3D Fingerprint Models (2012)

3D fingerprinting is an emerging technology with the distinct advantage of touchless operation. More important, 3D fingerprint models contain more biometric information than traditional 2D fingerprint images. However, current approaches to fingerprint feature detection usually must transform the 3D models to a 2D space through unwrapping or other methods, which might introduce distortions. A new approach directly extracts valley-ridge features from point-cloud-based 3D fingerprint models. It first applies the moving least-squares method to fit a local paraboloid surface and represent the local point cloud area. It then computes the local surface's curvatures and curvature tensors to facilitate detection of the potential valley and ridge points. The approach projects those points to the most likely valley-ridge lines, using statistical means such as covariance analysis and cross correlation. To finally extract the valley-ridge lines, it grows the polylines that approximate the projected feature points and removes the perturbations between the sampled points. Experiments with different 3D fingerprint models demonstrate this approach's feasibility and performance.
Abstract B011: Human IL-2 mutant exhibits a higher antitumor efficacy and lower toxicity than wildtype IL-2 in different preclinical contexts (2016)

Abstract High dose IL-2 is registered for the treatment of melanoma and renal cell carcinoma, however this therapy has limited efficacy and severe toxicity. It has been shown that in patients HD IL-2 drives preferential expansion of regulatory T cells, which dampen the antitumor immunity. This results explain at least partially the limited efficacy of this therapy. In this work, we characterize a human IL-2 mutant which differs from wildtype IL-2 by four mutations at the interface with the a-subunit of IL-2R. In vitro, IL-2 mutant induces proliferation of CD8+CD44hi and NK1.1 cells as efficiently as wtIL-2 does, but it shows a reduced capacity to induce proliferation of CD4+Foxp3+ regulatory T cells. In vivo, IL-2 mutant clearly induces preferential proliferation of CD8+CD44hi witha quite reduced proliferation of CD4+Foxp3+ regulatory T cells. The IL-2 mutant shows higher antimetastatic effect than wtIL-2 in several transplantable tumor models. i.e. the experimental metastasis model of MB16F0; the experimental and spontaneous metastasis models for the mouse pulmonary carcinoma 3LL-D1222 and the metastasis mammary carcinoma 4T1. Moreover initial data also support a higher potency of this IL2 mutant, when used in combination with other immune-therapies. Relevantly, the IL-2 mutant also exhibits lower lung and liver toxicity than does wtIL-2 when used at high doses in mice. The IL-2 mutant described could be a good candidate for improving cancer therapy based on IL-2. Citation Format: Tania Carmenate, Magela Montalvo, Gertrudis Rojas, Dasha Fuentes, Kalet Leon. Human IL-2 mutant exhibits a higher antitumor efficacy and lower toxicity than wildtype IL-2 in different preclinical contexts [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B011.
New aspects in the Bragg Glass-Disordered phase transition: an analysis based on the 3rd harmonics of the AC magnetic susceptibility (2007)

We analyse the phase transition between the Bragg Glass and the Disordered phase in the vortex lattice in type-II superconductors, both by analytical computations and experimental investigations. It is known that if the Peak Effect can be detected, a Bragg Glass/Disordered phase transition takes place. We show that, in some conditions, this transition can occur without the observation of the Peak Effect Phenomenon. We introduce a method based on the 3rd harmonics of the AC magnetic susceptibility to detect the transition also in these cases. Using this method, we obtain an experimental confirmation of the theoretical predictions on sphere shaped V3Si single crystals, in the high fields/low temperatures range too, where previous experimental studies failed to detect the Bragg/Disordered phase transition.