gebhart/patrepeval huggingface dataset:
In vitro evolution of an antibody fragment population to find high-affinity hapten binders (2008)

Recently, we constructed a focused antibody library tailored to interact with haptens. High functionality of this library was demonstrated, as specific binders could be retrieved to a range of different haptens. In the current study we have developed a mutagenesis and selection strategy in order to further fine-tune the hapten binding properties of these antibody fragments. Testosterone was chosen as model antigen for the investigation. A population, rather than a single clone, originating from this focused library and enriched for testosterone binders, was subjected to random mutagenesis and different phage display selection strategies of various stringencies. These included consecutively lowering the antigen concentration and having, or not having, soluble hapten present during the phage capture and elution steps. The different selection procedures resulted in a considerable increase in apparent affinities for several of the selected populations, from which the highest affinity antibody isolated had a K(D) of 2 nM, corresponding to an approximately 200-fold affinity improvement compared with the best clone of the starting population. Importantly, the polyclonal nature of the starting material allowed for the identification of novel unrelated variants that differed in fine-specificity, demonstrating that this approach is valuable for exploring different parts of structure space.
Enrichment of two isoflavone aglycones in black soymilk by Rhizopus oligosporus NTU 5 in a plastic composite support bioreactor (2015)

A repeated-batch PCS fermentation system was established to accelerate the deglycosylation rate of isoflavone in black soymilk. © 2015 Society of Chemical Industry.
Magnetization of ferromagnetic-antiferromagnetic double layers (1993)

Using a Green-function method the spin-wave excitation spectrum and the sublattice magnetizations of a system consisting of a ferro- and an antiferromagnetic layer are calculated. Both ferro- and antiferromagnetic interlayer couplings are considered. It is shown that in the extreme quantum case S=1/2 considered here interesting quantum effects appear at low temperatures.
Probing the higher order structure of RNA with peroxonitrous acid (1996)

Potassium peroxonitrite (ONOOK) and [Fe(EDTA)]2- were used to analyze the influence of chemically entirely different hydroxyl radical sources on tRNA cleavage profiles. [Fe(EDTA)]2- gives rise to hydroxyl radicals via a Fenton-like reaction during the oxidation of chelated Fe2+, while ONOOK generates hydroxyl radicals via its conjugate acid (ONOOH) when adding a stable alkaline solution of ONOOK in samples buffered at neutral pH. [Fe(EDTA)]2- is known to induce oxidative strand scission at sugar moieties thought to be solvent accessible, while those residues located in the 'inside' of structured RNAs are protected. Although ONOOH is neutral and significantly smaller than the metal complex, both reagents generate the same protection pattern on tRNAs, suggesting that access of the commonly formed hydroxyl radical, rather than access of its source, is the determining factor when probing the higher order structure of RNA. Strong difference in reactivity is only seen at the modified 2-thiouridine S34 of tRNA(Lys3) which shows hyperreactivity towards ONOOK treatment. This particular reaction may require interaction between the peroxonitrite anion and the thiocarbonyl group of the base, since hyperreactivity is not observed when probing the dethiolated tRNA(Lys3).
Trajectory planning issues in cuspidal commercial robots (2023)

A cuspidal serial robot can travel from one inverse kinematic solution to another without crossing a singularity. Cuspidal robots ask for extra care and caution in trajectory planning, as identifying an aspect related to one unique inverse kinematic solution is not possible. The issues related to motion planning with cuspidal robots are related to the inherent property arising from the geometric design of the robot. The cuspidality property has not been considered in recent industrial 6R robots with a non-spherical wrist. In this work, cuspidality is illustrated with the JACO robot (gen 2, non-spherical wrist), a serial arm by Kinova Robotics which is deployed in various applications and is cuspidal in nature. A nonsingular change of solutions for the robot is provided to highlight the effect of cuspidal robots on the interference with the environment. The pose with multiple inverse kinematic solutions in an aspect is presented. Problems in choosing the initial solution of the path in cuspidal robots, and its consequence, is illustrated with an example path in the workspace of the JACO robot. The paper presents the importance of cuspidality analysis of 6R robots and the implications of neglecting it.
Bundle-forming pilus retraction enhances enteropathogenicEscherichia coliinfectivity (2011)

Enteropathogenic Escherichia coli (EPEC) is an important human pathogen that causes acute infantile diarrhea. The type IV bundle-forming pili (BFP) of typical EPEC strains are dynamic fibrillar organelles that can extend out and retract into the bacterium. The bfpF gene encodes for BfpF, a protein that promotes pili retraction. The BFP are involved in bacterial autoaggregation and in mediating the initial adherence of the bacterium with its host cell. Importantly, BFP retraction is implicated in virulence in experimental human infection. How pili retraction contributes to EPEC pathogenesis at the cellular level remains largely obscure, however. In this study, an effort has been made to address this question using engineered EPEC strains with induced BFP retraction capacity. We show that the retraction is important for tight-junction disruption and, to a lesser extent, actin-rich pedestal formation by promoting efficient translocation of bacterial protein effectors into the host cells. A model is proposed whereby BFP retraction permits closer apposition between the bacterial and the host cell surfaces, thus enabling timely and effective introduction of bacterial effectors into the host cell via the type III secretion apparatus. Our studies hence suggest novel insights into the involvement of pili retraction in EPEC pathogenesis.
Functional data: local linear estimation of the conditional density and its application (2011)

International audience
MR Imaging Features of Isolated Cortical Vein Thrombosis: Diagnosis and Follow-Up (2008)

On T2*GE imaging, MSE of hemoglobin products within the thrombus was observed both at the early and late phases of ICoVT and appears to be of high diagnostic value compared with the other signal intensity changes detected on standard MR imaging.
Microelectrode-based probing of charge propagation and redox transitions in concentrated polyoxometallate electrolyte of potential utility for redox flow battery (2023)

Concentrated solutions of Keggin-type silicotungstic acid, as well as the system’s single crystals (H4SiW12O40*31H2O) and their colloidal suspensions have been tested using the microelectrode methodology to determine mass-transport, electron self-exchange and apparent (effective) diffusion-type coefficients for charge propagation and homogeneous (electron self-exchange) rates of electron transfers. Silicotungstic acid facilitates proton conductivity, and undergoes fast, reversible, multi-electron transfers leading to the formation of highly conducting, mixed-valence (tungsten(VI,V) heteropoly blue) compounds. To develop useful electroanalytical diagnostic criteria, electroanalytical approaches utilizing microdisk electrodes have been adapted to characterize redox transitions of the system and to determine kinetic parameters. Combination of microelectrode-based experiments performed in two distinct diffusional regimes: radial (long-term experiment; e.g., slow scan rate voltammetry or long-pulse chronoamperometry) and linear (short-term experiment; e.g., fast scan rate voltammetry or short-pulse chronocoulometry) permits absolute determination of such parameters as effective concentration of redox centers (C0) and apparent transport (diffusion) coefficient (Dapp). The knowledge of these parameters, in particular of [Dapp1/2 C0] seems to be of importance to the evaluation of utility of redox electrolytes for charge storage. For the colloidal suspension of silicotungstic acid (H4SiW12O40) crystals in the saturated solution, the following values have been obtained: Dapp = 1.8*10-6 cm2 s−1 and C0 = 1.1 mol dm−3, as well as the [Dapp1/2 C0] diagnostic parameter has reached the value as high as 6*10-3 mol/dm−3 cm s−1/2, provided that four electrons are involved in the H4SiW12O40 redox transitions. In this respect, the fact that crystals (dispersed solids) are characterized by high electron self-exchange rate (kex = 1.1*108 dm3 mol−1 s−1) and low activation energy (EA = 18.7 kJ mol−1) facilitating electron transfers between immobilized WVI and WV redox sites is also advantageous.
Complementary metal–oxide–semiconductor compatible 1060  nm photodetector with ultrahigh gain under low bias (2015)

Falling on the tail of the absorption spectrum of silicon, 1060 nm Si detectors often suffer from low responsivity unless an exceedingly thick absorption layer is used, a design that requires high operation voltage and high purity epitaxial or substrate material. We report an all-silicon 1060 nm detector with ultrahigh gain to allow for low operation voltage (<4 V) and thin (200 nm) effective absorption layer, using the recently discovered cycling excitation process. With 1% external quantum efficiency, a responsivity of 93 A/W was demonstrated in a p/n junction device compatible with the complementary metal-oxide-semiconductor process.
Digital Moiré Subtraction Interferometry (DMS) for Electronics Cooling Applications in Enclosures (2010)

Optical noninvasive temperature measurement techniques, such as interferometry, are particularly advantageous in obtaining temperature information noninvasively from enclosed low velocity flows induced by thermal sources, as commonly arise in electronic systems. The single greatest restriction in the application of interferometry as a standard measurement methodology has been the enormous cost associated with the optical equipment required. This cost is due to the quality of the optics required, which exhibits an exponential dependence on size. Digital Moiré subtraction is a technique, which removes the restriction on the use of high quality optics, thereby, enabling reasonably large fields of view. In this paper, a digital Moiré subtraction interferometer configuration is presented with a 140 mm field of view. First, the ability of the interferometer to accurately measure the free convection temperature field about an isothermal horizontal cylinder is examined through a comparison with measurements from literature using classical interferometry. The technique is then applied to the thermal interaction between 2D components representing BGAs mounted on a vertical printed circuit board (PCB). Qualitative and quantitative evaluation of the interferograms show the significant influence of in-plane PCB conductivity on the temperature field about the PCB. The spacing to length ratio above, which upstream components on a PCB experience enhanced cooling, is reduced from 4 to 3 for a PCB with a high effective in-plane conductivity (15 W/m K).
Source and Load Adaptive Design for a High-Power Soft-Switching Inverter (2006)

The operating range of a zero-voltage switched inverter is typically constrained by the source and load variation. This paper adopts a variable turns ratio coupled magnetic type soft-switching inverter for a wide-range source and load adaptability. The operating principle and design guideline are described in detail. Design examples have been verified with computer simulation and hardware implementation. Experimental results of a 120-kW hardware prototype are presented to show superiority of the proposed soft-switching inverter design and significant reduction on loss and dv/dt
Building Healthy Eating Knowledge and Behavior: An Evaluation of Nutrition Education in a Skill Training Course for Construction Apprentices (2019)

Background: Prior research has found poor health among construction workers is related to poor nutrition and low fruit and vegetable consumption. Promoting nutrition knowledge can improve dietary behaviors, but nutrition education among construction workers is limited. We evaluated the effectiveness of nutrition education on fruit and vegetable consumption among construction apprentices. In this pilot evaluative study, 36 construction apprentices enrolled in skill training programs received two 1.5-hour nutrition classes. Twelve questions addressing healthy eating knowledge and behavior were administered at baseline, after intervention, and at three months follow-up. After intervention, daily fruit consumption improved from baseline (mean (s.d.) =1.42 (0.55)) to post intervention (mean (s.d.) =1.72 (0.70)) (p &lt; 0.05) and to three months follow-up (mean(s.d.) =1.94 (0.83)) (p &gt; 0.05). After intervention, daily vegetable consumption improved from baseline (mean (s.d.) =1.67 (0.59)) to post intervention (mean (s.d.) =1.97 (0.74)) (p &lt; 0.05) and to three months follow-up (mean (s.d.) = 2.19 (0.82)) (p &gt; 0.05). Younger construction apprentices showed better healthy eating knowledge at post intervention and three months follow-up (p &gt; 0.05). Working in normal hours showed better healthy eating knowledge at post intervention but not at three months follow up (p &gt; 0.05). Both age groups and working hours did not show significant differences on healthy eating behaviour. Nutrition education implemented as a three-hour session within skill courses may possibly promote fruit and vegetable consumption among construction apprentices. Further research with control group is required to support the findings in this study.
Expression of genes involved in vascular development and angiogenesis in endothelial cells of adult lung (2003)

Profiling gene expression in endothelial cells advances the understanding of normal vascular physiology and disease processes involving angiogenesis. However, endothelial cell purification has been challenging because of the difficulty of isolating cells and their low abundance. Here we examine gene expression in endothelial cells freshly isolated from lung capillaries after in vivo labeling with fluorescent cationic liposomes and purification by fluorescence-activated cell sorting (FACS). Of the 39,000 genes and expressed sequence tags evaluated on custom oligonucleotide arrays, 555 were enriched in endothelial cell fraction. These included familiar endothelial cell-associated genes such as VEGF, VEGF receptor (VEGFR)-1, VEGFR-2, angiopoietin-2, Tie1, Tie2, Edg1 receptor, VE-cadherin, claudin 5, connexin37, CD31, and CD34. Also enriched were genes in semaphorin/neuropilin (Sema3c and Nrp1), ephrin/Eph (ephrin A1, B1, B2, and EphB4), delta/notch (Hey1, Jagged 2, Notch 1, Notch 4, Numb, and Siah1b), and Wingless (Frizzled-4 and Tle1) signaling pathways involved in vascular development and angiogenesis. Expression of representative genes in alveolar capillary endothelial cells was verified by immunohistochemistry. Such expression reflects features that endothelial cells of normal lung capillaries have in common with embryonic and growing blood vessels. About half of the enriched genes, including exostosin 2, lipocalin 7, phospholipid scramblase 2, pleckstrin 2, protocadherin 1, Ryk, scube 1, serpinh1, SNF-related kinase, and several tetraspanins, had little or no previous association with endothelial cells. This approach can readily be used to profile genes expressed in blood vessels in tumors, chronic inflammation, and other sites in which endothelial cells avidly take up cationic liposomes.
Hybrid pathway for chlorobenzoate metabolism in Pseudomonas sp. B13 derivatives (1980)

Derivatives of Pseudomonas sp. B13 which had acquired the capability to utilize 4-chloro- and 3,5-dichlorobenzoate as a consequence of the introduction of genes of the TOL plasmid of Pseudomonas putida mt-2 were studied. The utilization of these substrates, a property not shared by the parent strains, was shown to depend upon the combined activities of enzymes from the donor and from the recipient. During growth on 3-chloro-, 4-chloro-, and 3,5-dichlorobenzoate, predominantly the toluate 1,2-deoxygenase and both dihydrodihydroxybenzoate dehydrogenases of the parent strains were induced. On the other hand, no catechol 2,3-dioxygenase from P. putida mt-2 was detectable, so that degradation of chlorocatechols by the nonproductive meta-cleavage pathway was avoided. Instead of that, chlorocatechols were subject to ortho cleavage and totally degraded by the preexisting enzymes of Pseudomonas sp. B13.
Action of Endocrine Disruptors in Urogenital Development in Chicken Embryo (2006)

P-250 Abstract: The constant appearance of new chemical substances in the environment from industry (dioxin, surfactants, pesticides, heavy metals) and human activities (natural and synthetic hormones) are responsible for the increase of environmental pollution and resulting health risks. Among these substances, Endocrine Disruptors (ED) are particularly of interest because of their direct influence on human health and development, representing an underestimated major danger. Although emitted into the environment in very low quantity these substances can remain active at trace levels, especially through synergistic effects. They are suspected of disturbing the endocrine systems of animals, and more alarming, human endocrine systems as well. Epidemiological studies in France, Finland and Denmark have revealed the negative impact of these ED by an association with a high level of sexual abnormalities in male babies. In this context the objective of our work is to show the action of a family of ED, the estrogens, by use of our animal model - the chicken embryo. We have tested three main substances: Estrone and Estriol as natural hormones, and Ethynylestradiol as a synthetic one. The chicken embryo has been accepted for many years as a good model for studying embryologic development because: 1) each embryo develops independently of the environment; 2) its 21-day gestation period allows rapid results; 3) direct injection of potentially teratogenic substances at exact doses with precise timing provides excellent experimental control. Our work consisted of injecting the substance of interest into an embryo at an early development stage (4-days), stopping the development before maturation (18-days) and observing the effect on urological development. Estrone and Estriol lead to morphological defects, but none are observed with Ethynylestradiol. Estriol caused persistence of Müller ducts for 50% of the male embryos and oviduct hypertrophy for 71% of the females. Estrone caused the same phenomena at the same dosage but at lower percentages. However, a kidney dysfunction was only observed with Estrone in both males and females. Additional studies are planned to enable us to better determine the genetic elements that are disturbed by these ED during embryonic development. It will then be possible for us to identify the molecular targets that this system disrupts and develop it into a biodiagnostic assay for xenobiotic test substances.
Targeting abnormal ER stress responses in tumors: A new approach to cancer immunotherapy (2015)

Cancers thrive under adverse conditions and simultaneously inhibit antitumor immunity. We recently found that endoplasmic reticulum (ER) stress responses driven by the IRE1α-XBP1 pathway not only promote cancer cell survival, but also provoke severe dendritic cell (DC) dysfunction in tumors. Targeting IRE1α-XBP1 represents a two-pronged approach to restrain malignant cells while eliciting concomitant antitumor immunity.
Cold Sprayed Liners for Gun Tubes (2012)

Abstract The use of refractory materials is currently being developed for gun barrel coatings and liners. Explosive cladding, as well as a novel gun liner emplacement with elastomeric material (GLEEM) technique has been shown to be a successful method for bonding liners into 25-mm M242 Bushmaster barrels. The process relies on commercially available tube products that serve as the liner materials that are often difficult to manufacture. Cold spray is a novel process used to consolidate metal powders into both thin coatings and large bulk materials that is being investigated as a cost effective alternative to conventional processing techniques. This work examines the use of cold spray as it pertains to the consolidation of Ta donor tubes for explosively bonded gun liners. Ta tubes were consolidated and annealed to increase the ductility of the material from 0.2% to 35% strain as determined by tensile testing. Ta donor tube was successfully explosively clad to 25 mm gun barrel forging. Bond strength testing results of explosively clad cold spray tube were found to be comparable to commercially obtained liners. GLEEM was also successfully employed. However, the mechanical bond strength of this cladding was considerably lower than that of the explosively clad liner. The failure mechanism during GLEEM is slip between the liner and the forging and is due to the fact that the process relies on frictional bonding rather than metallurgical bonding.
Myositis overlap syndromes (1999)

Myositis-overlap syndromes are characterized by a heterogeneous group of clinical syndromes of which many are closely linked with specific autoantibodies. Clinical and laboratory-based research into this fascinating group of syndromes have given us clues in elucidating the role of immunogenetic, environmental influences on the etiopathogenesis of autoimmune disease. Patients positive for anti-snU1 RNP antibody often present with a constellation of "autoimmune-related" clinical features, often not fulfilling the diagnostic criteria for a single disease entity. Controversy remains as to whether this represents a single disease entity, namely mixed connective tissue disease, or an undifferentiated autoimmune rheumatic/overlap syndrome. Anti-PM-Scl antibodies are linked with myositis-scleroderma overlap and generally tend to follow a benign course, often responding well to minimal immunosuppression. More recently the number of anti-tRNA synthetase antibody-associated overlap syndromes has expanded; antibodies to the autoantigen histidyl-tRNA synthetase (Jo1) being the commonest and best characterized. Patients with these antibodies often have severe interstitial lung disease and the poorest prognosis, often necessitating aggressive immunosuppressive therapy.