gebhart/patrepeval huggingface dataset:
High frequency of intestinal T H 17 cells correlates with microbiota alterations and disease activity in multiple sclerosis (2017)

T helper 17 (T<sub>H</sub>17) cells are key players in multiple sclerosis (MS), and studies in animal models demonstrated that effector T<sub>H</sub>17 cells that trigger brain autoimmunity originate in the intestine. We validate in humans the crucial role of the intestinal environment in promoting T<sub>H</sub>17 cell expansion in MS patients. We found that increased frequency of T<sub>H</sub>17 cells correlates with high disease activity and with specific alterations of the gut mucosa-associated microbiota in MS patients. By using 16<i>S</i> ribosomal RNA sequencing, we analyzed the microbiota isolated from small intestinal tissues and found that MS patients with high disease activity and increased intestinal T<sub>H</sub>17 cell frequency showed a higher Firmicutes/Bacteroidetes ratio, increased relative abundance of <i>Streptococcus</i>, and decreased <i>Prevotella</i> strains compared to healthy controls and MS patients with no disease activity. We demonstrated that the intestinal T<sub>H</sub>17 cell frequency is inversely related to the relative abundance of <i>Prevotella</i> strains in the human small intestine. Our data demonstrate that brain autoimmunity is associated with specific microbiota modifications and excessive T<sub>H</sub>17 cell expansion in the human intestine.
Region-specific expression of the androgen receptor in the human epididymis (1997)

The expression of the androgen receptor in the human epididymis was analysed by ribonuclease protection, in-situ hybridization and immunohistochemistry. Androgen receptor mRNA and protein could be detected throughout the entire organ, albeit in different quantities, in the caput, corpus and cauda regions, respectively. Also positive, though only weakly, was the ductus deferens, while the efferent ducts were devoid of specific signals. In-situ transcript hybridization and immunocytochemistry localized androgen receptor mRNA and protein primarily to the epithelium of the epididymal duct. In the ductal epithelial cells androgen receptor immunoreactivity showed a distinct nuclear distribution. While peritubular cells occasionally displayed weak signals, interstitial cells as well as blood vessels were consistently negative throughout the entire organ. The observed pattern of androgen receptor expression in the human epididymis supports the notion that the structure and function of the epididymis is differentially controlled by androgens in a region-specific manner, whereas it would not seem compatible with a direct role for androgens in the regulation of epididymal blood flow.
Neurological and Neuroendocrine‐Cytokine Inter‐relationship in the Antiphospholipid Syndrome (2002)

Although many neurological deficits have been described in the antiphospholipid syndrome (APS), only stroke is well established and accepted as a diagnostic criterion in the disease. We presently review clinical data obtained from large series of cases regarding stroke, dementia, epilepsy, chorea, migraine, white-matter disease, and behavioral changes in APS, or linked-to-laboratory criteria such as antiphospholipid antibodies (aPL). The contribution of animal models to our understanding of these manifestations of APS is stressed, especially regarding the cognitive and behavioral aspects for which we have established model systems in the mouse. These models utilize immunization of mice with beta(2)-glycoprotein1, a central autoantigen in APS, which induces persistent high levels of aPLs. These mice develop hyperactive behavior after a period of four months, as well as deficits in learning and memory, and are potentially valuable as a system in which to study the pathogenesis and treatment of cognitive and behavioral aspects of APS. We have developed another model, in which IgGs from APS patients induce depolarization of brain synaptoneurosomes, and which may serve as a model for the pathogenesis of epilepsy in APS. Hormonal changes are another potential CNS manifestation of APS and this may be potentially linked to the systemic and central effects of cytokines such as interleukin-3. Better understanding of the link between APS and neurological or neuroendocrine manifestations other than stroke will reveal whether they can be used as clinical criteria for the diagnosis of APS and, it is hoped, lead to better treatment.
Secreted Tumor Antigens – Immune Biomarkers for Diagnosis and Therapy (2017)

With the advent of immunotherapies for cancer, there is growing interest in the identification of tumor antigens. Tumor antigens are self-molecules altered through e.g. genetic mutations (neoantigens), protein truncation, protein misfolding, or abnormal posttranslational modifications. To induce an immune response, tumor antigens need to be secreted into the tumor environment and presented to the immune system in the draining lymph nodes, resulting in the generation of tumor-specific effector cells and antibodies. Cytotoxic T cells are thought to be responsible for killing of tumor cells, and several recent studies have used MS, combined with exome/transcriptome sequencing and bioinformatics, to identify their cognate peptide ligands on tumor MHC class I molecules. Circulating (serum) antibodies have been more widely used to identify tumor antigens in a range of human cancers, using 2D Western blots, immunoaffinity, and microarray technologies. More specific antibody probes have been generated by harvesting antibodies directly from antibody-secreting cells through in vitro cultures of lymph node cells (antibody-secreting cells probes) or B-cell immortalization. Further identification and characterization of tumor antigens is likely to have important implications for cancer diagnostic and biomarker discovery, immune profiling, and the development of cancer vaccines and targeted immunotherapies.
Immunohistochemical Localization of Clostridium perfringens β2-Toxin in the Gastrointestinal Tract of Horses (2003)

Clostridia-associated intestinal disease in horses was generally reported to be due to infection with Clostridium perfringens type A, which harbors the cpa-encoded alpha-toxin. A recent study demonstrated a high incidence of beta2-toxigenic C. perfringens in horses suffering or dying from typhlocolitis, suggesting that this novel type of C. perfringens might play an important role in typhlocolitis and possibly other equine intestinal diseases. A retrospective study was conducted to assess the presence of the beta2-toxin in tissues of the equine gastrointestinal tract. Monospecific polyclonal antibodies against recombinant beta2-toxin were produced in rabbits and used to demonstrate the beta2-toxin in sections of the gastrointestinal tract by immunohistochemical methods. Sections from 69 horses were stained and beta2-toxin was observed immunohistochemically in 40 animals. Sections from the stomach, small intestine, and large intestine were positive. Immunopositivity for beta2-toxin was significantly associated with presence of beta2-toxigenic bacteria. This investigation demonstrates local production of beta2-toxin and suggests that immunohistochemistry using antitoxin antibodies represents a useful diagnostic method in those cases where isolation of bacteria and polymerase chain reaction typing is not feasible. Although the association between the presence of beta2-toxin and development of gastrointestinal disease in horses remains uncertain, the findings of this study indicate that the potential causal relationship warrants further investigation.
Effect of optical noise on retinal image and stochastic resonance (2010)

Stochastic Resonance (SR) is a phenomenon of optimization by noise in nonlinear systems [1]. It consists basically of that a weak signal, undetectable below a certain threshold, becomes detectable in the presence of an optimum amount of noise. SR has raised a great interest in biology given that noise may enhance the information processing in the nervous system, in particular in the visual system [2–4]. For example, the contrast threshold of a subject significantly decreases, reaching a minimum (resonance), when Gaussian noise is added. The SR phenomenon has also been observed in binocular rivalry when different stimuli are presented to each eye, and in depth perception. In this work, we study the effect of fluctuations in the eye's optical aberrations as a source of noise in the retinal image. Due to the temporal dynamics of the eye, the wave aberration was considered as the sum of an average reference wavefront and noise. Series of point-spread functions were calculated from aberrations and convolved with an object (sine-wave gratings) to simulate the retinal image. The improvement that occurs in image quality by adding extra defocus due to higher order aberrations may be view as a process of SR. Potential improvements in spatial vision due to optical noise, and the occurrence of processes mediated by SR are investigated.
Adaptive digital fuzzy hardware in application-specific integrated circuits (2003)

This paper presents a generic fuzzy logic system implementation in digital hardware. The architecture developed is oriented to Application-Specific Integrated Circuits (ASICs) and was therefore embedded within an ASIC for a simple control application. Furthermore, a distributed adaptation scheme is proposed for real-time environments. Performance/area tradeoffs for VLSI implementation are discussed.
ChemInform Abstract: Metal Oxo Clusters in Molybdenum and Vanadium Phosphate Solids (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Successful bi-enzyme stabilization for the biomimetic cascade transformation of carbon dioxide (2016)

In nature, carbon dioxide (CO<sub>2</sub>) conversion to valuable chemicals occurs <italic>via</italic> several metabolic pathways through multi-enzymatic reactions.
Association between breast cancer genetic susceptibility variants and terminal duct lobular unit involution of the breast (2016)

Terminal duct lobular units (TDLUs) are the predominant source of future breast cancers, and lack of TDLU involution (higher TDLU counts, higher acini count per TDLU and the product of the two) is a breast cancer risk factor. Numerous breast cancer susceptibility single nucleotide polymorphisms (SNPs) have been identified, but whether they are associated with TDLU involution is unknown. In a pooled analysis of 872 women from two studies, we investigated 62 established breast cancer SNPs and relationships with TDLU involution. Poisson regression models with robust variance were used to calculate adjusted per-allele relative risks (with the non-breast cancer risk allele as the referent) and 95% confidence intervals between TDLU measures and each SNP. All statistical tests were two-sided; P < 0.05 was considered statistically significant. Overall, 36 SNPs (58.1%) were related to higher TDLU counts although this was not statistically significant (p = 0.25). Six of the 62 SNPs (9.7%) were nominally associated with at least one TDLU measure: rs616488 (PEX14), rs11242675 (FOXQ1) and rs6001930 (MKL1) were associated with higher TDLU count (p = 0.047, 0.045 and 0.031, respectively); rs1353747 (PDE4D) and rs6472903 (8q21.11) were associated with higher acini count per TDLU (p = 0.007 and 0.027, respectively); and rs1353747 (PDE4D) and rs204247 (RANBP9) were associated with the product of TDLU and acini counts (p = 0.024 and 0.017, respectively). Our findings suggest breast cancer SNPs may not strongly influence TDLU involution. Agnostic genome-wide association studies of TDLU involution may provide new insights on its biologic underpinnings and breast cancer susceptibility.
Mechanisms Governing the Selection of Translation Initiation Sites on Foot-and-Mouth Disease Virus RNA (2011)

Translation initiation dependent on the foot-and-mouth disease virus (FMDV) internal ribosome entry site (IRES) occurs at two sites (Lab and Lb), 84 nucleotides (nt) apart. In vitro translation of an mRNA comprising the IRES and Lab-Lb intervening segment fused to a chloramphenicol acetyltransferase (CAT) reporter has been used to study the parameters influencing the ratio of the two products and the combined product yield as measures of relative initiation site usage and productive ribosome recruitment, respectively. With wild-type mRNA, ∼40% of initiation occurred at the Lab site, which was increased to 90% by optimization of its context, but decreased to 20% by mutations that reduced downstream secondary structure, with no change in recruitment in either case. Inserting 5 nt into the pyrimidine-rich tract located just upstream of the Lab site increased initiation at this site by 75% and ribosome recruitment by 50%. Mutating the Lab site to RCG or RUN codons decreased recruitment by 20 to 30% but stimulated Lb initiation by 20 to 40%. An antisense oligodeoxynucleotide annealing across the Lab site inhibited initiation at both sites. These and related results lead to the following conclusions. Recruitment by the wild-type IRES is limited by its short oligopyrimidine tract. At least 90% of internal ribosome entry occurs at the Lab AUG, but initiation at this site is restricted by its poor context, despite a counteracting effect of downstream secondary structure. Initiation at the Lb site is by ribosomes that access it by linear scanning from the original entry site, and not by an independent entry process.
Functional Role of Fe-Doping in Co-Based Perovskite Oxide Catalysts for Oxygen Evolution Reaction (2019)

Perovskite oxides have been at the forefront among catalysts for the oxygen evolution reaction (OER) in alkaline media offering a higher degree of freedom in cation arrangement. Several highly OER active Co-based perovskites have been known to show extraordinary activities and stabilities when the B-site is partially occupied by Fe. At the current stage, the role of Fe in enhancing the OER activity and stability is still unclear. In order to elucidate the roles of Co and Fe in the OER mechanism of cubic perovskites, two prospective perovskite oxides, La<sub>0.2</sub>Sr<sub>0.8</sub>Co<sub>1- x</sub>Fe <sub>x</sub>O<sub>3-δ</sub> and Ba<sub>0.5</sub>Sr<sub>0.5</sub>Co<sub>1- x</sub>Fe <sub>x</sub>O<sub>3-δ</sub> with x = 0 and 0.2, were prepared by flame spray synthesis as nanoparticles. This study highlights the importance of Fe in order to achieve high OER activity and stability by drawing relations between their physicochemical and electrochemical properties. Ex situ and operando X-ray absorption spectroscopy (XAS) was used to study the local electronic and geometric structure under oxygen evolving conditions. In parallel, density function theory computational studies were conducted to provide theoretical insights into our findings. Our findings show that the incorporation of Fe into Co-based perovskite oxides alters intrinsic properties rendering efficient OER activity and prolonged stability.
In incorporation improvement in InGaN based active region using InGaN pseudo substrate for monolithic white LED application (2018)

Les Diodes Electroluminescentes (DEL) à base de composés III-nitrures sont très efficaces pour les longueurs d’ondes correspondant à la couleur bleue. Ces DELs bleues sont très utilisées sur le marché car leur combinaison avec des phosphores produit une lumière blanche. Néanmoins, cette approche a plusieurs inconvénients tels que l’instabilité de la température de couleur ou les pertes liées à la conversion. Dans ce contexte la DEL blanche monolithique dont la lumière blanche est obtenue directement dans la zone active grâce à l’émission des puits quantiques à différentes longueurs d’ondes est envisagée.Pourtant, lorsque la longueur d’onde d’émission augmente, le rendement d’émission des puits quantiques InGaN/GaN diminue. Ceci est problématique pour l’application de la DEL blanche monolithique mais également pour l’application micro-display qui nécessite idéalement des DELs monochromatiques bleues, vertes et rouges fabriquées à partir de la même famille de matériaux. Ce problème est principalement du à la différence importante de paramètre de maille entre les puits quantiques InGaN et la couche GaN sur saphir utilisée comme substrat qui provoque une forte contrainte compressive. Cette contrainte est à l’origine d’un champ électrique interne dans les puits quantiques, préjudiciable au rendement d’émission, et d’un taux d’incorporation d’indium faible bien qu’originellement thermodynamiquement difficile.Cette thèse de doctorat propose de résoudre ce problème en réalisant la croissance de la DEL sur un pseudo-substrat InGaN appelé InGaNOS fabriqué par Soitec.Après avoir identifié les limitations des structures InGaN/GaN sur substrat GaN sur sapphire classique pour l’émission efficace à grande longueur d’onde, des structures « tout-InGaN » ont été crues par EPVOM sur substrats InGaNOS. Il a été démontré que la contrainte était partiellement relaxée et que l’incorporation d’indium était plus facile. Grâce à des caractérisations optiques et structurelles fines, les différentes étapes depuis la reprise de croissance InGaN jusqu’à la DEL complète ont été étudiées. En photoluminescence (PL), la longueur d’onde de 617 nm a été atteinte à température ambiante. Les performances optiques de ces structures de puits quantiques dans les régions spectrales correspondant au vert, jaune et ambre ont été mesurées et sont comparables aux meilleures valeurs de la littérature. Enfin, la croissance de la première DEL « tout InGaN » sur substrat InGaN a révélé les challenges restants qui nécessiteront des développements complémentaires.
Simulation of Biogas Conversion Using Porous Solid Oxide Electrochemical Cells: Virtual Prototyping (2022)

The computer-aided engineering approach has made it possible to achieve virtual prototypes and to describe expected performances of new apparatuses. In this study, a direct production of syngas with biogas using the configuration of the cascade conversion cell in the supply feed direction of the system was exhibited. Momentum, heat, mass and charge balances were solved using COMSOL Multiphysics® commercial software. These simulations allowed calculation of distributions of partial pressures for all gas species within the anode (CH4, H2, CO, CO2, H2O, N2), as well as velocity field and temperature. The conversion process included methane reforming (steam and dry) associated with the water–gas shift reaction. The computing results showed that the configuration of three porous oxide solid cells based on a solid oxide fuel cell (SOFC) system conferred a larger active surface area and limited thermal stress in oxide materials. In addition, depending on the production process of the biogas, feeding composition strongly influences the conversion rate of CO2 and CH4. We observed that production of syngas was optimal for a CO2/CH4 ratio = 1.
Economics of Gas-To-Liquid Processing (The Effect of Scaling on Profitability) (2011)

Abstract Previous economic studies of Gas-To-Liquids (GTL) processes have considered large scale plants for liquid production rates of 50,000 barrels of liquid per day (BLPD) (approximately the equivalent to 500 MMscf per day of gas consumption) or more. This paper is guided by the need to produce "stranded gas reserves" using small scale GTL technology. This study examined simple profitability indicators for small scale GTL plants. We made use of capital cost estimates supplied by a reputable company headquartered in Colorado, for a Fischer-Tropsch plant designed in the year 2000 with a production capacity of 50,000 BLPD. Exponential scaling was used for estimating the capital cost for a base case unit with a production capacity of 1000 BLPD, or an equivalent typical gas consumption rate of 10 MMscf per day. A base case set of parameters was assumed and the profitability indicators of net present value (NPV) and discounted cash flow rate of return (IRR) were calculated. A sensitivity study shown on a spider diagram was performed by varying five economic parameters; Capital Cost, Plant Capacity, Product Price, Feed Stock Price and Cost of Trucking. Each of these parameters was varied over an appropriate range while others were held constant. For each combination of parameters the NPV and IRR were calculated and a spider diagram for visualizing the sensitivity was prepared. Our calculations indicate that the profitability is most sensitive to changes in the product price. Changes in capital costs at a given unit capacity caused the next most sensitive profitability behavior. Profitability is nearly as sensitive to the plant capacity as with the capital cost for a given capacity. Profitability is less sensitive to changes in the cost of the feed gas but over the range of possible costs, it could be a deal breaker. Profitability is least sensitive to the cost of transporting the product. Our results indicate that under the right circumstances a relatively small GTL plant could be profitable. With success in ongoing work to develop more integrated Fischer-Tropsch (F-T) process, the capital cost could easily be reduced for such a small unit, making the economics even more profitable.
Alkene Hydrogenation Catalyzed by Nickel Hydride Complexes of an Aliphatic PNP Pincer Ligand (2012)

Abstract To investigate metal–ligand cooperativity as a strategy for promoting nickel‐catalyzed alkene hydrogenation, cationic and neutral nickel(II) hydride complexes of the aliphatic pincer ligand PNHP Cy {PNHP Cy = HN[CH 2 CH 2 P(Cy) 2 ] 2 } have been synthesized and characterized. Cationic hydride complex [(PNHP Cy )Ni(H)]BPh 4 ( 2 ) catalyzed the hydrogenation of styrene and 1‐octene under mild conditions. Only low conversion was observed in the hydrogenation of 3,5‐dimethoxybenzaldehyde using 2 . The neutral hydride complex (PNP Cy )Ni(H) ( 3 ) was also found to be an alkene hydrogenation catalyst. Mechanistic experiments suggest that for catalyst 2 , the hydrogenation reaction proceeds through a pathway involving initial insertion of the alkene into the Ni–H bond. Contrary to the initial hypothesis, reactivity comparisons with the methyl‐substituted hydride complex [(PNMeP Cy )Ni(H)]BPh 4 {PNMeP Cy = (CH 3 )N[CH 2 CH 2 P(Cy) 2 ] 2 } suggest that metal–ligand cooperativity is not involved in these rare examples of mild and homogeneous nickel hydrogenation catalysis.
Antifouling properties of 90/10 copper-nickel alloy. (1985)

The fouling of 90/10 copper-nickel alloys has been studied in the sea and in the Thames Estuary. Differences in fouling between these two sites and in the composition of corrosion products have been observed. In the sea, bacteria initially colonised the surface of the corrosion products and then became buried to form sheets of bacteria sandwiched between parallel corrosion layers. These corrosion layers are lined with bacterial mucilage which binds considerable amounts of copper. Further colonisation results in the development of slime films on the surface of the corrosion products. Evidence for the sloughing off of these and the slime film is presented and the success of the alloy in these environments is discussed.
[Regenerative medicine: history and perspectives]. (2008)

Regenerative medicine using stem cells is one of the most important topics today. Embryonic stem cells (ES cells) are useful in the studies of the differentiation of various cells or tissues for transplantation therapy, because of their pluripotency to differentiate into almost all types of cells in the body. However, it is controversial to use human ES cells, because it is necessary to sacrifice the life of human embryos for the establishment of these cells. Induced pluripotent stem cells (iPS cells) generated from somatic cells of patients are one of the alternative sources of human pluripotent stem cells while avoiding ethical problems. Epigenetic studies using iPS cells may be valuable to find the way to control cell differentiation more effectively.