gebhart/patrepeval huggingface dataset:
Chromatographic profiles of blood plasma free oligosaccharides in patients with cardiovascular disease (2015)

Free oligosaccharides (FOS) are unbound structural analogs of glycans of glycoconjugates. There are several sources of them inside the cell: 1) multistep pathways of N-glycosylation, 2) the cell quality control and endoplastic reticulum-associated degradation of mis-glycosylated and/or misfolded glycoproteins, 3) lysosomal degradation of mature glycoconjugates. Some of these FOS are the earliest indicators of potential glycosylation alterations that would be revealed in the course of the cell quality control and the endoplastic reticulum-associated degradation. Ischemia and hypertension cause stress of intracellular organelles leading to disruption of their functions. The main objective of the work was the characterization of free oligosaccharides (FOS) in plasma obtained from patients with cardiovascular diseases compared to those from healthy subjects to evaluate the potential of these compounds for diagnostics. Chromatographic profiles of FOS composed of 4–12 monosaccharides were obtained and analyzed for quantitative and qualitative differences between the samples. After plasma deproteinization and FOS purification the oligosaccharides were labelled with anthranilic acid (2-AA), separated into the neutral and charged with QAE Sephadex (Q25-120) chromatography and analysed using high-performance liquid chromatography (HPLC). Glucose unit values were determined following comparison with a 2-AA-labelled glucose oligomer ladder derived from a partial hydrolysate of dextran as an external standard. The data were collected and processed using Empower software. The charged FOS were digested with the sialidase from Arthrobacter ureafaciens. 2-AA – labelled free oligosaccharides from transferrin were used as an external standard for the structure decoding. The profiles obtained were compared with intracellular free oligosaccharides of known structures and with the glycan structures and their descriptions in the databases GlycoBase and EUROCarbDB. These approaches allowed predicting a range of glycan structures for each of the main peaks of HPLC profiles of plasma free oligosaccharides and managing ways for their future experimental analysis. In the case of cardiovascular disorders, HPLC profiles of FOS revealed a changing pattern of heterogeneity, depending on the severity of the disease. Three main enlarged glycan species in the netral fraction and one peak in the charged fraction distinguished the FOS of the patients from those of the healthy volunteers. It has been revealed that the neutral marker peaks were represented by polimannose glycans with 5–7 mannose residues and 1–2 residues of N-acetylglucosamine, and one of the major peaks of the charged fraction – by two-antennary complex N-glycan with two sialic acid residues. The study of free oligosaccharides of blood plasma is a new field of glycobiology allowing an evaluation of an organism state at the level of the cell organelle functional status and openning up broad prospects for finding early diagnostic and prognostic markers of cardiac insufficiency.
Patrice-François de Neny (1716-1784) : portrait d'un homme d'etat (1993)

info:eu-repo/semantics/published
Identification of miR-34a-target interactions by a combined network based and experimental approach (2016)

Circulating miRNAs have been associated with numerous human diseases. The lack of understanding the functional roles of blood-born miRNAs limits, however, largely their value as disease marker. In a systems biology analysis we identified miR-34a as strongly associated with pathogenesis. Genome-wide analysis of miRNAs in blood cell fractions highlighted miR-34a as most significantly up-regulated in CD3+ cells of lung cancer patients. By our in silico analysis members of the protein kinase C family (PKC) were indicated as miR-34a target genes. Using a luciferase assay, we confirmed binding of miR-34a-5p to target sequences within the 3'UTRs of five PKC family members. To verify the biological effect, we transfected HEK 293T and Jurkat cells with miR-34a-5p causing reduced endogenous protein levels of PKC isozymes. By combining bioinformatics approaches with experimental validation, we demonstrate that one of the most relevant disease associated miRNAs has the ability to control the expression of a gene family.
ChemInform Abstract: Palladium‐Catalyzed Direct Arylations of Heteroaromatics Bearing Dicyanovinyls at C‐2. (2013)

Abstract Substrates bearing a thiophene, furan, and N‐methylpyrrole unit undergo ready arylation at C‐5 to yield 2,5‐disubstituted derivatives.
Inter-relationship between ageing, body mass index, diabetes, systemic blood pressure and intraocular pressure in Asians: 6-year longitudinal study (2018)

Normal ageing and reduced systemic BP are associated with reduced IOP in Malay and Indian adults. Given that high IOP is a risk factor for glaucoma, our finding highlights the importance of controlling hypertension in older adults, where hypertension and glaucoma incidences are on a rise.
Deposition of Electrospun Fibers on Reactive Substrates for In Vitro Investigations (2008)

Recent in vitro studies with electrospun nanofibers have used a range of techniques. The in vitro system presented in this article describes electrospun fibers deposited onto chemically reactive substrates to provide fiber adherence and surface chemistry control of the substrate. Fibers of poly(epsilon-caprolactone) (PCL) or of a blend of PCL and collagen type I (C/PCL) were electrospun directly onto collectors coated with isocyanate-terminated star (polyethylene glycol) (sPEG). Alternatively, parallel electrospun fibers were collected on dual collectors in "dilute" quantities and transferred onto sPEG-coated substrates. The initial reactive nature of the substrates allows the collection of very few fibers, which adhere well during frequent washes. Furthermore, the sPEG layer transforms into protein-repellent substrates with the additional potential to include specific cellular mediators such as glycine-arginine-glycine-aspartate-serine (GRGDS) peptides to promote cell adhesion. Therefore, the fiber and substrate chemistry can be modified independently, which is particularly useful for in vitro studies of guided migrating cells. In the present work, dissociated cells of dorsal root ganglia seeded onto the substrates were investigated to assess the influence of different combinations of fiber material, fiber orientation, and surface functionalization. Cell adhesion was observed predominantly on the nanofibers, except when the sPEG layer on the substrate contained GRGDS. On the cell-repellent sPEG substrates, neurites were aligned in direct contact with parallel C/PCL fibers and less so with PCL fibers. In contrast, neurite alignment showed less guidance effect with C/PCL electrospun fibers on the GRGDS/sPEG-coated substrates. Therefore, the combination of oriented biologically active fibers on cell-repellent surfaces enhanced the guidance of such cells. These reactive substrate systems provide a multitude of in vitro combinations for providing cells with specific mediators and, in turn, defining the optimum environment of regenerating devices for in vivo studies.
Exploring the Promiscuity of Phenol Hydroxylase from Pseudomonas stutzeri OX1 for the Biosynthesis of Phenolic Compounds (2018)

Enzyme promiscuity plays an important role in developing biosynthetic pathways for novel target products. Phenol hydroxylase (PH) from Pseudomonas stutzeri OX1 is capable of ortho-hydroxylation of phenol and cresol isomers into counterpart catechols. A small ferredoxin-like protein PHQ was clustered together with the ph gene cluster in the genome of P. stutzeri OX1, and its function was not known. In this study, we found that the existence of PHQ has a promotion effect on the catalytic efficiency of PH. Then, we tested the substrate range of PH using nine different non-natural substrates. We found that PH was a promiscuous hydroxylase that could catalyze ortho-hydroxylation of several non-natural substrates, including catechol, 4-hydroxybenzoic acid and resorcinol. On this basis, linking the catechol biosynthetic pathway with the hydroxylation reaction catalyzed by PH enabled construction of a novel biosynthetic pathway for the synthesis of pyrogallol. This work not only characterized a well-performed PH, but also provided a promising hydroxylation platform for the production of high-value phenolic compounds.
Novel sulfonated poly(arylene ether sulfone) containing hydroxyl groups for enhanced proton exchange membrane properties (2014)

We here report a new sulfonated poly(arylene ether sulfone) modified with hydroxyl side groups for a proton exchange membrane fuel cell (PEMFC).
Density Functional Theory Study of the Alkali Metal Cation Adsorption on Pt(111), Pt(100), and Pt(110) Surfaces (2014)

We used density functional theory to study the adsorption of hydrogen, lithium, sodium, and potassium cations on different surfaces of platinum, namely the Pt(111), Pt(110), and Pt(100) surfaces. It was found that at low H + concentrations alkali metal cations can compete with hydrogen for adsorption on all the studied platinum surfaces leading to a site blocking effect during the electrochemical processes involving adsorption of hydrogen in alkaline media. The strongest site blocking effect is predicted to occur on the Pt(111) surface as hydrogen and alkali metal cations adsorb in the same fcc-hollow adsorption site. On the Pt(110) and Pt(100) surface hydrogen and alkali cations adsorb on different sites and can co-exist on the surface – the most favorable adsorption site for hydrogen is a bridge site, while the hollow site is favored for all the studied alkali metal cations. Based on the calculated adsorption Gibbs free energies and the number of available adsorption sites on different surfaces, the probability of the site blocking effect by alkali cations on different surfaces of platinum was determined as Pt(111)&gt;Pt(110)&gt;Pt(100).
Rare Earth Phosphate Glass and Glass-Ceramic Proton Conductors (2009)

The structure and conductivity of cerium and lanthanum phosphate glasses and glass-ceramics were investigated. The effects of varying the metal to phosphate ratio in the glasses, doping LaP3O9 glasses with Ce, and recrystallization of CeP3O9 glasses, on the glasses' microstructure and total conductivity were investigated using XRD, SEM, and AC impedance techniques. Strong increases in conductivity occurred when the glasses were recrystallized: the conductivity of a cerium metaphosphate glass increased conductivity after recrystallization from 10-7.5 S/cm to 10-6 S/cm at 400{degree sign}C.
Gold nanowires: Deposition, characterization and application to the Mass Spectrometry detection of low-molecular weight analytes (2009)

Nanowire fabrication methods are usually classified either as dasiatop downpsila, including for example photo- or electron beam-lithography, or dasiabottom uppsila, involving the synthesis of nanowires from smaller precursors. Lithographically patterned nanowire electrodeposition (LPNE) combines the attributes of the photolithography approach with the versatility of bottom-up electrodeposition methods. In the present study, gold nanowires (Au-NWs) have been electrodeposited using LPNE. The nanomaterials have been then subjected to a spectroscopic and morphological characterization by means of X-Ray Photoelectron Spectroscopy (XPS), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD) and Atomic Force Microscopy (AFM). Finally, Au-NWs have been successfully used as desorption/ionization promoters for the Laser-Induced Desorption-Ionization Mass Spectrometry (LDI-MS) detection of low-molecular weight analytes, such as amino acids and peptides.
Abstract 1648: ImmunoGraft® platform for the evaluation of Immuno-Oncology agents in PDX tumors models (2017)

Abstract Recent breakthroughs in Immunotherapy have given new hope to treating previously untreatable tumor types and provide a better tolerated alternative to standard agents. There is an unmet need for a pre-clinical platform to test potential immune-oncology therapeutics that would also provide a tool to examine the mechanisms of response to better predict clinical outcomes. We have previously presented the Champions ImmunoGraft®, an innovative pre-clinical model enabling immunotherapeutic agents to be evaluated for efficacy in solid tumors. This platform is more reflective of the human tumor microenvironment (both immune and non-immune cell-based) and may be one of the most translationally-relevant models to date for screening therapies targeting the immune system. However, optimization of humanization and PDX implantation protocols that allow a broader reconstitution of cell linage and higher engraftment rate are necessary to further improve the pre-clinical evaluation of immune-oncology therapeutics and enhance the value of this modality for patient’s benefit. To this end, immune-compromised NOG (PrkdcscidIl2rgtm1Sug) mice were reconstituted (humanized) with human CD34+ cells using optimized procedure and blood was collected at different time points post engraftment to check for the major leukocyte linages. At ten weeks after humanization, mature human CD45+ cells comprised close to 50% of the leukocytes detected in the circulation and secondary lymphoid tissues of the humanized animals. As a result of improved methodology of the reconstitution protocol we have achieved an 85% success rate of humanization with a shortened engraftment period utilizing fewer CD34+ cells that maintain humanization reconfirmed at 22 weeks post reconstitution. Champions TumorGraft® database contains more than one-thousand clinically relevant well-annotated PDX models. We have complied data from extensive genetic and protein expression analyses to design applicable ImmunoGraft® studies for testing of Immuno-Oncology agents. We have identified tumors expressing key markers that may predict response to immunotherapy agents including PDL-1, CD40, IDO-1 and IDO-2 as well as tumors that harbor a high mutational load. Here we present the efficacy and clinically relevant endpoints of two well-studied checkpoint inhibitors Ipilimumab and Pembrolizumab in this highly translational PDX platform. Citation Format: David Cerna, Daniel Ciznadija, Bhavna Verma, David Sidransky, Evgeny Izumchenko, Angela Davies, Maria Mancini. ImmunoGraft® platform for the evaluation of Immuno-Oncology agents in PDX tumors models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1648. doi:10.1158/1538-7445.AM2017-1648
Investigation of Bis-(3-sodiumsulfopropyl disulfide) (SPS) Decomposition in a Copper-Electroplating Bath Using Mass Spectroscopy (2008)

Bis-(3-sodiumsulfopropyl disulfide) (SPS) is a well-known accelerator used to promote "bottom-up filling" in the semiconductor copper (Cu) electroplating process. However, the gap-filling capability and the defect performance of Cu electroplating are impacted as the SPS molecules are decomposed or oxidized. In this study, by-products generated from SPS decomposition and oxidation were identified and quantized using mass spectroscopy. It was found that 1,3-propanedisulfonic acid (PDS) was the most stable species among the SPS by-products. The PDS concentration increased with the increasing surface area of immersed Cu metals. The relationship between the consumption rate of SPS and the generation rate of PDS with different surface areas of Cu metals was particularly investigated. Furthermore, an equivalent circuit was developed and then examined using electrochemical impedance spectroscopy to characterize the properties of the aged bath with the decomposition of SPS.
EXPERIMENTAL INFECTION OF CATTLE WITH A FELINE ISOLATE OF TRITRICHOMONAS FOETUS (2007)

Tritrichomonas foetus is the causative agent of bovine trichomoniasis, a sexually transmitted disease in cattle that can result in large profit losses for cattle producers. Increasing reports have suggested that T. foetus is also the causative agent of large-bowel diarrhea in cats. To determine if the trichomonads recovered from the reproductive tract of cattle and the large intestine of cats can thrive in the same host, 2 groups of virgin Angus heifers were inoculated with T. foetus. The first group of heifers was inoculated with a bovine T. foetus isolate cultured from a naturally infected cow, and heifers in the second group were inoculated with T. foetus organisms cultured from the feces of a naturally infected cat. Over an 11-wk period, vaginal, cervical, and uterine mucus samples were analyzed, along with a single transcervical uterine biopsy sample, to determine organism and disease presence. The mucus and biopsy samples collected from each group indicate that the disease caused by feline and bovine isolates of T. foetus are comparable, but not identical.
Mechanisms and applications of the anti-inflammatory effects of photobiomodulation (2017)

Photobiomodulation (PBM) also known as low-level level laser therapy is the use of red and near-infrared light to stimulate healing, relieve pain, and reduce inflammation. The primary chromophores have been identified as cytochrome c oxidase in mitochondria, and calcium ion channels (possibly mediated by light absorption by opsins). Secondary effects of photon absorption include increases in ATP, a brief burst of reactive oxygen species, an increase in nitric oxide, and modulation of calcium levels. Tertiary effects include activation of a wide range of transcription factors leading to improved cell survival, increased proliferation and migration, and new protein synthesis. There is a pronounced biphasic dose response whereby low levels of light have stimulating effects, while high levels of light have inhibitory effects. It has been found that PBM can produce ROS in normal cells, but when used in oxidatively stressed cells or in animal models of disease, ROS levels are lowered. PBM is able to up-regulate anti-oxidant defenses and reduce oxidative stress. It was shown that PBM can activate NF-kB in normal quiescent cells, however in activated inflammatory cells, inflammatory markers were decreased. One of the most reproducible effects of PBM is an overall reduction in inflammation, which is particularly important for disorders of the joints, traumatic injuries, lung disorders, and in the brain. PBM has been shown to reduce markers of M1 phenotype in activated macrophages. Many reports have shown reductions in reactive nitrogen species and prostaglandins in various animal models. PBM can reduce inflammation in the brain, abdominal fat, wounds, lungs, spinal cord.
Scalable Synthesis of the Desoxy-biphenomycin B Core (2011)

We describe the evolution of a kilogram-scale synthesis of the protected cyclic tripeptide desoxy-biphenomycin B, based on an early discovery route. The retrosynthetic concept included a macrolactamization strategy to build the core ring system of biphenomycin B in combination with a double catalytic asymmetric hydrogenation protocol for the construction of the ansa-tripeptide precursor. Eventually, the kilogram process comprised a 16-step sequence with an overall yield for the longest linear sequence of 19.5%.
Heterobimetallic Hydroxy Complexes: [Re3(CO)9(μ2‐OH)3(μ3‐OH)]− as a Novel Tripodal Ligand (1996)

A structure containing two cubes linked through a common metal atom (1) is formed on reaction of the novel tripodal ligand [{Re(CO)3}3(OH)4]− with MII salts (M = Mn, Cu). Crystals of 1 contain extended layers whose structures are determined by the type of coordination sphere of MII. • = Re(CO)3; Counterion: NEt.
Plasminogen Activator Inhibitor-1 Antagonist TM5441 Attenuates N ω -Nitro- l -Arginine Methyl Ester–Induced Hypertension and Vascular Senescence (2013)

Pharmacological inhibition of PAI-1 is protective against the development of hypertension, cardiac hypertrophy, and periaortic fibrosis in mice treated with L-NAME. Furthermore, PAI-1 inhibition attenuates the arterial expression of p16(Ink4a) and maintains telomere length. PAI-1 appears to play a pivotal role in vascular senescence, and these findings suggest that PAI-1 antagonists may provide a novel approach in preventing vascular aging and hypertension.
Softening of Rare Earth Orthophosphates by Transformation Plasticity: Possible Applications to Fiber‐Matrix Interphases in Ceramic Composites (2010)

This chapter contains sections titled: Introduction Transformation Plasticity Experiments Results and Discussion Summary and Conclusions
Sheep Exhibit Novel Variations in the Organization of the Mammalian Type II Gonadotropin-Releasing Hormone Receptor Gene (2004)

Species-specific differences in genes encoding type II GnRH receptor indicate that a functional hepta-helical receptor is produced in monkeys but not in rodents, cows, chimpanzees, or humans. To further investigate the extent of evolutionary differences, we sequenced the type II GnRH receptor gene from wild-type Soay sheep. The gene was isolated by long-distance PCR using primers to PEX11beta and RBM8A genes known to flank type II GnRH receptor gene homologues. The gene spans 5.7-kb DNA and was sequenced after shot-gun subcloning. Its novel features include absence of a Pit-1 transcription factor binding site, a premature stop codon (TAG) in exon 1, an in-frame deletion of 51 bp (17 codons) in exon 2, and several nonconservative codon changes. Sheep breed variation in the gene was assessed using genomic DNA in PCR-restriction digest assays for the premature stop codon and in a PCR assay for the deletion. Both characteristics were present in all 15 breeds tested. Receptor gene expression was investigated using poly-A(+) RNA Northern analysis, RT-PCR, and in situ hybridization. An oligonucleotide probe to exon 1 revealed an alternative transcript in testis but not in pituitary gland. No transcripts in testis or pituitary were detectable using an exon 2-3 probe. All tissues examined including multiple brain areas and gonadotrope-enriched cell cultures were negative for type II GnRH receptor in RT-PCR. Testis and pituitary sections were negative with exon 1 riboprobes and exon 1 or 2-3 oligonucleotide probes in in situ hybridization. A hepta-helical type II GnRH receptor is therefore not expressed from this sheep gene.
A Semantics-aware Transformer Model of Relation Linking for Knowledge Base Question Answering (2021)

Tahira Naseem, Srinivas Ravishankar, Nandana Mihindukulasooriya, Ibrahim Abdelaziz, Young-Suk Lee, Pavan Kapanipathi, Salim Roukos, Alfio Gliozzo, Alexander Gray. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 2: Short Papers). 2021.