gebhart/patrepeval huggingface dataset:
Enzymolysis of glomerular immune deposits in vivo with dextranase/protease ameliorates proteinuria, hematuria, and mesangial proliferation in murine experimental IgA nephropathy. (1990)

The therapeutic effects of saccharolytic and proteolytic enzymes were investigated in models of IgA nephropathy. Mesangial glomerulonephritis was induced in mice by intravenous injection of preformed soluble immune complexes of dextran sulfate and either IgA (J 558) or IgM (MOPC 104 E) anti-dextran MAb (passive model) or by immunization with DEAE dextran (active model). In the passive model, only 30-40% of dextranase-treated mice given IgA or IgM immune complexes had mesangial Ig or dextran deposits, compared with 100% of saline-treated controls (P less than 0.01). There was no significant difference in mice given only protease. In the active model, dextranase and protease separately each reduced glomerular dextran and C3 deposits, and hematuria (P less than 0.01). Dextranase also reduced the glomerular IgA deposits (20 vs. 100% of saline-treated mice) and the frequency and severity of mesangial matrix expansion (both P less than 0.02), but did not reduce the modest IgG or IgM codeposits. Protease reduced IgG and IgM deposits, proteinuria and mesangial hypercellularity compared with saline (P less than 0.02), but did not diminish IgA, and had no effect on mesangial matrix expansion. The combination of dextranase plus protease attenuated all components of glomerular injury as judged by clinical and pathological parameters, but inactivated dextranase plus inactivated protease had no effect on any parameter. We conclude that enzymatic digestion of antigen and antibody can reduce immune deposits, mesangial proliferation, proteinuria, and hematuria in experimental glomerulonephritis.
Three-Dimensional Organization of Block Copolymers on “DNA-Minimal” Scaffolds (2012)

Here, we introduce a 3D-DNA construction method that assembles a minimum number of DNA strands in quantitative yield, to give a scaffold with a large number of single-stranded arms. This DNA frame is used as a core structure to organize other functional materials in 3D as the shell. We use the ring-opening metathesis polymerization (ROMP) to generate block copolymers that are covalently attached to DNA strands. Site-specific hybridization of these DNA-polymer chains on the single-stranded arms of the 3D-DNA scaffold gives efficient access to DNA-block copolymer cages. These biohybrid cages possess polymer chains that are programmably positioned in three dimensions on a DNA core and display increased nuclease resistance as compared to unfunctionalized DNA cages.
Sub-50 nm gate length n-MOSFETs with 10 nm phosphorus source and drain junctions (2002)

Forty-nanometer gate length n-MOSFETs with ultra-shallow source and drain junctions of around 10 nm are fabricated for the first time. To achieve such shallow junctions, a technique of solid-phase diffusion (SPD) from phosphorous-doped silicated glass (PSG) gate sidewalls is used. The resulting 40 nm gate length n-MOSFETs operate quite normally at room temperature. Even in the sub-50 nm region, short-channel effects-V/sub th/ shift and S-factor degradation-are suppressed very well. The impact ionization rate falls significantly as Vd falls below 1.5 V. It is found that, in the case of Vd less than 1.5 V, hot-carrier degradation is not a serious problem even in the sub-50 nm region.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Determinant spreading during experimental autoimmune encephalomyelitis: is it potentiating, protecting or participating in the disease? (1998)

During many autoimmune conditions, a T-cell response initially focused to a self-antigen evolves towards the recruitment of T cells to multiple antigenic determinants. Here we discuss whether such determinant spreading involves T cells activated in the peripheral lymphoid organs, or alternatively, whether the diversification occurs after infiltration of the initiating T cells into the target organ, for example, into the central nervous system during experimental autoimmune encephalomyelitis, a prototype for multiple sclerosis. The expression of myelin antigens in the thymus and spleen may not only contribute to the induction of tolerance but also to determinant spreading. In this case, the outcome of in vivo diversification may ultimately be determined by the balance between type 1 and type 2 responses to antigenic determinants derived from myelin components. Thus, spreading T cells could modulate disease progression positively or negatively, depending upon the nature of the accompanying cytokine secretion profile.
A simulation model for the density of states and for incomplete ionization in crystalline silicon. II. Investigation of Si:As and Si:B and usage in device simulation (2006)

Building on Part I of this paper [Altermatt et al., J. Appl. Phys. 100, 113714 (2006)], the parametrization of the density of states and of incomplete ionization (ii) is extended to arsenic- and boron-doped crystalline silicon. The amount of ii is significantly larger in Si:As than in Si:P. Boron and phosphorus cause a similar amount of ii although the boron energy level has a distinctly different behavior as a function of dopant density than the phosphorus level. This is so because the boron ground state is fourfold degenerate, while the phosphorus ground state is twofold degenerate. Finally, equations of ii are derived that are suitable for implementation in device simulators. Simulations demonstrate that ii increases the current gain of bipolar transistors by up to 25% and that it decreases the open-circuit voltage of thin-film solar cells by up to 10mV. The simulation model therefore improves the predictive capabilities of device modeling of p-n-junction devices.
A Randomised Controlled Trial of a Probiotic Lactobacillus Strain in Healthy Adults: Assessment of its Delivery, Transit and Influence on Microbial Flora and Enteric Immunity (2002)

In several intestinal disease states, altered microflora, impaired gut barrier and/or intestinal inflammation offer a rationale for the effective therapeutic use of probiotic microorganisms. However, for most candidate probiotic organisms there is a lack of evidence detailing their characterisation and effects on host flora and immunity. We have previously reported the isolation and characterisation, from surgically resected segments of the human gastrointestinal tract (GIT), of potential probiotic lactic acid bacteria (LAB). We have also described subsequent animal experiments that evaluated the establishment, persistence and localisation of specific probiotic Lactobacillus strains within the murine intestinal tract, in addition to their ability to influence the development of murine inflammatory disorders. In these studies, transit and survival of Lactobacillus salivarius UCC118 at the ileum was demonstrated using enteral tube sampling of six healthy volunteers following consumption of a single dose (150 ml) of fermented milk-borne probiotic (10 8 colony forming units per ml (CFU/ml)). Subsequently, we performed a randomised controlled trial of 80 volunteers fed strain UCC118 (10 8 CFU/day for 21 d), using two oral delivery vehicles (fresh milk, n = 20 vs. fermented milk, n = 20; controls, n = 20 for each). Throughout this feeding period, and for up to 100 days following cessation of feeding, the numbers of total culturable lactobacilli and of the administered Lactobacillus UCC118 present in faeces were monitored. Five subjects (5/40; fresh milk, four; fermented milk, one) were still excreting the probiotic lactobacilli 21 days post-cessation of feeding, while one subject (fermented milk) was still colonised up to 100 days after feeding. Consumption of fermented milk-borne UCC118 cells resulted in significantly increased levels of faecal-borne enterococci and lactobacilli. Numbers of bifidobacteria, coliforms and bacteroides were not significantly altered. In addition, changes in salivary IgA levels against UCC118 cells and increased granulocyte phagocytic activity were observed following consumption of the fermented milk-borne probiotic. In summary, Lactobacillus UCC118 was found to effectively transit (and persist within) the human intestinal tract, to modify the faecal flora and to engage the immune system.
Clinical Applications of Photodynamic Therapy (1994)

This is a review of photodynamic therapy, which is a classic binary system involving the use of a photosensitizer and light of very specific wavelength, consistent with the absorption characteristics of that sensitizer. As a binary system, its effects are almost entirely limited to tumour cells, but the major drawback is its limited penetration because it utilizes physical light within the visible spectrum. For Photofrin II, which is the only approved sensitizer for clinical use in this country, the effects are limited to approximately 0.5 cm or less, depending on the tissue and the amount of blood, etc. Newer sensitizers offer more penetration and the opportunity to repeat treatments, because the newer sensitizers do not have the very long (up to 10 weeks) period of enhanced skin sensitivity to sunlight. A summary of the results of photodynamic therapy by individual sites is included. The use of newer sensitizers, which represent much purer substances than Photofrin II, should give an opportunity for repeated treatments, which should eventually make this form of treatment far more important than it has been up to now.
Inactivation of nuclear inhibitory polypeptides of protein phosphatase-1 (NIPP-1) by protein kinase A (1993)

We have recently purified two potent and specific inhibitory polypeptides of protein phosphatase-1 from the particulate fraction of bovine thymus nuclei (Beullens, M., Van Eynde, A., Stalmans, W., and Bollen, M. (1992) J. Biol. Chem. 267, 16538-16544). Here it is reported that these inhibitors, termed NIPP-1a (18 kDa) and NIPP-1b (16 kDa), are excellent substrates (Km = 0.1 microM) for phosphorylation by protein kinase A on both Ser and Thr residues. Phosphorylation was temporally closely related with an activation of NIPP-1. Maximal phosphorylation by protein kinase A (1.5 mol of phosphate/mol of NIPP-1) caused an 8-fold increase in the concentration of NIPP-1 required for half-complete inhibition of the catalytic subunit of protein phosphatase-1, irrespective of the concentration of the phosphatase. Phosphorylation decreased the binding of NIPP-1 to immobilized protein phosphatase-1. NIPP-1 could be efficiently and completely reactivated by incubation with the catalytic subunit of protein phosphatase-2A. The type-1 catalytic subunit was much less effective, however, even when present in a molar excess to NIPP-1. Chromatography of a salt extract of the particulate nuclear fraction of Mono Q revealed three species of PP-1. One of these species, termed PP-1N alpha, contained NIPP-1 as a subunit and could be activated 6-fold by incubation with protein kinase A under phosphorylating conditions. This activation of PP-1N alpha is opposite to the known inhibition of cytoplasmic species of protein phosphatase-1 by protein kinase A.
Vitamin D for the prevention and treatment of pancreatic cancer (2009)

Pancreatic cancer is ranked fifth among cancer-related deaths worldwide with a 5-year survival rate of less than 5%. Currently, surgery is the only effective therapy. However, most patients are diagnosed in the late stage and are not suitable for receiving curative surgery. Moreover, pancreatic cancer doesn't respond well to traditional chemotherapy and radiotherapy, leaving little effective treatment for advanced pancreatic cancer cases. 1alpha,25-dihydroxyvitamin D(3) [1alpha,25(OH)(2)D(3)], the biologically active form of vitamin D(3), was originally identified during studies of calcium and bone metabolism, though it is now recognized that it exerts biological effects in almost every tissue in the body. Abundant evidence has shown that 1alpha,25(OH)(2)D(3) has antiproliferative, apoptotic, pro-differentiation and antiangiogensis effects in many types of cancer cells in vivo and in vitro, including breast, prostate, and colon. Similarly, the antitumor growth effect of 1alpha,25(OH)(2)D(3) on pancreatic cells has been demonstrated. The clinical use of 1alpha,25(OH)(2)D(3) is impeded by the lethal side effects of hypercalcemia and hypercalciuria. Therefore, 1alpha,25(OH)(2)D(3) analogs, which are either equipotent or more potent than 1alpha,25(OH)(2)D(3) in inhibiting tumor cell growth but with fewer hypercalcemic and hypercalciuric side effects, have been developed for the treatment of different cancers. Recently, a pre-clinical study demonstrated that a less calcemic analog of 1alpha,25(OH)(2)D(3), 19-nor-1alpha,25(OH)(2)D(2) (Paricalcitol), is effective in inhibiting tumor growth in vitro and in vivo, via upregulation of p21 and p27 tumor suppressor genes. Studies on the anti-tumor effects of a more potent analog of Paricalcitol are underway. 1alpha,25(OH)(2)D(3) and its analogs are potentially attractive novel therapies for pancreatic cancer.
A strategy for identifying immunosuppressive therapies for Alzheimer disease. (1998)

There is increasing evidence that the immune system plays an important role in the pathology of Alzheimer disease (AD). The fundamental steps in this process involve induction of neurotoxic microglia by senile plaques. Recent studies have shown that microglia in contact with isolated plaque fragments secrete neurotoxins that can cause neuronal injury and brain damage typical of AD. In vitro models help to delineate individual steps of this activation cascade by which quiescent microglia become neuron-killing cells. Moreover, such model systems provide rapid screening assays to identify immunosuppressive drugs that might slow brain damage brought on by neurotoxic microglia.
Specificity of the zinc(ii), magnesium(ii) and calcium(ii) complexation by (pyridin-2-yl)aminomethane-1,1-diphosphonic acids and related 1,3-(thiazol-2-yl) and 1,3-(benzothiazol-2-yl) derivatives (2009)

The solution properties of a series of (pyridin-2-yl)aminomethane-1,1-diphosphonic acids 1-4 as well as closely related compounds 5 and 6 with 1,3-thiazolyl or 1,3-benzothiazolyl side chains and their influence on the complexation of Zn(II), Mg(II) and Ca(II) were studied by means of the 31P and 1H NMR spectroscopy, pH-potentiometry and ESI-MS methods. The crystal structures of 5 and 6 were determined by X-ray analysis. All the studied compounds exist in solution as mixtures of the Z and E isomers with respect to the C2-Namino bond. Compounds 1 and 2 exhibit higher overall basicities compared to 3-6 and have exceptionally basic pyridyl nitrogen (pK2 = 7.88 and 8.18, respectively). Dynamic NMR studies revealed that the nature of the aromatic side chain as well as the specificity and topology of the ring substituent account for the rotational barrier for the Z/E interconversion, which decreases in the order of 1 approximately 2 > 3 approximately 4 >> 5 (6). This is particularly important for aggregational properties of 1-6 in solution and for the complex-formation equilibria. Overall, compounds 1-6 demonstrate a strong tendency for the formation of protonated multinuclear complexes. Their formation is unexpectedly slow on the NMR time scale compared to previously studied bisphosphonate complexes. The stepwise release of protons upon the rise of pH leads to mononuclear species. The Z ligand conformation is preferred in multinuclear complexes of Zn(II), Mg(II) and Ca(II) with 1 and 2 whereas in the case of 3-6 the complexation processes are affected by the intramolecular Z/E interconversion.
Quantitative analysis of cell-free DNA in the plasma of gastric cancer patients (2012)

In the present study, an accurate and reproducible method for quantifying cell-free DNA (cfDNA) in human blood was established and tested for its ability to predict gastric cancer in patients. Using 'Alu81-qPCR' to amplify 81-bp Alu DNA sequences, we first estimated the amount of cfDNA in the serum or plasma of 130 patients with gastric cancer to identify which source of cfDNA is more suitable for the biomarker screening of these patients. The results of Alu81-qPCR revealed that the amount of cfDNA in the plasma was low compared with that in the serum, but was found at similar levels among the samples, indicating that the plasma may be a more suitable source of cfDNA for biomarker screening. For the 54 patients with gastric cancer and the 59 age-matched healthy controls, the mean levels of plasma cfDNA were 2.4-fold higher in the patient group compared with the control group, indicating that plasma cfDNA levels may be useful for predicting patients with gastric cancer. The results of our study suggest that Alu81-qPCR is a more reliable method than other techniques, such as the PicoGreen assay, for quantifying cfDNA in human blood, demonstrating the potential to complement current diagnostic procedures for the management of gastric cancer patients.
Butyric acid-producing anaerobic bacteria as a novel probiotic treatment approach for inflammatory bowel disease (2009)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Regional differences in the distribution of the proteoglycans biglycan and decorin in the extracellular matrix of atherosclerotic and restenotic human coronary arteries. (1994)

Proteoglycans are important constituents of blood vessels and accumulate in various forms of vascular disease. Little is known concerning the proteoglycan composition of restenotic lesions formed after angioplasty and whether the proteoglycan composition of these lesions differs from that of primary atherosclerosis. Accordingly, we sought to characterize the distribution of two proteoglycans, biglycan and decorin, in primary atherosclerotic and restenotic lesions of human coronary arteries. Restenosis (n = 37) and primary (n = 11) lesions obtained from 48 patients by directional atherectomy of human coronary arteries were stained with antibodies against biglycan and decorin. To further characterize the extracellular matrix of restenotic tissues, we studied the co-distribution of these proteoglycans with collagen types I, III, and IV. The loose fibroproliferative tissue seen predominantly in restenosis lesions consistently stained positively for biglycan in patterns of deposition ranging from disseminated to homogeneous. The density and intensity of biglycan staining was correlated with the density of collagen type I and III fiber networks, both of which were observed to interweave among the loose fibroproliferative tissue. The compact connective tissue of primary atherosclerotic plaque was characterized by strong biglycan staining which co-localized with intense collagen type I and III staining. Only basement membrane-like structures rich in collagen type IV demonstrated negative biglycan staining. In contrast, loose fibroproliferative tissue exhibited no significant staining for decorin. Strong immunostaining for decorin, however, was found in primary atherosclerotic plaque. There are thus regional differences in the distribution of extracellular matrix proteoglycans of restenotic and primary human atherosclerotic lesions; these observations suggest that differences established for the biological roles of biglycan and decorin in other organ systems may extend as well to pathologically altered human coronary arteries.
Correlation Analysis Between Disease Severity and Inflammation-related Parameters in Patients with COVID-19 Pneumonia (2020)

Abstract Aim The new coronavirus (COVID-19) pneumonia outbreaking at the end of 2019 is highly contagious. Crude mortality rate reached 49% in critical patients. Inflammation matters on disease progression. This study analyzed blood inflammation indicators among mild, severe and critical patients, helping to identify severe or critical patients early. Methods In this cross-sectional study, 100 patients were included and divided to mild, severe or critical groups. Correlation of peripheral blood inflammation-related indicators with disease criticality was analyzed. Cut-off values for critically ill patients were speculated through the ROC curve. Results Significantly, disease severity was associated with age (R=-0.564, P&lt;0.001), interleukin-2 receptor (IL2R) (R=-0.534, P&lt;0.001), interleukin-6 (IL-6) (R=-0.535, P&lt;0.001), interleukin-8 (IL-8) (R=-0.308, P&lt;0.001), interleukin-10 (IL-10) (R=-0.422, P&lt;0.001), tumor necrosis factor α (TNFα) (R=-0.322, P&lt;0.001), C-reactive protein (CRP) (R=-0.604, P&lt;0.001), ferroprotein (R=-0.508, P&lt;0.001), procalcitonin (R=-0.650, P&lt;0.001), white cell counts (WBC) (R=-0.54, P&lt;0.001), lymphocyte counts (LC) (R=0.56, P&lt;0.001), neutrophil count (NC) (R=-0.585, P&lt;0.001) and eosinophil counts (EC) (R=0.299, P=0.01). Conclusion With following parameters such as age &gt;67.5 years, IL2R &gt;793.5U/mL, CRP &gt;30.7ng/mL, ferroprotein &gt;2252μg/L, WBC&gt;9.5*10^9/L or NC &gt;7.305*10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented. Inflammation is closely related to severity of COVID-19, and IL-6, TNFα and IL-8 might be promising therapeutic targets.
Fabrication and testing of micro-lens arrays by all-liquid techniques (2004)

Various all-liquid fabrication strategies to construct polymer micro-lens arrays on glass substrates are presented. Wettability patterns were made on glass substrates and a monomer was deposited selectively on circular domains on the substrate by making use of the hydrophobic effect, resulting in liquid micro-lenses. The liquid micro-lenses were solidified by polymerization. Three different variations of the selective wetting process were developed. The polymer micro-lenses were characterized extensively by optical methods: focal length, surface roughness and optical aberrations of the lenses were determined by scanning white light interferometry. Due to their fabrication from the liquid phase, the root-mean-square surface roughness of the micro-lenses is between 10 and 35 nm, i.e. better than 1/10 wavelength. These measurements allowed comparison of the quality of lenses fabricated by these techniques.
Two helices plus a linker: a small model substrate for eukaryotic RNase P. (1995)

Using precursor tRNA molecules to study RNA-protein interactions, we have identified an RNA motif recognized by eukaryotic RNase P (EC 3.1.26.5). Analysis of circularly permuted precursors indicates that interruptions in the sugar-phosphate backbone are not tolerated in the acceptor stem, in the T stem-loop, or between residues A-9 and G-10. Prokaryotic RNase P will function with a minihelix consisting of the acceptor stem connected directly to the T stem-loop. Eukaryotic RNase P cannot use such a minimal substrate unless a linker sequence is added in the gap where the D stem and anticodon stem-loop were deleted.