gebhart/patrepeval huggingface dataset:
Patterned Immobilization of Thermoresponsive Polymer (1997)

The thermoresponsive polymer poly(N-isopropylacrylamide) was immobilized in a specific pattern on a polystyrene matrix by photolithography. N-Isopropylacrylamide was copolymerized with acrylic acid. The copolymer was coupled with azidoaniline. The low critical solution temperature of the copolymer was lowered by incorporation of azidophenyl groups. The derivatized copolymer was then immobilized on a polystyrene matrix. The surface wettability of the immobilized polystyrene matrix changed with temperature, whereas that of untreated polystyrene matrix was insensitive to temperature. The measurement of contact angle showed that the surface of the immobilized matrix was hydrophobic at 37 °C but hydrophilic at 10 °C. Micropatterned immobilization of the copolymer on the polystyrene matrix surface was carried out using a photomask. The surface micropattern was clearly observed by phase-contrast microscopy at 37 °C. At low temperatures, hydration of graft chains erased the micropattern. The polystyrene matrix with micropatterned surface was applied to tissue engineering. Mouse fibroblast STO cells grown on the surface area, on which thermosensitive polymers were immobilized, were selectively detached by lowering the temperature.
Isolation and characterisation of vascular endothelial growth factor-165 specific scFv fragments by phage display (2003)

Vascular endothelial growth factor (VEGF) is a multifunctional cytokine which plays a major role in angiogenesis. Alternative splicing causes the production of several different isoforms (VEGF-A 121, 145, 165, 189, 206). VEGF is essential for tumor angiogenesis and several studies have correlated elevated VEGF levels with tumor stage, metastases and progression. Antibody phage display was employed to isolate two scFv antibody fragments, D8 and F10, with specificity for the VEGF165 isoform. It was shown by ELISA and competitive immunohistochemistry that each clone bound to VEGF165 but not VEGF121. Immunohistochemistry with D8 and F10 on colorectal carcinoma and adenoma sections revealed positive staining similar to that shown by a polyclonal VEGF antibody. The scFv antibody fragments, D8 and F10, will be useful in specifically detecting circulating VEGF165 in cancer patients as most studies to date have quantified the total level of circulating VEGF (121 and 165). These reagents will allow further elucidation of the role of VEGF in tumor angiogenesis.
Neural Tissue Xenografting (2000)

Neural transplantation may become an important treatment alternative for focal brain disorders. To date, the most successful grafts have been obtained in patients with Parkinson's disease. Completely normalized dopamine production and reduction of Parkinsonian symptoms have been demonstrated 10 years after grafting. However, the allogeneic donor tissue has to be obtained from induced abortions, and there are logistical difficulties, risks of infection, and ethical constraints limiting a wider clinical use. Xenografting is an alternative that could bridge these limitations if immunological rejection could be prevented. Pig embryonic neural tissue has been grafted to patients with Parkinson's disease, but no functional benefits have clinically been proven so far. The immune reactions to neural xenografts were incompletely characterized at the time of these early clinical trials, and it is likely that the treatments used were insufficient and that the grafts were rejected. In this article we will review new experiments addressing the immune responses against porcine neural tissue grafted to the adult brain, including the role of antibodies, complement, natural killer (NK) cells, lymphocytes, as well as the effects of immunosuppressive drugs and donor tissue modifications.
Identification of some ectomycorrhizal basidiomycetes by PCR amplification of their gpd (glyceraldehyde-3-phosphate dehydrogenase) genes (1996)

Degenerated oligonucleotide primers designed to flank an approximately 1.2-kb fragment of the gene encoding glyceraldehyde-3-phosphate dehydrogenase (gpd) from ascomycetes and basidiomycetes were used to amplify the corresponding gpd fragments from several species of the ectomycorrhizal fungal taxa Boletus, Amanita, and Lactarius. Those from B. edulis, A. muscaria, and L. deterrimus were cloned and sequenced. The respective nucleotide sequences of these gene fragments showed a moderate degree of similarity (72 to 76%) in the protein-encoding regions and only a low degree of similarity in the introns (56 to 66%). Introns, where present, occurred at conserved positions, but the respective positions and numbers of introns in a given taxon varied. The amplified fragment from a given taxon could be distinguished from that of others by both restriction nuclease cleavage analysis and Southern hybridization. A procedure for labeling DNA probes with fluorescein-12-dUTP by PCR was developed. These probes were used in a nonradioactive hybridization assay, with which the gene could be detected in 2 ng of chromosomal DNA of L. deterrimus on slot blots. Taxon-specific amplification was achieved by the design of specific oligonucleotide primers. The application of the gpd gene for the identification of mycorrhizal fungi under field conditions was demonstrated, with Picea abies (spruce) mycorrhizal roots harvested from a northern alpine forest area as well as from a plant-breeding nursery. The interference by inhibitory substances, which sometimes occurred in the DNA extracted from the root-fungus mixture, could be overcome by using very diluted concentrations of template DNA for a first round of PCR amplification followed by a second round with nested oligonucleotide primers. We conclude that gpd can be used to detect ectomycorrhizal fungi during symbiotic interaction.
Serum erythropoietin concentration in chronic renal failure: relationship to degree of anemia and excretory renal function (1979)

By use of the fetal mouse liver cell assay, serum erythropoietin (SEp) concentration was measured in 135 patients at various stages of chronic renal failure and in 59 healthy subjects. In patients with creatinine clearances (CCr) ranging from 2 to 40 ml/min/1.73 sq m, endocrine renal function was found to deteriorate in parallel to excretory renal function. The known negative correlation between SEp and hematocrit (Hct) was not apparent, probably because of the loss of renal mass accompanying progress of anemia and renal insufficiency. In contrast, in patients with minimal variation of residual excretory renal function, as in individual patients investigated repeatedly within a short period of time, changes of Hct were always accompanied by opposite changes of corresponding SEp concentrations. Thus, patients with chronic renal failure have a sustained regulatory feedback mechanism between Hct and SEp, which probably works at a lower level.
Necrotic cells trigger a sterile inflammatory response through the Nlrp3 inflammasome (2009)

Dying cells are capable of activating the innate immune system and inducing a sterile inflammatory response. Here, we show that necrotic cells are sensed by the Nlrp3 inflammasome resulting in the subsequent release of the proinflammatory cytokine IL-1beta. Necrotic cells produced by pressure disruption, hypoxic injury, or complement-mediated damage were capable of activating the Nlrp3 inflammasome. Nlrp3 inflammasome activation was triggered in part through ATP produced by mitochondria released from damaged cells. Neutrophilic influx into the peritoneum in response to necrotic cells in vivo was also markedly diminished in the absence of Nlrp3. Nlrp3-deficiency moreover protected animals against mortality, renal dysfunction, and neutrophil influx in an in vivo renal ischemic acute tubular necrosis model. These findings suggest that the inhibition of Nlrp3 inflammasome activity can diminish the acute inflammation and damage associated with tissue injury.
Cartilage-derived morphogenetic proteins. New members of the transforming growth factor-beta superfamily predominantly expressed in long bones during human embryonic development. (1994)

Partially purified extracts from newborn calf articular cartilage were found to induce cartilage and bone when subcutaneously implanted in rats. This activity showed characteristics of bone morphogenetic proteins (BMPs). Degenerate oligonucleotide primer sets derived from the highly conserved carboxyl-terminal region of the BMP family were designed and used in reverse transcription-polymerase chain reactions with poly(A)+ RNA from articular cartilage as template to determine which BMPs are produced by chondrocytes. Two novel members of the transforming growth factor-beta (TGF-beta) superfamily were identified and designated cartilage-derived morphogenetic protein-1 (CDMP-1) and -2 (CDMP-2). Their carboxyl-terminal TGF-beta domains are 82% identical, thus defining a novel subfamily most closely related to BMP-5, BMP-6, and osteogenic protein-1. Northern analyses showed that both genes are predominantly expressed in cartilaginous tissues. In situ hybridization and immunostaining of sections from human embryos showed that CDMP-1 was predominantly found at the stage of precartilaginous mesenchymal condensation and throughout the cartilaginous cores of the developing long bones, whereas CDMP-2 expression was restricted to the hypertrophic chondrocytes of ossifying long bone centers. Neither gene was detectable in the axial skeleton during human embryonic development. The cartilage-specific localization pattern of these novel TGF-beta superfamily members, which contrasts with the more ubiquitous presence of other BMP family members, suggests a potential role for these proteins in chondrocyte differentiation and growth of long bones.
Reconfigurable optical directed-logic circuits using microresonator-based optical switches (2011)

We present a reconfigurable optical directed logic architecture that offers several significant improvements over the original directed logic presented by Hardy and Shamir. Specific embodiments of on-chip, waveguided, large-scale-integrated, cellular optical directed logic fabrics are proposed and analyzed. Five important logic functions are presented as examples to show that the same switch fabric can be reconfigured to perform different logic functions.
The state of the art of adeno-associated virus-based vectors in gene therapy (2007)

The adeno-associated virus (AAV) has rapidly gained popularity in gene therapy since the establishment of the first AAV2 infectious clone, in 1982, due to some of their distinguishing characteristics such as lack of pathogenicity, wide range of infectivity, and ability to establish long-term transgene expression. Notably over the past decade, this virus has attracted considerable interest as a gene therapy vector, and about 85% of the currently available 2,041 PubMed references on adeno-associated viruses have been published during this time. The exponential progress of AAV-based vectors has been made possible by the advances in the knowledge of the virology and biology of this virus, which allows great improvement in AAV vectors construction and a better comprehension of their operation. Moreover, with the recent discovery of novel AAV serotypes, there is virtually one preferred serotype for nearly every organ or tissue to target. Thus, AAV-based vectors have been successfully overcoming the main gene therapy challenges such as transgene maintenance, safety and host immune response, and meeting the desirable vector system features of high level of safety combined with clinical efficacy and versatility in terms of potential applications. Consequently, AAV is increasingly becoming the vector of choice for a wide range of gene therapy approaches. This report will highlight the state of the art of AAV-based vectors studies and the advances on the use of AAV vectors for several gene therapy approaches.
Complete Regression of Large Solid Tumors Using Engineered Drug-Resistant Hematopoietic Cells and Anti-CD137 Immunotherapy (2006)

Combining chemotherapy and immunotherapy is problematic because chemotherapy can ablate the immune responses initiated by modulators of the immune system. We hypothesized that protection of immunocompetent cells from the toxic effects of chemotherapy, using drug resistance gene therapy strategies, would allow the combined use of chemotherapy and immunotherapy. In wild-type mice, the antitumor effectiveness of an immunotherapy regimen employing an agonistic anti-CD137 antibody is diminished with escalating doses of the antifolate trimetrexate (TMTX). Using retroviral gene transfer of a mutant form of dihydrofolate reductase (L22Y-DHFR), hematopoietic stem cells were genetically engineered to withstand the toxic effects of TMTX. Mice transplanted with L22Y-DHFR-modified bone marrow were then challenged with AG104 sarcoma cells and treated with TMTX only, anti-CD137 only, or a combination of chemotherapy and immunotherapy. Although tumor burden was transiently decreased during TMTX administration, no mice treated with TMTX alone survived the tumor challenge, whereas approximately 40% of transplanted mice treated with anti-CD137 alone survived. However, 100% of mice survived with complete tumor regression after transplantation with L22Y-DHFR-transduced bone marrow followed by combined treatment with TMTX and anti-CD137. In addition, adoptive transfer of splenocytes from cured mice extended the survival of tumor- bearing animals by approximately 3 weeks compared with controls. Therefore, protection of the hematopoietic system can allow for the combined administration of chemotherapy and immunotherapy, which results in complete tumor clearance.
Lna (Locked Nucleic Acid) (1999)

Abstract LNA (Locked Nucleic Acid) forms duplexes with complementary DNA, RNA or LNA with unprecedented thermal affinities. CD spectra show that duplexes involving fully modified LNA (especially LNA:RNA) structurally resemble an A-form RNA:RNA duplex. NMR examination of an LNA:DNA duplex confirm the 3′-endo conformation of an LNA monomer. Recognition of double-stranded DNA is demonstrated suggesting strand invasion by LNA. Lipofectin-mediated efficient delivery of LNA into living human breast cancer cells has been accomplished.
Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic Cells (2006)

Transient infection of eukaryotic cells with commensal and extraintestinal pathogenic Escherichia coli of phylogenetic group B2 blocks mitosis and induces megalocytosis. This trait is linked to a widely spread genomic island that encodes giant modular nonribosomal peptide and polyketide synthases. Contact with E. coli expressing this gene cluster causes DNA double-strand breaks and activation of the DNA damage checkpoint pathway, leading to cell cycle arrest and eventually to cell death. Discovery of hybrid peptide-polyketide genotoxins in E. coli will change our view on pathogenesis and commensalism and open new biotechnological applications.
Intracellular Messengers Contributing to Persistent Nociception and Hyperalgesia Induced by L‐Glutamate and Substance P in the Rat Formalin Pain Model (1994)

The contribution of the intracellular messengers nitric oxide, arachidonic acid and protein kinase C to persistent nociception in response to tissue injury in rats was examined following the subcutaneous injection of formalin into the hindpaw. Formalin injury-induced nociceptive behaviours were reduced by intrathecal pretreatment with inhibitors of nitric oxide synthase (NG-nitro-L-arginine methyl ester, L-NAME), arachidonic acid (dexamethasone) or protein kinase C [protein kinase C (19-26) and 1-95-(isoquinolinesulphonyl)-2-methylpiperazine dihydrochloride, H-7]. Each of these agents affected the tonic, but not the acute, phase of the formalin response. Furthermore, none of these agents affected mechanical or thermal flexion reflex thresholds in rats not injected with formalin. Conversely, formalin-induced nociceptive responses were enhanced by stimulators of nitric oxide (sodium nitroprusside), arachidonic acid metabolism (arachidonic acid) or protein kinase C [(+/-)-1-oleoyl-2-acetyl-glycerol], and were slightly reduced by inositol trisphosphate. Mechanical flexion reflexes were also reduced by arachidonic acid, while thermal flexion reflexes were reduced after treatment with sodium nitroprusside, arachidonic acid or [(+/-)-1-oleoyl-2-acetyl-glycerol]. The enhancement of formalin nociceptive behaviours (hyperalgesia) in rats treated with L-glutamate or substance P was reversed by pretreatment with inhibitors of nitric oxide (L-NAME), arachidonic acid (dexamethasone) or protein kinase C (H-7). The results suggest that central sensitization and persistent nociception following formalin-induced tissue injury, and the hyperalgesia in the formalin test induced by L-glutamate and substance P, are dependent on the intracellular messengers nitric oxide, arachidonic acid and protein kinase C.
Structure−Activity Relationship of Triazafluorenone Derivatives as Potent and Selective mGluR1 Antagonists (2005)

SAR (structure-activity relationship) studies of triazafluorenone derivatives as potent mGluR1 antagonists are described. The triazafluorenone derivatives are non-amino acid derivatives and noncompetitive mGluR1 antagonists that bind at a putative allosteric recognition site located within the seven-transmembrane domain of the receptor. These triazafluorenone derivatives are potent, selective, and systemically active mGluR1 antagonists. Compound 1n, for example, was a very potent mGluR1 antagonist (IC50 = 3 nM) and demonstrated full efficacy in various in vivo animal pain models.
Use of acoustic prior information for confidence measure in ASR (automatic speech recognition) applications (2005)

In this paper, a new acoustic confidence measure of automatic speech recognition hypothesis is proposed and it is compared to approaches proposed in the literature. This approach takes into account prior information on the acoustic model performance specific to each phoneme. The new method is tested on two types of recognition errors: the out-of-vocabulary words and the errors due to additive noise. An efficient way to interpret the raw confidence measure as a correctness prior probability is also proposed in the paper. (C) 2005 Acoustical Society of America.
Optical Fiber Sensors Based on Polymeric Sensitive Coatings (2018)

Polymer technology is one of the fastest growing fields of contemporary research due to the possibility of using a wide variety of synthetic chemical routes for obtaining a polymeric network with a well-defined structure, resulting in materials with outstanding macroscopic properties. Surface engineering techniques based on the implementation of polymeric structures can be used as an interesting tool for the design of materials with functional properties. In this sense, the use of fabrication techniques for the design of nanostructured polymeric coatings is showing an important growth due to the intrinsic advantages of controlling the structure at a nanoscale level because physical, chemical, or optical properties can be considerably improved in comparison with the bulk materials. In addition, the presence of these sensitive polymeric coatings on optical fiber is a hot topic in the scientific community for its implementation in different market niches because a wide variety of parameters can be perfectly measured with a high selectivity, sensitivity, and fast response time. In this work, the two main roles that a polymeric sensitive matrix can play on an optical fiber for sensing applications are evaluated. In a first section, the polymers are used as a solid support for the immobilization of specific sensitive element, whereas in the second section the polymeric matrix is used as the chemical transducer itself. Additionally, potential applications of the optical fiber sensors in fields as diverse as biology, chemistry, engineering, environmental, industry or medicine will be presented in concordance with these two main roles of the polymeric sensitive matrices.
Small Intestinal Bacterial Overgrowth: A Possible Association with Fibromyalgia (2001)

Objectives: Subjects with fibromyalgia [FMS] frequently have non specific bowel complaints similar to subjects with small intestinal bacterial over growth [SIBO]. The aim of this study was to test whether 1. SIBO is prevalent in FMS and 2. If treatment of SIBO reduces bowel symptoms.Methods: Of 815 subjects under going lactulose hydrogen breath testing for assessment of SIBO, 123 patients had FMS. Those with SIBO were treated with antibiotics. At the initial and follow-up visits, subjects were asked to rate their symptoms. Symptom scores be fore and after treatment were com pared.Results: Of the 123 subjects with FMS, 96 [78%] were found to have SIBO. Returning subjects reported a 57 ± 29% over all improvement in symptoms with significant improvement in bloating, gas, abdominal pain, diarrhea, constipation, joint pains, and fatigue [P < 0.05].Conclusions: 1. Small intestinal bacterial over growth is associated with FMS, 2. Eradication of SIBO improves intestinal symptoms in FMS.
Genes de Neandertal (2005)

En mayo de 2006 el afamado paleogenetista Svante Paavo anunciaba durante una conferencia de prensa en Colorado Spring (USA) que su equipo habia logrado secuenciar, por primera vez, un fragmento de ADN nuclear de neandertal. Algo sumamente dificil e importante para conocer la historia y el destino evolutivo de esta especie humana; asi como para determinar su grado de parentesco con la humanidad actual (?Quienes fueron los neandertales en relacion con nosotros? ?Ancestros directos, hermanos o primos hermanos?) En noviembre de ese mismo ano el equipo que habia realizado esta investigacion publicaba un trabajo en el que exponian la tarea realizada y las conclusiones que extraian, destacando las puertas que abrian estos estudios. En efecto, la posibilidad de lograr descifrar el genoma neandertal (con todo lo que esto significa) esta, por primera vez, al alcance de los investigadores. Y no habra que esperar mucho puesto que, si todo va bien, sera algo que se concretara en el 2008.
A Novel Role for the Interleukin-1 Receptor Axis in Resistance to Anti-EGFR Therapy (2018)

Cetuximab (CTX) is a monoclonal antibody targeting the epidermal growth factor receptor (EGFR), commonly used to treat patients with metastatic colorectal cancer (mCRC). Unfortunately, objective remissions occur only in a minority of patients and are of short duration, with a population of cells surviving the treatment and eventually enabling CTX resistance. Our previous study on CRC xenopatients associated poor response to CTX with increased abundance of a set of pro-inflammatory cytokines, including the interleukins IL-1A, IL-1B and IL-8. Stemming from these observations, our current work aimed to assess the role of IL-1 pathway activity in CTX resistance. We employed a recombinant decoy TRAP IL-1, a soluble protein combining the human immunoglobulin Fc portion linked to the extracellular region of the IL-1-receptor (IL-1R1), able to sequester IL-1 directly from the medium. We generated stable clones expressing and secreting a functional TRAP IL-1 into the culture medium. Our results show that IL-1R1 inhibition leads to a decreased cell proliferation and a dampened MAPK and AKT axes. Moreover, CRC patients not responding to CTX blockage displayed higher levels of IL-1R1 than responsive subjects, and abundant IL-1R1 is predictive of survival in patient datasets specifically for the consensus molecular subtype 1 (CMS1). We conclude that IL-1R1 abundance may represent a therapeutic marker for patients who become refractory to monoclonal antibody therapy, while inhibition of IL-1R1 by TRAP IL-1 may offer a novel therapeutic strategy.