gebhart/patrepeval huggingface dataset:
Side Population Cells Isolated from Porcine Dental Pulp Tissue with Self‐Renewal and Multipotency for Dentinogenesis, Chondrogenesis, Adipogenesis, and Neurogenesis (2006)

Dental pulp has the potential to form dentin as a regenerative response to caries. This regeneration is mediated by stem/progenitor cells. Thus, stem cell therapy might be of potential utility in induction of reparative dentin. We isolated side population (SP) cells from dental pulp based on the exclusion of the DNA binding dye Hoechst 33342 by flow cytometry and compared its self-renewal capacities and multipotency with non-SP cells and primary pulp cells. The cumulative cell number of the SP cells was greater than the non-SP cells and primary pulp cells. Bmi1 was continuously expressed in SP cells, suggesting longer proliferative lifespan and self-renewal capacity of SP cells. Next, the maintenance of the multilineage differentiation potential of pulp SP cells was investigated. Expression of type II collagen and aggrecan confirmed chondrogenic conversion (30%) of SP cells. SP cells expressed peroxisome proliferator-activated receptor gamma and adaptor protein 2, showing adipogenic conversion. Expression of mRNA and proteins of neurofilament and neuromodulin confirmed neurogenic conversion (90%). These results demonstrate that pulp SP cells maintain multilineage differentiation potential. We further examined whether bone morphogenetic protein 2 (BMP2) could induce differentiation of pulp SP cells into odontoblasts. BMP2 stimulated the expression of dentin sialophosphoprotein (Dspp) and enamelysin in three-dimensional pellet cultures. Autogenous transplantation of the Bmp2-supplemented SP cells on the amputated pulp stimulated the reparative dentin formation. Thus, adult pulp contains SP cells, which are enriched for stem cell properties and useful for cell therapy with BMP2 for dentin regeneration.
Cystic Fibrosis Pigs Develop Lung Disease and Exhibit Defective Bacterial Eradication at Birth (2010)

Lung disease causes most of the morbidity and mortality in cystic fibrosis (CF). Understanding the pathogenesis of this disease has been hindered, however, by the lack of an animal model with characteristic features of CF. To overcome this problem, we recently generated pigs with mutated CFTR genes. We now report that, within months of birth, CF pigs spontaneously developed hallmark features of CF lung disease, including airway inflammation, remodeling, mucus accumulation, and infection. Their lungs contained multiple bacterial species, suggesting that the lungs of CF pigs have a host defense defect against a wide spectrum of bacteria. In humans, the temporal and causal relations between inflammation and infection have remained uncertain. To investigate these processes, we studied newborn pigs. Their lungs showed no inflammation but were less often sterile than controls. Moreover, after introduction of bacteria into their lungs, pigs with CF failed to eradicate bacteria as effectively as wild-type pigs. These results suggest that impaired bacterial elimination is the pathogenic event that initiates a cascade of inflammation and pathology in CF lungs. Our finding that pigs with CF have a host defense defect against bacteria within hours of birth provides an opportunity to further investigate CF pathogenesis and to test therapeutic and preventive strategies that could be deployed before secondary consequences develop.
Human NK cells at early stages of differentiation produce CXCL8 and express CD161 molecule that functions as an activating receptor (2012)

Human natural killer (NK) cell development is a step-by-step process characterized by phenotypically identified stages. CD161 is a marker informative of the NK cell lineage commitment, whereas CD56, CD117, and CD94/NKG2A contribute to define discrete differentiation stages. In cells undergoing in vitro differentiation from CD34(+) umbilical cord blood (UCB) progenitors, LFA-1 expression allowed to discriminate between immature noncytolytic CD161(+)CD56(+)LFA-1(-) and more differentiated cytolytic CD161(+)CD56(+)LFA-1(+) NK cells. CD161(+)CD56(+)LFA-1(-) NK cells produce large amounts of CXCL8 after phorbol myristate acetate (PMA) or cytokine treatment. Remarkably, CXCL8 mRNA expression was also detected in fresh stage III immature NK cells isolated from tonsils and these cells expressed CXCL8 protein on PMA stimulation. Within in vitro UCB-derived CD161(+)CD56(+)LFA-1(-) NK cells, CXCL8 release was also induced on antibody-mediated cross-linking of NKp44 and CD161. Such unexpected activating function of CD161 was confined to the CD161(+)CD56(+)LFA-1(-) subset, because it did not induce cytokine release or CD107a expression in CD161(+)CD56(+)LFA-1(+) cells or in mature peripheral blood NK cells. Anti-CXCL8 neutralizing antibody induced a partial inhibition of NK cell differentiation, which suggests a regulatory role of CXCL8 during early NK cell differentiation. Altogether, these data provide novel information that may offer clues to optimize NK cell maturation in hematopoietic stem cell transplantation.
Caloric restriction attenuates β‐amyloid neuropathology in a mouse model of Alzheimer's disease (2005)

This study was designed to explore the possibility that caloric restriction (CR) may benefit Alzheimer's disease (AD) by preventing beta-amyloid (Abeta) neuropathology pivotal to the initiation and progression of the disease. We report that a CR dietary regimen prevents Abeta peptides generation and neuritic plaque deposition in the brain of a mouse model of AD neuropathology through mechanisms associated with promotion of anti-amyloidogenic alpha-secretase activity. Study findings support existing epidemiological evidence indicating that caloric intake may influence risk for AD and raises the possibility that CR may be used in preventative measures aimed at delaying the onset of AD amyloid neuropathology.
Transient gene expression in HEK293 cells: Peptone addition posttransfection improves recombinant protein synthesis (2005)

Gene expression by large-scale transfection of mammalian cells is becoming an established technology for the fast production of milligram and even gram amounts of recombinant proteins (r-proteins). However, efforts are still needed to optimize production parameters in order to maximize volumetric productivities while maintaining product quality. In this study, transfection efficiency and volumetric productivity following transient gene expression in HEK293 cells were evaluated using green fluorescent protein (GFP) and human placental secreted alkaline phosphatase (SEAP) as reporter genes. We show that a single pulse of peptones (protein hydrolysates) to the cultures performed in a low serum (1%, v/v) and in serum-free medium results in a significant increase in volumetric protein productivity. Sixteen peptones from different sources were tested and almost all of them showed a positive effect on r-protein production. This effect, however, is time- and concentration-dependent. By using Tryptone N1 (a casein peptone, TN1) to feed the cultures at 24 h posttransfection (hpt), a 2-fold increase in volumetric SEAP productivity was obtained 5 days posttransfection. This effect was shown to be equal to that obtained when the culture was fed with a supplementary 4% (v/v) of serum. The positive effect of TN1 on protein production was also demonstrated with Tie2 protein ectodomain produced in serum-free medium. HPLC analysis of amino acids consumption/production during control batch and TN1 pulse culture showed some major differences in amino acid metabolism when using TN1 pulse. Asparagine, glycine, histidine, threonine, leucine, and valine show accumulation in the medium over the cultivation period instead of being consumed as observed in unfed sample (except for asparagine, which remained unchanged). Isoleucine, tyrosine, methionine, and phenylalanine all remained unchanged or slightly fluctuated in TN1-fed culture after the feeding pulse, while they were all steadily consumed in the control run. The relative abundance of SEAP's mRNA suggests that the improvement in protein yield results both from an increase of the translational activity and transcription efficiency. Further understanding of mechanisms by which amino acids/peptides regulate transcriptional and translational machinery in mammalian cells should facilitate the design of new strategies for the improvement of r-protein production by large-scale transfection.
Nanopatterning Biomolecules by Block Copolymer Self-Assembly (2012)

The fabrication of sub-100 nm features with bioactive molecules is a laborious and expensive process. To overcome these limitations, we present a modular strategy to create nanostructured substrates (ca. 25 nm features) using functional block copolymers (BCPs) based on poly(styrene-<i>b</i>-ethylene oxide) to controllably promote or inhibit cell adhesion. A single type of BCP was functionalized with a peptide, a perfluorinated moiety, and both compounds, to tune nanoscale phase separation and interactions with NIH3T3 fibroblast cells. The focal adhesion formation and morphology of the cells were observed to vary dramatically according to the functionality presented on the surface of the synthetic substrate. It is envisioned that these materials will be useful as substrates that mimic the extracellular matrix (ECM) given that the adhesion receptors of cells can recognize clustered motifs as small as 10 nm, and their spatial orientation can influence cellular responses.
Tissue factor initiates glomerular fibrin deposition and promotes major histocompatibility complex class II expression in crescentic glomerulonephritis. (1997)

Increased glomerular tissue factor (TF) expression is associated with glomerular fibrin deposition and renal failure in human and experimental crescentic glomerulonephritis (GN). However, the in vivo functional contribution of TF to the development of glomerular fibrin deposition, crescent formation, and renal failure in GN has not been established. The contribution of TF to fibrin deposition and renal injury was studied in a rabbit model of crescentic GN in which glomerular macrophage infiltration, augmented TF expression, and fibrin deposition are prominent. Administration of anti-TF antibody inhibited glomerular TF activity in nephritic glomeruli by 96%, without affecting macrophage accumulation or systemic indices of coagulation. Anti-TF antibody significantly reduced glomerular fibrin deposition (fibrin scores, 0.43 +/- 0.10 (treated) and 1.40 +/- 0.19 (control); P < 0.0005), crescent formation (0.33 +/- 0.05 (treated) and 1.0 +/- 0.06 (control); P < 0.0005), and development of renal failure (serum creatinine, 168 +/- 22 mumol/l (treated) and 267 +/- 35 mumol/l (control); P < 0.04). This was associated with significant reduction in proteinuria (1189 +/- 277 mg/24 hours (treated) and 2060 +/- 336 mg/24 hours (control); P < 0.03) and expression of MHC class II antigen in glomeruli (1.25 +/- 0.41 (treated) and 2.83 +/- 0.53 (control); P < 0.03) and in tubules and interstitial areas. These data demonstrate that TF is the major in vivo initiator of fibrin deposition in crescentic GN. The reduction in proteinuria and glomerular major histocompatibility class II antigen expression by TF inhibition suggests that TF may also activate other mediators that contribute to glomerular injury.
Analysis of the gluconate (gnt) operon of Bacillus subtilis (1991)

The gluconate (gnt) operon of Bacillus subtilis includes the gntR, gntK, gntP, and gntZ genes, respectively encoding the transcriptional repressor of the operon, gluconate kinase, the gluconate permease, and an unidentified open reading frame (Fujita and Fujita, 1987). We have compared the proteins encoded by the gnt operon of B.subtilis with published sequences and showed that (i) the gluconate repressor is homologous to several putative regulatory proteins in Escherichia coli, (ii) the gluconate kinase of B. subtilis is homologous to xylulose kinase, glycerol kinase and fucose kinase in E. coli (20-26% identity; 12-59 S.D.), (iii) the gluconate permease exhibits a C-terminal domain which is homologous to a hydrophobic protein encoded by an unidentified open reading frame (dsdAp) which precedes the dsdA gene of E. coli (39% identity; 19 S.D.), and (iv) the gntZ gene product is homologous to 6-phosphogluconate dehydrogenases of other bacteria and of animals (48-56%; 82-178 S.D.), thereby suggesting that the B. subtilis gntZ encodes 6-phosphogluconate dehydrogenase. Several conserved regions of the sequenced 6-phosphogluconate dehydrogenases can serve as signature patterns of this protein. Computer analyses have indicated that the previously reported sequences of the porcine and ovine 6-phosphogluconate dehydrogenases, as well as the hypothetical DsdAp protein, are probably erroneous. The probable reasons for the errors are reported along with the proposed revised sequences.
Receptor tyrosine phosphatase beta is expressed in the form of proteoglycan and binds to the extracellular matrix protein tenascin. (1994)

The extracellular domain of receptor type protein tyrosine phosphatase beta (RPTP beta) exhibits striking sequence similarity with a soluble, rat brain chondroitin sulfate proteoglycan (3F8 PG). Immunoprecipitation experiments of cells transfected with RPTP beta expression vector and metabolically labeled with [35S]sulfate and [35S]methionine indicate that the transmembrane form of RPTP beta is indeed a chondroitin sulfate proteoglycan. The 3F8 PG is therefore a variant form composed of the entire extracellular domain of RPTP beta probably generated by alternative RNA splicing. Previous immunohistochemical studies indicated that both RPTP beta and the extracellular matrix protein tenascin are localized in similar regions of the central nervous system. We have performed co-aggregation assays with red and green Co-vaspheres coated with tenascin and 3F8 PG, respectively, showing that the extracellular domain of RPTP beta (3F8 PG) binds specifically to tenascin. The interaction between a receptor tyrosine phosphatase and an extracellular matrix protein may have a role in development of the mammalian central nervous system.
Polyamine-linked oligonucleotides for DNA triple helix formation (1993)

The concept of antigene therapy of disease is based on the ability of an oligonucleotide (the therapeutic agent) to bind to double-stranded genomic DNA (the target associated with the disease). Examples are herein given of the linkage of a series of polyamines to a 21-mer homopyrimidine oligonucleotide. These conjugated 21-mers can each form a triple helix with an appropriate double-stranded homopurine-homopyrimidine DNA according to Hoogsteen base-pairing rules. No triple helix was found when unmodified third strand was used at 10 mM sodium phosphate, pH 6.5, 100 mM sodium chloride solution. In contrast, the spermine-conjugated oligonucleotide had a melting temperature of 42 degrees C. According to the melting profile, the appended spermine moiety was found to affect the Tm only of the triple helix, but not of the subsequent melting of the underlying double helix. The Tm enhancing ability of the spermine-conjugate was found to be better than that of other polyamine-conjugates.
Physicochemical characterization of the thermo-induced self-assembly of thermo-responsive PDMAEMA-b-PDEGMA copolymers (2015)

Diblock copolymers of poly[2-(dimethylamino)ethyl methacrylate]-block-poly[di(ethylene glycol) methyl ether methacrylate], PDMAEMA-b-PDEGMA, were synthesized by reversible addition–fragmentation chain transfer polymerization. The block ratio was varied to study the influence on the lower critical solution temperature and the corresponding phase transition in water. Therefore, turbidimetry, differential scanning calorimetry (DSC), dynamic light scattering (DLS), and laser Doppler velocimetry were applied. Additionally, asymmetric flow field-flow fractionation (AF4) coupled to DLS and multiangle laser light scattering (MALLS) was established as an alternative route to characterize these systems in terms of molar mass of the polymer chain and size of the colloids after the phase transition. It was found that AF4–MALLS allowed accurate determination of molar masses in the studied range. Nevertheless, some limitations were observed, which were critically discussed. The cloud point and phase transition of all materials, as revealed by turbidimetry, could be confirmed by DSC. For block copolymers with block ratios in the range of 50:50, a thermo-induced self-assembly into micellar and vesicular structures with hydrodynamic radii (Rh) of around 25 nm was observed upon heating. At higher temperatures, a reordering of the self-assembled structures could be detected. The thermo-responsive behavior was further investigated in dependence of pH value and ionic strength. Variation of the pH value mainly influences the solubility of the PDMAEMA segment, where a decrease of the pH value increases the transition temperature. An increase of ionic strength leads to a reduction of the cloud point due to the screening of electrostatic interactions. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015, 53, 924–935
50-Gb/s Silicon Optical Modulator (2011)

Optical modulators formed in silicon are the keystone to many low cost optical applications. Increasing the data rate of the modulator benefits the efficiency of channel usage and decreases power consumption per bit of data. Silicon-based modulators which operate via carrier depletion have to the present been demonstrated at data rates up to 40 Gb/s; however, here we present for the first time optical modulation at 50 Gb/s with a 3.1-dB extinction ratio obtained from carrier depletion based phase shifter incorporated in a Mach-Zehnder interferometer. A corresponding optical insertion loss of approximately 7.4 dB is measured.
Development and evaluation of AS03, an Adjuvant System containing α-tocopherol and squalene in an oil-in-water emulsion (2012)

AS03 is an Adjuvant System composed of α-tocopherol, squalene and polysorbate 80 in an oil-in-water emulsion. In various nonclinical and clinical studies, high levels of antigen-specific antibodies were obtained after administration of an AS03-adjuvanted vaccine, permitting antigen-sparing strategies. AS03 has been shown to enhance the vaccine antigen-specific adaptive response by activating the innate immune system locally and by increasing antigen uptake and presentation in draining lymph nodes, a process that is modulated by the presence of α-tocopherol in AS03. In nonclinical models of the AS03-adjuvanted prepandemic H5N1 influenza vaccine, increased levels of anti-influenza antibody afforded protection against disease and against virus replication of influenza strains homologous and heterologous to the vaccine strain. By incorporating AS03 in the pandemic H1N1/2009 vaccine, vaccine immunogenicity was increased compared with nonadjuvanted H1N1 vaccines. High H1N1/2009/AS03 vaccine effectiveness was demonstrated in several assessments in multiple populations. Altogether, the nonclinical and clinical data illustrate the ability of AS03 to induce superior adaptive responses against the vaccine antigen, principally in terms of antibody levels and immune memory. In general, these results support the concept of Adjuvant Systems as a plausible approach to develop new effective vaccines.
Functional analysis of the interaction of the antigen-specific T cell receptor with its ligands. (1986)

Increasing the number of antigen-specific T cell clones in a T cell proliferation assay resulted in a shift in the antigen dose-response curves toward higher amounts of antigen (i.e., more antigen was required to achieve a given degree of stimulation). The antigen dose-response curve shifts were found to reflect the competition that occurred between the antigen-specific T cell receptors for their ligand, a combination of antigen and Ia molecule. This observation made it possible to determine whether the difference in the potency with which several synthetic cytochrome c analogs could stimulate one cytochrome c-specific T cell clone was due to a difference in the avidity of the antigen-specific receptors on the T cell clone for the different Ia molecule-antigen combinations. It was demonstrated that a single amino acid substitution at position 103 (which greatly diminished the potency of the analog) did not significantly alter the avidity of the T cell antigen-specific receptor for its ligand. In contrast, a substitution at position 99 (which resulted in a comparable decrease in potency) caused a dramatic loss of avidity. These results are consistent with the previous designation of residue 99 as one site on the antigen that contacts the T cell antigen-specific receptor, and of residue 103 as one part of the antigen that contacts the Ia molecule.
New floating-gate AlGaAs/GaAs memory devices with graded-gap electron injector and long retention times (1988)

AlGaAs/GaAs floating-gate memory devices are reported. Compared with conventional Si-based floating-gate device this structure operates on a different injection method. Electrons are injected from the control gate into the floating gate using AlGaAs graded-gap barrier. This has the advantage of significantly smaller WRITE voltages. Charge retention times ranging from 2 s at 300 K to 4 h at 140 K have been measured. The extrapolated storage time at 77 K is approximately 700 years. From a functional point of view, these electrically alterable read-only memory (EAROM) structures are promising also for dynamic random-access memory (DRAM) or static random-access memory (SRAM) applications depending on the operating temperatures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bacterial adhesion and biofilms on surfaces (2008)

Bacterial adhesion has become a significant problem in industry and in the domicile, and much research has been done for deeper understanding of the processes involved. A generic biological model of bacterial adhesion and population growth called the bacterial biofilm growth cycle, has been described and modified many times. The biofilm growth cycle encompasses bacterial adhesion at all levels, starting with the initial physical attraction of bacteria to a substrate, and ending with the eventual liberation of cell clusters from the biofilm matrix. When describing bacterial adhesion one is simply describing one or more stages of biofilm development, neglecting the fact that the population may not reach maturity. This article provides an overview of bacterial adhesion, cites examples of how bacterial adhesion affects industry and summarises methods and instrumentation used to improve our understanding of the adhesive properties of bacteria.
Analgesic Effects of Vibration and Transcutaneous Electrical Nerve Stimulation Applied Separately and Simultaneously to Patients with Chronic Pain (1991)

The analgesic effects of transcutaneous electrical nerve stimulation (TENS) and vibratory stimulation (VS), used both separately and simultaneously, were compared in 24 patients suffering from chronic pain. We tested the hypothesis that these combined procedures might improve the pain reducing effects obtained with a single type of stimulation, since they make it possible to recruit a larger number of large diameter afferents and/or to increase the discharge frequencies. Four 35-minute treatment sessions (VS, TENS, VS + TENS, Sham stimulation) were run with each patient. The vibrations (100 Hz) and TENS (100 Hz) were applied to the surface of the painful region. The sham stimulation treatment consisted of positioning the TENS electrodes without actually delivering any current. The short form of the McGill pain questionnaire was used to assess the subjects' pain levels. The assessments took place immediately after any treatment (0h.), and again 4 hours and 24 hours later. The results showed that dual stimulation not only alleviated pain in more cases than either VS or TENS alone, but also had stronger and more long-lasting analgesic effects. On the other hand, all three types of stimulation used produced stronger analgesic effects than those obtained with the sham stimulation.