gebhart/patrepeval huggingface dataset:
Kinetic models for phycocyanin production by high cell density mixotrophic culture of the microalga Spirulina platensis (1998)

Phycocyanin production by high cell density cultivation of Spirulina platensis in batch and fed-batch modes in 3.7-L bioreactors with a programmed stepwise increase in light intensity program was investigated. The results showed that the cell density in fed-batch culture (10.2 g L -1 ) was 4.29-fold that in batch culture (2.38 g L -1 ), and the total phycocyanin production in the fed-batch culture (0.795 g L -1 ) was 3.05-fold that in the batch culture (0. An unstructured kinetic model to describe the microalga culture system including cell growth, phycocyanin formation, as well as glucose consumption was proposed. The data fitted the models well (r 2 0.99). Furthermore, based on the kinetic models, the potential effects of light limitation and photoinhibition on cell growth and phycocyanin formation can be examined in depth. The models demonstrated that the optimal light intensity for mixotrophic growth of Spirulina platensis in batch or fed-batch cultures using a 3.7-L bioreactor was 80160 E m -2 s -1 , and the stepwise increase in light intensity can be replaced by a constant light intensity mode.
Natural CD4+ CD25+ regulatory T cells. Their role in the control of superantigen responses (2001)

CD4 regulatory T cells have a major role in controlling the immune response to self and foreign antigens. Natural CD4+ CD25+ T cells are a major component of the regulatory subset. Their absence is associated with the development of autoimmune and inflammatory diseases and with abnormal peripheral T-cell homeostasis. Two main characteristics discriminate natural CD4+ CD25+ T cells from their CD4+ CD25- counterparts, namely their cytokine production profile and their behavior during tolerance induction. Natural CD4+ CD25+ T cells produce interleukin (IL)-10, a cytokine that contributes to their regulatory role. They do not produce IL-2 and are dependent on exogenous IL-2 for proliferation in vitro and in vivo. Studies of their response to superantigen administration in vivo show that they are resistant to clonal deletion but can be tolerized by anergy. Their resistance to apoptosis may contribute to their continuous regulatory function, as it allows them to maintain permanent control over effector T cells.
Granulocyte colony-stimulating factor gene transfer suppresses tumorigenicity of a murine adenocarcinoma in vivo. (1991)

We have investigated the effect of granulocyte colony-stimulating factor (G-CSF) delivery at the site of tumor growth by transducing, via retroviral vector, the human (hu) G-CSF gene into the colon adenocarcinoma C-26 and assaying the ability of transduced cells to form tumors when injected into syngeneic mice. As a control, the same tumor cells were infected with retroviruses engineered to transduce an unrelated gene, the human nerve growth factor receptor, or carry the neomycin resistance gene only. Only cells transduced with the huG-CSF were unable to develop tumors, although huG-CSF was expressed and produced at low level as estimated by both RNA analysis and enzyme-linked immunosorbent assay, indicating that G-CSF can exert an antitumor effect at a physiological dose. Implication of G-CSF as mediator of tumor inhibition was proven by reversing the nontumorigenic phenotype of G-CSF-expressing cells with anti-huG-CSF monoclonal antibody injected at the tumor site. No tumors were formed by injecting C-26 infected cells into nu/nu mice, while neoplastic nodules appeared after injection into sublethally irradiated mice; such tumors, however, regressed when mice normalized their leukocyte counts after irradiation. Tumors were also formed after injection of a mixture of infected and uninfected C-26 cells, although critical delay in tumor formation occurred when infected cells were 10 times more represented in the mixture. Histological examination of tissues surrounding the site of injection showed infiltration of neutrophilic granulocytes, whose number correlated with that of G-CSF-expressing C-26 cells in the injected mixture. These results indicate that G-CSF may have a potent antitumoral activity when released, even at low doses, at the tumor site. The antitumoral effect is mediated by recruitment and targeting of neutrophilic granulocytes to G-CSF-releasing cells.
Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus (2008)

Members of Norovirus, a genus in the family Caliciviridae, are causative agents of epidemic diarrhea in humans. Susceptibility to several noroviruses is linked to human histo-blood type, and its determinant histo-blood group antigens (HBGAs) are regarded as receptors for these viruses. Specificity for these carbohydrates is strain-dependent. Norwalk virus (NV) is the prototype genogroup I norovirus that specifically recognizes A- and H-type HBGA, in contrast to genogroup II noroviruses that exhibit a more diverse HBGA binding pattern. To understand the structural basis for how HBGAs interact with the NV capsid protein, and how the specificity is achieved, we carried out x-ray crystallographic analysis of the capsid protein domain by itself and in complex with A- and H-type HBGA at a resolution of approximately 1.4 A. Despite differences in their carbohydrate sequence and linkage, both HBGAs bind to the same surface-exposed site in the capsid protein and project outward from the capsid surface, substantiating their possible role in initiating cell attachment. Precisely juxtaposed polar side chains that engage the sugar hydroxyls in a cooperative hydrogen bonding and a His/Trp pair involved in a cation-pi interaction contribute to selective and specific recognition of A- and H-type HBGAs. This unique binding epitope, confirmed by mutational analysis, is highly conserved, but only in the genogroup I noroviruses, suggesting that a mechanism by which noroviruses infect broader human populations is by evolving different sites with altered HBGA specificities.
Spatial and temporal correlation of the interference in ALOHA ad hoc networks (2009)

Interference is a main limiting factor of the performance of a wireless ad hoc network. The temporal and the spatial correlation of the interference makes the outages correlated temporally (important for retransmissions) and spatially correlated (important for routing). In this letter we quantify the temporal and spatial correlation of the interference in a wireless ad hoc network whose nodes are distributed as a Poisson point process on the plane when ALOHA is used as the multiple-access scheme.
Factors influencing in vivo transduction by recombinant adeno-associated viral vectors expressing the human factor IX cDNA (2001)

Long-term expression of coagulation factor IX (FIX) has been observed in murine and canine models following administration of recombinant adeno-associated viral (rAAV) vectors into either the portal vein or muscle. These studies were designed to evaluate factors that influence rAAV-mediated FIX expression. Stable and persistent human FIX (hFIX) expression (> 22 weeks) was observed from 4 vectors after injection into the portal circulation of immunodeficient mice. The level of expression was dependent on promoter with the highest expression, 10% of physiologic levels, observed with a vector containing the cytomegalovirus (CMV) enhancer/beta-actin promoter complex (CAGG). The kinetics of expression after injection of vector particles into muscle, tail vein, or portal vein were similar with hFIX detectable at 2 weeks and reaching a plateau by 8 weeks. For a given dose, intraportal administration of rAAV CAGG-FIX resulted in a 1.5-fold or 4-fold higher level of hFIX compared to tail vein or intramuscular injections, respectively. Polymerase chain reaction analysis demonstrated predominant localization of the rAAV FIX genome in liver and spleen after tail vein injection with a higher proportion in liver after portal vein injection. Therapeutic levels of hFIX were detected in the majority of immunocompetent mice (21 of 22) following intravenous administration of rAAV vector without the development of anti-hFIX antibodies, but hFIX was not detected in 14 immunocompetent mice following intramuscular administration, irrespective of strain. Instead, neutralizing anti-hFIX antibodies were detected in all the mice. These observations may have important implications for hemophilia B gene therapy with rAAV vectors.
Inverse electron demand Diels–Alder reactions in chemical biology (2017)

The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
Using Bicellar Mixtures To Form Supported and Suspended Lipid Bilayers on Silicon Chips (2006)

Bicellar mixtures, planar lipid bilayer assemblies comprising long- and short-chain phosphatidylcholine lipids in suspension, were used to form supported lipid bilayers on flat silicon substrate and on nanotextured silicon substrates containing arrays of parallel troughs (170 nm wide, 380 nm deep, and 300 nm apart). Confocal fluorescence and atomic force microscopies were used to characterize the resulting lipid bilayer. Formation of a continuous biphasic undulating lipid bilayer membrane, where the crests and troughs corresponded to supported and suspended lipid bilayer regions, is demonstrated. The use of interferometric lithography to fabricate nanotexured substrates provides an advantage over other nanotextured substrates such as nanoporous alumina by offering flexibility in designing different geometries for suspending lipid bilayers.
Evidence that glucokinase regulatory protein is expressed  and interacts with glucokinase in rat brain (2001)

Our previous description of functional glucokinase isoforms in the rat brain has opened new questions concerning the presence of glucokinase regulatory protein in the brain and the functional role of its interactions with glucokinase. In this study, we found glucokinase regulatory protein mRNA in rat brain, pancreatic islets and liver. In addition, we found two other variant splicing isoforms, both identified in hypothalamus, pancreatic islets and liver. In situ hybridization studies revealed the presence of glucokinase regulatory protein mRNA, the highest number of positive cells being found in the paraventricular nucleus of the hypothalamus. Glucokinase regulatory protein gene expression gave rise to a protein of 69 kDa mainly in nuclear and soluble cell fractions. Glutathione S-transferase protein fused either to rat liver or human pancreatic islet glucokinase were able to precipitate glucokinase regulatory protein from liver or hypothalamic extracts in the presence of fructose-6-phosphate, the amount of protein co-precipitated being decreased with fructose-1-phosphate. These findings suggest that the presence of glucokinase and glucokinase regulatory protein in the rat brain would facilitate the adaptation of this organ to fluctuations in blood glucose concentrations, and both proteins may participate in glucose-sensing and metabolic regulation in the central nervous system.
Extensive Genome-wide Linkage Disequilibrium in Cattle (2000)

A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population. LD was measured between all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounced for closely linked marker pairs, extended over several tens of centimorgan. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies of the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long range disequilibrium between syntenic loci using low-density marker maps indicates that LD mapping has the potential to be very effective in livestock populations. The frequent occurrence of gametic associations between nonsyntenic loci, however, encourages the combined use of linkage and linkage disequilibrium methods to avoid false positive results when mapping genes in livestock.
Induction of endogenous human cytomegalovirus gene expression after differentiation of monocytes from healthy carriers (1994)

Monocytes are one site of carriage of the human cytomegalovirus (HCMV) genome in healthy human carriers. However, as there are conflicting data detailing the level of HCMV gene expression during persistence in these cells, we have analyzed monocytes for evidence of viral immediate-early, early, and late transcription by using reverse transcription followed by PCR. We were unable to find evidence of HCMV lytic gene transcription in freshly isolated peripheral blood monocytes from HCMV-seropositive subjects. However, as differentiation of monocytes to monocyte-derived macrophages results in increased permissiveness to infection with HCMV in vitro, we examined whether such differentiation could result in reactivation of endogenous viral gene expression. Here we show that in vitro differentiation of monocytes does result in expression of endogenous HCMV immediate-early genes. Although this differentiation led to reactivation of endogenous viral immediate-early expression, we were unable to detect any early or late viral transcription. Cocultivation experiments correlated with this level of gene induction, as no productive infection was detected. These data strongly suggest a mechanism of persistence of HCMV in the peripheral blood that is independent of HCMV lytic gene expression and that initial phases of lytic gene expression in monocytes can be induced by differentiation of these cells to monocyte-derived macrophages.
‘Laterally aggregated’ polyacrylamide gels for electrophoresis (1992)

A new method is described for producing highly porous polyacrylamide matrices: polymerization in presence of a preformed hydrophilic polymer. If a standard mixture of monomers (e.g., 5%T, 4%C) is polymerized in presence of, e.g., polyethylene glycol (PEG) 10 kDa, lateral chain aggregation occurs, with formation of large pore sizes. In PEG 10 kDa, the transition from a small- to a large-pore gel is clearly apparent at 0.5% PEG addition and reaches a plateau already at 2.5% PEG. Even with shorter PEG fragments (6.2 and 1 kDa) this transition occurs, but with progressively larger amounts of PEG in solution (up to 25% for the 1 kDa species). Other polymers such as hydroxymethyl cellulose (1000 kDa) and polyvinyl-pyrrolidone (360 kDa and 25 kDa) are also able to elicit this phenomenon. It appears that lateral chain aggregation (before the cross-linking event) is induced via intra-chain hydrogen bonding, since urea and temperature strongly inhibit it, whereas tetramethylurea (an agent quenching hydrophobic interactions) does not hamper it. By scanning electron microscope, it is found that the maximum pore size obtained in a 5%T, 4%C gel in presence of 2.5% PEG 10 kDA is of the order of 0.5 micron, whereas the same 5%T, 4%C control gel would have an average pore diameter of 5 nm. Thus, an increment of pore size of about 2 orders of magnitude is obtained: in these new matrices, a 21000 bp DNA fragment exhibits a much greater migration than in a control gel in which the sample is entrapped at the application site.
Plasmonic efficiencies of nanoparticles made of metal nitrides (TiN, ZrN) compared with gold (2016)

Abstract Metal nitrides have been proposed to replace noble metals in plasmonics for some specific applications. In particular, while titanium nitride (TiN) and zirconium nitride (ZrN) possess localized plasmon resonances very similar to gold in magnitude and wavelength, they benefit from a much higher sustainability to temperature. For this reason, they are foreseen as ideal candidates for applications in nanoplasmonics that require high material temperature under operation, such as heat assisted magnetic recording (HAMR) or thermophotovoltaics. This article presents a detailed investigation of the plasmonic properties of TiN and ZrN nanoparticles in comparison with gold nanoparticles, as a function of the nanoparticle morphology. As a main result, metal nitrides are shown to be poor near-field enhancers compared to gold, no matter the nanoparticle morphology and wavelength. The best efficiencies of metal nitrides as compared to gold in term of near-field enhancement are obtained for small and spherical nanoparticles, and they do not exceed 60%. Nanoparticle enlargements or asymmetries are detrimental. These results mitigate the utility of metal nitrides for high-temperature applications such as HAMR, despite their high temperature sustainability. Nevertheless, at resonance, metal nitrides behave as efficient nanosources of heat and could be relevant for applications in thermoplasmonics, where heat generation is not detrimental but desired.
Determination of body burden of uremic toxins. (1984)

The body burden of two uremic toxins, di- and trimethylamines, was determined in eight chronic renal failure patients, who received a renal transplant with immediate good function. The "pools" of these amines were calculated on the basis of serum concentration just prior to vascular anastomosis being established and compared to measured amines excreted over a period of five days following transplantation. The amount of DMA and TMA present intra-cellularly in eight muscle samples obtained from these patients was also studied. Both the measured to calculated ratios and intracellular to extracellular ratios of these amine concentrations suggests significant intracellular sequestration in end-stage renal disease. The possible effect on the intracellular milieu is discussed. Serum concentration of these uremic toxins under-estimates the total body burden.
An Official ATS Workshop Summary: Recent Advances and Future Directions in Pneumocystis Pneumonia (PCP) (2006)

Pneumocystis pneumonia (PCP) is a major cause of morbidity and mortality among immunocompromised persons, and it remains a leading acquired immune deficiency syndrome (AIDS)-defining opportunistic infection in human immunodeficiency virus (HIV)-infected individuals throughout the world. Pneumocystis has proven difficult to study, in part due to the lack of a reliable culture system for the organism. With the development of molecular techniques, significant advances in our understanding of the organism and the disease have been made over the past several years. These advances include an improved understanding of host-organism interactions and host defense, the development of noninvasive polymerase chain reaction (PCR)-based diagnostic assays, and the emerging data regarding the possible development of trimethoprim-sulfamethoxazole-resistant Pneumocystis. In addition, the recognition that patients without PCP may nevertheless be carriers of or colonized with Pneumocystis, and observations that suggest a role for Pneumocystis in the progression of pulmonary disease, combine to signal the need for a comprehensive and accessible review. In May 2005, the American Thoracic Society sponsored a one-day workshop, "Recent Advances and Future Directions in Pneumocystis Pneumonia (PCP)," which brought together 45 Pneumocystis researchers. The workshop included 21 presentations on diverse topics, which are summarized in this report. The workshop participants identified priorities for future research, which are summarized in this document.
Graphene oxide membranes with tunable permeability due to embedded carbon dots (2014)

In this communication, we fabricated graphene oxide membranes with tunable permeation by embedding carbon nanodots of controllable sizes.
Nanoscratch tester for thin film mechanical properties characterization (2000)

Quantitative instrumentation has become a necessity for adequate evaluation of material properties, particularly scratch resistance and adhesion at the film-substrate interface. The nanoscratch tester is a new instrument that combines the features of both the classical stylus scratch test (normal force range) and the scanning force microscope (SFM) (short sliding distances), allowing scratch lengths of up to 10 mm. Tangential force and penetration depth are measured during the scratching process. For high-resolution inspection of the scratched area, a SFM is integrated into the system. Typical uses are presented for a range of applications, particularly on curved sample geometries and the use of scratch mapping.
Tissue-Specific Induction of E-Selectin in Glomeruli Is Augmented following Diabetes mellitus (2001)

We recently demonstrated that induction of adhesion molecules is tissue, cell type, and blood vessel size specific. We examined here whether the glomeruli, a peculiar vascular system, express adhesion molecules in a specific manner in the murine kidney. In addition, since serum levels of soluble adhesion molecules have been reported to be elevated in diabetic patients, we examined the influence of diabetes mellitus on the induction of adhesion molecules in the kidney. Analysis of E-selectin mRNA expression by in situ hybridization indicated that it was selectively induced in glomeruli by intravenous administration of interleukin-1beta, while ICAM-1 mRNA expression was seen diffusely in endothelium lining the small arteries and capillaries or in glomeruli, and VCAM-1 mRNA expression was most prominent in endothelial cells of larger blood vessels. Induction of E-selectin mRNA expression in glomeruli by proinflammatory stimuli was augmented in streptozotocin-induced diabetic mice as compared with control mice, while ICAM-1 or VCAM-1 mRNA induction was only slightly influenced. Furthermore, immunohistochemical analysis showed that selective expression of E-selectin in glomeruli was augmented predominantly in epithelial cells, depending on the duration of diabetes mellitus, in KK-Ay mice. These findings suggest that glomerulus-specific expression of E-selectin is related to the development of diabetic nephropathy.