gebhart/patrepeval huggingface dataset:
Paper-Based Sensors: Emerging Themes and Applications (2018)

Paper is a versatile, flexible, porous, and eco-friendly substrate that is utilized in the fabrication of low-cost devices and biosensors for rapid detection of analytes of interest. Paper-based sensors provide affordable platforms for simple, accurate, and rapid detection of diseases, in addition to monitoring food quality, environmental and sun exposure, and detection of pathogens. Paper-based devices provide an inexpensive technology for fabrication of simple and portable diagnostic systems that can be immensely useful in resource-limited settings, such as in developing countries or austere environments, where fully-equipped facilities and highly trained medical staff are absent. In this work, we present the different types of paper that are currently utilized in fabrication of paper-based sensors, and common fabrication techniques ranging from wax printing to origami- and kirigami-based approaches. In addition, we present different detection techniques that are employed in paper-based sensors such as colorimetric, electrochemical, and fluorescence detection, chemiluminescence, and electrochemiluminescence, as well as their applications including disease diagnostics, cell cultures, monitoring sun exposure, and analysis of environmental reagents including pollutants. Furthermore, main advantages and disadvantages of different types of paper and future trends for paper-based sensors are discussed.
Catalytic Hydrothermal Conversion of Triglycerides to Non-ester Biofuels (2010)

This paper describes a catalytic hydrothermolysis (CH) process aimed at converting triglycerides to non-ester biofuels. The CH conversion was carried out at temperatures ranging from 450 to 475 °C and a pressure of 210 bar in the presence of water with and without a catalyst. The organic phase (biocrude) from the CH process underwent post-treatment involving decarboxylation and hydrotreating. Results derived from soybean oil, jatropha oil, and tung oil show that certain biofuel fractions met JP-8 specifications and Navy distillate specifications. One of the CH biofuel characteristics is their high levels of cyclics and aromatics. Tung-oil-based biofuels derived from the CH process contain up to 60% aromatics, which can be a desirable ingredient for fuel blends involving biofuels derived from other processes or feedstocks. Results from these crop oils also suggest that the CH process can be adapted to a variety of other triglyceride feedstocks.
Dynamic headspace enrichment/reinjection for open tubular GC/FTIR analysis of volatiles in polymers (1988)

Abstract An analytical system for the analysis of volatiles entrained in polymers is described. This system is based on a thermal desorption oven connected to a cold trap. After enrichment of headspace vapor, trapped material is reinjected and analyzed by open tubular gas chromatography/Fourier transform infrared spectroscopy, OTGC/FTIR. The thermal desorption oven is designed to provide different modes of sample introduction: use of a pyroprobe; insertion of a piece of quartz tubing with applied sample; or syringe injection. Headspace enrichment is carried out in a piece of fused silica capillary tubing filled with glass beads. The trap may be cooled either electrically using Peltier elements or with liquid nitrogen. A six‐port rotary valve is used for flow switching between enrichment and reinjection modes. All system parameters, temperatures, and timed events, are controlled from the gas chromatograph. Dynamic headspace analysis is demonstrated as a method for polymer characterization.
Theta-Glass Capillaries in Electrospray Ionization: Rapid Mixing and Short Droplet Lifetimes (2014)

Double-barrel wire-in-a-capillary electrospray emitters prepared from theta-glass capillaries were used to mix solutions during the electrospray process. The relative flow rate of each barrel was continuously monitored with internal standards. The complexation reaction of 18-crown-6 and K(+), introduced from opposite barrels, reaches equilibrium during the electrospray process, suggesting that complete mixing also occurs. A simplified diffusion model suggests that mixing occurs in less than a millisecond, and contributions of turbulence, estimated from times of coalescing ballistic microdroplets, suggest that complete mixing occurs within a few microseconds. This mixing time is 2 orders of magnitude less than in any mixer previously coupled to a mass spectrometer. The reduction of 2,6-dichloroindophenol by l-ascorbic acid was performed using the theta-glass emitters and monitored using mass spectrometry. On the basis of the rate constant of this reaction in bulk solution, an apparent reaction time of 274 ± 60 μs was obtained. This reaction time is an upper limit to the droplet lifetime because the surface area to volume ratio and the concentration of reagents increase as the droplet evaporates and some product formation occurs in the Taylor cone prior to droplet formation. On the basis of increases in reaction rates measured by others in droplets compared to rates in bulk solution, the true droplet lifetime is likely 1-3 orders of magnitude less than the upper limit, i.e., between 27 μs and 270 ns. The rapid mixing and short droplet lifetime achieved in these experiments should enable the monitoring of many different fast reactions using mass spectrometry.
Calcific Uremic Arteriolopathy in Peritoneal Dialysis Populations (2011)

Calciphylaxis or calcific uremic arteriolopathy is an infrequent complication of end stage kidney disease. It is characterized by arteriolar medial calcification, thrombotic cutaneous ischemia, tissue necrosis often leading to ulceration, secondary infection and increased mortality rates. Current, multimodality treatment involves local wound care, well-controlled calcium, phosphate and parathyroid hormone levels and combination therapy with sodium thiosulfate and hyperbaric oxygen therapy. This combination therapy may be changing the historically poor prognosis of calcific uremic arteriolopathy reported in the literature. Peritoneal dialysis is considered a risk factor based on limited publications, however this remains to be proven. Clinical presentation, diagnosis, pathogenesis and treatment of calcific uremic arteriolopathy in these patients are no different from other patients manifesting with this condition.
Collagen Fiber Diameter in the Rabbit Cornea After Collagen Crosslinking by Riboflavin/UVA (2004)

Collagen crosslinking using riboflavin and UVA leads to a significant increase in corneal collagen diameter. This alteration is the morphologic correlate of the crosslinking process leading to an increase in biomechanical stability. The crosslinking effect is strongest in the anterior half of the stroma because of the rapid decrease in UVA irradiance across the corneal stroma as a result of riboflavin-enhanced UVA absorption.
Deletion analysis identifies a region, upstream of the ADH2 gene of Saccharomyces cerevisiae, which is required for ADR1-mediated derepression. (1985)

Deletion analysis was used to identify sequences upstream of the ADH2 gene of Saccharomyces cerevisiae that are required for its regulation. 5' and 3' internal deletions of the ADH2 control region were created in vitro, and the fragments were ligated adjacent to the ADH1 promoter and structural gene. Hybrid genes with 3' deletions extending from -119 to -216 (the start site of ADH2 transcription is designated +1) were fully repressed and derepressed to high levels. Hybrid genes with 3' deletions extending from -119 to -257 were repressed but failed to significantly derepress. Hybrid genes lacking the -216 to -257 region also failed to respond to ADR1-5c, a mutant allele of the unlinked regulatory gene ADR1, which confers constitutive expression on ADH2. This implies that the region between these deletion endpoints, which includes a 22-base-pair sequence of dyad symmetry, is required for efficient derepression of an adjacent promoter. Internal deletions extending in the 3' direction from position -1141 confirmed these results. Deletion mutants lacking the region -1141 to -259 were normally regulated, whereas deletions extending from -1141 to -115 were not derepressible. These results support the hypotheses that the ADH2 promoter may normally be in an inactive conformation in the yeast chromosome and that derepression of ADH2 requires positive activation mediated through an upstream activation sequence located between 216 and 257 base pairs 5' to the start site of ADH2 transcription. No evidence for a DNA sequence mediating repression was obtained.
VEGF is an essential mediator of the neurogenic and behavioral actions of antidepressants (2007)

The neural mechanisms underlying the cellular and behavioral responses to antidepressants are not yet known. Up-regulation of growth factors and adult neurogenesis suggest a role for one or more of these factors in the action of antidepressants. One candidate of interest is vascular endothelial growth factor (VEGF), which was initially characterized for its role in angiogenesis, but also exerts direct mitogenic effects on neural progenitors in vitro. Results of this study demonstrate that VEGF is induced by multiple classes of antidepressants at time points consistent with the induction of cell proliferation and therapeutic action of these treatments. We find that VEGF signaling through the Flk-1 receptor is required for antidepressant-induced cell proliferation. We also show that VEGF-Flk-1 signaling is required and sufficient for behavioral responses in two chronic and two subchronic antidepressant models. Taken together, these studies identify VEGF and VEGF-Flk-1 signaling as mediators of antidepressant actions and potential targets for therapeutic intervention.
The capsular turnover product of Staphylococcus aureus strain Smith (1994)

The capsular polysaccharide released from the bacterial surface by cell wall turnover during growth exhibited less size heterogeneity and a higher average molecular mass than the polysaccharide extracted from the cell by treatment with lysostaphin or low pH. Treatment of turnover polysaccharide, radiolabelled by growth of the bacteria in the presence of N-acetyl-[3H]-glucosamine, with muramidase B from Chalaropsis released a low molecular weight product chromatographically identical to the peptidoglycan degradation products released from the peptidoglycan-teichoic acid complex by the same treatment. It is concluded that some or all of the capsular polysaccharide released into the culture fluid during growth is derived from peptidoglycan-linked capsular material, solubilised by cell wall turnover.
Escherichia coli Contains a Protein That Is Homologous in Function and N-terminal Sequence to the Protein Encoded by the nifS Gene of Azotobacter vinelandii and That Can Participate in the Synthesis of the Fe-S Cluster of Dihydroxy-acid Dehydratase (1996)

In this paper, I report the purification of a protein from Escherichia coli that is very similar in sequence, molecular weight, and the reactions it can catalyze to the protein encoded by the Azotobacter vinelandii nifS gene. This E. coli protein contains pyridoxal phosphate as a cofactor and catalyzes the removal of sulfur from cysteine to form alanine and S0. When dithiothreitol is present along with cysteine, the S0 formed is reduced to S2-. This protein has a reactive sulfhydryl group that is essential for activity. As isolated, this sulfhydryl group appears to be in a disulfide linkage with the sulfhydryl group from the phosphopantetheine moiety of the acyl carrier protein. The purified E. coli protein can mobilize the sulfur from cysteine and contribute it to the formation of a [4Fe-4S] cluster on the apoprotein of E. coli dihydroxy-acid dehydratase. A mechanism is proposed for the early stages of the synthesis of Fe-S clusters using this protein and sulfur in the S0 oxidation state.
Mathematical descriptions of hybridoma culture kinetics: I. Initial metabolic rates (1988)

The lack of quantitative descriptions of mammalian culture kinetics limits the ability to optimally design and control cell culture bioreactors. This limitation is ad dressed by developing mathematical equations relating the initial growth rate and the antibody productivity of the hybridoma cell line, CRL-1606, to its environmental state. This initial rate approach, in contrast with steady state analysis of chemostat cultures, approximates steady state behavior, since the rates were measured over brief time intervals and at low cell concentrations (< 50,000 cells/mL). The advantage of this approach is that it is much faster than the chemostat approach.An equation for the growth rate was developed that superimposed Monod equations in serum and glutamine with "noncompetitive" -type inhibition constants were inversely proportional to the lactate and ammonium concentrations. The Monod constant is critical for relating initial, low cell level culture states to other states.Lactate was found to be the only environmental parameter that significantly inhibited antifibronectin monoclonal antibody production by the CRL-1606 hybridomas. Volumetric productivity was strictly related to culture viability, which was observed to decline at growth rates below 0.02 h(-1). Lactate was also found to significantly inhibit ammonium production.
Trophectoderm: the first epithelium to develop in the mammalian embryo. (1988)

The first epithelium to appear during mammalian embryogenesis is the trophectoderm, a polarized transporting single cell layer that comprises the wall of the blastocyst. The trophectoderm develops concurrently with blastocoele fluid production as the morula develops into a blastocyst. The process whereby the morula becomes a fluid-filled cyst is called 'cavitation', which can be regarded as the first functional expression of the trophectoderm phenotype. The outer layer of cells of the morula comprise the nascent trophectoderm and are already morphologically polarized prior to the onset of cavitation. A major working hypothesis in the field of mammalian embryogenesis is that such polarization is a prerequisite for the initiation of cavitation. To test this hypothesis we examined morulae for their ability to cavitate during treatments that modify morphological polarity in nascent trophectoderm cells. These treatments included ouabain, different concentrations of extracellular K and Na, cytochalasins and colcemid. Ouabain and extracellular K and Na affect the activity of Na/K-ATPase, which has been implicated in the maintenance of morphological polarity of nascent trophectoderm cells. Cytochalasins and colcemid also modify apical-basal polarity of nascent trophectoderm cells and impair cavitation. The endpoints that were monitored included incidence of cavitation, rate of cavitation and the status of morphological polarity of nascent trophectoderm cells. Collectively, all of these treatments indicate that there is a functional association between an asymmetric distribution of organelles along the apical-basal axis of nascent trophectoderm cells and the ability of the embryo to produce nascent blastocoele fluid efficiently. In addition, the preimplantation embryo appears to possess two mechanisms for accumulating blastocoele fluid.
A review of micropumps (2004)

We survey progress over the past 25 years in the development of microscale devices for pumping fluids. We attempt to provide both a reference for micropump researchers and a resource for those outside the field who wish to identify the best micropump for a particular application. Reciprocating displacement micropumps have been the subject of extensive research in both academia and the private sector and have been produced with a wide range of actuators, valve configurations and materials. Aperiodic displacement micropumps based on mechanisms such as localized phase change have been shown to be suitable for specialized applications. Electroosmotic micropumps exhibit favorable scaling and are promising for a variety of applications requiring high flow rates and pressures. Dynamic micropumps based on electrohydrodynamic and magnetohydrodynamic effects have also been developed. Much progress has been made, but with micropumps suitable for important applications still not available, this remains a fertile area for future research.
Phase II trials of recombinant leukocyte A interferon in disseminated malignant melanoma: results in 96 patients. (1986)

Ninety-six patients with advanced malignant melanoma received thrice weekly im recombinant leukocyte A interferon (Roferon-A) in three consecutive phase II trials utilizing doses of 12 X 10(6) U/m2, 50 X 10(6) U/m2, and 50 X 10(6) U/m2 plus cimetidine. The overall response rate was 22%, with median times to disease progression and survival of 3.9 and 11.3 months, respectively. For all study participants, the median times to disease progression and survival were 1.5 and 5 months, respectively. Most regressions occurred within the first month of treatment and were predominantly in soft tissue, although three patients are responding 2-3 years after onset of treatment. The most noteworthy toxic effects included a flu-type illness, anorexia, and fever (38.3-39.4 degrees C). The median weight loss was 2.1 kg on the low-dose regimen and 5.6 kg on the high-dose program. Recombinant leukocyte A interferon in the dosages and schedule that we used has definite but limited efficacy for patients with disseminated malignant melanoma.
Effect of annealing treatment on electroluminescence from GaN/Si nanoheterostructure array (2012)

A GaN/Si nanoheterostructure array was prepared by growing GaN nanostructures on silicon nanoporous pillar array (Si-NPA). Based on as-grown and annealed GaN/Si-NPA, two light-emitting diodes (LEDs) were fabricated. It was found that after the annealing treatment, both the turn-on voltage and the leakage current density of the nanoheterostructure varied greatly, together with the electroluminescence (EL) changed from a yellow band to a near infrared band. The EL variation was attributed to the radiative transition being transformed from a defect-related recombination in GaN to an interfacial recombination of GaN/Si-NPA. Ours might have provided an effective approach for fabricating GaN/Si-based LEDs with different emission wavelengths.
MRP3, an organic anion transporter able to transport anti-cancer drugs (1999)

The human multidrug-resistance protein (MRP) gene family contains at least six members: MRP1, encoding the multidrug-resistance protein; MRP2 or cMOAT, encoding the canalicular multispecific organic anion transporter; and four homologs, called MRP3, MRP4, MRP5, and MRP6. In this report, we characterize MRP3, the closest homolog of MRP1. Cell lines were retrovirally transduced with MRP3 cDNA, and new monoclonal antibodies specific for MRP3 were generated. We show that MRP3 is an organic anion and multidrug transporter, like the GS-X pumps MRP1 and MRP2. In Madin-Darby canine kidney II cells, MRP3 routes to the basolateral membrane and mediates transport of the organic anion S-(2,4-dinitrophenyl-)glutathione toward the basolateral side of the monolayer. In ovarian carcinoma cells (2008), expression of MRP3 results in low-level resistance to the epipodophyllotoxins etoposide and teniposide. In short-term drug exposure experiments, MRP3 also confers high-level resistance to methotrexate. Neither 2008 cells nor Madin-Darby canine kidney II cells overexpressing MRP3 showed an increase in glutathione export or a decrease in the level of intracellular glutathione, in contrast to cells overexpressing MRP1 or MRP2. We discuss the possible function of MRP3 in (hepatic) physiology and its potential contribution to drug resistance of cancer cells.
CAL-101, a Potent Selective Inhibitor of the p110δ Isoform of Phosphatidylinositol 3-kinase, Attenuates Pathway Signaling, Induces Apoptosis, and Overcomes Signals From the Microenvironment In Cellular Models of Hodgkin Lymphoma (2010)

Abstract Abstract 3926 Phosphatidylinositide 3-kinases (PI3Ks) are a family of lipid kinases that are involved in signaling events which control a diverse number of cellular processes. The class I kinases contain 4 isoforms designated p110α, β, δ, γ, and are activated by cell surface receptors. Aberrant regulation of the PI3K signaling pathway is frequently observed in human malignancies including those of hematological origin. CAL-101 is an oral p110δ-specific inhibitor which has shown preclinical and clinical activity in non-Hodgkin lymphoma (NHL) and chronic lymphocytic leukemia (CLL). This compound is a potent p110δ inhibitor (EC50 of 65 nM in a whole-blood assay) with &gt;200-fold selectivity over the other class I PI3K isoforms and no activity against Class II and III PI3K family members or other PI3K-related proteins, including mTOR and DNA-PK. Prior in vitro NHL studies revealed that CAL-101 induces caspase-dependent apoptosis, and inhibits CD40L-, BAFF-, CXCL12- and CXCL13-derived survival signals in cellular models (Lannutti BJ, et al., Blood 2010). To investigate the potential role of p110δ in Hodgkin lymphoma (HL) we screened a number of HL cell lines for p110δ isoform expression and constitutive PI3K pathway activation. We report high levels of p110δ protein and activated Akt in 5 of 5 HL cell lines evaluated (L428, L540, L591, L1236, KM-H2). Inhibition of p110δ with CAL-101 treatment of cell lines resulted in a reduction of Akt phosphorylation and a decrease in cellular viability. Because previous studies have established the importance of signals from the microenvironment for the survival and proliferation of malignant cells as well as for their resistance to standard therapies, we investigated the effect of p110δ inhibition by CAL-101 in HL cell line-stroma cocultures. In this setting, CAL-101 overcame tumor cell growth induced by coculture of HL cells with bone marrow stromal cells. In addition, CAL-101 induced dose-dependent apoptosis of HL cells at 48 hours. Furthermore, stromal cell coculture resulted in increased CCL5, CCL17, and CCL22 levels; productions of these chemokines by HL cells cultured in the presence of stromal cells were reduced by CAL-101 in a dose-dependent manner. These results indicate that specific inhibition of p110δ may disrupt signals between HL cells and their microenvironment, thereby providing the preclinical rationale for clinical evaluation of CAL-101 as a novel therapeutic approach in patients with Hodgkin lymphoma. Disclosures: Meadows: Calistoga Pharmaceuticals: Employment. Kashishian:Calistoga Pharmaceuticals: Employment. Johnson:Calistoga Pharmaceuticals: Employment. Lannutti:Calistoga Pharmaceutical Inc.: Employment.
Characterization of the Histone Acetyltransferase (HAT) Domain of a Bifunctional Protein with Activable O-GlcNAcase and HAT Activities (2004)

Histones and transcription factors are regulated by a number of post-translational modifications that in turn regulate the transcriptional activity of genes. These modifications occur in large, multisubunit complexes. We have reported previously that mSin3A can recruit O-GlcNAc transferase (OGT) along with histone deacetylase into such a corepressor complex. This physical association allows OGT to act cooperatively with histone deacetylation in gene repression by catalyzing the O-GlcNAc modification on specific transcription factors to inhibit their activity. For rapid, reversible gene regulation, the enzymes responsible for the converse reactions must be present. Here, we report that O-GlcNAcase, which is responsible for the removal of O-GlcNAc additions on nuclear and cytosolic proteins, possesses intrinsic histone acetyltransferase (HAT) activity in vitro. Free as well as reconstituted nucleosomal histones are substrates of this bifunctional enzyme. This protein, now termed NCOAT (nuclear cytoplasmic O-GlcNAcase and acetyltransferase) has a typical HAT domain that has both active and inactive states. This finding demonstrates that NCOAT may be regulated to reduce the state of glycosylation of transcriptional activators while increasing the acetylation of histones to allow for the concerted activation of eukaryotic gene transcription.