gebhart/patrepeval huggingface dataset:
Field Amplified Separation in Capillary Electrophoresis:  A Capillary Electrophoresis Mode (2006)

In field-amplified injection in capillary electrophoresis (CE), the capillary is filled with two buffering zones of different ionic strength; this induces an amplified electrical field in the low ionic strength zone and a lower field in the high ionic strength zone, making sample stacking feasible. The electroosmotic flow (eof) usually observed in CE, however, displaces the low field zone and induces an extra band broadening preventing any CE separation in the field-amplified zone. These limitations have originated the restricted use of field amplification in CE only for stacking purposes. For the first time, in this work it is theoretically shown and experimentally corroborated that CE separation speed and efficiency can simultaneously be increased if the whole separation is performed in the field-amplified zone, using what we have called field amplified separation in capillary electrophoresis (FAsCE). The possibilities of this new CE mode are investigated using a new and simple coating able to provide near-zero eof at the selected separation pH. Using FAsCE, improvements of 20% for separation speed and 40% for efficiency are achieved. Moreover, a modified FAsCE approach is investigated filling the capillary with the high ionic strength buffer up to the interior of the detection window. Under these conditions, an additional 3-fold increase in sensitivity is also observed. The most interesting results were obtained combining the short-end injection mode and this modified FAsCE approach. Under these conditions, a part of a 3-fold improvement in efficiency and sensitivity, the total analysis time was drastically reduced to 40 s, giving rise to a time reduction of more than 7-fold compared to normal CE. This speed enhancement brings about one of the fastest CE separations achieved using capillaries, demonstrating the great possibilities of FAsCE as a new, sensitive, efficient, and fast CE separation mode.
In vivo activation of melanoma-specific CD8+ T cells by endogenous tumor antigen and peptide vaccines. A comparison to virus-specific T cells (2002)

Many new types of vaccines against infectious or malignant diseases are currently being proposed. Careful characterization of the induced immune response is required in assessing their efficiency. While in most studies human tumor antigen-specific T cells are analyzed after in vitro re-stimulation, we investigated these T cells directly ex vivo using fluorescent tetramers. In peripheral blood lymphocytes from untreated melanoma patients with advanced disease, a fraction of tumor antigen (Melan-A/MART-1)-specific T cells were non-naive, thus revealing tumor-driven immune activation. After immunotherapy with synthetic peptides plus adjuvant, we detected tumor antigen-specific T cells that proliferated and differentiated to memory cells in vivo in some melanoma patients. However, these cells did not present the features of effector cells as found in cytomegalovirus specific T cells analyzed in parallel. Thus, peptide plus adjuvant vaccines can lead to activation and expansion of antigen specific CD8(+) T cells in PBL. Differentiation to protective CD8(+) effector cells may, however, require additional vaccine components that stimulate T cells more efficiently, a major challenge for the development of future immunotherapy.
Induction of Apoptosis by the Oolong Tea Polyphenol Theasinensin A through Cytochrome c Release and Activation of Caspase-9 and Caspase-3 in Human U937 Cells (2000)

This study examined the growth inhibitory effects of theasinensin A (from oolong tea) and black tea polyphenols, including theaflavin (TF-1), a mixture (TF-2) of theaflavin-3-gallate (TF-2a) and theaflavin-3'-gallate (TF-2b), and theaflavin-3,3'-digallate (TF-3) in human cancer cells. Theasinensin A, TF-1, and TF-2 displayed strong growth inhibitory effects against human histolytic lymphoma U937, with estimated IC50 values of 12 microM, but were less effective against human acute T cell leukemia Jurkat, whereas TF-3 and (-)-epigallocatechin-3-gallate (EGCG) had lower activities. The molecular mechanisms of tea polyphenol-induced apoptosis as determined by annexin V apoptosis assay, DNA fragmentation, and caspase activation were further investigated. Loss of membrane potential and reactive oxygen species (ROS) generation were also detected by flow cytometry. Treatment with tea polyphenols caused rapid induction of caspase-3, but not caspase-1, activity and stimulated proteolytic cleavage of poly(ADP-ribose) polymerase (PARP). Pretreatment with a potent caspase-3 inhibitor, Z-Asp-Glu-Val-Asp-fluoromethyl ketone, inhibited theasinensin A induced DNA fragmentation. Furthermore, it was found that theasinensin A induced loss of mitochondrial transmembrane potential, elevation of ROS production, release of mitochondrial cytochrome c into the cytosol, and subsequent induction of caspase-9 activity. These results indicate that theasinensin A allows caspase-activated deoxyribonuclease to enter the nucleus and degrade chromosomal DNA and induces DFF-45 (DNA fragmentation factor) degradation. The results suggest that induction of apoptosis by theasinensin A may provide a pivotal mechanism for their cancer chemopreventive function.
The Contribution of Bone Marrow–Derived Cells to the Tumor Vasculature in Neuroblastoma Is Matrix Metalloproteinase-9 Dependent (2005)

The contribution of the tumor stroma to cancer progression has been increasingly recognized. We had previously shown that in human neuroblastoma tumors orthotopically implanted in immunodeficient mice, stromal-derived matrix metalloproteinase-9 (MMP-9) contributes to the formation of a mature vasculature by promoting pericyte recruitment along endothelial cells. Here we show that MMP-9 is predominantly expressed by bone marrow-derived CD45-positive leukocytes. Using a series of bone marrow transplantation experiments in MMP-9(+/+) and MMP-9(-/-) mice xenotransplanted with human neuroblastoma tumors, we show that bone marrow-derived MMP-9 is critical for the recruitment of leukocytes from bone marrow into the tumor stroma and for the integration of bone marrow-derived endothelial cells into the tumor vasculature. Expression of MMP-9 by bone marrow-derived cells in the tumor stroma is also critical for the formation of a mature vasculature and coverage of endothelial cells with pericytes. Furthermore, in primary human neuroblastoma tumor specimens of unfavorable histology, we observed a higher level of tumor infiltration with MMP-9 expressing phagocytic cells and a higher degree of coverage of endothelial cells by pericytes when compared with tumor specimens with a favorable histology. Taken together, the data show that in neuroblastoma, MMP-9 plays a critical role in the recruitment of bone marrow-derived cells to the tumor microenvironment where they positively contribute to angiogenesis and tumor progression.
Clostridium difficile in a pediatric outpatient population (1982)

Clostridium difficile has been implicated as one cause of hospital-acquired diarrhea in children, yet the prevalence of this organism in outpatient children with diarrhea has not been established. Over a 1-year period, 306 outpatient children ranging in age from 2 weeks to 16 years were cultured for C. difficile and potential bacterial pathogens. C. difficile was isolated from 7.0% of patients with diarrhea (12 of 171) and 14.8% of controls with nondiarrheal illnesses (20 of 135). The 32 patients yielding C. difficile were significantly younger than the other study patients. C. difficile was isolated in conjunction with another enteric pathogen in only one case. Antibiotic exposure in the month prior to culture was no different between the 32 positive patients and the overall population. Moreover the patients yielding C. difficile were clinically indistinguishable from the other study patients. C. difficile appears to comprise part of the normal bowel flora in some children beyond the neonatal period and despite a negative history of recent antibiotic usage.
Robust and Efficient Regulation of Transgene Expression in Vivo by Improved Tetracycline-Dependent Lentiviral Vectors (2002)

We developed a panel of lentiviral vectors that displayed tetracycline-regulated transgene expression over two orders of magnitude in bulk, non-selected populations of transduced cells in vitro and in vivo. The robust expression and homogeneous response indicated that most transduced vector genomes were transcription competent and responsive to regulation, providing the lentiviral vector with a novel competitive advantage for gene transfer. After ex vivo transduction and transplantation of cord blood CD34+ cells into NOD/SCID mice, reporter gene expression could be switched "on" and "off" in human hematopoietic cells in vivo for prolonged times, proving integration of the regulated expression system into long-term repopulating cells. By vector injection into established tumor grafts, we achieved efficient delivery and quantitative regulation of transgene expression in vivo. By these approaches, gene function studies can now be performed in in vivo models of human hematopoiesis and cancer. In the future, regulated lentiviral vectors will improve the safety and efficacy of gene therapy.
Polyethyleneimine Functionalized Single-Walled Carbon Nanotubes as a Substrate for Neuronal Growth (2005)

We report the synthesis of a single-walled carbon nanotube (SWNT) graft copolymer. This polymer was prepared by the functionalization of SWNTs with polyethyleneimine (PEI). We used this graft copolymer, SWNT-PEI, as a substrate for cultured neurons and found that it promotes neurite outgrowth and branching.
Organizational Design Trade-Offs at the DRAM, Memory Bus, and Memory Controller Level: Initial Results (1999)

This paper presents initial results in a study of organization level parameters associated with the design of the primary memory system—the DRAM system beneath the lowest level of the cache hierarchy. These parameters are orthogonal to architecture-level parameters such as DRAM core speed, bus arbitration protocol, etc. and include bus width, bus speed, number of independent channels, degree of banking, read burst width, write burst width, etc; this study presents the effective cross-product of varying each of these parameters independently. The simulator is based on SimpleScalar 3.0a and models a fast (simulated as 2GHz), highly aggressive out-of-order uniprocessor. The interface to the primary memory system is fully non-blocking, supporting up to 32 outstanding misses at both the level-1 and level-2 caches. Our simulations show the following: (a) the choice of primary memory-system organization is critical, as it can effect total execution time by a factor of 3x for a constant CPU organization and DRAM speed; (b) the most important factors in the performance of the primary memory system are the channel speed (bus cycle time) and the granularity of data access, the burst width—each of these can independently affect total execution time by a factor of 2x; (c) for small bursts, multiple narrow independent channels to the memory system exhibit better performance than a single wide channel; for large bursts, channel cycle time is the most important factor; (d) the degree of DRAM multi-banking plays a secondary role in its impact on total execution time; (e) the optimal burst width tends to be high (large enough to fetch an L2 cache block in 2 bursts) and scales with the block size of the level 2 cache; and (f) the memory queue sizes can be extremely large, due to the bursty nature of references to the primary memory system and the promotion of reads ahead of writes. Among other things, we conclude that the scheduling of the memory bus is the primary bottleneck and that it should be the focus of further study.
The Effect of Ammonium Salt and Matrix in the Detection of DNA by Matrix-assisted Laser Desorption/Ionization Time-of-flight Mass Spectrometry (1996)

The effect of ammonium salt in the detection of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been systematically investigated using several matrices with ammonium salt additives. The results show that the presence of ammonium salt in the matrix has a beneficial effect on protonation and deprotonation of oligonucleotides in addition to suppressing alkali-ion adducts. These observations indicate that a good matrix for DNA detection could be made from two components; i.e. one component for desorption, which has a relatively large absorption coefficient at the incident laser wavelength, and another component for ionization, which has good protonation and deprotonation ability. Experimental results show that ammonium citrate and ammonium tartrate are good ionization components. Experimental results also indicate that large numbers of chemicals can be used as desorption components. The concept of a two-component matrix system opens many possibilities in the search for a good matrix to be used in the detection of biopolymers. The selection criteria for good matrices in this two-component system are discussed.
Phase II study of dual 131I-labeled monoclonal antibody therapy with interferon in patients with metastatic colorectal cancer. (1996)

The combination of COL-1 (anti-CEA) and CC49 (anti-TAG-72) has shown an increase in binding and distribution in colon cancer by immunoperoxidase staining compared to either antibody alone. To overcome tumor heterogeneity and allow delivery of higher radiation dose, 131I-labeled COL-1 and CC49 at a total dose of 75 mCi/m2 (2775 MBq/m2) were simultaneously administered to 14 patients with metastatic colon cancer. alpha-IFN (3 x 10(6) IU) was given s.c. on days -5 to +3 to increase carcinoembryonic antigen and TAG-72 antigen expression. Most patients had mild symptoms during IFN therapy, including mild neutropenia, fever, and malaise, which rapidly subsided after IFN cessation. No acute allergic reactions occurred with radioimmunotherapy; two patients experienced transient, delayed grade 2 arthralgias. Transient neutropenia and/or thrombocytopenia, which was maximal at 4-6 weeks, were consistent side effects without adverse events. All patients had tumor localization, and 13 of 14 patients achieved 4+ (highest grade) localization readings to at least one known site of disease. No objective responses occurred; 4 patients were stable and 10 progressed. Tumor dose estimates varied from 393 to 1327 cGy, including liver and extrahepatic sites. Combining two complementary antibodies and IFN administration appeared to increase localization intensity and radiation doses at tumor sites as compared to historical controls. The amount of radiation delivered to tumor sites was still below that required to cause tumor regressions in metastatic colorectal cancer.
Distribution of Cell-Free and Cell-Associated HIV Surrogates in the Colon After Simulated Receptive Anal Intercourse in Men Who Have Sex With Men (2011)

Our HIV surrogates stayed within the rectosigmoid colon for 24 hours. Exogenously dosed autologous lymphocytes and HIV-sized particles migrate to similar locations and associate with the colonic tissue in the lumen.
Heat-resistant singlemode optical waveguides using fluorinated polyimides (1993)

Singlemode polymer optical waveguides are fabricated using fluorinated polyimides. The optical waveguides exhibit a low loss of less than 0.3dB/cm parallel to the waveguide plane (TE polarisation) at 1.3μm, and have thermal and moisture stability.
Sodium Butyrate Induces Neuroendocrine Cytodifferentiation in the Insulinoma Cell Line RINm5F (1994)

The differentiating agent sodium butyrate inhibits proliferation and stimulates cell-specific hormone expression in rat insulinoma cells. In this study, we investigated the effect of sodium butyrate on neuroendocrine cytodifferentiation in the rat insulinoma subclone, RINm5F. The cells were cultured with 0.5, 1, or 1.5 mM sodium butyrate for up to 72 h. Ultrastructurally, cells cultured with 1 mM sodium butyrate revealed a more differentiated appearance with an induction of cellular compartments involved in regulated insulin secretion. Morphometric analysis showed a significant elevation of neuroendocrine granule density. The total area of the specific granules was increased after incubation with 1 mM sodium butyrate for 48 and 72 h. Proliferation of RINm5F cells was inhibited by sodium butyrate in a dose-dependent manner. DNA production ceased completely within 24 h at 1.5 mM sodium butyrate. This concentration of sodium butyrate increased the cellular insulin content 8.9-fold and the insulin production 2-fold after 72 h. The insulin release was reduced from 79 +/- 3.5% in controls to 37 +/- 5.6% of total in a 24-h incubation period after 3 days of culture with 1.5 mM sodium butyrate. Insulin mRNA levels increased to a maximum of 324% compared with controls after 48 h of culture with 1.5 mM sodium butyrate. Chromogranin A mRNA levels increased to a similar extent (368 +/- 26%), whereas sodium butyrate did not stimulate the expression of synaptophysin, a major membrane component of small neuroendocrine vesicles. In conclusion, our data suggest the selective induction of neuroendocrine cytodifferentiation by sodium butyrate in RINm5F cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Enzyme replacement therapy for infantile-onset Pompe disease (2017)

The search found no trials comparing the effectiveness and safety of enzyme replacement therapy to another intervention, no intervention or placebo. One small randomized controlled trial provided no robust evidence for which dosing schedule of alglucosidase alfa was more effective to treat infantile-onset Pompe disease. It is not deemed ethical to proceed with new placebo-controlled trials, therefore a randomized controlled trial with a large sample size comparing different dosing schedules of enzyme replacement therapy is needed. The main clinical outcomes (i.e. cardiac function, invasive ventilation, survival, motor development, adverse events (e.g. the development of antibodies)) should be standardized when evaluated and reported.
Erythrocyte-dependent regulation of human skeletal muscle blood flow: role of varied oxyhemoglobin and exercise on nitrite, S-nitrosohemoglobin, and ATP (2010)

The erythrocyte is proposed to play a key role in the control of local tissue perfusion via three O(2)-dependent signaling mechanisms: 1) reduction of circulating nitrite to vasoactive NO, 2) S-nitrosohemoglobin (SNO-Hb)-dependent vasodilatation, and 3) release of the vasodilator and sympatholytic ATP; however, their relative roles in vivo remain unclear. Here we evaluated each mechanism to gain insight into their roles in the regulation of human skeletal muscle blood flow during hypoxia and hyperoxia at rest and during exercise. Arterial and femoral venous hemoglobin O(2) saturation (O(2)Hb), plasma and erythrocyte NO and ATP metabolites, and leg and systemic hemodynamics were measured in 10 healthy males exposed to graded hypoxia, normoxia, and graded hyperoxia both at rest and during submaximal one-legged knee-extensor exercise. At rest, leg blood flow and NO and ATP metabolites in plasma and erythrocytes remained unchanged despite large alterations in O(2)Hb. During exercise, however, leg and systemic perfusion and vascular conductance increased in direct proportion to decreases in arterial and venous O(2)Hb (r(2) = 0.86-0.98; P = 0.01), decreases in venous plasma nitrite (r(2) = 0.93; P < 0.01), increases in venous erythrocyte nitroso species (r(2) = 0.74; P < 0.05), and to a lesser extent increases in erythrocyte SNO (r(2) = 0.59; P = 0.07). No relationship was observed with plasma ATP (r(2) = 0.01; P = 0.99) or its degradation compounds. These in vivo data indicate that, during low-intensity exercise and hypoxic stress, but not hypoxic stress alone, plasma nitrite consumption and formation of erythrocyte nitroso species are associated with limb vasodilatation and increased blood flow in the human skeletal muscle vasculature.
From Single Atoms to Nanoparticles: Autocatalysis and Metal Aggregation in Atomic Layer Deposition of Pt on TiO2 Nanopowder (2018)

A fundamental understanding of the interplay between ligand-removal kinetics and metal aggregation during the formation of platinum nanoparticles (NPs) in atomic layer deposition of Pt on TiO<sub>2</sub> nanopowder using trimethyl(methylcyclo-pentadienyl)platinum(IV) as the precursor and O<sub>2</sub> as the coreactant is presented. The growth follows a pathway from single atoms to NPs as a function of the oxygen exposure (P<sub>O2</sub> × time). The growth kinetics is modeled by accounting for the autocatalytic combustion of the precursor ligands via a variant of the Finke-Watzky two-step model. Even at relatively high oxygen exposures (<120 mbar s) little to no Pt is deposited after the first cycle and most of the Pt is atomically dispersed. Increasing the oxygen exposure above 120 mbar s results in a rapid increase in the Pt loading, which saturates at exposures >> 120 mbar s. The deposition of more Pt leads to the formation of NPs that can be as large as 6 nm. Crucially, high P<sub>O2</sub> (≥5 mbar) hinders metal aggregation, thus leading to narrow particle size distributions. The results show that ALD of Pt NPs is reproducible across small and large surface areas if the precursor ligands are removed at high P<sub>O2</sub> .
Direct evidence that sulfhydryl groups of Keap1 are the sensors regulating induction of phase 2 enzymes that protect against carcinogens and oxidants (2002)

Coordinate induction of phase 2 proteins and elevation of glutathione protect cells against the toxic and carcinogenic effects of electrophiles and oxidants. All inducers react covalently with thiols at rates that are closely related to their potencies. Inducers disrupt the cytoplasmic complex between the actin-bound protein Keap1 and the transcription factor Nrf2, thereby releasing Nrf2 to migrate to the nucleus where it activates the antioxidant response element (ARE) of phase 2 genes and accelerates their transcription. We cloned, overexpressed, and purified murine Keap1 and demonstrated on native gels the formation of complexes of Keap1 with the Neh2 domain of Nrf2 and their concentration-dependent disruption by inducers such as sulforaphane and bis(2-hydroxybenzylidene)acetone. The kinetics, stoichiometry, and order of reactivities of the most reactive of the 25 cysteine thiol groups of Keap1 have been determined by tritium incorporation from [(3)H]dexamethasone mesylate (an inducer and irreversible modifier of thiols) and by UV spectroscopy with sulforaphane, 2,2'-dipyridyl disulfide and 4,4'-dipyridyl disulfide (titrants of thiol groups), and two closely related Michael reaction acceptors [bis(2- and 4-hydroxybenzylidene)acetones] that differ 100-fold in inducer potency and the UV spectra of which are bleached by thiol addition. With large excesses of these reagents nearly all thiols of Keap1 react, but sequential reaction with three successive single equivalents (per cysteine residue) of dipyridyl disulfides revealed excellent agreement with pseudo-first order kinetics, rapid successive declines in reaction velocity, and the stoichiometric formation of two equivalents of thiopyridone per reacted cysteine. This finding suggests that reaction of cysteine thiols is followed by rapid formation of protein disulfide linkages. The most reactive residues of Keap1 (C(257), C(273), C(288), and C(297)) were identified by mapping the dexamethasone-modified cysteines by mass spectrometry of tryptic peptides. These residues are located in the intervening region between BTB and Kelch repeat domains of Keap1 and probably are the direct sensors of inducers of the phase 2 system.
A texture-based method for modeling the background and detecting moving objects (2006)

This paper presents a novel and efficient texture-based method for modeling the background and detecting moving objects from a video sequence. Each pixel is modeled as a group of adaptive local binary pattern histograms that are calculated over a circular region around the pixel. The approach provides us with many advantages compared to the state-of-the-art. Experimental results clearly justify our model.