gebhart/patrepeval huggingface dataset:
Studies employing Saccharomyces cerevisiae cpt1 and ept1 null mutants implicate the CPT1 gene in coordinate regulation of phospholipid biosynthesis. (1994)

The Saccharomyces cerevisiae CPT1 and EPT1 genes are structural genes encoding sn-1,2-diacylglycerol choline phosphotransferase and sn-1,2-diacylglycerol choline/ethanolamine phosphotransferase, respectively. Incorporation of 32Pi into phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine in wild type and ept1 strains was decreased in the presence of exogenous inositol. In contrast, inositol did not affect 32Pi incorporation into phospholipid in cpt1 or cpt1ept1 strains. In membranes isolated from wild type and ept1 strains grown in the presence of inositol or inositol/choline, the CPT1-derived cholinephosphotransferase activities were reduced 40-50 and 65%, respectively. Inositol-dependent reductions in CPT1 derived choline-phosphotransferase activity correlated with transcript levels in both wild type and ept- backgrounds. The ethanolaminephosphotransferase activity of the EPT1 gene product in wild type cells was reduced 40% by exogenous inositol alone and 50% by inositol/choline. In the cpt1 strain, however, the ethanolaminephosphotransferase activity was unaffected by exogenous inositol or inositol/choline. The inositol-dependent reduction of ethanolaminephosphotransferase activity observed in wild type cells correlated with reduced levels of EPT1 transcripts; in the cpt1 strain, EPT1 transcript levels were not affected by inositol. These results indicate that 1) a functional CPT1 gene or gene product is required for inositol-dependent regulation of phospholipid synthesis; 2) the enzyme activities of both the CPT1 and EPT1 gene products are repressed by inositol and inositol/choline, and require an intact CPT1 gene; 3) inositol mediates its regulatory effects on phospholipid synthesis via a transcriptional mechanism.
Zirconocene-MAO catalyzed homo- and copolymerizations of linear asymmetrically substituted dienes with propene: a novel strategy to functional (co)poly(α-olefin)s (1998)

The polymerization behavior of three linear asymmetrically substituted dienes, i.e. 6-phenyl-1,5-hexadiene (A), 7-methyl-1,6-octadiene (B) and R(+)-5,7-dimethyl-1,6-octadiene (isocitronellene, C) is reported in order to study the effect of substitution at one vinylic group. Homopolymerization of these monomers with the catalyst system rac-Et[Ind]2ZrCl2/MAO resulted in no reaction products in the case of monomer A and in polymers with Mw = 3.5 kg/mol and Mw = 14.0 kg/mol with the monomers B and C, respectively. According to NMR analysis, the vinylene end group of isocitronellene remained untouched during polymerization, which excludes the possibility of cyclopolymerization or crosslinking. Copolymerization of isocitronellene with propene resulted in incorporation of the diene (15.6 mol-%) equal to the stoichiometric ratio in the monomer feed, with a relatively high catalyst activity. The degree of incorporated isocitronellene is inversely related to the polymerization temperature, providing control over crystallinity (isotacticity) and molecular weight of the copolymer. The isocitronellene homo- and copolymers could be epoxidized quantitatively and brominated to an extent of 90%. Perfluorohexyl iodide was grafted onto the isocitronellene/propene copolymer by radical reaction (conversion 80%), yielding a poly(α-olefin) with fluorinated side chains.
Classical Complement Pathway Components C1r and C1s: Purification from Human Serum and in Recombinant Form and Functional Characterization (2013)

C1r and C1s are the proteases responsible for the activation and proteolytic activity of the C1 complex of the classical complement pathway, respectively. They are assembled into a Ca(2+)-dependent C1s-C1r-C1r-C1s tetramer which in turn associates with the recognition protein C1q. The C1 complex circulates in serum as a zymogen and is activated upon binding of C1q to appropriate targets, such as antigen-antibody complexes. This property is used for the purification of C1r and C1s from human serum after binding of C1 to insoluble immune complexes. Disruption of the bound C1 complex by EDTA releases C1r and C1s which are further separated by ion-exchange chromatography; both proteins can be reassembled in the presence of calcium ions and the reconstituted tetramer isolated by gel filtration. In this chapter, we describe the purification of the activated and proenzyme forms of C1r and C1s and of the proenzyme C1s-C1r-C1r-C1s tetramer as well as methods for their biochemical and functional characterization. The production of recombinant C1s and of the proenzyme tetramer in a baculovirus-insect cell system, and their purification by affinity chromatography is also presented.
Characterization of acute lymphoblastic leukemia progenitor cells (2004)

Only some acute lymphoblastic leukemia (ALL) cells are thought to be capable of proliferating to maintain the leukemic clone, and these cells may be the most relevant to target with treatment regimens. We have developed a serum-free suspension culture (SC) system that supported growth of B-ALL cells from 33 patients for up to 6 weeks. ALL cells from 28 cases (85%) were expanded in this system, and growth was superior in SC than in long-term bone marrow culture. To characterize ALL progenitors, cells were sorted for expression of CD34 and CD10 or CD19 and the subfractions assayed in SC and in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. Cells capable of long-term proliferation in vitro and NOD/SCID repopulation were derived only from the CD34(+)/CD10(-) and CD34(+)/CD19(-) subfractions, and these cells could engraft secondary recipients. The engrafted cells had the same immunophenotype and karyotype as was seen at diagnosis, suggesting they had differentiated in vivo. These results demonstrate that ALL cells capable of long-term proliferation in vitro and in vivo are CD34(+)/CD10(-)/CD19(-). This suggests that cells with a more immature phenotype, rather than committed B-lymphoid cells, may be the targets for transformation in B-ALL.
Identification of Cytomegalovirus-Specific Cytotoxic T Lymphocytes In Vitro Is Greatly Enhanced by the Use of Recombinant Virus Lacking the US2 to US11 Region or Modified Vaccinia Virus Ankara Expressing Individual Viral Genes (2005)

Cytomegalovirus (CMV) elicits a potent T-cell response in humans that appears to protect the host from virus-associated disease. Despite facing strong host defense mechanisms, CMV remains as a lifelong infection that may reactivate and cause life-threatening disease in immunocompromised individuals. This persistence is probably assisted by expression of immune subversion proteins of the virus encoded by genes belonging to the US gene family. These proteins modulate major histocompatibility complex expression in infected cells and bias in vitro experiments toward the detection of only certain specificities. We have combined the use of recombinant CMV, lacking the US2 to US11 region genes, and cytoplasmic gamma interferon staining to define a more accurate assessment of CMV-specific responses in vivo. Recombinant CMV stimulation reveals a CD8 response much larger than that of parental virus in all donors tested. In some cases, this represented up to 10-fold increases in the number of cells detected. Responses were directed mainly against pp65, IE-1, and pp50 in the majority of donors. In addition, previously unreported IE-2-specific T-cell responses could be detected in a minority of cases. Furthermore, we observed a less marked increase in the response to mutant CMV by CD4 T cells in some donors. This suggests that a much broader T-cell response to CMV exists in vivo than is revealed by restimulation with wild-type virus and adds to the evidence that the efficacy of immune evasion strategies may not be as absolute as previously believed.
The effects of impurities and temperature on amorphous silicon solar cells (1977)

Amorphous silicon (a-Si) solar cells have been fabricated in SiH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> glow discharges containing various impurity gases such as N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O, CH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> , etc. The effect of these impurity gases on the photovoltaic properties are discussed. Experimental data are also presented for the variation of photovoltaic properties with deposition temperature, annealing temperature in air, and temperature during operation.
Metalloporphyrin Nanotube Fabrication Using Peptide Nanotubes as Templates (2001)

Protoporphyrin IX Zn(II) has been demonstrated to form metalloporphyrin coatings on peptide nanotubes via hydrogen bonds and produce metalloporphyrin nanotubes. This diacid metalloporphyrin was stabilized on the peptide nanotube surfaces with two types of hydrogen bonds, intermolecular hydrogen bond between the carboxylic acid of metalloporphyrins and the amide of peptide nanotube and intermolecular hydrogen bond between the carboxylic acids of neighboring metalloporphyrins. Since previous study indicates that the peptide nanotubes can potentially be assembled as arrays, the applications of metalloporphyrin nanotubes to nanoscale chemical sensors or photonics may be possible.
Prediction and Outcomes of Impossible Mask Ventilation (2009)

Impossible mask ventilation is an infrequent airway event that is associated with difficult intubation. Neck radiation changes represent the most significant clinical predictor of impossible mask ventilation in the patient dataset.
Solid Freeform Fabrication Symposium Proceedings, September 1996. (1996)

Abstract : The Seventh Solid Freeform Fabrication (SFF) Symposium, held at The University of Texas in Austin on August 12-14, 1996, was attended by over 200 national and international researchers. Papers, addressed SFF issues in computer software, machine design, materials synthesis and processing, and integrated manufacturing. The continued growth in the research, application and development of SFF approaches was readily apparent from the increased participation over previous years and the diverse domestic and foreign attendees from industrial users, SFF machine manufacturers, universities, and government. The excitement generated at the Symposium reflects the participants' total involvement in SFF and the future technical health of this growing technology. The Symposium was again organized in a manner to allow the multi-disciplinary nature of the SFF research to be presented coherently, with various sessions emphasizing computer issues, machine topics, and the variety of materials aspects of SFF. We believe that documenting the constantly changing state of SFF art as represented by these Proceedings will serve both the people presently involved in this fruitful technical area as well as the large flux of new researchers and users entering the field.
From Marrow to Brain: Expression of Neuronal Phenotypes in Adult Mice (2000)

After intravascular delivery of genetically marked adult mouse bone marrow into lethally irradiated normal adult hosts, donor-derived cells expressing neuronal proteins (neuronal phenotypes) developed in the central nervous system. Flow cytometry revealed a population of donor-derived cells in the brain with characteristics distinct from bone marrow. Confocal microscopy of individual cells showed that hundreds of marrow-derived cells in brain sections expressed gene products typical of neurons (NeuN, 200-kilodalton neurofilament, and class III beta-tubulin) and were able to activate the transcription factor cAMP response element-binding protein (CREB). The generation of neuronal phenotypes in the adult brain 1 to 6 months after an adult bone marrow transplant demonstrates a remarkable plasticity of adult tissues with potential clinical applications.
Interchangeable Hebbian and Anti-Hebbian STDP Applied to Supervised Learning in Spiking Neural Network (2018)

This work provides a complete framework, including device, architecture, and algorithm, for implementing bio-inspired supervised spiking neural networks (SNNs) on hardware. An analog synapse with atypical dual bipolar resistive-switching (D-BRS) modes demonstrates interchangeable Hebbian spiking-timing-dependent plasticity (STDP) and anti-Hebbian STDP, and it is capable of implementing supervised ReSuMe SNNs in crossbar arrays. By using an “exchange” update scheme, accurate supervised learning (~96% for MNIST) is achieved in a compact network.
Vacuuming the Periplasm (2005)

Ever since their discovery multidrug resistance (MDR) transporters have provided a plethora of fascinating and challenging topics for fundamental and applied research. Recognized first as a cause of resistance of tumor cells to anticancer agents (reviewed in reference 5), they were later discovered in all living organisms, from bacteria to humans. In bacteria the expression of MDR transporters can raise antibiotic resistance by several orders of magnitude, rendering some antibiotics clinically useless, especially against gram-negative pathogens (reviewed in reference 30). The structural diversity of substrates for some MDR pumps is striking: a single efflux system may accommodate positively or negatively charged compounds, as well as compounds that are neutral or zwitterionic (reviewed in reference 20). Establishing the basis for multidrug recognition and transport, which provides a single protein with both broad specificity and high selectivity, is a fundamentally intriguing challenge. Aside from being intellectually rewarding, unraveling the mechanistic details will greatly facilitate the fight to combat antibiotic resistance. The results of the study by Aires and Nikaido published in this issue of the Journal of Bacteriology (1a), demonstrating that MDR transporter AcrD could capture its substrates directly from the periplasm and extrude them into the external medium, bring us one step closer to elucidation of this fascinating biochemical process.
Cells adapted to the proteasome inhibitor 4-hydroxy- 5-iodo-3-nitrophenylacetyl-Leu-Leu-leucinal-vinyl sulfone require enzymatically active proteasomes for continued survival (2001)

The proteasome is the primary protease used by cells for degrading proteins and generating peptide ligands for class I molecules of the major histocompatibility complex. Based on the properties of cells adapted to grow in the presence of the proteasome inhibitor 4-hydroxy-5-iodo-3-nitrophenylacetyl-Leu-Leu-leucinal-vinyl sulfone (NLVS), it was proposed that proteasomes can be replaced by alternative proteolytic systems, particularly a large proteolytic complex with a tripeptidyl peptidase II activity. Here we show that NLVS-adapted cells retain sensitivity to a number of highly specific proteasome inhibitors with regard to antigenic peptide generation, accumulation of polyubiquitinated proteins, degradation of p53, and cell viability. In addition, we show that in the same assays (with a single minor exception), NLVS-adapted cells are about as sensitive as nonselected cells to Ala-Ala-Phe-chloromethylketone, a specific inhibitor of tripeptidyl peptidase II activity. Based on these findings, we conclude that proteasomes still have essential proteolytic functions in adapted cells that are not replaced by Ala-Ala-Phe-chloromethylketone-sensitive proteases.
Scanning Neural Network for Text Line Recognition (2012)

Optical character recognition (OCR) of machine printed Latin script documents is ubiquitously claimed as a solved problem. However, error free OCR of degraded or noisy text is still challenging for modern OCR systems. Most recent approaches perform segmentation based character recognition. This is tricky because segmentation of degraded text is itself problematic. This paper describes a segmentation free text line recognition approach using multi layer perceptron (MLP) and hidden markov models (HMMs). A line scanning neural network-trained with character level contextual information and a special garbage class-is used to extract class probabilities at every pixel succession. The output of this scanning neural network is decoded by HMMs to provide character level recognition. In evaluations on a subset of UNLV-ISRI document collection, we achieve 98.4% character recognition accuracy that is statistically significantly better in comparison with character recognition accuracies obtained from state-of-the-art open source OCR systems.
Interdigitated back contact solar cells with polycrystalline silicon on oxide passivating contacts for both polarities (2017)

We demonstrate an independently confirmed 25.0%-efficient interdigitated back contact silicon solar cell with passivating polycrystalline silicon (poly-Si) on oxide (POLO) contacts that enable a high open circuit voltage of 723 mV. We use n-type POLO contacts with a measured saturation current density of J0n = 4 fA cm−2 and p-type POLO contacts with J0p = 10 fA cm−2. The textured front side and the gaps between the POLO contacts on the rear are passivated by aluminum oxide (AlOx) with J0AlOx = 6 fA cm−2 as measured after deposition. We analyze the recombination characteristics of our solar cells at different process steps using spatially resolved injection-dependent carrier lifetimes measured by infrared lifetime mapping. The implied pseudo-efficiency of the unmasked cell, i.e., cell and perimeter region are illuminated during measurement, is 26.2% before contact opening, 26.0% after contact opening and 25.7% for the finished cell. This reduction is due to an increase in the saturation current density of the AlOx passivation during chemical etching of the contact openings and of the rear side metallization. The difference between the implied pseudo-efficiency and the actual efficiency of 25.0% as determined by designated-area light current–voltage (I–V) measurements is due to series resistance and diffusion of excess carriers into the non-illuminated perimeter region.
Gut solutions to a gut problem: bacteriocins, probiotics and bacteriophage for control of Clostridium difficile infection (2013)

Clostridium difficile infection (CDI) is a major cause of morbidity and mortality among hospitalized patients and imposes a considerable financial burden on health service providers in both Europe and the USA. The incidence of CDI has dramatically increased in recent years, partly due to the emergence of a number of hypervirulent strains. The most commonly documented risk factors associated with CDIs are antibiotic usage leading to alterations of the gut microbiota, age >65 years and long-term hospital stay. Since standard therapies for antibiotic-associated diarrhoea and CDI have limited efficacy, there is now an urgent need for alternative therapeutics. In this review, we outline the current state of play with regard to the potential of gut-derived bacteriocins, probiotics and phage to act as antimicrobial agents against CDI in the human gut.
Transglutaminase amine substrates for photochemical labeling and cleavable cross-linking of proteins. (1980)

A new procedure for the photochemical labeling of peptides and for the production of cleavable cross-links between protein molecules is given. This method is mediated through the catalytic action of the enzyme guinea pig liver transglutaminase. Each of the labeling and cross-linking reagents described here is an amine substrate for transglutaminases and, because of the narrow specificity of these enzymes, is introduced covalently only at the gamma-carboxamide group of available peptide-bound glutamine residues. Cross-linking results either solely through the action of the enzyme in the case of a diamine substrate, or by subsequent photolysis in the case of photosensitive amine substrates. Cleavable bonds in several of the substrates are disulfide or vicinal hydroxyl groups. The validity of the procedure is demonstrated by the preparation of photosensitive derivatives of substance P and glucagon 1-6 and in the cleavable covalent cross-linking of guanidinated beta-casein.
Isolation and analysis of thermotolerant mutants of wheat (2000)

Thermotolerant mutants of wheat cv. Guardian were isolated by selecting survivors from 5-d-old seedlings of M2 populations exposed to 47 degrees C for 90 min. Progeny testing, using triphenyl tetrazolium chloride reduction as a measure of tissue viability, following heat stress treatment for 120 min at each of three temperatures (32, 38 and 50 degrees C), confirmed the thermotolerant nature of seedlings of 13 mutants. Mutants were isolated at frequencies of 0.1% and 0.2% following the use of sodium azide and ethyl methanesulphonate, respectively. The relative thermotolerance of ten of the mutants and 'Guardian' was then tested by exposing plants to heat stresses of 38 degrees C for 6 h in every 24 h for five successive days at one of four growth stages between seedling and anthesis. Pmax (light-saturated net photosynthetic rate) and chlorophyll content were compared in stressed and unstressed plants. The Pmax of 'Guardian' was depressed by at least 23% by heat stress at each stage; this inhibition was least at ear emergence and greatest at anthesis, the latter being associated with reduced sink size as a result of lowered seed set. The stress-induced inhibition of Pmax in 'Guardian' plants at anthesis had not recovered 3 d after removal of the stress. Mutant lines exhibited different developmental profiles of Pmax thermostability. Mutant tht (thermotolerant) 10, for example, exhibited partial thermostability at each growth stage tested while the Pmax of mutant tht 2 was completely unaffected by heat stress at second node and ear emergence, but was as inhibited as that of 'Guardian' at anthesis; heat stress applied at anthesis in tht 2, but not tht 10, was associated with reduced seed set. Generally, the inhibitory effect of heat stress on Pmax in the mutants was reflected in declines in chlorophyll content. The ten mutants were grouped into nine categories, on the basis of thermotolerance characteristics.
Spectroscopic approach for monitoring two-photon excited fluorescence resonance energy transfer from homodimers at the subcellular level (2003)

We have employed a spectroscopic approach for monitoring fluorescence resonance energy transfer (FRET) in living cells. This method provides excellent spectral separation of green fluorescent protein (GFP) mutant signals within a subcellular imaging volume using two-photon excited fluorescence imaging and spectroscopy (TPIS-FRET). In contrast to current FRET-based methodologies, TPIS-FRET does not rely on the selection of optical filters, ratiometric image analysis, or bleedthrough correction algorithms. Utilizing the intrinsic optical sectioning capabilities of TPIS-FRET, we have identified protein-protein interactions within discrete subcellular domains. To illustrate the applicability of this technique to the detection of homodimer formation, we demonstrated the in vivo association of promyleocyte (PML) homodimers within their corresponding nuclear body.