gebhart/patrepeval huggingface dataset:
Growth of Mesenchymal Stem Cells on Electrospun Type I Collagen Nanofibers (2006)

We reconstituted type I collagen nanofibers prepared by electrospin technology and examined the morphology, growth, adhesion, cell motility, and osteogenic differentiation of human bone marrow-derived mesenchymal stem cells (MSCs) on three nano-sized diameters (50-200, 200-500, and 500-1,000 nm). Results from scanning electron microscopy showed that cells on the nanofibers had a more polygonal and flattened cell morphology. MTS (3-[4,5-dimethythiazol-2-yl]-5-[3-carboxy-methoxyphenyl]-2-[4-sul-fophenyl]-2H-tetrazolium compound) assay demonstrated that the MSCs grown on 500-1,000-nm nanofibers had significantly higher cell viability than the tissue culture polystyrene control. A decreased amount of focal adhesion formation was apparent in which quantifiable staining area of the cytoplasmic protein vinculin for the 200-500-nm nanofibers was 39% less compared with control, whereas the area of quantifiable vinculin staining was 45% less for both the 200-500-nm and 500-1,000-nm nanofibers. The distances of cell migration were quantified on green fluorescent protein-nucleofected cells and was 56.7%, 37.3%, and 46.3% for 50-200, 200-500, and 500-1,000 nm, respectively, compared with those on the control. Alkaline phosphatase activity demonstrated no differences after 12 days of osteogenic differentiation, and reverse transcription-polymerase chain reaction (RT-PCR) analysis showed comparable osteogenic gene expression of osteocalcin, osteonectin, and ostepontin between cells differentiated on polystyrene and nanofiber surfaces. Moreover, single-cell RT-PCR of type I collagen gene expression demonstrated higher expression on cells seeded on the nanofibers. Therefore, type I collagen nanofibers support the growth of MSCs without compromising their osteogenic differentiation capability and can be used as a scaffold for bone tissue engineering to facilitate intramembranous bone formation. Further efforts are necessary to enhance their biomimetic properties.
Failure Identification of Induction Motors by Sensing Unbalanced Stator Currents (1989)

The maintenance of electric drives is essential to their efficient and safe operation in any industry. The lack of an effectively designed and implemented maintenance policy will result in increased downtime, increased capital losses from catastrophic failures, and in some cases, a reduced level of personnel safety. Traditional approaches to maintenance include statistical-replacement policies and preventive-maintenance testing. The relative success or failure of these approaches is dependent on the specific industrial setting. However both have inherent limitations. For example, replacement policies tend to increase costs because motors are often taken out of service while still in good condition. Off-line testing procedures, such as insulation-resistance measurements, have limited value since they can be difficult to interpret and are applicable to the detection of a limited number of failure modes. On-line and continuous monitoring methods offer significant advantages in this regard, since incipient failures can be detected, and appropriate maintenance actions can be scheduled, thereby avoiding the costs and problems associated with unexpected failures. Thus far, research in this area has focused on sensing magnetic flux, stator current, rotor current, shaft flux, ground fault current, vibrations, temperature, and speed fluctuations. The first five methods are based on sensing electrical or magnetic parameters, and the remaining are based on monitoring mechanical quantities. A classical type of current transformer is found very effective in sensing the unbalanced currents in the three-phase power system where highresistance grounding is used, such as in an underground coal mine.
Label-Embedding for Attribute-Based Classification (2013)

Attributes are an intermediate representation, which enables parameter sharing between classes, a must when training data is scarce. We propose to view attribute-based image classification as a label-embedding problem: each class is embedded in the space of attribute vectors. We introduce a function which measures the compatibility between an image and a label embedding. The parameters of this function are learned on a training set of labeled samples to ensure that, given an image, the correct classes rank higher than the incorrect ones. Results on the Animals With Attributes and Caltech-UCSD-Birds datasets show that the proposed framework outperforms the standard Direct Attribute Prediction baseline in a zero-shot learning scenario. The label embedding framework offers other advantages such as the ability to leverage alternative sources of information in addition to attributes (e.g. class hierarchies) or to transition smoothly from zero-shot learning to learning with large quantities of data.
Estimating geological CO2 storage security to deliver on climate mitigation (2018)

Carbon capture and storage (CCS) can help nations meet their Paris CO<sub>2</sub> reduction commitments cost-effectively. However, lack of confidence in geologic CO<sub>2</sub> storage security remains a barrier to CCS implementation. Here we present a numerical program that calculates CO<sub>2</sub> storage security and leakage to the atmosphere over 10,000 years. This combines quantitative estimates of geological subsurface CO<sub>2</sub> retention, and of surface CO<sub>2</sub> leakage. We calculate that realistically well-regulated storage in regions with moderate well densities has a 50% probability that leakage remains below 0.0008% per year, with over 98% of the injected CO<sub>2</sub> retained in the subsurface over 10,000 years. An unrealistic scenario, where CO<sub>2</sub> storage is inadequately regulated, estimates that more than 78% will be retained over 10,000 years. Our modelling results suggest that geological storage of CO<sub>2</sub> can be a secure climate change mitigation option, but we note that long-term behaviour of CO<sub>2</sub> in the subsurface remains a key uncertainty.
Daytime Exposure to Bright Light, as Compared to Dim Light, Decreases Sleepiness and Improves Psychomotor Vigilance Performance (2003)

Daytime bright light exposure can reduce the impact of sleep loss on sleepiness levels and performance, as compared to dim light. These effects appear to be mediated by mechanisms that are separate from melatonin suppression. The results may assist in the development of treatments for daytime sleepiness.
Nanocapillary Array Interconnects for Gated Analyte Injections and Electrophoretic Separations in Multilayer Microfluidic Architectures (2003)

An electrokinetic injection technique is described which uses a nuclear track-etched nanocapillary array to inject sample plugs from one layer of a microfluidic device into another vertically separated layer for electrophoretic separations. Gated injection protocols for analyte separations, reported here, establish nanocapillary array interconnects as a route to multilevel microfluidic analytical designs. The hybrid nanofluidic/microfluidic gated injection protocol allows sample preparation and separation to be implemented in separate horizontal planes, thereby achieving multilayer integration. Repeated injections and separations of FITC-labeled arginine and tryptophan, using 200-nm pore-diameter capillary array injectors in place of traditional cross injectors are used to demonstrate gated injection with a bias configuration that uses relay switching of a single high-voltage source. Injection times as rapid as 0.3 s along with separation reproducibilities as low as 1% for FITC-labeled arginine exemplify the capability for fast, serial separations and analyses. Impedance analysis of the micro-/nanofluidic network is used to gain further insight into the mechanism by which this actively controlled nanofluidic-interconnect injection method works. Gated sample introduction via a nanocapillary array interconnect allows the injection and separation protocols to be optimized independently, thus realizing the versatility needed for real-world implementation of rapid, serial microchip analyses.
Novel structural features of autoantibodies in murine lupus: A possible superantigen binding site? (1994)

The stimulus for the production of anti-DNA autoantibodies in lupus remains unknown. Since double-stranded DNA (dsDNA) is a weak immunogen, other stimuli such as B cell superantigens or anti-idiotypic antibodies may provide an alternative mechanism for their production. The presence of regulatory determinants on autoantibodies might be revealed through their structural characterization, but they have eluded detection, perhaps because they may be three-dimensional and require closer analysis. In this report we cloned and sequenced the heavy chain variable region (VH) of a monoclonal anti-dsDNA antibody, mAb 3E10, derived from MRL/lpr mice with lupus nephritis previously shown to express an idiotype associated with nephritis in murine and human lupus. We now show that mAb 3E10 VH contains novel structural features unrelated to DNA binding which are shared only by a subset of autoantibodies expressed in murine lupus. These lupus autoantibodies can be distinguished from antibodies of non-autoimmune strains by the presence of a specific sequence at the junction of the diversity and joining genes combined with the use of variable region genes with conserved sequences in framework 1 (FR1) and FR3. The location of the novel sequences indicates the possibility of a three-dimensional solvent-exposed determinant located distant from the classical antigen binding site that could regulate their production, possibly through binding B cell superantigens or other infectious agents.
Species‐specific transfer of plasma albumin from blood into different cerebrospinal fluid compartments in the fetal sheep. (1991)

1. The blood-cerebrospinal fluid (CSF) transfer of endogenous sheep albumin and several exogenous species of albumin has been investigated in different CSF compartments of the immature fetal sheep brain, at an early stage of development (60 days gestation, term is 150 days) when the CSF concentration of total protein is high. 2. There were marked differences in the steady-state CSF/plasma ratios for all species of albumin (including endogenous sheep albumin) between different CSF compartments. Ratios measured in the cisterna magna were significantly higher than those in the dorsal subarachnoid space, which in turn were higher than those in the lateral ventricles. The ratios for endogenous sheep albumin were (%; mean +/- S.E.M.): lateral ventricle (LV), 4.0 +/- 0.03; dorsal subarachnoid (DSA), 6.1 +/- 1.0; cisterna magna (CM), 13.7 +/- 0.8. 3. Three hours after I.V. injection, the CSF/plasma ratios for bovine albumin (LV, 2.0 +/- 0.2; DSA, 2.4 +/- 0.1; CM, 7.2 +/- 0.7%) were significantly lower than the ratio for endogenous sheep albumin in all three compartments. The ratios for human albumin (LV, 0.7 +/- 0.2; DSA, 1.0 +/- 0.2; CM, 3.9 +/- 0.4%) were significantly lower than those for bovine albumin. 4. In all three CSF compartments, the endogenous sheep albumin ratios were higher than would be expected on the basis of transfer by passive mechanisms. Conversely, steady-state CSF/plasma ratios for [3H]sucrose and [14C]inulin were consistent with passive transfer, and there were no differences between the ratios for these markers measured in each of the three CSF regions. 5. Goat albumin and [35S]sheep albumin ratios were not significantly different, 5 h after injection, from the endogenous sheep albumin levels in each of the three CSF compartments. 6. It is concluded that in the 60-day-old fetal sheep, all of the endogenous albumin in CSF is derived from the plasma by a specific transfer mechanism that can distinguish between different species of the same protein. There is also some evidence of a small passive component of blood-CSF albumin transfer. 7. Immunocytochemical evidence suggests that the route of transfer from blood to CSF is transcellular, through the choroid plexus epithelial cells. 8. Regional variations in albumin ratios are probably due to differences in specific transfer into each CSF compartment. This is reflected in a differential immunocytochemical staining for albumin in choroid plexus epithelial cells from different regions of the brain. 9. The results are discussed in terms of differences in albumin amino acid sequences, structural homologies, and transfer by a specific transcellular mechanism.
Microstructure of Ethene/Norbornene Copolymers (1999)

The microstructure of ethene/norbornene copolymers produced by metallocene/methylaluminoxane catalysts is investigated by 13C NMR spectroscopy. The microstructure of alternating copolymers is assigned on the pentad level by comparison of the pentad distribution in 13C NMR spectra with the calculated distribution according to the alternating mechanism. Norbornene block structures produced with different catalysts are compared, and norbornene diblock structures are assigned. Triad distributions for the alternating copolymers and diad distributions for copolymers containing diblocks were obtained.
Altered Ligand Binding Properties and Enhanced Stability of a Constitutively Active Estrogen Receptor:  Evidence That an Open Pocket Conformation Is Required for Ligand Interaction (1997)

To elucidate the ligand binding properties of the estrogen receptor (ER) and how ligand access to and release from the ligand binding pocket is affected by the conformational state of the receptor, we have measured the rates of estradiol association and dissociation, the equilibrium binding, and the stability of estradiol binding to denaturants, comparing wild-type human ER and a point mutant (Y537S ER) that shows full constitutive activity, i.e., the same full transcriptional activity in the absence or presence of estrogen. Ligand binding kinetics and affinity were measured with the full-length (1-595) ERs and with truncated forms of both receptors containing domains C through F (including the DNA binding, hinge, and ligand binding domains, amino acids 175-595) or domains E and F (the ligand binding domain; amino acids 304-595). With all ERs, the rates of ligand association and dissociation were considerably slower with the Y537S mutant ER than with wild-type ER (6-fold and 3-4-fold, respectively). These marked differences in ligand on and off rates for the wild-type and Y537S receptors result in a predicted (k-1/k+1) and measured Kd that is 2-fold lower for Y537S ER compared to wild-type ER. The binding of estradiol by wild-type ER was disrupted by high concentrations of urea (above 2 M), whereas the Y537S ER was distinctly more resistant to this disruption. These results are consistent with a model in which wild-type ER in the absence of ligand adopts a transcriptionally inactive collapsed pocket conformation, stabilized by specific interactions of Y537 with nearby regions of ER. When estradiol is bound, the wild-type ER adopts a transcriptionally active, closed pocket (ligand occupied) conformation. By contrast, the Y537S mutant ER favors the transcriptionally active closed pocket conformation, whether occupied by ligand or not, the latter state (closed pocket but unoccupied) accounting for its constitutive activity. Our findings suggest that the entry or exit of ligand from the binding pocket requires that ER adopt an open pocket conformation. The reduced rates of ligand association and dissociation in the constitutively active form of the ER, as well as its greater resistance to disruption of ligand binding by urea, support the supposition that the rate at which this open pocket conformation can be accessed from the unoccupied or ligand-occupied Y537S ER is slower than from the unoccupied or occupied forms of wild-type ER. Thus, the binding and release of ligand by ER require that the receptor access an open pocket state, and the ease with which this state can be accessed is affected by mutations that alter receptor conformation.
Regulation of Aquaporin-2 Trafficking by Vasopressin in the Renal Collecting Duct (2000)

In the renal collecting duct, vasopressin increases osmotic water permeability (P(f)) by triggering trafficking of aquaporin-2 vesicles to the apical plasma membrane. We investigated the role of vasopressin-induced intracellular Ca(2+) mobilization in this process. In isolated inner medullary collecting ducts (IMCDs), vasopressin (0.1 nm) and 8-(4-chlorophenylthio)-cAMP (0.1 mm) elicited marked increases in [Ca(2+)](i) (fluo-4). Vasopressin-induced Ca(2+) mobilization was completely blocked by preloading with the Ca(2+) chelator BAPTA. In parallel experiments, BAPTA completely blocked the vasopressin-induced increase in P(f) without affecting adenosine 3',5'-cyclic monophosphate (cAMP) production. Previously, we demonstrated the lack of activation of the phosphoinositide-signaling pathway by vasopressin in IMCD, suggesting an inositol 1,4,5-trisphosphate-independent mechanism of Ca(2+) release. Evidence for expression of the type 1 ryanodine receptor (RyR1) in IMCD was obtained by immunofluorescence, immunoblotting, and reverse transcription-polymerase chain reaction. Ryanodine (100 microm), a ryanodine receptor antagonist, blocked the arginine vasopressin-mediated increase in P(f) and blocked vasopressin-stimulated redistribution of aquaporin-2 to the plasma membrane domain in primary cultures of IMCD cells, as assessed by immunofluorescence immunocytochemistry. Calmodulin inhibitors (W7 and trifluoperazine) blocked the P(f) response to vasopressin and the vasopressin-stimulated redistribution of aquaporin-2. The results suggest that Ca(2+) release from ryanodine-sensitive stores plays an essential role in vasopressin-mediated aquaporin-2 trafficking via a calmodulin-dependent mechanism.
Resolution of Racemic Amino Acids by Gas Chromatography (1965)

Journal Article Resolution of Racemic Amino Acids by Gas Chromatography Get access Glenn E. Pollock, Glenn E. Pollock Search for other works by this author on: Oxford Academic PubMed Google Scholar Vance I. Oyama, Vance I. Oyama Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard D. Johnson Richard D. Johnson Exobiology Division, National Aeronautics and Space Administration, Ames Research Center, Moffett Field, California Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Chromatographic Science, Volume 3, Issue 5, May 1965, Pages 174–176, https://doi.org/10.1093/chromsci/3.5.174 Published: 01 May 1965
Programmed Adsorption and Release of Proteins in a Microfluidic Device (2003)

A microfluidic device has been developed that can adsorb proteins from solution, hold them with negligible denaturation, and release them on command. The active element in the device is a 4-nanometer-thick polymer film that can be thermally switched between an antifouling hydrophilic state and a protein-adsorbing state that is more hydrophobic. This active polymer has been integrated into a microfluidic hot plate that can be programmed to adsorb and desorb protein monolayers in less than 1 second. The rapid response characteristics of the device can be manipulated for proteomic functions, including preconcentration and separation of soluble proteins on an integrated fluidics chip.
Charge-dependent translocation ofBordetella pertussisadenylate cyclase toxin into eukaryotic cells: Implication for thein vivodelivery of CD8+T cell epitopes into antigen-presenting cells (1998)

Bordetella pertussis secretes a calmodulin-activated adenylate cyclase toxin, CyaA, that is able to deliver its N-terminal catalytic domain (400-aa residues) into the cytosol of eukaryotic target cells, directly through the cytoplasmic membrane. We have previously shown that CyaA can be used as a vehicle to deliver T cell epitopes, inserted within the catalytic domain of the toxin, into antigen-presenting cells and can trigger specific class I-restricted CD8(+) cytotoxic T cell responses in vivo. Here, we constructed a series of recombinant toxins harboring at the same insertion site various peptide sequences of 11-25 amino acids, corresponding to defined CD8(+) T cell epitopes and differing in the charge of the inserted sequence. We show that inserted peptide sequences containing net negative charges (-1 or -2) decreased or completely blocked (charge of -4) the internalization of the toxin into target cells in vitro and abolished the induction of cytotoxic T cell responses in vivo. The blocking of translocation due to the inserted acidic sequences can be relieved by appropriate mutations in the flanking region of CyaA that counterbalance the inserted charges. Our data indicate that (i) the electrostatic charge of the peptides inserted within the catalytic domain of CyaA is critical for its translocation into eukaryotic cells and (ii) the delivery of T cell epitopes into the cytosol of antigen-presenting cells by recombinant CyaA toxins is essential for the in vivo stimulation of specific cytotoxic T cells. These findings will help to engineer improved recombinant CyaA vectors able to stimulate more efficiently cellular immunity.
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS (2003)

A need exists for technologies that permit the direct quantification of differences in protein and posttranslationally modified protein expression levels. Here we present a strategy for the absolute quantification (termed AQUA) of proteins and their modification states. Peptides are synthesized with incorporated stable isotopes as ideal internal standards to mimic native peptides formed by proteolysis. These synthetic peptides can also be prepared with covalent modifications (e.g., phosphorylation, methylation, acetylation, etc.) that are chemically identical to naturally occurring posttranslational modifications. Such AQUA internal standard peptides are then used to precisely and quantitatively measure the absolute levels of proteins and posttranslationally modified proteins after proteolysis by using a selected reaction monitoring analysis in a tandem mass spectrometer. In the present work, the AQUA strategy was used to (i) quantify low abundance yeast proteins involved in gene silencing, (ii) quantitatively determine the cell cycle-dependent phosphorylation of Ser-1126 of human separase protein, and (iii) identify kinases capable of phosphorylating Ser-1501 of separase in an in vitro kinase assay. The methods described here represent focused, alternative approaches for studying the dynamically changing proteome.
Efficient Neural Audio Synthesis (2018)

Sequential models achieve state-of-the-art results in audio, visual and textual domains with respect to both estimating the data distribution and generating high-quality samples. Efficient sampling for this class of models has however remained an elusive problem. With a focus on text-to-speech synthesis, we describe a set of general techniques for reducing sampling time while maintaining high output quality. We first describe a single-layer recurrent neural network, the WaveRNN, with a dual softmax layer that matches the quality of the state-of-the-art WaveNet model. The compact form of the network makes it possible to generate 24kHz 16-bit audio 4x faster than real time on a GPU. Second, we apply a weight pruning technique to reduce the number of weights in the WaveRNN. We find that, for a constant number of parameters, large sparse networks perform better than small dense networks and this relationship holds for sparsity levels beyond 96%. The small number of weights in a Sparse WaveRNN makes it possible to sample high-fidelity audio on a mobile CPU in real time. Finally, we propose a new generation scheme based on subscaling that folds a long sequence into a batch of shorter sequences and allows one to generate multiple samples at once. The Subscale WaveRNN produces 16 samples per step without loss of quality and offers an orthogonal method for increasing sampling efficiency.