gebhart/patrepeval huggingface dataset:
Threat of the Spores (2004)

It is difficult
to get the news from poems
yet men die miserably every day
for lack
of what is found there.
“Asphodel, That Greeny Flower” by William Carlos Williams, a physician and poet
Beware the threat of the spores,
Bad news parcels bide their time.
They lurk to enter the unsuspecting
And unleash dormant evil that multiplies.
The twin rings of code within are culprits
Spawning the Unholy Trinity of toxins.
Inject to bleed, swell, and destroy,
While the “protective” antigen does anything but.
Skin lesions black as the namesake coal,
Pale in comparison to the inhaled disease.
Finely milled, known simply as Ames strain
Artificial and abhorrent agents of terror.
“Alpha” bacteria,
Germs of the germ theory.
Origin of the famous postulates,
Crafty bugs made cruel by man.
Brought home the nesting-doll syndrome,
Envelopes, spores, bacilli, plasmids.
With it the fear and the frenzy
To cure what we create.
Statistical demonstration of silicide-like uniform and ultra-low specific contact resistivity using a metal/high-k/Si stack in a sidewall contact test structure (2014)

We demonstrate a 300mm wafer scale conformal contact process to achieve uniform ultra-low specific contact resistivity (ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) for metal/high-k/n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> Si (MIS) contacts. To achieve conformal contacts, we use a sidewall TLM (STLM) test structure that helps to minimize current crowding effect and variability. A systematic study is provided by varying doping density (N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> ), high-k material (LaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> , ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> and TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> ) and high-k thickness (t <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> ) to optimize ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> . The obtained ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> and its uniformity are found to be comparable with standard nickel silicide technology, with a possibility of further improvement by use of lower work-function metal.
Reversal of charge selectivity in transmembrane protein pores by using noncovalent molecular adapters (2000)

In this study, the charge selectivity of staphylococcal alpha-hemolysin (alphaHL), a bacterial pore-forming toxin, is manipulated by using cyclodextrins as noncovalent molecular adapters. Anion-selective versions of alphaHL, including the wild-type pore and various mutants, become more anion selective when beta-cyclodextrin (betaCD) is lodged within the channel lumen. By contrast, the negatively charged adapter, hepta-6-sulfato-beta-cyclodextrin (s(7)betaCD), produces cation selectivity. The cyclodextrin adapters have similar effects when placed in cation-selective mutant alphaHL pores. Most probably, hydrated Cl(-) ions partition into the central cavity of betaCD more readily than K(+) ions, whereas s(7)betaCD introduces a charged ring near the midpoint of the channel lumen and confers cation selectivity through electrostatic interactions. The molecular adapters generate permeability ratios (P(K+)/P(Cl-)) over a 200-fold range and should be useful in the de novo design of membrane channels both for basic studies of ion permeation and for applications in biotechnology.
Nucleoside synthesis : organosilicon methods (1991)

General methods of nucleoside synthesis glycosylation of silylated heterocyclic bases synthesis of pyrimidine nucleosides synthesis of nucleosides containing condensed pyrimidine systems synthesis of nucleosides dervived from other heterocyclic bases the synthesis of nucleotides.
General Relationship for the Thermal Oxidation of Silicon (1965)

The thermal-oxidation kinetics of silicon are examined in detail. Based on a simple model of oxidation which takes into account the reactions occurring at the two boundaries of the oxide layer as well as the diffusion process, the general relationship x02+Ax0=B(t+τ) is derived. This relationship is shown to be in excellent agreement with oxidation data obtained over a wide range of temperature (700°–1300°C), partial pressure (0.1–1.0 atm) and oxide thickness (300–20 000 Å) for both oxygen and water oxidants. The parameters A, B, and τ are shown to be related to the physico-chemical constants of the oxidation reaction in the predicted manner. Such detailed analysis also leads to further information regarding the nature of the transported species as well as space-charge effects on the initial phase of oxidation.
A Dialogue Process for Choosing Value-Creating Strategies (1999)

A decision process has proven effective in three activities that are key to value creation: choosing an excellent strategy, actually bringing about change, and operating effectively with the new strategy. The dialogue is between a decision board and the strategy team as they work through six steps of a decision process. This process is focused on alternatives and implementation and is founded in decision analysis. Strategy frame-works and structuring tools are key to assessing the business situation. Risk and value trade-offs are made explicit, leading to concrete proposals to add value and reduce risk. Explicit plans for action are developed as the strategic alternative is chosen. Companies have developed strategy insights using this process, as we illustrate with examples from the pharmaceutical industry.
Probing the Functional Equivalence of Otoferlin and Synaptotagmin 1 in Exocytosis (2011)

Cochlear inner hair cells (IHCs) use Ca(2+)-dependent exocytosis of glutamate to signal sound information. Otoferlin (Otof), a C(2) domain protein essential for IHC exocytosis and hearing, may serve as a Ca(2+) sensor in vesicle fusion in IHCs that seem to lack the classical neuronal Ca(2+) sensors synaptotagmin 1 (Syt1) and Syt2. Support for the Ca(2+) sensor of fusion hypothesis for otoferlin function comes from biochemical experiments, but additional roles in late exocytosis upstream of fusion have been indicated by physiological studies. Here, we tested the functional equivalence of otoferlin and Syt1 in three neurosecretory model systems: auditory IHCs, adrenal chromaffin cells, and hippocampal neurons. Long-term and short-term ectopic expression of Syt1 in IHCs of Otof (-/-) mice by viral gene transfer in the embryonic inner ear and organotypic culture failed to rescue their Ca(2+) influx-triggered exocytosis. Conversely, virally mediated overexpression of otoferlin did not restore phasic exocytosis in Syt1-deficient chromaffin cells or neurons but enhanced asynchronous release in the latter. We further tested exocytosis in Otof (-/-) hippocampal neurons and in Syt1(-/-) IHCs but found no deficits in vesicle fusion. Expression analysis of different synaptotagmin isoforms indicated that Syt1 and Syt2 are absent from mature IHCs. Our data argue against a simple functional equivalence of the two C(2) domain proteins in exocytosis of IHC ribbon synapses, chromaffin cells, and hippocampal synapses.
Global reconstruction of the human metabolic network based on genomic and bibliomic data (2007)

Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computational approaches are required to elucidate and understand metabolic genotype-phenotype relationships. We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50 years of legacy data (i.e., bibliomic data). Herein we describe the reconstruction process and demonstrate how the resulting genome-scale (or global) network can be used (i) for the discovery of missing information, (ii) for the formulation of an in silico model, and (iii) as a structured context for analyzing high-throughput biological data sets. Our comprehensive evaluation of the literature revealed many gaps in the current understanding of human metabolism that require future experimental investigation. Mathematical analysis of network structure elucidated the implications of intracellular compartmentalization and the potential use of correlated reaction sets for alternative drug target identification. Integrated analysis of high-throughput data sets within the context of the reconstruction enabled a global assessment of functional metabolic states. These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology.
Folding of Proteins with WD-Repeats:  Comparison of Six Members of the WD-Repeat Superfamily to the G Protein β Subunit (1996)

The family of WD-repeat proteins comprises over 30 different proteins that share a highly conserved repeating motif [Neer, E. J., Schmidt, C. J., Nambudripad, R., & Smith, T. F. (1994) Nature 371, 297-300]. Members of this family include the signal-transducing G protein beta subunit, as well as other proteins that regulate signal transduction, transcription, pre-mRNA splicing, cytoskeletal organization, and vesicular fusion. The crystal structure of one WD-repeat protein (G beta) has now been solved (Wall et al., 1995; Sondek et al, 1996) and reveals that the seven repeating units form a circular, propeller-like structure with seven blades each made up of four beta strands. It is very likely that all WD-repeat proteins form a similar structure. If so, it will be possible to use information about important surface regions of one family member to predict properties of another. If WD proteins form structures similar to G beta, their hydrodynamic properties should be those of compact, globular proteins, and they should be resistant to cleavage by trypsin. However, the only studied example of a WD-repeat protein, G beta, synthesized in vitro in a rabbit reticulocyte lysate, is unable to fold into a native structure without its partner protein G gamma. The non-WD-repeat amino terminal alpha helix of G beta does not inhibit folding because G beta does not fold even when this region is removed. It is not known whether all WD-repeat proteins are unable to fold when synthesized in an in vitro system. We synthesized seven members of the family in a rabbit reticulocyte lysate, determined their Stokes radius, sedimentation coefficient, and frictional ratio, and assayed their stability to trypsin. Our working definition of folding was that the proteins from globular, trypsin-resistant structures because, except for G beta gamma, their functions are not known or cannot be assayed in reticulocyte lysates. We chose proteins that include amino and carboxyl extensions as well as proteins that are made up entirely of WD-repeats. We show that unlike G beta, several proteins with WD-repeats are able to fold into globular proteins in a rabbit reticulocyte lysate. One protein, beta Trcp, formed large aggregates like G beta, suggesting that it may also require a partner protein. Despite the presence of many potential tryptic cleavage sites, all of the proteins that did fold gave stable large products on tryptic proteolysis, as predicted on the basis of the structure of G beta. These studies suggest that other WD-repeat proteins are likely to form propeller structures similar to G beta.
Long-term clinical relevance of criteria for designating multiple sclerosis as benign after 10 years of disease (2008)

Although designating patients as having a benign course after 10 years has a poor predictive value, three factors at presentation indicate a better prognosis.
Hyaluronic acid stimulates human fibroblast proliferation within a collagen matrix (1998)

Human dermal fibroblasts suspended in a collagen matrix exhibit a 4-day delay in cell division, while the same cells in monolayer divided by day 1. The initial rates of 3H-thymidine incorporation by cells in monolayer or suspended in collagen were not significantly different. When suspended in collagen, there was a threefold increase in the proportion of cells in a tetraploidal (4N) DNA state compared to the same cells in monolayer. Flow cytometry analysis and 3H-thymidine incorporation studies identified the delay of cell division as a consequence of a block in the G2/M of the cell cycle and not an inhibition of DNA synthesis. The inclusion of 150 microg/ml of hyaluronic acid (HA) in the manufacture of fibroblast populated collagen lattices (FPCL) caused a stimulation of cell division, as determined by cell counting; increased the expression of tubulin, as determined by Western blot analysis; and reduced the proportion of cells in a 4N state, as determined by flow cytometry. HA added to the same cells growing in monolayer produced a minimal increase in the rate of cell division or DNA synthesis. HA supplementation of FPCLs stimulated cell division as well as tubulin concentrations, but it did not enhance lattice contraction. The introduction of tubulin isolated from pig brain or purchased tubulin into fibroblasts by electroporation prior to their transfer into collagen lattices promoted cell division in the first 24 hours and enhanced FPCL contraction. It is proposed that tubulin protein, the building blocks of microtubules, is limited in human fibroblasts residing within a collagen matrix. When human fibroblasts are suspended in collagen, one effect of added HA may be to stimulate the synthesis of tubulin which assists cells through the cell cycle.
Detection of viable and dead Listeria monocytogenes on gouda-like cheeses by real-time PCR (2005)

The significance of this work is that we have developed a novel concept for detection of viable and potentially infectious L. monocytogenes.
Computational prediction of methylation status in human genomic sequences (2006)

Epigenetic effects in mammals depend largely on heritable genomic methylation patterns. We describe a computational pattern recognition method that is used to predict the methylation landscape of human brain DNA. This method can be applied both to CpG islands and to non-CpG island regions. It computes the methylation propensity for an 800-bp region centered on a CpG dinucleotide based on specific sequence features within the region. We tested several classifiers for classification performance, including K means clustering, linear discriminant analysis, logistic regression, and support vector machine. The best performing classifier used the support vector machine approach. Our program (called hdfinder) presently has a prediction accuracy of 86%, as validated with CpG regions for which methylation status has been experimentally determined. Using hdfinder, we have depicted the entire genomic methylation patterns for all 22 human autosomes.
Thermostability of bacterial luciferase expressed in different microbes (1994)

Bacterial luciferase was used to investigate the relationship between the thermostability of a cytoplasmic reporter molecule and cellular heat resistance. The luciferase activity of Vibrio fischeri was expressed in strains of Escherichia coli, Salmonella typhimurium, Listeria monocytogenes and Brochothrix thermosphacta following transformation with plasmid pSP13 carrying the luxAB genes. The thermostability of intracellular luciferase varied depending on the organism in which it was expressed, but was not related to the cellular heat resistance of the different organisms. Addition of xylitol to the heating medium protected against loss of viability and inactivation of intracellular luciferase. Glycerol also protected against loss of viability but was less effective at preventing thermal denaturation of luciferase.
Identification of a promiscuous inflammatory peptide receptor on the surface of red blood cells (1993)

Erythrocytes have long been appreciated as transporters and exchangers of O2 and CO2 between the lungs and the tissues. Here we examine the role of erythrocytes as potential mediators of inflammatory processes by assessing their ability to bind to a number of inflammatory peptides of the chemokine (for chemoattractant cytokine) superfamily. Radiolabeled chemokines of either the C-X-C (IL-8, MGSA/gro, NAP-2) or C-C (RANTES, MCP-1) class bind reversibly to red cell surface receptors numbering 1000-9000 sites/cell with a Kd of approximately 5 nM. In contrast to what is seen for chemokine binding to target inflammatory cells, chemokines of either class displace heterologous chemokines, indicating that the proteins are competing for a promiscuous receptor. Chemical cross-linking with radiolabeled chemokines reveals a 30-38-kilodalton protein on the red cell surface, and cross-linking is inhibited in the presence of heterologous unlabeled chemokines. These data show that red blood cells possess a multispecific receptor for the newly identified chemokine superfamily of inflammatory cytokines, and thus the red cell may play a novel role as a regulator of inflammatory processes.
Sickle cell disease diagnosis based on spatio-temporal cell dynamics analysis using 3D printed shearing digital holographic microscopy (2018)

We present a spatio-temporal analysis of cell membrane fluctuations to distinguish healthy patients from patients with sickle cell disease. A video hologram containing either healthy red blood cells (h-RBCs) or sickle cell disease red blood cells (SCD-RBCs) was recorded using a low-cost, compact, 3D printed shearing interferometer. Reconstructions were created for each hologram frame (time steps), forming a spatio-temporal data cube. Features were extracted by computing the standard deviations and the mean of the height fluctuations over time and for every location on the cell membrane, resulting in two-dimensional standard deviation and mean maps, followed by taking the standard deviations of these maps. The optical flow algorithm was used to estimate the apparent motion fields between subsequent frames (reconstructions). The standard deviation of the magnitude of the optical flow vectors across all frames was then computed. In addition, seven morphological cell (spatial) features based on optical path length were extracted from the cells to further improve the classification accuracy. A random forest classifier was trained to perform cell identification to distinguish between SCD-RBCs and h-RBCs. To the best of our knowledge, this is the first report of machine learning assisted cell identification and diagnosis of sickle cell disease based on cell membrane fluctuations and morphology using both spatio-temporal and spatial analysis.
Are Selective Macromolecule Removal Plasmapheresis Systems Useful for Autoimmune Diseases or Hyperlipidemia? (1993)

Although technical limitations exist with existing selective removal systems, very few products are available and no major clinical trials have demonstrated the superiority or equivalence of selective removal systems over plasma exchange. It is generally recognized that selective removal systems are preferable, and that selective macromolecule removal plasmapheresis systems are useful for autoimmune diseases or hyperlipidemia. In the treatment of a disease with a selective removal device, the disease pathogen should be identified and the efficacy of removal demonstrated. In general, for plasmapheresis applications, there is a need to better understand the pathophysiology of the disease states and to identify the pathogenic molecules. With such information, development of the optimal selective removal method will be possible. There is the need for clinical studies to compare selective removal and plasma exchange for specific disease states. Incentives for the development of improved selective removal technologies where cost effectiveness could be demonstrated should be encouraged.
Monometallic, homo-, and hetero-bimetallic complexes of a siloxy-bis(phosphinimide) ligand (2006)

Deprotonation of Me 3 SiNP(t-Bu) 2 Me with BuLi generates [Me 3 SiNP(t-Bu) 2 CH 2 Li] (1), which reacts with (Me 2 SiCl) 2 O to give the new siloxyl-bis(phosphinimine) ligand [Me 3 SiNP(t-Bu) 2 CH 2 SiMe 2 ] 2 O (2). This ligand reacts with 1 or 2 equiv. of CpTiCl 3 to give [CpTiCl 2 NP(t-Bu) 2 CH 2 SiMe 2 OCH 2 SiMe 2 P(t-Bu) 2 NSiMe 3 ] (3) and [CpTiCl 2 NP(t-Bu) 2 CH 2 SiMe 2 ] 2 O (4), similar to the species [CpNbCl 3 NP(t-Bu) 2 CH 2 SiMe 2 ] 2 O (5) and [CpTiCl 2 NP(t-Bu) 2 (µ-O-(CH 2 SiMe 2 ) 2 )- P(t-Bu) 2 NCpNbCl 3 ] (6). Subsequent alkylations of these metal-halide derivatives afforded the analogous permethylated analogs 7–10, respectively. Reaction of 8 with B(C 6 F 5 ) 3 generates [(CpTiMe 2 NP(t-Bu) 2 CH 2 SiMe 2 )(CpTiMeNP(t-Bu) 2 CH 2 SiMe 2 )O][MeB(C 6 F 5 )] (11). Benzylation of 4 give the species [CpTiBz 2 NP(t-Bu) 2 CH 2 SiMe 2 ] 2 O (12), which reacts subsequently with NC(2,6-Me 2 C 6 H 3 ) to give a 1:1 mixture of the diastereoisomers of [CpTiBz(N=C(CH 2 Ph)(2,6-Me 2 C 6 H 3 ))NP(t-Bu) 2 CH 2 SiMe 2 ] 2 O 13a and 13b. These synthetic routes are described and the implications considered. X-ray structural data for compounds 2, 4, 8, and 10 are reported.Key words: phosphinimide ligands, bimetallic species, heterobimetallic compounds.
The Personal Health Inventory: Current Use, Perceived Barriers, and Benefits. (2017)

A survey of primary care providers at a VA hospital helped to understand respondents' barriers to and benefits of using a personal health inventory with patients.
Symmetry-based inhibitors of HIV protease. Structure-activity studies of acylated 2,4-diamino-1,5-diphenyl-3-hydroxypentane and 2,5-diamino-1,6-diphenylhexane-3,4-diol (1993)

The structure-activity relationships in two series of novel, symmetry-based inhibitors of HIV protease, the enzyme responsible for maturation of the human immunodeficiency virus, are described. Beginning with lead compounds 3-6, the effect of adding polar, heterocyclic end groups to one or both ends of the symmetric or pseudosymmetric inhibitors was probed. Aqueous solubility was enhanced > 1000-fold while maintaining potent inhibition of purified HIV-1 protease and anti-HIV activity in vitro. Pharmacokinetic studies in rats indicated a substantial difference in the absorption properties of mono-ol-based and diol-based inhibitors. The oral bioavailability of inhibitor 19 in rats was 19%; however, the Cmax obtained failed to exceed the anti-HIV EC50 in vitro. Substantial plasma levels of potent inhibitors of the diol class were not obtained after oral administration in rats; however, the optimal combination of aqueous solubility and in vitro antiviral activity of several inhibitors support their potential use in intravenous therapy.
A fuzzy ontology-based abstract search engine and its user studies (2002)

Query refinement can help users find information on the Internet more effectively. This feature has been implemented in a PASS (personalized abstract search services) system, a Web-based, domain-specific search engine for searching abstracts of research papers. The system uses a fuzzy ontology of term associations to support the feature. The ontology is automatically built in two stages using information obtained from the system's collection. A preliminary user study reveals that query refinement is one of the most important features of the system.