gebhart/patrepeval huggingface dataset:
Iron-suppressible production of hydroxamate by Escherichia coli isolates (1982)

A total of 476 strains of Escherichia coli isolated from humans, pigs, cattle, poultry, potable water, or effluent were examined for iron-suppressible ability to produce hydroxamate. Isolates able to produce such material (Hyd+ isolates) are presumed to be able to carry out hydroxamate-dependent transport of iron. The percentages of Hyd+ isolates found among E. coli isolated from the feces of breast-fed babies (71%), adults (46%), milk-fed calves (32%), or poultry (28%) were significantly greater (P less than 0.01) than the percentages isolated from potable water and effluent (6%) or from the feces of suckling piglets (6%), weaned pigs (6%), or weaned cattle (4%). The percentages of Hyd+ isolates found among E. coli associated with diarrhea in humans (51%), weaned pigs (7%) or calves (25%) were not significantly different (P greater than 0.1) from those found among strains isolated from corresponding nondiarrheic hosts. Many of the E. coli isolated from cases of E. coli bacteremia in humans and poultry were Hyd+ (64% and 83%, respectively). We conclude that ability to carry out hydroxamate-mediated transport of iron is widely distributed among natural isolates of E. coli but that the distribution of Hyd+ E. coli is not random. E. coli isolated from sources where levels of available iron might be expected to be low tend to be Hyd+. It seems that a link may exist between prevalence of Hyd+ E. coli and active host-defense based on restricted availability of iron.
5-Aminolevulinic acid-based photodynamic therapy (1997)

Promising results of ALA-based clinical PDT and diagnosis have been obtained. The modality has advantages over conventional treatments. However, some improvements need to be made, such as optimization of parameters of ALA-based PDT and diagnosis; increased tumor selectivity of ALA-derived PpIX; better understanding of light distribution in tissue: improvement of light dosimetry procedure; and development of simpler, cheaper, and more efficient light delivery systems.
Selective H atom sensors using ultrathin Ag/Si Schottky diodes (1999)

Schottky diodes with ultrathin silver films on n-Si(111) are used for selective detection of atomic hydrogen. The exothermic adsorption of H atoms on the Ag surface creates hot electrons which may travel ballistically through the metal film and traverse the Schottky barrier. The chemically induced current is measurable (≈0.001 electrons/H atom) as a chemicurrent. After saturation of the adsorption sites, this chemicurrent achieves a steady-state value due to a balance of removal of adsorbed hydrogen and readsorption. The detection limit of the sensors is approximately 1010 H atoms cm−2 s−1. The detectors are completely insensitive to H2 molecules.
Welcome to Y2K: Is Art Therapy a Profession or an Idea? (2000)

(2000). Welcome to Y2K: Is Art Therapy a Profession or an Idea? Art Therapy: Vol. 17, Is art therapy a profession or an idea?, pp. 2-3.
A system for simulation and monitoring of robot-assisted and navigation-assisted surgical interventions (Part 1) (2002)

Location monitoring systems for surgical applications are getting more and more common in clinical daily life. Navigation treatment systems are also a form of a location monitoring system. These systems always consist of an optical, US-, electromagnetic or mechanical navigation system. If two or more navigation systems are combined or one navigations system is combined with a robot system the kinematic model of the entire system consists of closed kinematic loops. In this paper, an approach is presented to gain more information from the closed kinematic chains instead of breaking the kinematic loops.
A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA (2001)

The 21-nucleotide small temporal RNA (stRNA) let-7 regulates developmental timing in Caenorhabditis elegans and probably in other bilateral animals. We present in vivo and in vitro evidence that in Drosophila melanogaster a developmentally regulated precursor RNA is cleaved by an RNA interference-like mechanism to produce mature let-7 stRNA. Targeted destruction in cultured human cells of the messenger RNA encoding the enzyme Dicer, which acts in the RNA interference pathway, leads to accumulation of the let-7 precursor. Thus, the RNA interference and stRNA pathways intersect. Both pathways require the RNA-processing enzyme Dicer to produce the active small-RNA component that represses gene expression.
Atom Transfer Radical Polymerization (ATRP): Current Status and Future Perspectives (2012)

Current status and future perspectives in atom transfer radical polymerization (ATRP) are presented. Special emphasis is placed on mechanistic understanding of ATRP, recent synthetic and process development, and new controlled polymer architectures enabled by ATRP. New hybrid materials based on organic/inorganic systems and natural/synthetic polymers are presented. Some current and forthcoming applications are described.
Expansion of spleen myeloid suppressor cells represses NK cell cytotoxicity in tumor-bearing host (2007)

Tumor growth promotes the expansion of myeloid suppressor cells. An inverse correlation between natural killer (NK) cell activation and myeloid suppressor cell (MSC) expansion in tumor-bearing patients and mice prompted us to investigate the role of MSCs in controlling NK antitumor cytotocixity. After adoptive transfer to naive recipients, CD11b(+)Gr-1(+) MSCs freshly isolated from spleens of tumor-bearing mice but not naive mice were able to inhibit NK cell cytotoxicity. An in vivo imaging analysis indicates that the removal of tumors resulted in a significant increased ability (P < .05) in NK cell cytotoxicity to eliminate injected YAC-1 cells from the lungs. Fluorescence-activated cell sorter (FACS) analysis of the composition of lung leukocytes further indicates that the removal of tumors also leads to the reduction of MSCs accumulated in the lung. These data suggest that MSCs suppress NK cell cytotoxicity. The inhibition of NK cell cytotoxicity is cell-cell contact dependent. Inhibition of perforin but not granzyme B production was responsible for MSC-mediated inhibition of NK cytotoxicity. Western blot analyses further suggests that MSCs suppress IL-2-mediated NK cell cytotoxicity by affecting the activity of Stat5.
Interleukin‐13 receptor α2 chain (2006)

IL-13Ralpha2 is a promising target for ovarian cancer therapy, and the soluble form of IL-13R may be a possible surrogate marker for disease monitoring.
ICL670A: a new synthetic oral chelator: evaluation in hypertransfused rats with selective radioiron probes of hepatocellular and reticuloendothelial iron stores and in iron-loaded rat heart cells in culture (2001)

ICL670A (formerly CGP 72 670) or 4-[3,5-bis-(hydroxyphenyl)-1,2,4-triazol-1-yl]- benzoic acid is a tridentate iron-selective synthetic chelator of the bis-hydroxyphenyl-triazole class of compounds. The present studies used selective radioiron probes of hepatocellular and reticuloendothelial (RE) iron stores in hypertransfused rats and iron-loaded heart cells to define the source of iron chelated in vivo by ICL670A and its mode of excretion, to examine its ability to remove iron directly from iron-loaded myocardial cells, and to examine its ability to interact with other chelators through a possible additive or synergistic effect. Results indicate that ICL670A given orally is 4 to 5 times more effective than parenteral deferoxamine (DFO) in promoting the excretion of chelatable iron from hepatocellular iron stores. The pattern of iron excretion produced by ICL670A is quite different from that of DFO and all iron excretion is restricted to the bile regardless of whether it is derived from RE or hepatocellular iron stores. Studies in heart cell cultures have shown a favorable interaction between DFO and ICL670A manifested in improved chelating efficiency of ICL670A, which is most probably explained by an exchange of chelated iron between ICL670A and DFO. These unique chelating properties of ICL670A may have practical implications for current efforts to design better therapeutic strategies for the management of transfusional iron overload.
The Parasitome of the Phytonematode Heterodera glycines (2003)

Parasitism genes expressed in the esophageal gland cells of phytonematodes encode secretions that control the complex process of plant parasitism. In the soybean cyst nematode, Heterodera glycines, the parasitome, i.e., the secreted products of parasitism genes, facilitate nematode migration in soybean roots and mediate the modification of root cells into elaborate feeding cells required to support the growth and development of the nematode. With very few exceptions, the identities of these secretions are unknown, and the mechanisms of cyst nematode parasitism, therefore, remain obscure. The most direct and efficient approach for cloning parasitism genes and rapidly advancing our understanding of the molecular interactions during nematode parasitism of plants is to create gland cell-specific cDNA libraries using cytoplasm microaspirated from the esophageal gland cells of various parasitic stages. By combining expressed sequence tag analysis of a gland cell cDNA library with high throughput in situ expression localization of clones encoding secretory proteins, we obtained the first comprehensive parasitome profile for a parasitic nematode. We identified 51 new H. glycines gland-expressed candidate parasitism genes, of which 38 genes constitute completely novel sequences. Individual parasitome members showed distinct gland cell expression patterns throughout the parasitic cycle. The parasitome complexity discovered paints a more elaborate picture of host cellular events under specific control by the nematode parasite than previously hypothesized.
Functional trait complementarity and dominance both determine benthic secondary production in temperate seagrass beds (2021)

Abstract Defining relationships between biodiversity and ecosystem functioning (BEF) is key to understanding the consequences of biodiversity loss. Although species functional traits are strongly linked to ecosystem processes, their integration into BEF models has been focused mainly on terrestrial ecosystems. Application is limited because functional trait‐based BEF models typically have small‐sample sizes and highly correlated predictors, making it difficult for model selection and identifying underlying drivers. We examine the BEF relationship between secondary production and benthic invertebrate taxonomic and functional diversity for seagrass beds located across a range of environmental conditions. Specifically, we evaluate the role of complementarity (i.e., dissimilarity in species or traits) and dominance (disproportional importance of traits) in determining secondary production at 20 sites using 34 metrics of taxonomic diversity, functional diversity, and functional traits. Here, diversity metrics represent complementarity and functional traits represent dominance. We used elastic‐net regression and commonality analysis to evaluate the BEF model, because its properties (i.e., few observations and many potential, and highly correlated, predictors) precluded more standard approaches and it is well suited to this situation. Functional richness and five functional traits (crawling, surface deposit feeding [SurDF], location on sediment surface, lifespan 1–3 yr, and semi‐continuous breeding) were identified as important determinants of secondary production, explaining 74% of the variance. SurDF was the most important predictor that acted in isolation to influence secondary production, while all other predictors acted together. All six selected variables in three different combinations explained 68% of the total variance in the BEF model. These results indicate that both dominance and complementarity mechanisms were important for the BEF relationship. Our study highlights elastic‐net regression and commonality analysis as a powerful approach to model functional trait‐based BEF relationships. We further show that inclusion of the functional landscape into BEF models is highly valuable, allowing the implications of species loss for ecosystem functioning to be mechanistically understood.
Adaptive ray packet reordering (2008)

Modern high-performance ray tracers use large ray packets and SIMD instruction sets to decrease both the computational and bandwidth cost compared to a single ray implementation. Current global illumination renderers, however, are still based around single ray implementations and interfaces. The presumption is that while packets have been shown to work well for highly coherent rays, in the presence of less coherent secondary ray distributions the gains of both packet and SIMD techniques dwindle rapidly. With low enough coherence, performance can be reduced to being as slow as reasonable single ray code - if not worse - so the benefit of packets for a global illumination system is assumed to be next to none. With SIMD width expanding in future architectures, leaving SIMD units underutilized means a massive loss in performance compared to the maximum performance achievable. In this paper, we present a method for recovering packet and SIMD coherence for incoherent secondary ray distributions through demand-driven reordering of rays into more coherent packets. We demonstrate that the reordering overhead is outweighed by the increased coherence within a prototypical implementation in the Manta realtime ray tracer among a wide variety of ray distributions, including diffuse path tracing.
A Pilot Study of IL-2Rα Blockade during Lymphopenia Depletes Regulatory T-cells and Correlates with Enhanced Immunity in Patients with Glioblastoma (2012)

ClinicalTrials.gov NCT00626015.
Attaching and effacing locus of a Citrobacter freundii biotype that causes transmissible murine colonic hyperplasia (1993)

Citrobacter freundii biotype 4280 produces attaching and effacing (AE) lesions in the large intestine of laboratory mice and is the causative agent of transmissible murine colonic hyperplasia. AE lesions are also produced by enteropathogenic Escherichia coli in humans. Southern analysis revealed that biotype 4280, but not 20 other strains of C. freundii, contained DNA homologous to the eae (E. coli attaching and effacing) gene which is necessary for AE activity by enteropathogenic E. coli in vitro. We have cloned and determined the nucleotide sequence of the C. freundii eae homolog. Our findings suggest that the eae locus of C. freundii biotype 4280 is necessary for AE activity and has a role in the pathogenesis of transmissible murine colonic hyperplasia.
Structure-function studies of the adenylate cyclase toxin of Bordetella pertussis and the leukotoxin of Pasteurella haemolytica by heterologous C protein activation and construction of hybrid proteins (1997)

The adenylate cyclase toxin (CyaA) from Bordetella pertussis and the leukotoxin (LktA) from Pasteurella haemolytica are members of the RTX (stands for repeats in toxin) family of cytolytic toxins. They have pore-forming activity and share significant amino acid homology but show marked differences in biological activity. CyaA is an invasive adenylate cyclase and a weak hemolysin which is active on a wide range of mammalian cells. LktA is a cytolytic protein with a high target cell specificity and is able to lyse only leukocytes and platelets from ruminants. Each toxin is synthesized as an inactive protoxin encoded by the A gene, and the product of the accessory C gene is required for posttranslational activation. Heterologous activation of LktA by CyaC did not result in a change in its specificity for nucleated cells, although the toxin showed a greater hemolytic-to-cytotoxic ratio. LktC was unable to activate CyaA. A hybrid toxin (Hyb1), which contained the N-terminal enzymic domain and the pore-forming domain from CyaA (amino acids [aa] 1 to 687), with the remainder of the protein derived from the C-terminal end of LktA (aa 379 to 953), showed no toxic activity. Replacement of part of the LktA C-terminal domain of Hyb1 by the CyaA C-terminal domain (aa 919 to 1706) to create hybrid toxin 2 (Hyb2) partially restored toxic activity. In contrast to CyaA, Hyb2 was activated more efficiently by LktC than by CyaC, showing the importance of the region between aa 379 and 616 of LktA for activation by LktC. LktC-activated Hyb2 was more active against ruminant than murine nucleated cells, whereas CyaC-activated Hyb2 displayed a similar, but lower, activity against both cell types. These data indicate that LktC and the region with which it interacts have an influence on the target cell specificity of the mature toxin.
Gut microbiome-host interactions in health and disease (2011)

The gut microbiome is the term given to describe the vast collection of symbiotic microorganisms in the human gastrointestinal system and their collective interacting genomes. Recent studies have suggested that the gut microbiome performs numerous important biochemical functions for the host, and disorders of the microbiome are associated with many and diverse human disease processes. Systems biology approaches based on next generation 'omics' technologies are now able to describe the gut microbiome at a detailed genetic and functional (transcriptomic, proteomic and metabolic) level, providing new insights into the importance of the gut microbiome in human health, and they are able to map microbiome variability between species, individuals and populations. This has established the importance of the gut microbiome in the disease pathogenesis for numerous systemic disease states, such as obesity and cardiovascular disease, and in intestinal conditions, such as inflammatory bowel disease. Thus, understanding microbiome activity is essential to the development of future personalized strategies of healthcare, as well as potentially providing new targets for drug development. Here, we review recent metagenomic and metabonomic approaches that have enabled advances in understanding gut microbiome activity in relation to human health, and gut microbial modulation for the treatment of disease. We also describe possible avenues of research in this rapidly growing field with respect to future personalized healthcare strategies.
Rapid Evolution of H5N1 Influenza Viruses in Chickens in Hong Kong (1999)

The H5N1 avian influenza virus that killed 6 of 18 persons infected in Hong Kong in 1997 was transmitted directly from poultry to humans. Viral isolates from this outbreak may provide molecular clues to zoonotic transfer. Here we demonstrate that the H5N1 viruses circulating in poultry comprised two distinguishable phylogenetic lineages in all genes that were in very rapid evolution. When introduced into new hosts, influenza viruses usually undergo rapid alteration of their surface glycoproteins, especially in the hemagglutinin (HA). Surprisingly, these H5N1 isolates had a large proportion of amino acid changes in all gene products except in the HA. These viruses maybe reassortants each of whose HA gene is well adapted to domestic poultry while the rest of the genome arises from a different source. The consensus amino acid sequences of "internal" virion proteins reveal amino acids previously found in human strains. These human-specific amino acids may be important factors in zoonotic transmission.
Field Test of a Unique Phosphonate Scale Inhibitor for Extended-Life Squeeze Treatment in Sandstone (1999)

Abstract The Chevron field at Rangely Colorado is a mature field that is currently under water alternating gas (WAG) Carbon Dioxide flood. There is continuing concern that barium sulfate may form in the wells and calcite may form in surface facilities. Squeezing the wells to protect them from barium sulfate scale has been the best method of controlling the barium sulfate problem. Production is from sandstone, which makes it difficult to obtain optimal performance from scale squeeze treatments. For ten years these wells have been treated with good success using an acidic Diethylene Triamine PentaMethylene Phosponic Acid (DETPMP) type inhibitor. Likewise good squeeze results had been obtained in the North Sea sandstones for many years using DETPMP type inhibitors, but improved results were seen with PhosphonoMethylated PolyAmines (PMPA). Therefore it seemed logical to try the PMPA in this Colorado sandstone. Four wells were squeezed with PMPA. Initial return curves were very promising. No large return spikes were seen, indicating that the inhibitor adsorbed very well. Within a few weeks residual levels fell to a very desirable level of 10 mg/l. Residuals then continued to fall to levels below the target level of about 5 ppm. However, there are no reports of scale in the well indicating that sufficient inhibitor is returning to control scale. By mass balance, 20 to 30% of the squeezed chemical returned after nine months. Most of that returned in the first few months after the squeeze. At current return levels, inhibitor could return for many years.
Complement factor D, a novel serine protease (1996)

Factor D is unique among serine proteases in that it requires neither enzymatic cleavage for expression of proteolytic activity nor inactivation by a serpin for its control. Regulation of factor D activity is instead attained by a novel mechanism that depends on reversible conformational changes for expression and control of catalytic activity. These conformational changes are believed to be induced by the single natural substrate, C3bB, and to result in realignment of the catalytic triad, the specificity pocket, and the nonspecific substrate binding site, all of which have atypical conformations. Mutational studies have defined structural determinants responsible for these unique structural features of factor D and for the resultant low reactivity with synthetic esters.
Function of Cd3ε-Mediated Signals in T Cell Development (2000)

The T cell antigen receptor (TCR) and pre-TCR complexes are composed of multiple signal-transducing subunits (CD3 gamma, CD3 delta, CD3 epsilon, and zeta) that each contain one or more copies of a semiconserved functional motif, the immunoreceptor tyrosine-based activation motif (ITAM). Although biochemical studies indicate that individual TCR-ITAMs may bind selectively or with different affinity to various effector molecules, data from other experiments suggest that at least some ITAMs are functionally equivalent. In this study, we examined the role of CD3straightepsilon ITAM-mediated signals in T cell development by genetically reconstituting CD3 epsilon-deficient mice with transgenes encoding either wild-type or ITAM-mutant (signaling defective) forms of the protein. The results demonstrate that signals transduced by CD3 epsilon are not specifically required for T cell maturation but instead contribute quantitatively to TCR signaling in a manner similar to that previously observed for zeta chain. Unexpectedly, analysis of TCR-transgenic/CD3 epsilon-mutant mice reveals a potential role for CD3 epsilon signals in T cell survival.