gebhart/patrepeval huggingface dataset:
An Ionization Process in a Low-Energy Cesium Plasma (1965)

The mechanisms of ion formation in cesium plasmas at relatively low electron temperatures (3500°K) and pressures of a few Torr are investigated. It is concluded that most of the ions are molecular and that they are formed by collisions between cesium atoms in the first excited state. The excited atoms are predominantly produced by inelastic electron collisions. The excitation cross section is computed by means of the impact parameter method. It has a maximum value of 100×10−16 cm2 at 7 eV. The de-excitation cross section is computed and found to be approximately constant at 50×10−16 cm2. Radiation trapping and diffusion of excited atoms are also studied. The ionization cross section is calculated by means of statistical thermodynamics from the measured recombination coefficient for the inverse of the ionizing process. It is found to be 1450×10−16 cm2. The plasma is uniform throughout its volume except in the immediate vicinity of the bounding electrodes. The proposed mechanism results in performance characteristics for cesium thermionic converters, operating in the ``ignited mode,'' which are in qualitative and quantitative agreement with experimental data.
Surface Complexation and Oxidation of SnII by Nanomagnetite (2013)

The long-lived fission product 126Sn is of substantial interest in the context of nuclear waste disposal in deep underground repositories. However, the prevalent redox state, the aqueous speciation as well as the reactions at the mineral-water interface under the expected anoxic and reducing conditions are a matter of debate. We therefore investigated the reaction of Sn(II) with a relevant redox-reactive mineral, magnetite (Fe(II)Fe(III)2O4) at <2 ppmv O2, and monitored Sn uptake as a function of pH and time. Tin redox state and local structure were investigated by Sn–K X-ray absorption spectroscopy (XAS). We observed a rapid uptake (<30 min) and oxidation of Sn(II) to Sn(IV) by magnetite. The local structure determined by XAS showed two Sn–Fe distances of about 3.15 and 3.60 Å in line with edge and corner sharing arrangements between octahedrally coordinated Sn(IV) and the magnetite surface, indicative of formation of tetradentate inner-sphere complexes between pH 3 and 9. Based on the EXAFS-derived surface structure, we could successfully model the sorption data with two different complexes, (Magn_sO)4Sn(IV)(OH)2–2 (logK(2,0)(–2) −14.97 ± 0.35) prevailing from pH 2 to 9, and (Magn_sO)4Sn(IV)(OH)2Fe (logK(2,1)(0) −17.72 ± 0.50), which forms at pH > 9 by coadsorption of Fe(II), thereby increasing sorption at this high pH.
cAMP signaling in neurons: patterns of neuronal expression and intracellular localization for a novel protein, AKAP 150, that anchors the regulatory subunit of cAMP-dependent protein kinase II beta. (1992)

In mammalian brain, physiological signals carried by cyclic AMP (cAMP) seem to be targeted to effector sites via the tethering of cAMP-dependent protein kinase II beta (PKAII beta) to intracellular structures. Recently characterized A kinase anchor proteins (AKAPs) are probable mediators of the sequestration of PKAII beta because they contain a high-affinity binding site for the regulatory subunit (RII beta) of the kinase and a distinct intracellular targeting domain. To establish a cellular basis for this targeting mechanism, we have employed immunocytochemistry to 1) identify the types of neurons that are enriched in AKAPs, 2) determine the primary intracellular location of the anchor protein, and 3) demonstrate that an AKAP and RII beta are coenriched and colocalized in neurons that utilize the adenylate cyclase-cyclic AMP-dependent protein kinase (PKA) signaling pathway. Antibodies directed against rat brain AKAP 150 were used to elucidate the regional, cellular and intracellular distribution of a prototypic anchor protein in the CNS. AKAP 150 is abundant in Purkinje cells and in neurons of the olfactory bulb, basal ganglia, cerebral cortex, and other forebrain regions. In contrast, little AKAP 150 is detected in neurons of the thalamus, hypothalamus, midbrain, and hindbrain. A high proportion of total AKAP 150 is concentrated in primary branches of dendrites, where it is associated with microtubules. We also discovered that the patterns of accumulation and localization of RII beta (and PKAII beta) in brain are similar to those of AKAP 150. The results suggest that bifunctional AKAP 150 tethers PKAII beta to the dendritic cytoskeleton, thereby creating a discrete target site for the reception and propagation of signals carried by cAMP.
Role of oxidised low density lipoprotein in atherogenesis (1993)

* What is oxidised LDL? * What is the evidence for the presence in vivo of oxidised LDL? * What are the potential mechanisms by which oxidised LDL may be atherogenic? * What measures may be taken to inhibit the oxidative modification process?
KLF2 exerts antifibrotic and vasoprotective effects in cirrhotic rat livers: behind the molecular mechanisms of statins (2014)

Exogenous hepatic KLF2 upregulation improves liver fibrosis, endothelial dysfunction and portal hypertension in cirrhosis.
Polydrug- and Methadone-Addicted Newborns: A Continuum of Impairment? (1982)

Two groups of infants born to drug-addicted mothers were evaluated in a prospective controlled study and compared with a third control group. Group I infants (N = 39) were born to mothers on well-controlled low-dose methadone maintenance. Group II infants (N = 19) were born to polydrug-abusing mothers, and group III infants (N = 27) were born to control mothers who had no history or evidence of drug abuse. All three groups were matched for maternal factors that might affect neonatal outcome. Group I infants were significantly smaller than control infants for all growth measurements and had a significantly smaller head circumference than group II infants. Utilizing the Brazelton Neonatal Behavioral Assessment Scale, group I infants showed more depression of interactive behaviors and state controls than group II infants, who in turn were more depressed than group III infants. The effects of nonnarcotic drugs on intrauterine growth and neonatal behavior appear to place the polydrug-addicted newborn in an intermediate zone of deficit between normal and opiate-addicted newborns.
Gas chromatographic/mass spectrometric analysis of stable isotopes of 3-methylhistidine in biological fluids: Application to plasma kineticsin vivo (1992)

A simple and rapid method for measuring 3-methylhistidine (3MH) in plasma and urine is described. Internal standard, 1-methylhistidine (1MH), was added to plasma, acidified and absorbed onto cation-exchange columns. It was then eluted from columns, dried, and derivatized for gas chromatography/mass spectrometry. A major fragment of 3MH was monitored at 238 u and 3-methyl-(methyl-2H3)histidine (d3-3MH) (used for in vivo kinetics) at 241 u, whereas 1MH was monitored at 340 u and eluted 0.5 min later than 3MH. Standard curves for plasma analysis were linear and nanamole amounts of 3MH in plasma were determined with a precision of 3.5%. 3MH was also quantitated in urine; however, because of substantial amounts of 1MH, (18O2)1MH was used as the internal standard. Nanamole amounts of 3MH were determined in urine with a precision of 2.7%. Application of the 3MH analytical method was used to develop a kinetic compartmental model by using the stable isotope of 3MH, d3-3MH. Cattle, like humans, quantitatively excrete 3MH in the urine. A young bovine was injected with d3-3MH and the enrichment curve in plasma was evaluated in order to obtain a steady-state production rate of 3MH. The decay curve was modeled through the use of NIH-SAAM modeling program. The kinetics of d3-3MH from plasma were adequately described by a three-pool compartmental model. The de novo production rate of 3MH estimated in the calf was 665 mumol per day. This corresponded to an estimated fractional turnover rate of 1.56% per day, which was similar to estimates obtained from urine collections.(ABSTRACT TRUNCATED AT 250 WORDS)
High-performance electrical signaling (2002)

This paper reviews the technology of high-performance electrical signaling, presents the current state of the art, and projects future directions. We have demonstrated equalized electrical signaling between CMOS integrated circuits at data rates of 4Gb/s. As the factors that determine this signaling rate all scale with improving technology we expect the data rates of high-performance electrical signaling systems to improve on a Moore's Law curve. The frequency-dependent attenuation of copper wires sets a bandwidth-distance squared (Bd/sup 2/) limit on the distance one can signal at a given data rate. Equalizing the channel cancels inter-symbol interference caused by this attenuation and greatly increases signaling distance. In the limit of perfect equalization, distance is ultimately limited by thermal noise in the receiver. At this limit, we calculate that a 4Gb/s system will be capable of operating over 100m of 24-gauge cable without repeaters.
Blockade of the natriuretic peptide receptor guanylyl cyclase-A inhibits NF-κB activation and alleviates myocardial ischemia/reperfusion injury (2001)

Acute myocardial infarction (AMI) remains the leading cause of death in developed countries. Although reperfusion of coronary arteries reduces mortality, it is associated with tissue injury. Endothelial P-selectin–mediated infiltration of neutrophils plays a key role in reperfusion injury. However, the mechanism of the P-selectin induction is not known. Here we show that infarct size after ischemia/reperfusion was significantly smaller in mice lacking guanylyl cyclase-A (GC-A), a natriuretic peptide receptor. The decrease was accompanied by decreases in neutrophil infiltration in coronary endothelial P-selectin expression. Pretreatment with HS-142-1, a GC-A antagonist, also decreased infarct size and P-selectin induction in wild-type mice. In cultured endothelial cells, activation of GC-A augmented H2O2-induced P-selectin expression. Furthermore, ischemia/reperfusion–induced activation of NF-κB, a transcription factor that is known to promote P-selectin expression, is suppressed in GC-A–deficient mice. These results suggest that inhibition of GC-A alleviates ischemia/reperfusion injury through suppression of NF-κB–mediated P-selectin induction. This novel, GC-A–mediated mechanism of ischemia/reperfusion injury may provide the basis for applying GC-A blockade in the clinical treatment of reperfusion injury.
Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations (2017)

Fecal microbiota transplantation is a compelling treatment for recurrent Clostridium difficile infections, with potential applications against other diseases associated with changes in gut microbiota. But variability in fecal bacterial communities-believed to be the therapeutic agent-can complicate or undermine treatment efficacy. To understand the effects of transplant preparation methods on living fecal microbial communities, we applied a DNA-sequencing method (PMA-seq) that uses propidium monoazide (PMA) to differentiate between living and dead fecal microbes, and we created an analysis pipeline to identify individual bacteria that change in abundance between samples. We found that oxygen exposure degraded fecal bacterial communities, whereas freeze-thaw cycles and lag time between donor defecation and transplant preparation had much smaller effects. Notably, the abundance of Faecalibacterium prausnitzii-an anti-inflammatory commensal bacterium whose absence is linked to inflammatory bowel disease-decreased with oxygen exposure. Our results indicate that some current practices for preparing microbiota transplant material adversely affect living fecal microbial content and highlight PMA-seq as a valuable tool to inform best practices and evaluate the suitability of clinical fecal material.
Enhancement of Cancer Vaccine Therapy by Systemic Delivery of a Tumor-Targeting Salmonella- Based STAT3 shRNA Suppresses the Growth of Established Melanoma Tumors (2011)

Cancer vaccine therapies have only achieved limited success when focusing on effector immunity with the goal of eliciting robust tumor-specific T-cell responses. More recently, there is an emerging understanding that effective immunity can only be achieved by coordinate disruption of tumor-derived immunosuppression. Toward that goal, we have developed a potent Salmonella-based vaccine expressing codon-optimized survivin (CO-SVN), referred to as 3342Max. When used alone as a therapeutic vaccine, 3342Max can attenuate growth of aggressive murine melanomas overexpressing SVN. However, under more immunosuppressive conditions, such as those associated with larger tumor volumes, we found that the vaccine was ineffective. Vaccine efficacy could be rescued if tumor-bearing mice were treated initially with Salmonella encoding a short hairpin RNA (shRNA) targeting the tolerogenic molecule STAT3 (YS1646-shSTAT3). In vaccinated mice, silencing STAT3 increased the proliferation and granzyme B levels of intratumoral CD4(+) and CD8(+) T cells. The combined strategy also increased apoptosis in tumors of treated mice, enhancing tumor-specific killing of tumor targets. Interestingly, mice treated with YS1646-shSTAT3 or 3342Max alone were similarly unsuccessful in rejecting established tumors, whereas the combined regimen was highly potent. Our findings establish that a combined strategy of silencing immunosuppressive molecules followed by vaccination can act synergistically to attenuate tumor growth, and they offer a novel translational direction to improve tumor immunotherapy.
p38 MAPK signalling cascades: ancient roles and new functions (2000)

p38 MAPKs are a conserved subfamily of MAPKs involved in the response to stress found in eukaryotic cells from yeast to mammals. The recent isolation of genes coding for members of this signalling cascade in Drosophila has provided us with the genetic tools to study their various biological roles and their regulatory interactions with other signalling pathways. This cascade participates in the immune response, a function that is remarkably conserved between flies and humans. Additionally, it appears to exert other fundamental roles during development, in cell fate specification in imaginal discs, and in cell polarity during oogenesis. These functions involve genetic and biochemical interactions with other signalling cascades, the decapentaplegic/TGFbeta, the wingless/Wnt and the torpedo/Ras-ERK pathways. In the near future, we can expect a flurry of information that will allow us to draw a comprehensive picture of the roles of signalling networks mediated by p38s during development.
MIRD Pamphlet No 19: absorbed fractions and radionuclide S values for six age-dependent multiregion models of the kidney. (2003)

The multiregion model described here permits estimates of regional kidney dose not previously supported by current single-region models. Full utilization of the new model, however, requires serial imaging of the kidneys with regions of interest assigned to the renal cortex and medulla.
Virus-induced Interferon α Production by a Dendritic Cell Subset in the Absence of Feedback Signaling In Vivo (2002)

An effective type I interferon (IFN-alpha/beta) response is critical for the control of many viral infections. Here we show that in vesicular stomatitis virus (VSV)-infected mouse embryonic fibroblasts (MEFs) the production of IFN-alpha is dependent on type I IFN receptor (IFNAR) triggering, whereas in infected mice early IFN-alpha production is IFNAR independent. In VSV-infected mice type I IFN is produced by few cells located in the marginal zone of the spleen. Unlike other dendritic cell (DC) subsets, FACS((R))-sorted CD11c(int)CD11b(-)GR-1(+) DCs show high IFN-alpha expression, irrespective of whether they were isolated from VSV-infected IFNAR-competent or -deficient mice. Thus, VSV preferentially activates a specialized DC subset presumably located in the marginal zone to produce high-level IFN-alpha largely independent of IFNAR feedback signaling.
Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem (2015)

Woody plant encroachment has become a global threat to grasslands and has caused declines in aboveground richness and changes in ecosystem function; yet we have a limited understanding on the effects of these phenomena on belowground microbial communities. We completed riparian woody plant removals at Konza Prairie Biological Station, Kansas and collected soils spanning land-water interfaces in removal and woody vegetation impacted areas. We measured stream sediments and soils for edaphic variables (C and N pools, soil water content, pH) and bacterial (16S rRNA genes) and fungal (ITS2 rRNA gene repeat) communities using Illumina MiSeq metabarcoding. Bacterial richness and diversity decreased with distance from streams. Fungal richness decreased with distance from the stream in wooded areas, but was similar across landscape position while Planctomycetes and Basidiomycota relative abundance was lower in removal areas. Cyanobacteria, Ascomycota, Chytridiomycota and Glomeromycota relative abundance was greater in removal areas. Ordination analyses indicated that bacterial community composition shifted more across land-water interfaces than fungi yet both were marginally influenced by treatment. This study highlights the impacts of woody encroachment restoration on grassland bacterial and fungal communities which likely subsequently affects belowground processes and plant health in this ecosystem.
Parametric Response Map As an Imaging Biomarker to Distinguish Progression From Pseudoprogression in High-Grade Glioma (2010)

Purpose To assess whether a new method of quantifying therapy-associated hemodynamic alterations may help to distinguish pseudoprogression from true progression in patients with high-grade glioma. Patients and Methods Patients with high-grade glioma received concurrent chemoradiotherapy. Relative cerebral blood volume (rCBV) and blood flow (rCBF) maps were acquired before chemoradiotherapy and at week 3 during treatment on a prospective institutional review board–approved study. Pseudoprogression was defined as imaging changes 1 to 3 months after chemoradiotherapy that mimic tumor progression but stabilized or improved without change in treatment or for which resection revealed radiation effects only. Clinical and conventional magnetic resonance (MR) parameters, including average percent change of rCBV and CBF, were evaluated as potential predictors of pseudoprogression. Parametric response map (PRM), an innovative, voxel-by-voxel method of image analysis, was also performed. Results Median radiation dose was 72 Gy (range, 60 to 78 Gy). Of 27 patients, stable disease/partial response was noted in 13 patients and apparent progression was noted in 14 patients. Adjuvant temozolomide was continued in all patients. Pseudoprogression occurred in six patients. Based on PRM analysis, a significantly reduced blood volume (PRM rCBV ) at week 3 was noted in patients with progressive disease as compared with those with pseudoprogression (P &lt; .01). In contrast, change in average percent rCBV or rCBF, MR tumor volume changes, age, extent of resection, and Radiation Therapy Oncology Group recursive partitioning analysis classification did not distinguish progression from pseudoprogression. Conclusion PRM rCBV at week 3 during chemoradiotherapy is a potential early imaging biomarker of response that may be helpful in distinguishing pseudoprogression from true progression in patients with high-grade glioma.
Purification and characterization of a novel metalloendopeptidase from Saccharomyces cerevisiae (1993)

We previously identified an activity in the soluble fraction of the yeast Saccharomyces cerevisiae that is a candidate for catalyzing the proteolytic maturation of farnesylated-CXXX precursor polypeptides. We describe here a 1259-fold purification of this activity by chromatography on DEAE-cellulose, hydroxylapatite, phenyl-Sepharose, and Sephacryl S-200. Sodium dodecyl sulfate gel electrophoresis of this preparation demonstrated a single 68-kDa polypeptide chain. The experimentally determined N-terminal amino acid sequence was identical at all 20 positions with residues 28-47 of the deduced sequence of the S. cerevisiae YCL57w gene product. This analysis suggests that the YCL57w gene encodes this enzyme and that the initial translation product may contain a leader peptide. Its complete deduced amino acid sequence shows significant homology to a number of zinc metallopeptidases and is most closely related to rat metalloendopeptidase 24.15 (E.C. 3.4.24.15), an enzyme that preferentially cleaves after hydrophobic residues. Using the purified yeast enzyme, we show a unique cleavage site in the peptides bradykinin and beta-neoendorphin four residues from the C-terminus on the carboxyl side of a hydrophobic amino acid. The cleavage pattern for neurotensin revealed a major site three residues from the C-terminus also on the carboxyl side of a hydrophobic residue and a minor site four residues from the C-terminus of the peptide. This specificity is similar to that of rat endopeptidase 24.15 and may explain why the farnesylated peptide employed in our studies is a good substrate for the yeast enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)
Helper T-Cell Responses and Clinical Activity of a Melanoma Vaccine With Multiple Peptides From MAGE and Melanocytic Differentiation Antigens (2008)

Results of this study support the safety and immunogenicity of a vaccine comprised of six melanoma helper peptides. There is also early evidence of clinical activity.
Novel developments on cervical length screening and progesterone for preventing preterm birth (2008)

Cervical length (CL) measured by transvaginal ultrasound is an effective screening test for the prevention of preterm birth (PTB). The criteria for an effective screening test are all met by CL. It studies an important condition (PTB); it is safe and acceptable by >99% of women; it recognises an early asymptomatic phase that precedes PTB by many weeks; it has a well-described technique, is reproducible, is predictive of PTB in all populations studies so far; and, perhaps most importantly, it has been shown that 'early' treatment is effective in prevention. These two interventions, effective only in specific populations, are ultrasound-indicated cerclage and vaginal progesterone.
ADAMTS2 gene dysregulation in T/myeloid mixed phenotype acute leukemia (2014)

Detailed molecular cytogenetic characterization of the complex rearrangement in the reported T/My MPAL case allowed us to observe ADAMTS2 gene overexpression, identifying a molecular marker that may be useful for monitoring minimal residual disease. To our knowledge, this is the first evidence of gene dysregulation due to a chromosomal rearrangement in T/My MPAL NOS.