gebhart/patrepeval huggingface dataset:
A metadata calculus for secure information sharing (2009)

In both commercial and defense sectors a compelling need is emerging for rapid, yet secure, dissemination of information to the concerned actors. Traditional approaches to information sharing that rely on security labels (e.g., Multi-Level Security (MLS)) suffer from at least two major drawbacks. First, static security labels do not account for tactical information whose value decays over time. Second, MLS-like approaches have often ignored information transform semantics when deducing security labels (e.g., output security label = max over all input security labels). While MLS-like label deduction appears to be conservative, we argue that this approach can result in both underestimation and overestimation of security labels. We contend that overestimation may adversely throttle information flows, while underestimation incites information misuse and leakage.
Field-Flow Fractionation: Addressing the Nano Challenge (2010)

Field-flow fractionation is coming of age as a family of analytical methods for separating and characterizing macromolecules, nanoparticles, and particulates. The capabilities and versatility of these techniques are discussed in light of the challenges that are being addressed in analyzing nanometer-sized sample components and the insights gained through their use in applications ranging from materials science to biology. (To listen to a podcast about this feature, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html .).
Saccharification of steam‐exploded poplar wood (1991)

Effects of time, temperature, and pH during the steam explosion of poplar wood were studied with the aim of optimize both pentoses recovery and enzymatic hydrolysis efficiency. Steam explosion of acid impregnated wood chips allowed the recovery of 70% of potential xylose as monomers (217 degrees C, 120 s) Enzymatic hydrolysis of pretreated fiber with Trichoderma reesei CL-847 cellulase system increased progressively with the severity of the steam treatment conditions. The best yield in term of glucose recovery after 24 h of enzymatic hydrolysis was 70% of potential glucose (225 degrees C, 120 s). Deactivation by adsorption on lignin of Trichoderma reesei cellulases and inhibition of these enzymes by low-molecular-weight phenols and trihydroxybutyric acids were noticed.
A Hammerhead Ribozyme That Cleaves Perforin and Fas-ligand RNAsin Vitro (1996)

Polyfunctional ribozymes targeting more than one RNA might be ideal for treatment of diseases caused by the expression of more than one mRNA. This is the case of Graft versus Host Disease, which in the mouse model is due to the action of two proteins responsible for different lytic pathways: perforin and fasligand. We have created a bifunctional ribozyme fusing two antiperforin and antifas-ligand hammerhead ribozymes with a stretch of CA dinucleotides. This bifunctional ribozyme is able to recognize and cleave in vitro perforin and fas-ligand mRNA in a specific and selective fashion, with a catalytic efficiency similar to that of its individual components.
Mathematical Model of the lac Operon: Inducer Exclusion, Catabolite Repression, and Diauxic Growth on Glucose and Lactose (1997)

A mathematical model of the lactose (lac) operon was developed to study diauxic growth on glucose and lactose. The model includes catabolite repression, inducer exclusion, lactose hydrolysis to glucose and galactose, and synthesis and degradation of allolactose. Two models for catabolite repression were tested: (i) cyclic AMP (cAMP) synthesis inversely correlated with the external glucose concentration and (ii) synthesis inversely correlated with the glucose transport rate. No significant differences in the two models were observed. In addition to synthesis, degradation and secretion of cAMP were also included in the model. Two models for the phosphorylation of the glucose produced from lactose hydrolysis were also tested: (i) phosphorylation by intracellular hexokinase and (ii) secretion of glucose and subsequent phosphorylation upon transport back into the cell. The latter model resulted in weak catabolite repression when the glucose produced from lactose was transported out of the cell, whereas the former model showed no catabolite repression during growth on lactose. Parameter sensitivity analysis indicates the importance of key parameters to lac operon expression and cell growth: the lactose and allolactose transformation rates by beta-galactosidase and the glucose concentrations that affect catabolite repression and inducer exclusion. Large values of the allolactose hydrolysis rate resulted in low concentrations of allolactose, low-level expression of the lac operon, and slow growth due to limited import and metabolism of lactose; small values resulted in a high concentration of allolactose, high-level expression of the lac operon, and slow growth due to a limiting concentration of glucose 6-phosphate formed from allolactose. Changes in the rates of all beta-galactosidase-catalyzed reactions showed similar behavior, but had more drastic effects on the growth rate. Changes in the glucose concentration that inhibited lactose transport could extend or contract the diauxic growth period during growth in the presence of glucose and lactose. Moreover, changes in the glucose concentration that affected catabolite repression affected the cAMP levels and lac operon expression, but had a lesser effect on the growth rate.
Calcium/Calmodulin Activation of Soybean Glutamate Decarboxylase (1995)

Recently, we provided preliminary evidence for calcium (Ca2+)/calmodulin (CaM) stimulation of plant glutamate decarboxylase (GAD; EC 4.1.1.15). In the present study, a detailed characterization of the phenomenon is described. GAD was partially purified from various soybean (Glycine max L. Merr.) tissues (developing seed coat and cotyledons, leaf, and root) in the presence of EDTA by a combination of ammonium sulfate precipitation and anion-exchange fast protein liquid chromatography. GAD activity showed a sharp optimum at pH 5.8, with about 12% of maximal activity at pH 7. It was stimulated 2- to 8-fold (depending on the tissue source) in the presence of Ca2+/CaM at pH 7 but not at pH 5.8. Furthermore, when the protease inhibitor phenylmethylsulfonyl fluoride was omitted from the purification procedure, GAD activity was insensitive to Ca2+/CaM but was similar in magnitude to CaM-stimulated activity. The stimulation by Ca2+/CaM was fully inhibited by the CaM antagonists N-(6-aminohexyl)-5-chloro-1-naphthalenesulfon-amide and trifluoperazine. With saturating CaM or Ca2+, the concentrations of Ca2+ and CaM required for half-maximal stimulation were about 7 to 11 [mu]M and 25 nM, respectively. The effect of Ca2+ and CaM appeared to be through a 2.4-fold stimulation of Vmax and a 55% reduction in Km. The results suggested that GAD is activated via Ca2+ signal transduction.
Targeted therapy for NSCLC with driver mutations (2013)

Oncogenic products represent reliable targets for drug therapy and the expanding knowledge of molecular pathways involved in lung tumorigenesis is resulting in a dramatic change of treatment strategies leading to an improvement in disease and symptom control, extending life duration and improving quality of life.
Nuclear transplantation of ectodermal cells in pig oocytes: Ultrastructure and radiography (1996)

This study investigated the changes in nucleolar fine structure and the synthesis of both heterogeneous nuclear RNA (hnRNA) and ribosomal RNA (rRNA) in pig reconstructed embryos obtained by electrofusion of a single pig ectodermal cell to an enucleated metaphase-II oocyte. The nucleolar morphological changes and the pattern of transcription were examined in the ectodermal cells before fusion and in the nuclear transfer reconstructed embryos 16-18 hr after fusion. Before fusion the ectodermal cells exhibited a reticulated nucleolus with active RNA synthesis. In the reconstructed embryos, modifications of the nucleolar structure were observed, as assessed by the presence of either round-shaped, compact, dense nucleolar precursor bodies, or reticulated nucleoli. However, in both cases there was no RNA synthesis. Blebbing activity of the nuclear envelope was not observed. These results indicate that the nucleus of pig ectodermal cells exhibited either a complete or an incomplete remodelling when transferred to an enucleated metaphase-II oocyte, with no detectable RNA synthesis. Cell-cycle synchronization of ectodermal cell donor nuclei may play an important role in nuclear reprogramming after fusion.
Trophoblast differentiation during embryo implantation and formation of the maternal-fetal interface (2004)

Trophoblasts, the specialized cells of the placenta, play a major role in implantation and formation of the maternal-fetal interface. Through an unusual differentiation process examined in this review, these fetal cells acquire properties of leukocytes and endothelial cells that enable many of their specialized functions. In recent years a great deal has been learned about the regulatory mechanisms, from transcriptional networks to oxygen tension, which control trophoblast differentiation. The challenge is to turn this information into clinically useful tests for monitoring placental function and, hence, pregnancy outcome.
Mass Spectrometric Approaches for Elucidation of Antigen—Antibody Recognition Structures in Molecular Immunology (2007)

Mass spectrometric approaches have recently gained increasing access to molecular immunology and several methods have been developed that enable detailed chemical structure identification of antigen-antibody interactions. Selective proteolytic digestion and MS-peptide mapping (epitope excision) has been successfully employed for epitope identification of protein antigens. In addition, "affinity proteomics" using partial epitope excision has been developed as an approach with unprecedented selectivity for direct protein identification from biological material. The potential of these methods is illustrated by the elucidation of a beta-amyloid plaque-specific epitope recognized by therapeutic antibodies from transgenic mouse models of Alzheimer's disease. Using an immobilized antigen and antibody-proteolytic digestion and analysis by high resolution Fourier transform ion cyclotron resonance mass spectrometry has lead to a new approach for the identification of antibody paratope structures (paratope-excision; "parex-prot"). In this method, high resolution MS-peptide data at the low ppm level are required for direct identification of paratopes using protein databases. Mass spectrometric epitope mapping and determination of "molecular antibody-recognition signatures" offer high potential, especially for the development of new molecular diagnostics and the evaluation of new vaccine lead structures.
Space−Velocity Correlation Focusing (1996)

An algorithm is developed for identifying optimal focusing conditions in time-of-flight mass spectrometers with certain ionization source geometries. Ions are extracted from the source using time-dependent electric fields. Calculations and experiments demonstrate that use of these optimum conditions can significantly improve mass spectrometer resolution. Matrix-assisted laser desorption/ionization (MALDI) represents an application that is of considerable interest. Because the identification of optimum conditions depends on a correlation between the spatial and velocity distributions of ions in the source region of the instrument, we call this approach space−velocity correlation focusing.
Bicarbonate Enhances the Peroxidase Activity of Cu,Zn-Superoxide Dismutase (1999)

We examined the effect of bicarbonate on the peroxidase activity of copper-zinc superoxide dismutase (SOD1), using the nitrite anion as a peroxidase probe. Oxidation of nitrite by the enzyme-bound oxidant results in the formation of the nitrogen dioxide radical, which was measured by monitoring 5-nitro-gamma-tocopherol formation. Results indicate that the presence of bicarbonate is not required for the peroxidase activity of SOD1, as monitored by the SOD1/H(2)O(2)-mediated nitration of gamma-tocopherol in the presence of nitrite. However, bicarbonate enhanced SOD1/H(2)O(2)-dependent oxidation of tocopherols in the presence and absence of nitrite and dramatically enhanced SOD1/H(2)O(2)-mediated oxidation of unsaturated lipid in the presence of nitrite. These results, coupled with the finding that bicarbonate protects against inactivation of SOD1 by H(2)O(2), suggest that SOD1/H(2)O(2) oxidizes the bicarbonate anion to the carbonate radical anion. Thus, the amplification of peroxidase activity of SOD1/H(2)O(2) by bicarbonate is attributed to the intermediary role of the diffusible oxidant, the carbonate radical anion. We conclude that, contrary to a previous report (Sankarapandi, S., and Zweier, J. L. (1999) J. Biol. Chem. 274, 1226-1232), bicarbonate is not required for peroxidase activity mediated by SOD1 and H(2)O(2). However, bicarbonate enhanced the peroxidase activity of SOD1 via formation of a putative carbonate radical anion. Biological implications of the carbonate radical anion in free radical biology are discussed.
Distributions of Exons and Introns in the Human Genome (2004)

The human genome is revisited using exon and intron distribution profiles. The 26,564 annotated genes in the human genome (build October, 2003) contain 233,785 exons and 207,344 introns. On average, there are 8.8 exons and 7.8 introns per gene. About 80% of the exons on each chromosome are < 200 bp in length. < 0.01% of the introns are < 20 bp in length and < 10% of introns are more than 11,000 bp in length. These results suggest constraints on the splicing machinery to splice out very long or very short introns and provide insight to optimal intron length selection. Interestingly, the total length in introns and intergenic DNA on each chromosome is significantly correlated to the determined chromosome size with a coefficient of correlation r = 0.95 and r = 0.97, respectively. These results suggest their implication in genome design.
Formation of the initial C3 convertase of the alternative complement pathway. Acquisition of C3b-like activities by spontaneous hydrolysis of the putative thioester in native C3. (1981)

Activation of the alternative pathway of complement commences with the formation of an initial fluid-phase C3 convertase. Treatment of C3 with the nucleophilic reagent methylamine has previously been shown to result in the cleavage of an intramolecular thioester bond and to induce C3b-like properties, including the ability to form a fluid-phase C3 convertase. This report examines the hypothesis that spontaneous hydrolysis of the thioester generates a derivative of C3 that is responsible for the formation of the initial C3 convertase of the alternative pathway. The rate of spontaneous decay of C3 hemolytic activity in buffer was found to be between 0.2 and 0.4%/h. In the presence of other alternative pathway proteins, the rate of inactivation was 1%/h. The rate of spontaneous inactivation was greatly accelerated by low concentrations of chaotrophic agents such as KSCN or guanidine. Liberation of a sulfhydryl group, not present in native C3, correlated with loss of hemolytic activity, indicating that exposure to chaotropic agents resulted in thioester hydrolysis. Unlike native C3, C3 bearing a single reactive sulfhydryl group was capable of generating fluid-phase C3 convertase with Factors B, D, and P and was cleaved by Factor I (C3b inactivator) in the presence of Factor H (beta 1H). The fragmentation patterns indicated that the C3a domain was covalently associated with the functionally C3b-like C3. Organomercurial agarose was employed for the rapid removal of sulfhydryl-bearing, hemolytically inactive forms of C3 and C3b from native hemolytically active C3.
Neutralizing antibodies against the V3 loop of human immunodeficiency virus type 1 gp120 block the CD4-dependent and -independent binding of virus to cells (1997)

The CD4 molecule is an essential receptor for human immunodeficiency virus type 1 (HIV-1) through high-affinity interactions with the viral external envelope glycoprotein gp120. Previously, neutralizing monoclonal antibodies (MAbs) specific to the third hypervariable domain of gp120 (the V3 loop) have been thought to block HIV infection without affecting the binding of HIV particles to CD4-expressing human cells. However, here we demonstrate that this conclusion was not correct and was due to the use of soluble gp120 instead of HIV particles. Indeed, neutralizing anti-V3 loop MAbs inhibited completely the binding and entry of HIV particles into CD4+ human cells. In contrast, the binding of virus was only partially inhibited by neutralizing anti-CD4 MAbs against the gp120 binding site in CD4, which, like the anti-V3 loop MAbs, completely inhibited HIV entry and infection. Nonneutralizing control MAbs against either the V3 loop or the N or C terminus of gp120 had no significant effect on HIV binding and entry. HIV-1 particles were also found to bind human and murine cells expressing or not expressing the human CD4 molecule. Interestingly, the binding of HIV to CD4+ murine cells was inhibited by both anti-V3 and anti-CD4 MAbs, whereas the binding to human and murine CD4- cells was affected only by anti-V3 loop MAbs. The effect of anti-V3 loop neutralizing MAbs on the HIV binding to cells appears not to be the direct consequence of gp120 shedding from HIV particles or of a decreased affinity of CD4 or gp120 for binding to its surface counterpart. Taken together, our results suggest the existence of CD4-dependent and -independent binding events involved in the attachment of HIV particles to cells; in both of these events, the V3 loop plays a critical role. As murine cells lack the specific cofactor CXCR4 for HIV-1 entry, other cell surface molecules besides CD4 might be implicated in stable binding of HIV particles to cells.
Dysregulation of Allergic Airway Inflammation in the Absence of Microbial Colonization (2011)

These data demonstrate that the presence of commensal bacteria is critical for ensuring normal cellular maturation, recruitment, and control of allergic airway inflammation.
Mechanics of Deformation and Acoustic Propagation in Porous Media (1962)

A unified treatment of the mechanics of deformation and acoustic propagation in porous media is presented, and some new results and generalizations are derived. The writer's earlier theory of deformation of porous media derived from general principles of nonequilibrium thermodynamics is applied. The fluid-solid medium is treated as a complex physical-chemical system with resultant relaxation and viscoelastic properties of a very general nature. Specific relaxation models are discussed, and the general applicability of a correspondence principle is further emphasized. The theory of acoustic propagation is extended to include anisotropic media, solid dissipation, and other relaxation effects. Some typical examples of sources of dissipation other than fluid viscosity are considered.
Genetic determination of telomere size in humans: a twin study of three age groups. (1994)

Reduction of telomere length has been postulated to be a causal factor in cellular aging. Human telomeres terminate in tandemly arranged repeat arrays consisting of the (TTAGGG) motif. The length of these arrays in cells from human mitotic tissues is inversely related to the age of the donor, indicating telomere reduction with age. In addition to telomere length differences between different age cohorts, considerable variation is present among individuals of the same age. To investigate whether this variation can be ascribed to genetic influences, we have measured the size of terminal restriction fragments (TRFs) in HaeIII-digested genomic DNA from 123 human MZ and DZ twin pairs 2-95 years of age. The average rate of telomere shortening was 31 bp/year, which is similar to that observed by others. Statistical analysis in 115 pairs 2-63 years of age indicates a 78% heritability for mean TRF length in this age cohort. The individual differences in mean TRF length in blood, therefore, seem to a large extent to be genetically determined.
Trigeminal neuralgia: the diagnosis and management of this excruciating and poorly understood facial pain (2011)

Trigeminal neuralgia is defined as sudden, usually unilateral, severe, brief, stabbing recurrent episodes of pain within the distribution of one or more branches of the trigeminal nerve, which has a profound effect on quality of life. The diagnosis is made on history alone, and time needs to be taken to elicit the key features and differentiate from toothache or one of the trigeminal autonomic cephalalgias. Most trigeminal neuralgia is idiopathic, but a small percentage is due to secondary causes-for example, tumours or multiple sclerosis-which can be picked up on CT or MRI. Recently published international guidelines suggest that carbamazepine and oxcarbazepine are the first-line drugs. There is limited evidence for the use of lamotrigine and baclofen. If there is a decrease in efficacy or tolerability of medication, surgery needs to be considered. A neurosurgical opinion should be sought early. There are several ablative, destructive procedures that can be carried out either at the level of the Gasserian ganglion or in the posterior fossa. The only non-destructive procedure is microvascular decompression (MVD). The ablative procedures give a 50% chance of patients being pain free for 4 years, compared with 70% of patients at 10 years after MVD. Ablative procedures result in sensory loss, and MVD carries a 0.2-0.4% risk of mortality with a 2-4% chance of ipsilateral hearing loss. Surgical procedures result in markedly improved quality of life. Patient support groups provide information and support to those in pain and play a crucial role.
Comparison of azathioprine, methotrexate, and the combination of both in the treatment of rheumatoid arthritis (1992)

Abstract Objective. To compare the relative safety and efficacy of azathioprine (AZA), methotrexate (MTX), and the combination of both in the treatment of active rheumatoid arthritis (RA). Methods. Two hundred twelve patients with active RA were entered into a 24‐week prospective, controlled, double‐blind, multicenter trial and were randomly assigned to 1 of 3 treatment groups. Results. One hundred fifty‐eight patients finished 24 weeks of the study. There were no remissions seen but response rates were greater than 30% for all outcome measures. Combination therapy was not statistically superior to MTX therapy alone, but both combination therapy and MTX alone were superior to AZA alone when patients were analyzed by intent‐to‐treat and with withdrawals treated as therapy failures. If only patients who continued taking the therapy were analyzed, the mean improvement was greater for AZA therapy than for MTX, while the combination remained the most active. Adverse effects on the gastrointestinal tract and elevations of liver enzyme levels were the most frequent causes for discontinuations. Conclusion. Both combination therapy and MTX alone were superior to therapy with AZA alone for active RA but were not statistically different in their effect on outcome assessment.