gebhart/patrepeval huggingface dataset:
Graphene oxide for effective radionuclide removal (2012)

Here we show the efficacy of graphene oxide (GO) for rapid removal of some of the most toxic and radioactive long-lived human-made radionuclides from contaminated water, even from acidic solutions (pH < 2). The interaction of GO with actinides including Am(III), Th(IV), Pu(IV), Np(V), U(VI) and typical fission products Sr(II), Eu(III) and Tc(VII) were studied, along with their sorption kinetics. Cation/GO coagulation occurs with the formation of nanoparticle aggregates of GO sheets, facilitating their removal. GO is far more effective in removal of transuranium elements from simulated nuclear waste solutions than other routinely used sorbents such as bentonite clays and activated carbon. These results point toward a simple methodology to mollify the severity of nuclear waste contamination, thereby leading to effective measures for environmental remediation.
Knowledge-based automatic topic identification (1995)

As the first step in an automated text summarization algorithm, this work presents a new method for automatically identifying the central ideas in a text based on a knowledge-based concept counting paradigm. To represent and generalize concepts, we use the hierarchical concept taxonomy WordNet. By setting appropriate cutoff values for such parameters as concept generality and child-to-parent frequency ratio, we control the amount and level of generality of concepts extracted from the text.
Subbreakdown drain leakage current in MOSFET (1987)

Significant drain leakage current can be detected at drain voltages much lower than the breakdown voltage. This subbreakdown leakage can dominate the drain leakage current at zero V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</inf> in thin-oxide MOSFET's. The mechanism is shown to be band-to-band tunneling in Si in the drain/gate overlap region. In order to limit the leakage current to 0.1 pA/µm, the oxide field in the gate-to-drain overlap region must be limited to 2.2 MV/cm. This may set another constraint for oxide thickness or power supply voltage.
BREAK THE FLAME CHAIN REACTION (1962)

Since man first discovered how to start fires he has been trying to find better ways to put them out. Water, if properly applied, is effective but is not always readily available at the fire site and may be difficult to transport over the required distance. Many investigations have been made and others are in progress to discover some effective chemical fire suppressant.
How Dangerous Is Looking Away From the Road? Algorithms Predict Crash Risk From Glance Patterns in Naturalistic Driving (2012)

The results inform the design of algorithms to monitor driver state that support real-time distraction mitigation systems.
Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity (1993)

Multiple RNA splicing sites exist within human immunodeficiency virus type 1 (HIV-1) genomic RNA, and these sites enable the synthesis of many mRNAs for each of several viral proteins. We evaluated the biological significance of the alternatively spliced mRNA species during productive HIV-1 infections of peripheral blood lymphocytes and human T-cell lines to determine the potential role of alternative RNA splicing in the regulation of HIV-1 replication and infection. First, we used a semiquantitative polymerase chain reaction of cDNAs that were radiolabeled for gel analysis to determine the relative abundance of the diverse array of alternatively spliced HIV-1 mRNAs. The predominant rev, tat, vpr, and env RNAs contained a minimum of noncoding sequence, but the predominant nef mRNAs were incompletely spliced and invariably included noncoding exons. Second, the effect of altered RNA processing was measured following mutagenesis of the major 5' splice donor and several cryptic, constitutive, and competing 3' splice acceptor motifs of HIV-1NL4-3. Mutations that ablated constitutive splice sites led to the activation of new cryptic sites; some of these preserved biological function. Mutations that ablated competing splice acceptor sites caused marked alterations in the pool of virus-derived mRNAs and, in some instances, in virus infectivity and/or the profile of virus proteins. The redundant RNA splicing signals in the HIV-1 genome and alternatively spliced mRNAs provides a mechanism for regulating the relative proportions of HIV-1 proteins and, in some cases, viral infectivity.
The Pathology of Influenza Virus Infections (2008)

Influenza viruses are significant human respiratory pathogens that cause both seasonal, endemic infections and periodic, unpredictable pandemics. The worst pandemic on record, in 1918, killed approximately 50 million people worldwide. Human infections caused by H5N1 highly pathogenic avian influenza viruses have raised concern about the emergence of another pandemic. The histopathology of fatal influenza virus pneumonias as documented over the past 120 years is reviewed here. Strikingly, the spectrum of pathologic changes described in the 1918 influenza pandemic is not significantly different from the histopathology observed in other less lethal pandemics or even in deaths occurring during seasonal influenza outbreaks.
Emergence of resistant variants of HIV in vivo during monotherapy with the proteinase inhibitor saquinavir (1997)

We examined the phenotypic and genotypic properties of virus from the peripheral blood mononuclear cells (PBMC) and plasma of eight HIV-1-infected asymptomatic patients before and during monotherapy with the proteinase inhibitor saquinavir. Susceptibility of primary isolates to drug was assessed in PBMC culture by deriving IC50 and IC90 values. The observed increases in IC50 and IC90 after approximately one year of therapy with a dosage of 600 mg tds suggests the presence of virus resistant to saquinavir in vivo. The magnitude of this altered susceptibility ranged from three-fold to in one case 100-fold. In two patients a greater than eight-fold decrease in susceptibility to saquinavir was observed. Sequencing of the proteinase genes in viral RNA obtained from patient plasma and/or PBMC was carried out by PCR in parallel with sensitivity testing. In each case between nine and 12 clones were analysed. In the two patients from whom virus had greater than eight-fold reduction in susceptibility, a point mutation was observed in the viral proteinase (Leu90--> Met/Ile). Further mutations were observed at residues 36, 71 and 84 in these subjects. In a third patient, in whom an eight-fold increase in HIV IC50 of saquinavir was observed, no mutations were detected in the proteinase; sequencing of proteinase cleavage sites in viral gag-pol revealed no significant mutations. In no patient was a Gly48-->Val mutation observed, although this has been associated with resistance in vitro. The Leu90-->Met mutation was observed in five subjects, but a greater than eight-fold phenotypic change in antiviral susceptibility was seen in only two of these. Hence, in vivo, the Leu90-->Met but not the Gly48-->Val mutation is necessary, but not sufficient, for phenotypic resistance to saquinavir in HIV.
The human fatty acid-binding protein family: Evolutionary divergences and functions (2011)

Fatty acid-binding proteins (FABPs) are members of the intracellular lipid-binding protein (iLBP) family and are involved in reversibly binding intracellular hydrophobic ligands and trafficking them throughout cellular compartments, including the peroxisomes, mitochondria, endoplasmic reticulum and nucleus. FABPs are small, structurally conserved cytosolic proteins consisting of a water-filled, interior-binding pocket surrounded by ten anti-parallel beta sheets, forming a beta barrel. At the superior surface, two alpha-helices cap the pocket and are thought to regulate binding. FABPs have broad specificity, including the ability to bind long-chain (C16-C20) fatty acids, eicosanoids, bile salts and peroxisome proliferators. FABPs demonstrate strong evolutionary conservation and are present in a spectrum of species including Drosophila melanogaster, Caenorhabditis elegans, mouse and human. The human genome consists of nine putatively functional protein-coding FABP genes. The most recently identified family member, FABP12, has been less studied.
Immunostimulatory DNA Reverses Established Allergen-Induced Airway Remodeling (2004)

To determine whether immunostimulatory sequences of DNA (ISS) can reverse established airway remodeling, mice that had developed airway remodeling following 3 mo of repetitive OVA challenges, were treated with ISS for 1-3 mo. Systemic administration of ISS to mice that had already developed established airway remodeling significantly reduced the degree of airway collagen deposition (assessed by lung collagen content, peribronchial trichrome staining, and immunostaining with anticollagen type III and type V Abs). ISS reduced bronchoalveolar lavage and lung levels of TGF-beta1 and reduced the number of TGF-beta1-positive eosinophils and TGF-beta1-positive mononuclear cells recruited to the airway. In vitro studies demonstrated that ISS inhibited TGF-beta1 expression by macrophages (RAW 264.7 cell line and bone marrow-derived macrophages). In addition, ISS significantly reduces lung levels of expression of the chemokine thymus- and activation-regulated chemokine, as well as the number of peribronchial CD4(+) lymphocytes that express Th2 cytokines that promote peribronchial fibrosis. Overall, these studies demonstrate that ISS can reverse features of airway collagen deposition by reducing levels of lung TGF-beta1, as well as by reducing levels of the chemokine thymus- and activation-regulated chemokine and the numbers of peribronchial CD4(+) lymphocytes that drive the ongoing Th2 immune response.
TheTRP4gene ofSaccharomyces cerevisiae: isolation and structural analysis (1986)

The TRP4 gene of Saccharomyces cerevisiae, encoding the anthranilate phosphoribosyl transferase, was isolated and subcloned by functional complementation in yeast. A 2 kb fragment containing information for a polypeptide of 380 amino acids and the 5'- and 3'-flanking regions was sequenced. The TRP4 transcript was identified and mapped with S1 nuclease. Homologies to two prokaryotic genes encoding the same function, and sequences potentially involved in transcription start and termination and in regulation of TRP4 gene expression are discussed.
Angle Independent Ultrasonic Detection of Blood Flow (1987)

We present a new technique for blood velocity imaging based on tracking the motion of the speckle pattern produced by blood. Unlike Doppler velocity determinations, these are angle independent. Initial in vivo experiments yield promising results.
Development of functional biomaterials with micro- and nanoscale technologies for tissue engineering and drug delivery applications (2012)

Micro- and nanotechnologies have emerged as potentially effective fabrication tools for addressing the challenges faced in tissue engineering and drug delivery. The ability to control and manipulate polymeric biomaterials at the micron and nanometre scale with these fabrication techniques has allowed for the creation of controlled cellular environments, engineering of functional tissues and development of better drug delivery systems. In tissue engineering, micro- and nanotechnologies have enabled the recapitulation of the micro- and nanoscale detail of the cell's environment through controlling the surface chemistry and topography of materials, generating 3D cellular scaffolds and regulating cell-cell interactions. Furthermore, these technologies have led to advances in high-throughput screening (HTS), enabling rapid and efficient discovery of a library of materials and screening of drugs that induce cell-specific responses. In drug delivery, controlling the size and geometry of drug carriers with micro- and nanotechnologies have allowed for the modulation of parametres such as bioavailability, pharmacodynamics and cell-specific targeting. In this review, we introduce recent developments in micro- and nanoscale engineering of polymeric biomaterials, with an emphasis on lithographic techniques, and present an overview of their applications in tissue engineering, HTS and drug delivery.
Cloning and characterization of the cDNAs for human and rabbit interleukin-1 precursor (1985)

DNA sequence complementary to the mRNA for rabbit interleukin-1 precursor (preIL-1) has been cloned from the cDNA library constructed using partially purified poly(A)+RNA from induced rabbit alveolar macrophages by mRNA hybridization-translation assay. By using this cDNA as a probe, human IL-1 cDNA was isolated from the cDNA library prepared using poly(A)+RNA from induced HL-60 cells, a human monocyte-like cell line. The amino acid sequences of the human and rabbit preIL-1 deduced from the cDNA sequences reveal their primary structures which consists of 271 and 267 amino acid residues, respectively. The amino acid sequence is 64% conserved between human and rabbit. The difference in number of amino acid residues results from the carboxy-terminal extention of 4 amino acid residues in human preIL-1. Expression of the cloned human cDNA in E. coli yielded biologically active IL-1.
Potential Mechanism for Sustained Antiretroviral Efficacy of AZT-3TC Combination Therapy (1995)

Combinations of antiretroviral drugs that prevent or delay the appearance of drug-resistant human immunodeficiency virus-type 1 (HIV-1) mutants are urgently required. Mutants resistant to 3'-azidothymidine (AZT, zidovudine) became phenotypically sensitive in vitro by mutation of residue 184 of viral reverse transcriptase to valine, which also induced resistance to (-)2'-deoxy-3'-thiacytidine (3TC). Furthermore, AZT-3TC coresistance was not observed during extensive in vitro selection with both drugs. In vivo AZT-3TC combination therapy resulted in a markedly greater decreased in serum HIV-1 RNA concentrations than treatment with AZT alone, even though valine-184 mutants rapidly emerged. Most samples assessed from the combination group remained AZT sensitive at 24 weeks of therapy, consistent with in vitro mutation studies.
Effect of Different Fractions of Heparin on Plasmodium falciparum Merozoite Invasion of Red Blood Cells in Vitro (1992)

Heparin and various heparin fractions were separated according to differences in molecular weight or affinity for antithrombin III and used for the inhibition of Plasmodium falciparum merozoite invasion of red blood cells in vitro. No variation in sensitivity to heparin was found among the four strains of P. falciparum tested; all required approximately 5 micrograms/ml (0.5 U/ml) of heparin for 50% inhibition of invasion. The most efficient fraction of heparin was the one with low affinity for antithrombin III. Its 50% inhibition concentration was 1 microgram/ml, indicating that it was more efficient than unfractionated heparin and other heparin fractions. The effect of heparin was reversible, since washing of heparin-treated cultures containing mainly schizonts showed no inhibition of merozoite invasion. The results suggest that a heparin fraction with no anticoagulant effect might be useful in the treatment of patients with falciparum malaria.
Applying Method of Moments to Model Reliability of Pavements Infrastructure (2006)

Even though the concepts of pavement reliability and risk-based design have been recognized for a long time, probabilistic pavement design methods are often limited to the application of Monte Carlo simulation or Taylor expansion to evaluate reliability measures. This paper presents a comprehensive framework for establishing pavement reliability functions that consider various uncertainties associated with a pavement, starting from design assumptions to construction process and finally to utilization. With the recent development in the theory of structural reliability, in particular, the introduction of the standard normal point-estimate method for approximation of moments of the limit state function and the standardized functions for obtaining moment reliability indices, analytical evaluation of the probability integral for reliability has become feasible. The primary advantage of the analytical approach is its suitability for implementing optimization models of classical nonlinear algorithms. Finally, a numerical study was conducted to demonstrate the applicability of the method of moments for predicting pavement reliability.
Genome-wide DNA methylation profiling of chronic lymphocytic leukemia allows identification of epigenetically repressed molecular pathways with clinical impact (2010)

We performed a genome-wide analysis of aberrant DNA methylation in chronic lymphocytic leukemia (CLL) using methylated CpG island amplification (MCA) coupled with a promoter microarray. We identified 280 potential targets of aberrant DNA methylation in CLL. These genes were located more frequently in chromosomes 19 (16%, p=0.001), 16 (11%, p=0.001), 17 (10%, p=0.02) and 11 (9%, p=0.02) and could be grouped in several functional networks. Methylation status was confirmed for 22 of these genes (SOX11, DLX1, FAM62C, SOX14, RSPO1, ADCY5, HAND2,SPOCK, MLL, ING1, PRIMA1, BCL11B, LTBP2, BNC1, NR2F2, SALL1, GALGT2, LHX1, DLX4, KLK10, TFAP2 and APP) in 78 CLL patients by pyrosequencing. As a proof of principle, we analyzed the expression of 2 genes, PRIMA1 and APP, in primary cells and of GALGT2, TFAP2C and PRIMA1 in leukemia cells. There was an inverse association between methylation and gene expression. This could be reversed by treatment with 5-aza-2'-deoxycytidine in cell lines. Treatment in a clinical trial with 5-azacitidine resulted in decreased methylation of LINE, DLX4 and SALL1 in the peripheral blood B-cells of patients with CLL. IgVH mutational status or ZAP-70 expression were not associated with specific methylation profiles. By multivariate analysis, methylation of LINE and APP was associated with shorter overall survival (p = 0.045 and 0.0035, respectively). This study demonstrates that aberrant DNA methylation is common and has potential prognostic and therapeutic value in CLL.
Estimates of disease effects on soybean yields in the United States 2003 to 2005. (2006)

Research must focus on management of diseases that cause extensive losses, especially when funds for research are limited. Knowledge of the losses caused by various soybean diseases is essential when prioritizing research budgets. The objective of this project was to compile estimates of soybean yields suppressed due to diseases for each soybean-producing state in the US from 2003 to 2005. The goal was to provide this information to help funding agencies and scientists prioritize research objectives and budgets. Yield suppression due to individual diseases varied among regions in the US, and the total of soybean yields suppressed due to diseases in the US varied among years. Soybean cyst nematode suppressed US soybean yield more during 2003 to 2005 than any other disease. Phytophthora root and stem rot, sudden death syndrome, and seedling diseases ranked in the top four on the list of diseases that suppressed soybean yield during these years. This is the first report of soybean yield suppression due to Asian soybean rust in the United States.
Specific cellular stimulation in the primary immune response: a quantized model. (1982)

A general theory for the initial phase of T cell independent immune response is derived from elementary physical-chemical considerations and from the premise that response entails a quantized linkage of cell surface receptors. The theory leads to the construction of explicit antigen dose--response and antigen dose--suppression curves, to the calculation of intrinsic affinities for receptors, and to the deduction that receptors are divalent in character. The theory may be applicable to other cell surface phenomena wherein requirements for stimulation and suppression are equivalent to those found in the immune system.
Chemical Approaches to Triggerable Lipid Vesicles for Drug and Gene Delivery (2003)

Effective drug delivery requires the precise spatial and temporal delivery of therapeutic agents to the target site. To this end, a variety of chemical and physicochemical approaches have been devised to create lipid vesicles (liposomes) that can be triggered to release their contents in a controlled fashion. The triggers include changes in pH, redox potential, temperature, or the level of specific enzymes. We review the chemistries that have recently been applied to exploit the pH and redox potential triggers so as to release vesicle contents in the appropriate biological location.
Protocol for Dengue Infections in Mosquitoes (A. aegypti) and Infection Phenotype Determination (2007)

The purpose of this procedure is to infect the Aedes mosquito with dengue virus in a laboratory condition and examine the infection level and dynamic of the virus in the mosquito tissues. This protocol is routinely used for studying mosquito-virus interactions, especially for identification of novel host factors that are able to determine vector competence. The entire experiment must be conducted in a BSL2 laboratory. Similar to Plasmodium falciparum infections, proper attire including gloves and lab coat must be worn at all times. After the experiment, all the materials that came in contact with the virus need to be treated with 75% ethanol and bleached before proceeding with normal washing. All other materials need to be autoclaved before discarding them.
CD28, Ox-40, LFA-1, and CD4 Modulation of Th1/Th2 Differentiation Is Directly Dependent on the Dose of Antigen (2000)

The involvement of specific accessory/costimulatory molecules in differentiation to Th1 and Th2 phenotypes is controversial. Reports suggest that molecules such as CD4, CD28, and Ox-40 support Th2 differentiation and suppress Th1 differentiation, whereas others such as LFA-1 support Th1 responses and suppress Th2 responses. We have previously defined an in vitro model of differentiation that is absolutely dependent on the initial dose and affinity of peptide presented to a naive CD4 cell. The dose and affinity of Ag regulate autocrine production of IL-2, IL-4, and IFN-gamma, which in turn govern differentiation to Th1 and Th2 phenotypes. We have used this system to confirm that CD4, CD28, and Ox-40 interactions can promote, and LFA-1 interactions can suppress, differentiation of cells secreting the Th2 cytokines IL-5 and IL-13. However, for CD4 and LFA-1, this is only seen over a certain range of peptide doses. In addition, CD28 and Ox-40 interactions also promote Th1 differentiation. In general, agonist Abs to accessory molecules shifted the response curves for IFN-gamma, IL-5, and IL-13 to lower doses, whereas antagonist reagents resulted in similar curves shifted toward the higher doses. We conclude that ligation of cell surface accessory receptors enables low doses of Ag to promote responses normally induced only by higher doses. Individual receptors do not intrinsically regulate one cytokine phenotype or another, suggesting that differentiation is controlled by the level of expression of multiple accessory molecule pairs integrated with the number and affinity of peptide/MHC complexes.