gebhart/patrepeval huggingface dataset:
myExperiment: A Web 2.0 Virtual Research Environment for Research using Computation and Services (2009)

Recent challenges in monitoring subsurface geological repositories intended for disposal of radioactive materials such as spent nuclear fuel call for new, innovative concepts that are facility independent, cost-effective, passive, and reliable. Once nuclear material is in place at these facilities, reverifying the inventory may no longer be feasible if continuity of knowledge is lost or unavailable to the inspectors. Using cosmic ray muons may present several potential advantages over conventional photon/neutron signatures, and their use in safeguards applications have only received attention in the past decade. However, there have been limited efforts to explore the integration of cosmic ray muons into repository safeguards and study potential gains, risks, and costs. This paper presents a Monte Carlo-based methodology to characterize the cosmic ray muon flux, including muon angular and energy differential distributions at depths representative of subsurface geological repositories. Since there have been limited measurements at these sites and a measurement made in one site is not always transferable to another site, the objective is to develop an efficient simulation method and useful parametrizations to provide a convenient tool for enabling muon simulations at any geological repository site. It is expected these results will provide a better understanding of how muons can be integrated into an existing geological repository safeguards framework.
Assembly of a tRNA splicing complex: evidence for concerted excision and joining steps in splicing in vitro. (1986)

Splicing of tRNA precursors in Saccharomyces cerevisiae extracts proceeds in two steps; excision of the intervening sequence and ligation of the tRNA halves. The ability to resolve these two steps and the distinct physical properties of the endonuclease and ligase suggested that the splicing steps may not be concerted and that these two enzymes may act independently in vivo. A ligase competition assay was developed to examine whether the excision and ligation steps in tRNA splicing in vitro are concerted or independent. The ability of either yeast ligase or T4 ligase plus kinase to join the tRNA halves produced by endonuclease and the distinct structures of the reaction products provided the basis for the competition assay. In control reactions, joining of isolated tRNA halves formed by preincubation with endonuclease was measured. The ratio of yeast to T4 reaction products in these control assays reflected the ratio of the enzyme activities, as would be expected if each has equal access to the substrate. In splicing competition assays, endonuclease and pre-tRNA were added to ligase mixtures, and joining of the halves that were formed was measured. In these assays the products were predominantly those of the yeast ligase even when the T4 enzymes were present in excess. These results demonstrate preferential access of yeast ligase to the endonuclease products and provide evidence for the assembly of a functional tRNA splicing complex in vitro. This observation has important implications for the organization of the splicing components and of the gene expression pathway in vivo.
Cytotoxicity of human macrophages for tumor cells. Enhancement by human lymphocyte mediators. (1979)

Human macrophages, derived from peripheral blood monocytes, acquire enhanced cytotoxicity for human target cells after incubation in mediator-rich supernates from antigen-stimulated lymphocytes. Maximum cytotoxicity was observed after 24-h incubation in mediators. In comparison to normal macrophages, mediator-activated macrophages were cytotoxic to five of the six malignant cell lines tested but had no effect on five nonmalignant cell lines. In 20 experiments with one target (SK-BR-3), mean cytotoxicity was 23 +/- 2.7% and with another target (MA-160), was 29 +/- 3.4%. Macrophages became cytotoxic after 8-h incubation with mediators and the enhanced cytotoxicity persisted for at least 40 h after the lymphocyte mediators were removed. These findings are consistent with the hypothesis that macrophages, activated by antigen-induced lymphocyte mediators, can contribute to the host resistance to tumor growth in man.
Efficient Incorporation of Unsaturated Methionine Analogues into Proteins in Vivo (2000)

A set of eight methionine analogues was assayed for translational activity in Escherichia coli. Norvaline and norleucine, which are commercially available, were assayed along with 2-amino-5-hexenoic acid (2), 2-amino-5-hexynoic acid (3), cis-2-amino-4-hexenoic acid (4), trans-2-amino-4-hexenoic acid (5), 6,6,6-trifluoro-2-aminohexanoic acid (6), and 2-aminoheptanoic acid (7), each of which was prepared by alkylation of diethyl acetamidomalonate with the appropriate tosylate, followed by hydrolysis. The E. coli methionine auxotroph CAG18491, transformed with plasmids pREP4 and pQE15, was used as the expression host, and translational activity was assayed by determination of the capacity of the analogue to support synthesis of the test protein dihydrofolate reductase (DHFR) in the absence of added methionine. The importance of amino acid side chain length was illustrated by the fact that neither norvaline (8) nor 7 showed translational activity, in contrast to norleucine (9), which does support protein synthesis under the assay conditions. The internal alkene functions of 4 and 5 prevented incorporation of these analogues into test protein, and the fluorinated analogue 6 yielded no evidence of translational activity. The terminally unsaturated compounds 2 and 3, however, proved to be excellent methionine surrogates: 1H NMR spectroscopy, amino acid analysis, and N-terminal sequencing indicated ∼85% substitution of methionine by 2, while 3 showed 90−100% replacement. Both analogues also function efficiently in the initiation step of protein synthesis, as shown by their near-quantitative occupancy of the N-terminal amino acid site in DHFR. Enzyme kinetics assays were conducted to determine the rate of activation of each of the methionine analogues by methionyl tRNA synthetase (MetRS); results of the in vitro assays corroborate the in vivo incorporation results, suggesting that success or failure of analogue incorporation in vivo is controlled by MetRS.
Characterization of the ribonuclease activity on the skin surface (2006)

The rapid degradation of ribonucleic acids (RNA) by ubiquitous ribonucleases limits the efficacy of new therapies based on RNA molecules. Therefore, our aim was to characterize the natural ribonuclease activities on the skin and in blood plasma i.e. at sites where many drugs in development are applied. On the skin surfaces of Homo sapiens and Mus musculus we observed dominant pyrimidine-specific ribonuclease activity. This activity is not prevented by a cap structure at the 5'-end of messenger RNA (mRNA) and is not primarily of a 5'- or 3'-exonuclease type. Moreover, the ribonuclease activity on the skin or in blood plasma is not inhibited by chemical modifications introduced at the 2'OH group of cytidine or uridine residues. It is, however, inhibited by the ribonuclease inhibitor RNasin although not by the ribonuclease inhibitor SUPERase* In. The application of our findings in the field of medical science may result in an improved efficiency of RNA-based therapies that are currently in development.
Polymers to treat brain tumours (1990)

Brain tumours are difficult to treat by conventional methods. A biodegradable polymer, poly-[bis(p-carboxyphenoxy)propane sebacic acid] with a nitrosourea, carmustine, has been demonstrated to be biocompatible in the brains of experimental animals and to release drugs in a predictable sustained manner. Carmustine impregnated in polymers appears to be more effective than when delivered by standard methods. A Phase I clinical study has demonstrated the safety of this approach in treating brain tumours and a Phase III placebo-controlled study is currently underway. Other applications of the polymer in the treatment of brain diseases are discussed.
In Silico Discovery of Androgen Receptor Antagonists with Activity in Castration Resistant Prostate Cancer (2012)

Previously available androgen receptor (AR) antagonists (bicalutamide, flutamide, and nilutamide) have limited activity against AR in prostate cancers that relapse after castration [castration resistant prostate cancer (CRPC)]. However, recent AR competitive antagonists such as MDV3100, generated through chemical modifications to the current AR ligands, appear to have increased activity in CRPC and have novel mechanisms of action. Using pharmacophore models and a refined homology model of the antagonist-liganded AR ligand binding domain, we carried out in silico screens of small molecule libraries and report here on the identification of a series of structurally distinct nonsteroidal small molecule competitive AR antagonists. Despite their unique chemical architectures, compounds representing each of six chemotypes functioned in vitro as pure AR antagonists. Moreover, similarly to MDV3100 and in contrast to previous AR antagonists, these compounds all prevented AR binding to chromatin, consistent with each of the six chemotypes stabilizing a similar AR antagonist conformation. Additional studies with the lead chemotype (chemotype A) showed enhanced AR protein degradation, which was dependent on helix 12 in the AR ligand binding domain. Significantly, chemotype A compounds functioned as AR antagonists in vivo in normal male mice and suppressed AR activity and tumor cell proliferation in human CRPC xenografts. These data indicate that certain ligand-induced structural alterations in the AR ligand binding domain may both impair AR chromatin binding and enhance AR degradation and support continued efforts to develop AR antagonists with unique mechanisms of action and efficacy in CRPC.
Achievement of essentially full spatial coherence in a high-average-power soft-x-ray laser (2001)

We report an observation of essentially full spatial coherence in a high average power soft-x-ray laser. Rapid coherence buildup due to strong refractive antiguiding in a long plasma column is experimentally demonstrated. This allows the generation of fully coherent, milliwatt-level average power soft-x-ray radiation by a tabletop device. The peak brightness of this laser reaches $2\ifmmode\times\else\texttimes\fi{}{10}^{25}{\mathrm{photons}\mathrm{}\mathrm{s}}^{\ensuremath{-}1}{\mathrm{mm}}^{\ensuremath{-}2}{\mathrm{mrad}}^{\mathrm{\ensuremath{-}}2}$ within 0.01% spectral bandwidth, making it one of the brightest soft-x-ray sources available.
Thermodynamic and Kinetic Effects in the Aggregation Behavior of a Poly(ethylene glycol-b-propylene sulfide-b-ethylene glycol) ABA Triblock Copolymer (2005)

We explore the effects of preparation protocol on the morphology and stability of aggregates from a poly(ethylene glycol-b-propylene sulfide-b-ethylene glycol) triblock copolymer, PEG44−PPS76−PEG44. Fluorescence spectra and excimer formation of the probe molecule pyrene elucidated the various stages of aggregate formation, and cryo-TEM yielded insight into aggregate morphology. When prepared by direct hydration of polymer films, an extraordinary variety of morphologies was formed, ranging from spherical micelles to wormlike micelles, Y-junctions, blackberry micelles, and vesicles. Aging produced more uniform structural ensembles, including wormlike micelles with undulations and eventually spherical micelles, indicating the nonequilibrium nature of the system as initially formed. On the contrary, preparation by dilution from organic solvent yielded only structures that were closer to equilibrium distributions.
비만인의 UCP-2 유전자 다형에 따른 운동 중 지방대사의 변화 (2005)

본 연구의 목적은 UCP2 유전자 1/D 다형성에 따른 트레이드밀 운동 중 지질대사를 비교하는 것이었다. 본 연구의 피험자는 의학적 질환을 가지고 있지않은 총 39명(ID, n=10; DD, n=29; 연령 20-30대)으로 하였다. 신체계측은 신장, 체중, 체지방율을 측정하였고 운동 부하 검사를 통해서 심폐체력을 측정하였다 모든 피험자는 12시간 공복 후, 최대산소섭취량의 40% 강도로 한 시간 동안 운동하였다. 채혈은 전완정맥을 통해 안정, 운동 30분, 운동 60분, 그리고 회복기 1시간에 각각 채혈하였다. 채혈 후 혈중 젖산, 글루코스, 중성지방, 그리고 유리지방산을 분석하였다. 그리고 호흡교환을은 안정 시를 포함하여 운동 10분마다 측정하였다. 측정변인의 Two way ANOVA 결과, 혈중 젖산에서 집단과 반복 간에 유의한 삼호작용이 나타났다. 그리고 유전형질 간의 비교에서 안정 시 중성지방과 젖산 농도는 DD 농형접합자 집단이 ID 이형접합자 집단보다 유의하게 높게 나타났다. 본 연구에서 나타난 결과로 볼 때 비록 UCP2 유전자 다형에 따른 운동 중 지질대사에 영향을 미치지 않는 것으로 보이지만 UCP2 유전자 다형은 비만과 심혈관질환의 유전적 지표가 될 수 있음을 의미할 것이다.
1-[(1-Methyl-1H-imidazol-2-yl)methyl]-4-phenylpiperidines as mGluR2 Positive Allosteric Modulators for the Treatment of Psychosis (2011)

A novel series of mGluR2 positive allosteric modulators (PAMs), 1-[(1-methyl-1H-imidazol-2-yl)methyl]-4-phenylpiperidines, is herein disclosed. Structure-activity relationship studies led to potent, selective mGluR2 PAMs with excellent pharmacokinetic profiles. A representative lead compound (+)-17e demonstrated dose-dependent inhibition of methamphetamine-induced hyperactivity and mescaline-induced scratching in mice, providing support for potential efficacy in treating psychosis.
GFP‐tagging of cell components reveals the dynamics of subcellular re‐organization in response to infection of Arabidopsis by oomycete pathogens (2003)

Cytoplasmic aggregation, the rapid translocation of cytoplasm and subcellular components to the site of pathogen penetration, is one of the earliest reactions of plant cells against attack by microorganisms. We have investigated cytoplasmic aggregation during Arabidopsis-oomycete interactions. Infection by non-pathogenic Phytophthora sojae was prevented in the plant epidermal cell layer, whereas Peronospora parasitica isolates Cala2 (avirulent) and Noks1 (virulent) could both penetrate into the mesophyll cell layer. Epidermal cell responses to penetration by these oomycetes were examined cytologically with a range of transgenic Arabidopsis plants expressing Green Fluorescent Protein (GFP)-tagged cell components. These included plants containing GFP-TUA6 for visualizing microtubules, GFP-hTalin for actin microfilaments, GFP-tm-KKXX for endoplasmic reticulum (ER), and STtmd-GFP for the Golgi apparatus. In all interactions, actin microfilaments were actively re-arranged and formed large bundles in cytoplasmic strands focused on the penetration site. Aggregation of ER membrane and accumulation of Golgi bodies at the infection site were observed, suggesting that production and secretion of plant materials were activated around the penetration site. Microtubules did not become focused on the penetration site. No difference was evident between the responses of epidermal cells in the non-host, incompatible and compatible interactions. This result indicates that the induction of cytoplasmic aggregation in Arabidopsis epidermal cells was neither suppressed by the virulent strain of Peronospora, nor effective in stopping infection.
Mannose-binding lectin as part of the complement pathway: characterization in non-inflamed and inflamed human eyes (2011)

Our study demonstrated that mannose-binding lectin is significantly elevated in inflamed human eyes but virtually undetectable in non-inflamed control eyes, suggesting a role in sight-threatening ocular inflammation.
Acyclovir-Resistant Herpes Simplex Virus Infections in Patients with the Acquired Immunodeficiency Syndrome (1989)

RECURRENT herpes simplex virus (HSV) infections are frequent in patients with the acquired immunodeficiency syndrome (AIDS). Although they are usually self-limiting in the normal host, such infections may produce extensive and persistent ulcerative disease in compromised hosts.1 Several studies have demonstrated the beneficial effects of systemic acyclovir in severe HSV infections in immunodeficient patients, and this drug has become the antiviral agent of choice in the treatment of such infections.2 3 4 5 6 Virtually all HSV strains isolated from patients with acute HSV infections are highly susceptible to acyclovir, but acyclovir-resistant strains have been recovered occasionally from persons who have received prolonged therapy . . .
Polyclonal expansion of T-cell receptor-gamma delta+ T lymphocytes associated with neutropenia and thrombocytopenia. (1992)

A patient with large granular lymphocyte (LGL) expansion (T-gamma lymphocytosis), neutropenia and thrombocytopenia was studied longitudinally. Analysis of peripheral blood mononuclear cells (PBMC) demonstrated an unusual large proportion of CD3+ T-lymphocytes expressing a gamma delta T-cell receptor (TcR-gamma delta). Immunofluorescence (IF) stainings with subset-specific monoclonal antibodies showed a fluctuating expansion of TcR-gamma delta+ T-cells expressing V gamma 9 and V delta 2 variable (V) gene segments. Biochemical characterization of PBMC showed the presence of a disulphide-linked TcR-gamma delta. TcR gene rearrangement studies on sorted TcR-gamma delta+ T-cells showed rearrangements of V gamma 9-J gamma 1.2 and V delta 2-J delta 1 V and joining (J) gene segments, thereby confirming the IF staining results. These data alone did not allow us to determine whether the TcR-gamma delta+ LGL expansion represented a polyclonal or monoclonal proliferation, because the combinatorial repertoire of TcR-gamma delta receptors is limited due to the availability of only a few V and J segments within the TcR-gamma and TcR-delta genes and because of the preferential usage of V gamma 9-J gamma 1.2 and V delta 2-J delta 1 rearrangements by TcR-gamma delta+ T-cells in blood of healthy individuals. We therefore used polymerase chain reaction (PCR)-mediated amplification of the TcR-gamma delta rearrangements, using specific V gamma 9, J gamma 1.2, V delta 2, and J delta 1 oligonucleotides to determine the junctional diversity of the TcR-gamma delta+ T-cell population. Sequence analysis of the PCR products obtained revealed a mixture of different junctional region sequences compatible with a polyclonal expansion. This is in contrast to the few reported TcR-gamma delta+ LGL and the majority of TcR-alpha beta+ LGL expansions, which appeared to consist of monoclonal proliferations.
Sensitive detection of occult breast cancer by the reverse-transcriptase polymerase chain reaction. (1994)

RT-PCR of K19 is a sensitive, specific, and rapid method for detection of occult mammary carcinoma cells in the peripheral blood and bone marrow of patients with breast cancer. The presence of residual breast cancer cells in histologically normal bone marrow aspirates but not in stem-cell apheresis harvests is a frequent finding. This assay may be useful in diagnosing metastatic disease, as well as in monitoring the effectiveness of systemic therapy.
High Rate Filtration of Solids-Stabilized Oil-in-Water Emulsions (1973)

This paper explores the biopsychosocial and spiritual needs of adolescents and young adults (AYA) with life-threatening or terminal illnesses. AYA are situated between childhood and adulthood (ages 15-25) and have distinct biopsychosocial and spiritual needs unique to their developmental stage. Having a life-threatening or terminal illness directly challenges normal AYA developmental tasks and identity formation. AYA experience more troubling physical symptoms during the dying process compared to other age groups, which leads to significant psychological distress and an increased need for pharmacological treatments. In general, AYA desire to be fully informed and involved in the health care decision-making process, leading to ethical dilemmas when the AYA is a minor and their wishes differ from the wishes of their legal guardian(s). Social workers are especially well-equipped to serve this population due to aligning professional standards and ability to advocate for holistic care within interdisciplinary teams. Additional research is needed to tailor holistic interventions to meet the needs of this population.
Microbial resistance in relation to catalase activity to oxidative stress induced by photolysis of hydrogen peroxide (2011)

ABSTRACT The purpose of the present study was to evaluate the mechanism of microbial resistance to oxidative stress induced by photolysis of hydrogen peroxide (H 2 O 2 ) in relation to microbial catalase activity. In microbicidal tests, Staphylococcus aureus and Candida albicans were killed and this was accompanied by production of hydroxyl radicals. C. albicans was more resistant to hydroxyl radicals generated by photolysis of H 2 O 2 than was S. aureus . A catalase activity assay demonstrated that C. albicans had stronger catalase activity; accordingly, catalase activity could be one of the reasons for the resistance of the fungus to photolysis of H 2 O 2 . Indeed, it was demonstrated that C. albicans with strong catalase activity was more resistant to photolysis of H 2 O 2 than that with weak catalase activity. Kinetic analysis using a modified Lineweaver‐Burk plot also demonstrated that the microorganisms reacted directly with hydroxyl radicals and that this was accompanied by decomposition of H 2 O 2 . The results of the present study suggest that the microbicidal effects of hydroxyl radicals generated by photolysis of H 2 O 2 can be alleviated by decomposition of H 2 O 2 by catalase in microorganisms.
Airway surface fluid composition in the rat determined by capillary electrophoresis (1997)

The apical surface of respiratory epithelial cells is covered by a thin layer of low-viscosity fluid termed airway surface fluid (ASF), about which relatively little is known. We collected samples of ASF from anesthetized rats, which were then analyzed using capillary electrophoresis, a method that enables extremely small quantities of fluid to be analyzed. We found values for Na+ (40.57 +/- 3.08 mM), K+ (1.74 +/- 0.36 mM), and Cl- (45.16 +/- 1.81 mM), indicating that this fluid is hypotonic compared with rat plasma. In contrast, the concentrations of nitrite and nitrate within ASF were higher than reported plasma values. Additionally, intravenous administration of the cholinergic agonist methacholine (MCh) resulted in a dose-dependent increase in the concentration of Na+ and Cl- within the ASF. This increase is approximately 50% in these ions after a dose of 100 ng MCh/g body wt. This animal model, together with this microanalytical technique, may be useful for investigating the in vivo regulation of ASF composition.
Clinical Outcomes after Transfusion-Associated Hepatitis C (1995)

In a group of patients seen at a referral center, chronic post-transfusion hepatitis C was a progressive disease and, in some patients, led to death from either liver failure or hepatocellular carcinoma.
Amplified potentiometric transduction of DNA hybridization using ion-loaded liposomes (2010)

Amplified potentiometric transduction of DNA hybridization based on using liposome 'nanocarriers' loaded with the signaling ions is reported. The liposome-amplified potentiometric bioassay involved the duplex formation, followed by the capture of calcium-loaded liposomes, a surfactant-induced release and highly-sensitive measurements of the calcium signaling ions using a Ca(2+) ion-selective electrode (ISE). The high loading yield of nearly one million signaling ions per liposome leads to sub-fmol DNA detection limits. Factors affecting the ion encapsulation efficiency and signal amplification are evaluated and discussed. The influence of the surfactant lysing agent is also examined. Such use of 'green' calcium signaling ions addresses the inherent toxicity of Ag and CdS nanoparticle tags used in previous potentiometric bioassays. The new strategy was applied for the detection of low levels of E. coli bacteria. It could be readily extended to trace measurements of other important biomolecules in connection to different biorecognition events. The attractive analytical performance makes liposomes a useful addition to the armory of potentiometric bioassays.