gebhart/patrepeval huggingface dataset:
Construction and behavior of biologically contained bacteria for environmental applications in bioremediation (1995)

The survival of microorganisms can be predicted through the use of active biological containment systems. We have constructed contained Pseudomonas putida strains that degrade alkylbenzoates. The modified strain carries a fusion of the Plac promoter to the gef gene, which encodes a killing protein. Expression from Plac is controlled through a regulatory cascade, so that Plac is switched on or off by the absence or presence of alkylbenzoates, respectively. Similar uncontained strains were also constructed and tested as a control. Contained and uncontained strains were genetically stable, and their survival and functionality in soil microcosms were as expected. Both contained and uncontained strains survived well in soils supplemented with alkylaromatics, whereas survival of the contained strain in soil microcosms without methylbenzoates was markedly reduced, in contrast to the control strain, which survived in these soils in the absence of alkylbenzoates. The TOL plasmid was transferred in soils between Pseudomonas strains but was not able to mobilize the elements of the containment system.
MR Elastography Demonstrates Unique Regional Brain Stiffness Patterns in Dementias (2017)

Quantitative MRE of changes in brain viscoelastic structure shows unique regional brain stiffness patterns between common dementia subtypes.
MUC5B Promoter Variant and Rheumatoid Arthritis with Interstitial Lung Disease (2018)

We found that the MUC5B promoter variant was associated with RA-ILD and more specifically associated with evidence of usual interstitial pneumonia on imaging. (Funded by Société Française de Rhumatologie and others.).
Supplementary Table S5 from Sex Differences in Cancer Driver Genes and Biomarkers (2023)

&lt;p&gt;Summary of all sex-bias analysis of copy number aberrations and point mutations&lt;/p&gt;
Characterization of recombinant Mal d 4 and its application for component‐resolved diagnosis of apple allergy (2006)

Apple profilin complementary DNAs were identified. The physicochemical and allergenic properties of purified recombinant Mal d 4.0101 were evaluated showing that the recombinant protein was equal to the natural protein as shown by inhibition assays. Thus, Mal d 4 represents another example suitable for component-resolved diagnosis of food allergy.
Trigger-Loaded Microcapsules Containing Additives for Enhanced Performance of Lithium-Ion Batteries (2010)

Abstract not Available.
Figure S4 from The PET-Tracer <sup>89</sup>Zr-Df-IAB22M2C Enables Monitoring of Intratumoral CD8 T-cell Infiltrates in Tumor-Bearing Humanized Mice after T-cell Bispecific Antibody Treatment (2023)

&lt;p&gt;Figure S4 shows the IHC analysis for tumor density, necrosis and blood vessels.&lt;/p&gt;
Micro-interconnection reliability: Thermal, electrical and mechanical stress (2012)

The results of stress tests on 50 μm-pitch Pb-free microbump interconnect 3D Si structures are summarized. It was found that thermal processes alone compete strongly with electromigration at stress currents of 50 and 100 mA. Typical test sites exhibited a gradual increase in relative resistance increase over time. While large changes in bump interconnection resistance did occur for some sites, the interconnections were resistant to full open electrical failure, even after subjected to mechanical shock following long-term EM stress. Underfilled samples were more robust than non-underfilled samples. Overall, the results suggest that for application in 3D Si stacks, microbumps can support higher power densities than those used currently with standard pitch bump interconnections.
Hybrid dielectric/metal reflector for low thresholdvertical-cavity surface-emitting lasers (1997)

Data are presented on a hybrid dielectric/metal reflector made from MgF/ZnSe/MgF/Au for use on vertical-cavity surface-emitting lasers. This hybrid design can reduce the thickness of the top mirror to &lt; 0.75 µm for a wavelength of 1 µm, while also achieving high reflectivity. The authors demonstrate a mirror on vertical-cavity surface-emitting lasers with a sub 100 µA threshold.
Leukemia Inhibitory Factor is Augmented in the Heart in Experimental Heart Failure (2003)

Leukemia inhibitory factor (LIF) is a pleiotropic cytokine that induces cardiac myocyte hypertrophy through the signal transducing molecule, glycoprotein 130. To date, localization of LIF in the heart and regulation of cardiac LIF expression in congestive heart failure (CHF) remain undefined. The present study investigates the potential activation of LIF expression in the failing canine heart that was produced by progressive rapid ventricular pacing. Immunohistochemistry for LIF revealed that LIF immunoreactivity was present in the atrial and ventricular myocytes of the normal heart and was markedly increased in the failing heart as compared to the normal heart. Northern blot analysis demonstrated that cardiac LIF mRNA was increased in both atrium and ventricle in CHF as compared to the normal heart (P<0.01). Linear regression analysis revealed a positive correlation between atrial LIF mRNA and atrial pressure (r=0.87, P<0.001 in right atrium and r=0.86, P<0.001 in left atrium). Positive correlations between left ventricular LIF mRNA and left ventricular dimensions (r=0.91, P<0.0001 in end-systolic diameter; r=0.86, P<0.001 in end-diastolic diameter), and an inverse correlation between left ventricular LIF mRNA and left ventricular ejection fraction (EF) were observed (r=-0.93, P<0.0001). There was a positive correlation between left ventricular LIF mRNA and left ventricular mass index (LVMI) (r=0.85, P<0.001). The present study demonstrates that cardiac LIF immunoreactivity and its gene expression are increased in a canine model of experimental CHF and suggests a potential role for LIF in the pathophysiology of CHF.
Average Liouvillian theory revisited: cross-correlated relaxation between chemical shift anisotropy and dipolar couplings in the rotating frame in nuclear magnetic resonance (1999)

A review is given of the mathematical foundations of average Liouvillian theory and examples are provided of average Liouvillian expressions derived for sequences in nuclear magnetic resonance which possess temporal symmetry or antisymmetry. The utility of this approach is demonstrated in the design of pulse sequences to measure the effect of cross-correlation between chemical shift anisotropy and dipolar couplings on relaxation rates in biomolecules. Experimental verification of the theory is carried out on a 15N labelled sample of ubiquitin.
Translational Molecular Self-Diffusion in Magnetic Resonance Imaging (1984)

By varying slice-selective gradients in successive data acquisitions, the first in vitro measurements of molecular self-diffusion coefficients were performed in a magnetic resonance imager at 0.35 Tesla. Reasonably accurate measurements were found by the MRI method in comparison with 2.3 T NMR spectrometer measurements on the same samples, and in comparison to reported literature values. Thus, in addition to T1, T2, mobile proton density, flow velocity, magnetic susceptibility, and chemical shift, molecular self-diffusion coefficients are now added to the list of biophysical parameters measurable by magnetic resonance imaging in the noninvasive characterization of biological systems.
Supplemental Materials from The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients (2023)

&lt;p&gt;Supplemental Methods, Supplemental References, Supplemental Figure Legends, Figure S1-13, Table S1-5 and S14&lt;/p&gt;
ChemInform Abstract: STUDIES ON THE REACTION OF 1,2‐DICARBONYL COMPOUNDS WITH DIMETHYL 3‐KETOGLUTARATE. STERIC AND ELECTRONIC EFFECTS (1985)

Abstract Dicarbonylverbindungen (I) reagieren mit Acetondicarbonsäuredimethylester (II) zuvden Primär‐Addukten (III) bzw. im Fall von (Id) zum Bicyclus (IV).
The abnormal phosphorylation of tau protein at Ser-202 in Alzheimer disease recapitulates phosphorylation during development. (1993)

Tau is a neuronal phosphoprotein whose expression is developmentally regulated. A single tau isoform is expressed in fetal human brain but six isoforms are expressed in adult brain, with the fetal isoform corresponding to the shortest of the adult isoforms. Phosphorylation of tau is also developmentally regulated, as fetal tau is phosphorylated at more sites than adult tau. In Alzheimer disease, the six adult tau isoforms become abnormally phosphorylated and form the paired helical filament, the major fibrous component of the characteristic neurofibrillary lesions. We show here that Ser-202 (in the numbering of the longest human brain tau isoform) is a phosphorylation site that distinguishes fetal from adult tau and we identify it as one of the abnormal phosphorylation sites in Alzheimer disease. The abnormal phosphorylation of tau at Ser-202 in Alzheimer disease thus recapitulates normal phosphorylation during development.
European Initiative Towards Advances in Fourth Generation (2004)

This paper reviews in brief four on-going European research projects in the field of mobile and wireless communications.
Haemodynamic unloading reverses occlusive vascular lesions in severe pulmonary hypertension (2016)

Our results indicate that haemodynamic stress is prerequisite to the development and progression of occlusive neointimal lesions in this rat model of severe pulmonary hypertension. We conclude that perivascular inflammation and occlusive neointimal arteriopathy are driven by haemodynamic stress.
Supplementary Figure 2 from Small-Molecule RA-9 Inhibits Proteasome-Associated DUBs and Ovarian Cancer <i>In Vitro</i> and <i>In Vivo</i> via Exacerbating Unfolded Protein Responses (2023)

&lt;p&gt;PDF file - 322KB, Ovarian cancer cells sensitivity to cisplatin and to RA 9/cisplatin combination.&lt;/p&gt;
Potassium superoxide chemical transformation/mass spectrometry detection of covalent damage to the DNA of cultured human lymphocytes exposed to benzo[a]pyrene (1993)

Cultured human lymphocytes were exposed to benzo[a]pyrene (B[a]P), and diol epoxide-type DNA adducts arising from this chemical were detected by a method consisting of the following sequence of steps: (1) isolate the DNA; (2) subject the DNA to mild acid hydrolysis to release the polyaromatic moiety as a tetrahydrotetrol; (3) add an internal standard; (4) oxidize the tetrahydrotetrol with potassium superoxide to pyrene-2,3-dicarboxylic acid; (5) derivatize the latter with pentafluorobenzyl bromide; (6) purify the diester product on a silica cartridge; and (7) detect this product by gas chromatography electron capture negative ion mass spectrometry. From the dose (1 microgram/mL) of B[a]P applied, five adducts in 10(7) normal nucleotides were found. Largely because steps 2-5 of the method take place sequentially in a single vial, the procedure is convenient and affords precise results. To demonstrate the potential of the method to detect KO2-susceptible polyaromatic hydrocarbon DNA adducts in general, including unknowns, it was also applied to picomole and femtomole amounts of a standard of chrysene-1,4-quinone using scanning and selected ion monitoring conditions, respectively, in the MS. Since standard products can be detected with selected ion monitoring at levels 10(4) below those encountered here (prior work), it should be possible in the future to extend the method to samples containing smaller amounts of such adducts.
Supplemental Figure 2 from Mast Cell–Derived Prostaglandin D<sub>2</sub> Inhibits Colitis and Colitis-Associated Colon Cancer in Mice (2023)

&lt;p&gt;Supplemental Figure 2&lt;/p&gt;
Enhanced Aging Model for Supercapacitors Taking Into Account Power Cycling: Application to the Sizing of an Energy Storage System in a Direct Wave Energy Converter (2014)

This paper proposes an original model for supercapacitors that takes into account both calendar aging and cycling aging. A state variable is used to quantify the state of aging. This model is based on a series of recent experiments conducted in various research laboratories on the same technology (Maxwell Technology) and serves to represent the degradation of equivalent series resistance and capacitance. This model is particularly useful in an aging-aware life-cycle cost analysis. We show that an accurate aging model is critical to the design of an energy storage system that optimizes the economic life-cycle cost. Such an optimization is particularly applicable for smoothing in offshore systems such as direct wave energy converters, which require both cost reduction and high reliability. The influence of an aging model in the sizing process is investigated toward the end of this paper.
ChemInform Abstract: Diaryl Indenes and Benzofurans: Novel Classes of Potent and Selective Cyclooxygenase‐2 Inhibitors. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
HIV-1 envelope glycoproteins proteolytic cleavage protects infected cells from ADCC mediated by plasma from infected individuals (2021)

ABSTRACT The HIV-1 envelope glycoprotein (Env) is synthesized in the endoplasmic reticulum as a trimeric gp160 precursor, which requires proteolytic cleavage by a cellular furin protease to mediate virus-cell fusion. Env is conformationally flexible, but controls its transition from the unbound “closed” conformation (State 1) to downstream CD4-bound conformations (States 2/3), which are required for fusion. In particular, HIV-1 has evolved several mechanisms that reduce the premature “opening” of Env which exposes highly conserved epitopes recognized by non-neutralizing antibodies (nnAbs) capable of mediating antibody-dependent cellular cytotoxicity (ADCC). Env cleavage decreases its conformational transitions favoring the adoption of the “closed” conformation. Here we altered the gp160 furin cleavage site to impair Env cleavage and to examine its impact on ADCC responses mediated by plasma from HIV-1-infected individuals. We found that infected primary CD4+ T cells expressing uncleaved, but not wildtype, Env are efficiently recognized by nnAbs and become highly susceptible to ADCC responses mediated by plasma from HIV-1-infected individuals. Thus, HIV-1 limits the exposure of uncleaved Env at the surface of HIV-1-infected cells at least in part to escape ADCC responses.
Michael Addition Reactions between Chiral Ni(II) Complex of Glycine and 3-(trans-Enoyl)oxazolidin-2-ones. A Case of Electron Donor−Acceptor Attractive Interaction-Controlled Face Diastereoselectivity1 (2001)

This study has demonstrated that the readily available and inexpensive 3-(trans-3'-alkyl/arylpropenoyl)oxazolidin-2-ones, featuring high electrophilicity and conformational homogeneity, are synthetically superior Michael acceptors over the conventionally used alkyl enoylates, allowing for a remarkable improvement in reactivity and, in most cases, diastereoselectivity of the addition reactions with a Ni(II) complex of the chiral Schiff base of glycine with (S)-o-[N-(N-benzylprolyl)amino]benzophenone. Kinetically controlled diastereoselectivity in the corresponding Michael addition reactions between the Ni(II) complex of glycine and the oxazolidin-2-ones was systematically studied as a function of steric, electronic, and position effects of the substituents on the starting Michael acceptor. In both aliphatic and aromatic series the simple diastereoselectivity was found to be virtually complete, affording the products via the corresponding TSs with the approach geometry like. The face diastereoselectivity of the reactions between the Ni(II) complex of glycine and the 3-(trans-3'-alkylpropenoyl)oxazolidin-2-ones was found to depend exclusively on the steric bulk of the alkyl group on the starting Michael acceptor. In contrast, the face diastereoselectivity in the reactions of aromatic oxazolidin-2-ones with the Ni(II) complex of glycine was shown to be controlled predominantly by the electronic properties of the aryl ring. In particular, the additions of the Ni(II) complex of glycine with 3-(trans-3'-arylpropenoyl)oxazolidin-2-ones, bearing electron-withdrawing substituents on the phenyl ring, afforded the (2S,3R)-configured products with synthetically useful diastereoselectivity and in quantitative chemical yields, thus allowing for an efficient access to the sterically constrained beta-aryl-substituted pyroglutamic and glutamic acids.
Security Assessment in Gas-Electric Networks (2018)

In many parts of the world, electricity systems are experiencing an increasing amount of gas-fired generation being installed due to its cheap fuel. The flexibility offered by gas generators is considered to be beneficial for electric grids, particularly in the face of increasing renewable generation. However, gas generators are often problematic for the gas network, as they induce large, rapid changes in the demand. The objective of this paper is to investigate the interaction between electrical and gas networks, and how security criteria for gas system operations implicitly impact the operation of the electric grid. Special attention is paid to the incorporation of the gas system dynamics, which have profound impact on the security assessment. To facilitate the assessment, the paper proposes an analysis framework which considers i) preventive security assessment for the gas system, ii) determination of remedial actions and gas load shedding after a contingency occurs, and iii) the impact of the load shedding on the electric grid, given different operating rules for the gas system. A case study shows that the preventive security assessment is beneficial both for the gas and electric grid, and that the security criterion used to determine the required gas system remedial actions impacts the cost of the electric grid.
Behavior of Segmental Jacked Pipe Piles in Stiff Clay (2018)

Small diameter segmental jacked pipe piles are one option for underpinning lightly to heavily loaded structures to reduce settlement and even restore the structure to near original condition. In most cases, short sections of steel pipe are jacked into the ground through poor soils to achieve the desired load capacity from end bearing on a firm layer. The mass of the structure is used as the reaction to jacking. A study was conducted to evaluate the influence of end configuration on the installation jacking force and load behavior on jacked segmental pipe piles in a stiff overconsolidated clay. Four different configurations of the pipe end were tested: two closed ends (flush and oversized plate) and two open ends (no end plate and oversized ring). Plugging measurements were made of the open end piles during installation. Compression tests were conducted one day after installation to determine short-term axial capacity. The results show that the pile plugging of open end piles occurs very quickly and that substantial side resistance can develop for flush end pipes. Results of the site characterization, pile installation forces, and load tests are presented.
Hydrodynamic tensor density functional theory with correct susceptibility (2007)

In a previous work the authors developed a family of orbital-free tensor equations for the density functional theory [J. Chem. Phys. 124, 024105 (2006)]. The theory is a combination of the coupled hydrodynamic moment equation hierarchy with a cumulant truncation of the one-body electron density matrix. A basic ingredient in the theory is how to truncate the series of equation of motion for the moments. In the original work the authors assumed that the cumulants vanish above a certain order (N). Here the authors show how to modify this assumption to obtain the correct susceptibilities. This is done for N=3, a level above the previous study. At the desired truncation level a few relevant terms are added, which, with the right combination of coefficients, lead to excellent agreement with the Kohn-Sham Lindhard susceptibilities for an uninteracting system. The approach is also powerful away from linear response, as demonstrated in a nonperturbative study of a jellium with a repulsive core, where excellent matching with Kohn-Sham simulations is obtained, while the Thomas-Fermi and von Weiszacker methods show significant deviations. In addition, time-dependent linear response studies at the new N=3 level demonstrate the author's previous assertion that as the order of the theory is increased new additional transverse sound modes appear mimicking the random phase approximation transverse dispersion region.
Supplementary Table 1 from Metronomic Docetaxel in PRINT Nanoparticles and EZH2 Silencing Have Synergistic Antitumor Effect in Ovarian Cancer (2023)

&lt;p&gt;PDF - 312K, Storage stability of PLGA-PRINT nanoparticles.&lt;/p&gt;
Properties and Applications of Ceramic Composites Containing Silicon Carbide Whiskers (2011)

In the early 1980s, researchers at Oak Ridge National Laboratory developed a new type of ceramic composite reinforced with dispersed silicon carbide (SiC) whiskers. The majorityphase (“matrix”) material of these composites was aluminum oxide (Al2O3) and the minority-phase (“filler”) SiC was grown in whisker-form by a pyrolysis technique using organic waste such as rice hulls. Inclusion of a small volume fraction of silicon carbide whiskers (SiCw) in Al2O3 had a large impact on the properties and allowed for interesting applications which otherwise would not be possible with Al2O3 alone. The whisker form of SiC made the composites exceptionally non-brittle compared to conventional monolithic ceramics due to a variety of toughening mechanisms within the composites. Many years later, it was discovered that the whiskers also imparted useful electrical properties.
Lymphoid interstitial pneumonia after allogeneic bone marrow transplantation. A possible manifestation of chronic graft-versus-host disease (1985)

Interstitial pneumonia (IP) is a frequent and serious complication of bone marrow transplantation with a median time of onset about 2 months posttransplant. Most cases result either from toxicity of radiation and chemotherapy or from infection with pathogens such as cytomegalovirus. Described are two patients with chronic graft-versus-host disease (GVHD) who presented with late-onset IP 242 and 632 days posttransplant. Histologic examination of lung biopsy specimens disclosed a lymphoid interstitial pneumonia (LIP) in both cases. The major lymphocyte subset found in bronchoalveolar lavages and lung tissue was OKT8(+) and showed a positive dot staining for acid phosphatase. Contrary to peripheral blood mononuclear cells, most OKT8(+) lymphocytes in the lungs were OKT3(-). Since acute GVHD lesions are mediated mainly by cytotoxic T-lymphocytes, our data suggest that LIP in marrow-grafted patients may be a manifestation of chronic GVHD. It should be distinguished from the more common types of IP encountered following bone marrow transplantation.
Subtleties in tolerating correlated failures in wide-area storage systems (2006)

High availability is widely accepted as an explicit requirement for distributed storage systems. Tolerating correlated failures is a key issue in achieving high availability in today’s wide-area environments. This paper systematically revisits previously proposed techniques for addressing correlated failures. Using several real-world failure traces, we qualitatively answer four important questions regarding how to design systems to tolerate such failures. Based on our results, we identify a set of design principles that system builders can use to tolerate correlated failures. We show how these lessons can be effectively used by incorporating them into IRISSTORE, a distributed read-write storage layer that provides high availability. Our results using IRISSTORE on the PlanetLab over an 8-month period demonstrate its ability to withstand large correlated failures and meet preconfigured availability targets. 1