gebhart/patrepeval huggingface dataset:
Expression and characterization of the protein Rv1399c from <i>Mycobacterium tuberculosis</i> (2004)

The Mycobacterium tuberculosis genome contains an unusually high number of proteins involved in the metabolism of lipids belonging to the Lip family, including various nonlipolytic and lipolytic hydrolases. Driven by a structural genomic approach, we have biochemically characterized the Rv1399c gene product, LipH, previously annotated as a putative lipase. Rv1399c was overexpressed in E. coli as inclusion bodies and refolded. Rv1399c efficiently hydrolyzes soluble triacylglycerols and vinyl esters. It is inactive against emulsified substrate and its catalytic activity is strongly inhibited by the diethyl paranitrophenyl phosphate (E600). These kinetic behaviors unambiguously classify Rv1399c as a nonlipolytic rather than a lipolytic hydrolase. Sequence alignment reveals that this enzyme belongs to the alpha/beta hydrolase fold family and shares 30-40% amino acid sequence identity with members of the hormone-sensitive lipase subfamily. A model of Rv1399c derived from homologous three-dimensional structures reveals a canonical catalytic triad (Ser162, His290 and Asp260) located at the bottom of a solvent accessible pocket lined by neutral or charged residues. Based on this model, kinetic data of the Arg213Ala mutant partially explain the role of the guanidinium moiety, located close to His290, to confer an unusual low pH shift of the catalytic histidine in the wild type enzyme. Overall, these data identify Rv1399c as a new nonlipolytic hydrolase from M. tuberculosis and we thus propose to reannotate its gene product as NLH-H.
Harmonic generation by intense ultrashort laser pulses in rare gases (2000)

The interaction of intense ultrashort laser pulses with a gas of argon atoms in numerically investigated. The investigation utilizes a model that solves both the time- dependent Schroedinger equation and the wave equation self- consistently. The time-dependent Schroedinger equation for a single-active electron in the effective static potential and in the potential of electron-laser interaction is solved using alternating direction implicit method. The Maxwell's wave equation is solved using an explicit finite-different technique. We show that, under some conditions, propagation effects significantly clean up the single-atom spectrum providing new spectrum with well-resolved harmonic structure.
<title>Wavelets: what kind of signal processing is that?</title> (1996)

We introduce fundamentals of wavelet signal processing. We review the wavelet transform and multiresolution analysis. We illustrate their properties by simple examples.
SURGICAL TREATMENT OF MITRAL AND AORTIC STENOSES (1954)

Although Samways<sup>1</sup>suggested over 50 years ago that mitral stenosis should be surgically correctible since it is a mechanical obstruction, 25 years elapsed before the first clinical attempt at mitral valvotomy was reported by Cutler and Levine.<sup>2</sup>Soon thereafter, mitral commissurotomies were attempted by Allen and Graham,<sup>3</sup>Pribram,<sup>4</sup>and Souttar.<sup>5</sup>Of 10 patients operated on by these surgeons, only 2 survived, and only one of these 2 was improved by the operation.<sup>5</sup>Such disheartening results discouraged further clinical trials until the recent constructive efforts of pioneers like Smith,<sup>6</sup>Bailey,<sup>7</sup>Harken and associates,<sup>8</sup>and Baker, Brock, and Campbell,<sup>9</sup>who made successful surgical relief of mitral stenosis a reality. Their success may be attributed to the fact that, in performing valvotomies by making the incision at the point of fusion of the leaflets (commissures), instead of inserting the valvotome into the heart
A novel hypothesis-testing technique for resolving overlapping peaks in DNA sequencing (2003)

The accuracy of determining the Deoxyribo Nucleic Acid (DNA) sequence is limited by overlapping peaks of the same base-type (A, C, G or T). Commonly used iterative method to resolve these peaks tends to generate false peaks and has limited resolution. This paper presents a novel hypothesis-testing method, which uses a statistical model of DNA time series, to estimate position and amplitude of the overlapping peaks. The new method has better resolution than the iterative method and does not generate false peaks.
Viral Inhibition of the IFN-Induced JAK/STAT Signalling Pathway: Development of Live Attenuated Vaccines by Mutation of Viral-Encoded IFN-Antagonists (2016)

The interferon (IFN) induced anti-viral response is amongst the earliest and most potent of the innate responses to fight viral infection. The induction of the Janus kinase/signal transducer and activation of transcription (JAK/STAT) signalling pathway by IFNs leads to the upregulation of hundreds of interferon stimulated genes (ISGs) for which, many have the ability to rapidly kill viruses within infected cells. During the long course of evolution, viruses have evolved an extraordinary range of strategies to counteract the host immune responses in particular by targeting the JAK/STAT signalling pathway. Understanding how the IFN system is inhibited has provided critical insights into viral virulence and pathogenesis. Moreover, identification of factors encoded by viruses that modulate the JAK/STAT pathway has opened up opportunities to create new anti-viral drugs and rationally attenuated new generation vaccines, particularly for RNA viruses, by reverse genetics.
A high temperature superconductor filter/low-noise amplifier MIC (1994)

This paper presents the design and performance of a hybrid semiconductor/superconductor amplifier and filter integrated circuit. The circuit combines the high frequency, low noise advantages of a cryogenically cooled GaAs HEMT with the low loss, high Q properties of a narrowband HTSC filter and matching networks. The HTSC filter/amplifier combination produced 7.2dB gain at the passband centre frequency of 19.8 GHz, with a 3dB bandwidth of 2%. A minimum noise figure of 1.5dB was achieved at this frequency.
ASCA X-Ray Observation of the Lobe Dominant Radio Galaxy NGC 612 (1998)

The radio galaxy NGC 612 ( z = 0.0290; Spinrad et al. 1985) exhibits bright (~ 11 Jy at 843 MHz) double lobes at a large scale of about 500 kpc x 130 kpc with a very faint core (Jones & McAdam 1992). We performed ASCA observations (AO-4; PI = Kaneda) of NGC 612 on July 12-14, 1996, in search for inverse-Compton (IC) X-rays from the radio lobes.
Study of the use of linear predictor and related methods of speech analysis for measuring vocal-tract area functions (1974)

The linear predictor (LP) and partial correlation (PARCOR) methods of speech analysis have been applied to sounds produced by acoustic horns with inside cross-sectional shapes comparable to the human vocal tract. Our experience with human speech suggests that the area functions obtained from both methods are variable and depend strongly on the type of speech sounds, the sampling rate, the method of windowing and compensation of the signal, and other factors. To evaluate these methods in a controlled situation, the horns are driven with a known input volume velocity. The output volume velocity is measured, sampled at a 20-kHz rate, and analyzed with a computer program using either an LP of PARCOR algorithm. The computed area function and transfer function are compared with the known geometry and measured frequency response of the horn. Implications of these results on the use of LP and related methods for studying vocal-tract area functions in hearing and nonhearing subjects are discussed.
Multi‐scaled microstructures in natural rubber characterized by synchrotron X‐ray scattering and optical microscopy (2008)

Abstract Multi‐scaled microstructures induced by natural impurities (i.e., proteins, phospholipids, carbohydrates) in natural rubber (NR) were investigated by synchrotron small‐angle X‐ray scattering (SAXS), wide‐angle X‐ray diffraction (WAXD), and optical microscopy using several kinds of untreated and chemically treated un‐vulcanized samples. These microstructures include large aggregates (size less than 50 μm), well‐defined crystals (size less than a few 10 μm), and micelles (size much less than 10 μm). In un‐vulcanized NR samples, even though the concentrations of natural impurities are relatively low, the dispersion of these microstructures significantly affects the mechanical properties. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 2456–2464, 2008
Thermal Stability of Nanocrystalline Sm <sub>2</sub> O <sub>3</sub> and Sm <sub>2</sub> O <sub>3</sub> –MgO (2006)

Nanocrystalline Sm 2 O 3 and Sm 2 O 3 –MgO powders have been prepared by spray pyrolysis of aqueous precursor solutions containing citric acid as a complexant. Synthesized powders consist of hollow spheres with thin shells. The two‐phase samples exhibit an improved microstructural stability compared with pure Sm 2 O 3 . The microstructure before and after various heat treatments has been investigated by high‐resolution transmission electron microscopy, scanning electron microscopy, nitrogen adsorption, and X‐ray diffraction.
Quantitative Analysis of the Key Factors Affecting Yeast Growth (2003)

Yeast growth is affected not only by the operative conditions (temperature, pH, sugar concentration) but also by the intrinsic properties of the investigated system, namely, type of strain, culture medium, and physiological state of the inoculum. Several authors describe the influence of the operative conditions quantitatively, whereas the effects of the intrinsic properties are in general reported as qualitative observations. In order to investigate these aspects, which are very important in the optimization of industrial baker's yeast production, several yeast growth runs were carried out varying the type of strain, the culture medium, and the physiological state of the inoculum employed. Experimental data on both batch and fed-batch baker's yeast growth were interpreted quantitatively using a modified and improved suitable cybernetic model. The results of a sensitivity analysis performed on the kinetic parameters of the model have shown that parameters related to the different culture medium and strain can be obtained by mathematical regression on experimental data. The parameters relating to the different physiological state of the inoculum are independent from strain and culture medium employed, so that one batch and one fed-batch growth run, carried out in defined operative conditions, are sufficient to determine the whole set of model parameters. Moreover, the improved model has been tested by simulating fed-batch growth runs, performed under different operative conditions, demonstrating its predictive power.
Accelerated growth of syngeneic tumors in mice treated with methylcholanthrene (1978)

BALB/c and C3H- mice were given a single injection of methylcholanthrene (MCA) and were tested at various times thereafter for immunologic reactivity and resistance to syngeneic tumor challenge. MCA treatment did not affect the rejection of H-2-incompatible tumor allografts, the rejection of H-2-compatible skin allografts, or the induction of delayed hypersensitivity to DNCB as measured by footpad challenge. In contrast, mice treated with MCA exhibited an increase susceptibility to challenge with several syngeneic ultraviolet-induced and MCA-induced fibrosarcomas. These studies demonstrate that in the autochthonous host the measurement of host immune status by in vivo cell-mediated immune responses to exogenous antigens does not necessarily predict the host response to tumor growth.
Attenuated <i>Salmonella typhimurium</i> Containing Interleukin-2 Decreases MC-38 Hepatic Metastases: A Novel Anti-tumor Agent (1996)

Currently, there is no long-term effective treatment for unresectable hepatic malignancies. Salmonella sp. are known to naturally track to the liver during active infection. To develop a biological vector for delivery of Interleukin-2 (IL-2) to the liver for anti-tumor purposes, the avirulent and highly immunogenic chi 4550 strain of Salmonella typhimurium was used as a vector for IL-2. The gene for human IL-2 was cloned into plasmid pYA292 (renamed pIL-2) and inserted into the attenuated Salmonella typhimurium and renamed [chi 4550 (pIL-2)]. This transformant was found to produced biologically active IL-2 demonstrated by NK cell activation in a 4 hour chromium release cytotoxicity assay. To determine anti-tumor potential, MCA-38 murine adenocarcinoma cells were injected intrasplenically into C57BL/6 mice to produce hepatic metastases and metastases were subsequently enumerated after 12 days. Statistical significance was determined by ANOVA with Fisher's test for significance. Hepatic metastases enumerated by blinded observers revealed that the mean number of metastases was 106.4 in control mice, 103.7 in mice gavage fed attenuated salmonella without IL-2 [chi 4550(pYA292)], and 44.3 in mice fed the chi 4550(pIL2); (ANOVA: p < 0.01). Culture of livers and spleens in mice administered a single gavage dose of salmonella demonstrated persistent colonization for up to 4 weeks. No observable toxicity was seen to either IL-2 or salmonella. These studies demonstrate that the chi 4550(pIL2) is a novel form of in vivo biotherapy which produces biologically active IL-2 and employs the oral route of administration to stimulate an immune response against malignancy in the liver.
Structure and compression of crystalline methane at high pressure and room temperature (1980)

Methane, CH4, crystallizes in the face-centered cubic metal structure (space group Fm3m) at 15.9 kbar and 20 °C. Cubic unit-cell edges at 16.1, 28.9, 39.5, and 52.1 kbar are 5.4434, 5.3064, 5.1963, and 5.0947 Å, respectively. The isothermal bulk modulus, calculated from a first-order Murnaghan equation of state (K′=4), is 49±9 kbar. Methane transforms to a second as yet unidentified high-pressure solid phase at 52.5 kbar (20 °C).
Protective Coatings for SOFC Metallic Interconnects (2019)

Corrosion and chromium evaporation from commonly used metallic interconnects in humidified oxidizing environment during SOFC operation remains an issue. We have studied the role of pretreatment of AISI 430 alloy with or without nickel coating on the oxidation resistance and formation of interfacial compounds at 650-800°C in moisture-saturated air. It is found that electrodeposited nickel coated AISI 430 alloy pretreated in dry hydrogen (Ar-3% H2) improves the oxidation resistance but not pre-oxidized alloy. The underlying mechanisms for improved oxidation resistance are discussed using structural and microstructural analysis.
Use of high-dose human intravenous immunoglobulin therapy in sensitized patients awaiting transplantation: the Cedars-Sinai experience. (2003)

Cedars Sinai Medical Center has developed a protocol using high-dose (2 mg/kg) IVIG to desensitize and transplant patients who are broadly sensitized to HLA antigens. Since 2000, we have evaluated and transplanted 57 broadly sensitized patients (19 with deceased donor and 38 with living donor kidneys) following IVIG treatment. The incidence of allograft rejection was 38.5% and 4-year patient and graft survival rates were 96.5% and 82.5%, respectively. We have also used IVIG in combination with pulse steroids to treat antibody-mediated rejection episodes in 18 patients with C4d deposition in rejection biopsies. Thirteen responded to treatment and 5 grafts were lost in this group with severe antibody-mediated rejection. These results suggest that in many cases high-dose IVIG treatment can neutralize or mitigate antibody responses to eliminate positive donor-specific crossmatches and permit transplantation of broadly sensitized patients and offers a means to treat antibody-mediated rejection successfully.
<title>Image segmentation by region-contour cooperation as a basis for efficient coding scheme</title> (1992)

International audience
PD-1/CTLA-4 Blockade Inhibits Epstein-Barr Virus-Induced Lymphoma Growth in a Cord Blood Humanized-Mouse Model (2016)

Epstein-Barr virus (EBV) infection causes B cell lymphomas in humanized mouse models and contributes to a variety of different types of human lymphomas. T cells directed against viral antigens play a critical role in controlling EBV infection, and EBV-positive lymphomas are particularly common in immunocompromised hosts. We previously showed that EBV induces B cell lymphomas with high frequency in a cord blood-humanized mouse model in which EBV-infected human cord blood is injected intraperitoneally into NOD/LtSz-scid/IL2Rγnull (NSG) mice. Since our former studies showed that it is possible for T cells to control the tumors in another NSG mouse model engrafted with both human fetal CD34+ cells and human thymus and liver, here we investigated whether monoclonal antibodies that block the T cell inhibitory receptors, PD-1 and CTLA-4, enhance the ability of cord blood T cells to control the outgrowth of EBV-induced lymphomas in the cord-blood humanized mouse model. We demonstrate that EBV-infected lymphoma cells in this model express both the PD-L1 and PD-L2 inhibitory ligands for the PD-1 receptor, and that T cells express the PD-1 and CTLA-4 receptors. Furthermore, we show that the combination of CTLA-4 and PD-1 blockade strikingly reduces the size of lymphomas induced by a lytic EBV strain (M81) in this model, and that this anti-tumor effect requires T cells. PD-1/CTLA-4 blockade markedly increases EBV-specific T cell responses, and is associated with enhanced tumor infiltration by CD4+ and CD8+ T cells. In addition, PD-1/CTLA-4 blockade decreases the number of both latently, and lytically, EBV-infected B cells. These results indicate that PD-1/CTLA-4 blockade enhances the ability of cord blood T cells to control outgrowth of EBV-induced lymphomas, and suggest that PD-1/CTLA-4 blockade might be useful for treating certain EBV-induced diseases in humans.
COMPARISON OF PALAEO OIL CHARGES WITH CURRENTLY RESERVOIRED HYDROCARBONS USING MOLECULAR AND ISOTOPIC ANALYSES OF OIL-BEARING FLUID INCLUSIONS: JABIRU OIL FIELD, TIMOR SEA (1997)

Geochemical techniques have been used to compare the composition of oil trapped in fluid inclusions from the Jabiru oil field with currently reservoired oil. The inclusion oil is preferentially enriched in polar compounds, probably due to an adsorption effect during trapping, but this has not affected the hydrocarbon composition of the trapped oil. Source characterisation using biomarker and gasoline range hydrocarbon parameters shows that the fluid inclusion oils have the same source affinity as the current production oil. This is corroborated by the carbon isotopic compositions of high molecuJar weight n-alkanes trapped in oil-bearing fluid inclusions, which are similar to those of the production oil. Both oils have maturities in the peak oil generative window, but aromatic hydrocarbon ratios demonstrate that the fluid inclusion oil is less mature (calculated reflectance [RJ = 0.84 per cent) than the currently reservoired charge (0.92 per cent Rc). Fluid inclusion abundance data and residual oil saturations indicate the Jabiru oil column was previously significantly larger, with subsequent leakage reducing the column to its present size. The geochemical data collected for the fluid inclusion oil suggests that it is representative of early charge to the Jabiru structure. The difference between the fluid inclusion oil and the production oil is thought to reflect continued charging of the trap with progressively more mature oil from the same or similar source rock facies. The change in the molecular composition of the oil in the Jabiru structure probably occurred by dilution of earlier, lower maturity charge with larger volumes of more mature oil.
ChemInform Abstract: CHLORINOLYSES OF ALKYL (OR ARYL) PHTHALIMIDOMETHYL SULFOXIDES WITH SULFURYL CHLORIDE, CHLORINE AND THIONYL CHLORIDE (1979)

Abstract Die auf dem skizzierten Wege hergestellten Phthalimidomethylsulfoxide (IV) werden mit Sulfurylchlorid oder Chlor chlorolytisch gespalten.
Direct Molecular Identification of the Mouse Pink-Eyed Unstable Mutation by Genome Scanning (1991)

DNA sequences associated with the mouse pink-eyed unstable mutation were identified in the absence of closely linked molecular markers and without prior knowledge of the encoded gene product. This was accomplished by "genome scanning," a technique in which high-resolution Southern blots of genomic DNAs were hybridized to a dispersed and moderately repetitive DNA sequence. In this assay, pink-eyed unstable DNA was distinguished from the DNA of wild-type and revertant mice by enhanced hybridization to one of several hundred resolved fragments. The fragment showing enhanced hybridization in pink-eyed unstable DNA was cloned and found to lie within a DNA duplication that is located close to, or within, the pink-eyed dilution locus. The duplication associated with the mouse pink-eyed unstable mutation may mediate the high reversion frequency characteristic of this mutation.
<i>In situ</i> Stimulation of CD40 and Toll-like Receptor 3 Transforms Ovarian Cancer–Infiltrating Dendritic Cells from Immunosuppressive to Immunostimulatory Cells (2009)

Boosting therapeutically relevant immunity against lethal epithelial tumors may require targeting tumor-induced immunosuppression on an individualized basis. Here, we show that, in the ovarian carcinoma microenvironment, CD11c(+)MHC-II(+) dendritic cells spontaneously engulf tumor materials but, rather than enhancing antitumor immunity, suppress T-cell function. In situ costimulation of CD40 and Toll-like receptor (TLR) 3 on tumor-infiltrating dendritic cells decreased their L-arginase activity, enhanced their production of type I IFN and interleukin-12 (p70), augmented their capacity to process antigens, and up-regulated costimulatory molecules in vivo in mice and in vitro in human dissociated tumors. Synergistic CD40/TLR activation also induced the migration of activated dendritic cells to lymphatic locations and promoted their capacity to present antigens. Correspondingly, without exogenous antigen, combined CD40/TLR agonists boosted measurable T-cell-mediated antitumor immunity and induced the rejection of otherwise lethal i.p. ovarian carcinomas. Our results highlight the potential of transforming tumor-infiltrating dendritic cells (the most abundant leukocyte subset in the solid ovarian carcinoma microenvironment) from an immunosuppressive to an immunostimulatory cell type. Combined administration of synergistic CD40 and TLR3 agonists could enhance their individual therapeutic effects against ovarian and other lethal epithelial cancers.
Impaired Sociability of the Balb/c Mouse, an Animal Model of Autism Spectrum Disorders, is Attenuated by NMDA Receptor Agonist Interventions: Clinical Implications (2011)

Impaired Sociability of the Balb/c Mouse, an Animal Model of Autism Spectrum Disorders, is Attenuated by NMDA Receptor Agonist Interventions: Clinical Implications