gebhart/patrepeval huggingface dataset:
Towards universal influenza vaccines? (2011)

Vaccination is the most cost-effective way to reduce the considerable disease burden of seasonal influenza. Although seasonal influenza vaccines are effective, their performance in the elderly and immunocompromised individuals would benefit from improvement. Major problems related to the development and production of pandemic influenza vaccines are response time and production capacity as well as vaccine efficacy and safety. Several improvements can be envisaged. Vaccine production technologies based on embryonated chicken eggs may be replaced by cell culture techniques. Reverse genetics techniques can speed up the generation of seed viruses and new mathematical modelling methods improve vaccine strain selection. Better understanding of the correlates of immune-mediated protection may lead to new vaccine targets besides the viral haemagglutinin, like the neuraminidase and M2 proteins. In addition, the role of cell-mediated immunity could be better exploited. New adjuvants have recently been shown to increase the breadth and the duration of influenza vaccine-induced protection. Other studies have shown that influenza vaccines based on different viral vector systems may also induce broad protection. It is to be expected that these developments may lead to more universal influenza vaccines that elicit broader and longer protection, and can be produced more efficiently.
Quantized overcomplete expansions in IR/sup N/: analysis, synthesis, and algorithms (1998)

Coefficient quantization has peculiar qualitative effects on representations of vectors in IR with respect to overcomplete sets of vectors. These effects are investigated in two settings: frame expansions (representations obtained by forming inner products with each element of the set) and matching pursuit expansions (approximations obtained by greedily forming linear combinations). In both cases, based on the concept of consistency, it is shown that traditional linear reconstruction methods are suboptimal, and better consistent reconstruction algorithms are given. The proposed consistent reconstruction algorithms were in each case implemented, and experimental results are included. For frame expansions, results are proven to bound distortion as a function of frame redundancy r and quantization step size for linear, consistent, and optimal reconstruction methods. Taken together, these suggest that optimal reconstruction methods will yield O(1/r/sup 2/) mean-squared error (MSE), and that consistency is sufficient to insure this asymptotic behavior. A result on the asymptotic tightness of random frames is also proven. Applicability of quantized matching pursuit to lossy vector compression is explored. Experiments demonstrate the likelihood that a linear reconstruction is inconsistent, the MSE reduction obtained with a nonlinear (consistent) reconstruction algorithm, and generally competitive performance at low bit rates.
A Fast Numerical Method for Solving Large Sparse Linear Systems (2014)

This paper applies the extrapolated homotopy method to solve large sparse linear systems. An optimal extrapolation parameter obtained in this paper makes the approximate solution convergent rapidly. Numerical results demonstrate that the homotopy method embedded with the optimal extrapolation parameter is more accurate than the direct and iterative numerical methods.
Promoter Structure and Transcriptional Regulation of Human &#946;-Galactoside &#945;2, 3-Sialyltransferase Genes (2008)

Six human beta-galactoside alpha2,3-sialyltransferase genes, which are hST3Gal I-VI, have been cloned. Multiple genes encode enzymes with closely related catalytic specificities but different patterns of tissue expression. The multiple genes correspond to the control of various tissue specific regulators. Several studies have examined the transcriptional regulation of some human beta-galactoside alpha2,3-sialyltransferases genes. Multiple mRNA forms differing only in the 5'-untranslated regions have been identified in hST3Gal II, hST3Gal III, hST3Gal IV, hST3Gal V, and hST3Gal VI. These transcripts are produced by a combination of alternative splicing and promoter utilization, suggesting the transcriptional regulation of this gene depends on the use of alternative promoters, further suggesting that tissue-specific transcriptional regulation of these genes depends on the use of multiple genes and multiple promoters. The multiple regulatory pathways of these ubiquitous sialyltransferases may be differentially modulated in various cell types.
Activity of the triazole SCH 56592 against disseminated murine coccidioidomycosis (1997)

SCH 56592 (SCH) is a new triazole antifungal with a broad spectrum of activity. In vitro susceptibility testing against five strains of Coccidioides immitis revealed MICs from 0.39 to 3.13 microg/ml and minimal fungicidal concentrations from 1.56 to 3.13 microg/ml. A murine model of systemic coccidioidomycosis was established in female CD-1 mice. Groups received either no treatment or oral therapy with fluconazole at 10 or 100 mg/kg of body weight; itraconazole at 10 or 100 mg/kg; SCH at 0.5, 2, 10, or 25 mg/kg; or its methylcellulose diluent alone. Therapy began 2 days postinfection and continued once daily for 19 days. Surviving mice were euthanized 49 days postinfection, and infectious burdens were determined by culture. All drugs were superior to no-treatment or diluent-treatment controls (P < 0.001) in prolonging survival but were not significantly different from one another. Itraconazole at 100 mg/kg was superior to fluconazole in reduction of CFU in the spleen, liver, and lung (P < 0.01 to 0.001). SCH at 0.5 mg/kg was superior to either fluconazole or itraconazole at 10 mg/kg in reduction of CFU in all three organs (P < 0.05 to 0.001). SCH at 2 mg/kg was not significantly different from itraconazole at 100 mg/kg in all three organs. SCH at 10 and 25 mg/kg was superior to either dose of fluconazole or itraconazole in all three organs (P < 0.05 to 0.001). In terms of reduction of CFU, SCH was > or = 200-fold as potent as fluconazole and > or = 50-fold as potent as itraconazole. There was a clear dose-responsive relationship for SCH in each of the organs. It is noteworthy that SCH effected cures (no detectable C. immitis in any organ) in 1 of 9, 6 of 10, or 9 of 9 surviving mice in animals given 2, 10, or 25 mg/kg, respectively. Neither fluconazole nor itraconazole cured any survivor. SCH has potent, fungicidal activity in vivo against C. immitis. It should be considered for clinical trials in patients with coccidioidomycosis.
Formation of aminals from amines via Pummerer rearrangement (1979)

Reaction of 2-amino-3-nitropyridine with acid chlorides in the presence of dimethyl sulfoxide and a tertiary base, such as pyridine, unexpectedly yielded the aminal N,N′-bis(3-nitro-2-pyridinylimino)methylene 5. A similar aminal 6 formed when 2-amino-5-nitropyridine was treated under the same conditions. However, simple aminopyridines such as 2-aminopyridine or 2-amino-6-methylpyridine gave only the 2-N-methylenethiomethyl derivatives. It was proved that the aminals are formed by the attack of a suitable base on the N-methylenethiomethyl intermediates with expulsion of methyl mercaptan. The formation of these unusual aminals may be explained to be taking place via a Pummerer type rearrangement.
Metadata management for federated databases (2007)

A federated database consists of several loosely integrated databases, where each database may contain hundreds of tables and thousands of columns,interrelated by complex foreign key relationships. In general, there exists a lot of semistructured data elements outside the database represented by documents (files), created and updated by multiple users and programs. Documents have references to multiple databases and subsets of their tables and columns. Manually tracking which specific tables and columns are referred to by a document, accessed by a specific program or user is a daunting task. With such a goal in mind, we present a system that builds metadata models for a federated database using a relational database as a central object type and metadata repository. Metadata includes table and columns coming from logical data models corresponding to each database, as well as documents representing external semistructured data sources. SQL statements assemble metadata and data types to create objects and relationships as relational tables for easy querying. We discuss potential applications in federated scientific databases.
Reactor Characterization for an SiO2 Plasma Etchback Process with Response‐Surface Methodology: Effects of Interelectrode Spacing (1990)

The characteristics of plasmas which are used to etch composite layers of sacrificial photoresist and underlying have been examined with experimental design and modeled empirically by response‐surface methodology using a Lam Research Autoetch 480 single‐wafer system. The effects of variations of process gas flow rates for (150–200 sccm) and (0–50 sccm), reactor pressure (900–2000 mtorr), and interelectrode spacing (4–6 mm) on the etch rates of and photoresist were explored at fixed radio frequency power (500W at 13.56 MHz) at . Variation in spacing shows different effects for these two materials; whereas the etch rates generally increase with increasing spacing as the other parameters are varied, the photoresist etch rates exhibit more complex behavior. At the lower spacing of 4 mm, neither film has a measurable etch rate for low settings of the other variables. The etch rates are virtually constant with increasing flow rate for low, middle, and high settings of the other variables. At low settings of the other variables, the photoresist etch rates are zero over the range of flow rates but increase with increasing flow rates for middle and high settings of the other variables. At a spacing of 4 mm, the etch rates of both films are negligible over the range of flow rates and the range of reactor pressure. At larger spacings the etch rates of photoresist increase with increasing flow rate, while the etch rates of are similar for middle and high settings of the other variables over the range of flow rates. Process optimization using the empirical models to attain suitable etch rates for both films for planarization of a composite layer of photoresist and with high etch uniformity was achieved at 500W of RF power, 1450 mtorr, 150 sccm of , 0 sccm , and a spacing of 5.5 mm. Hence, for a plasma with this reactor adequate planarization is obtained without the use of . The addition of small concentrations of to a plasma resulted in increasingly higher etch rates for photoresist as the process progressed.
Depression and immune function (1988)

Abstract Clinical studies have demonstrated that measures of cell‐mediated immune function are altered in bereaved persons and depressed patients. This review article focuses on our recent observations of changes in T cell subpopulations and natural killer cytotoxicity in women undergoing adverse life events including conjugal bereavement. A reduction in natural cytotoxicity has also been found in depressed patients. The mechanism by which psychologic states might influence immune function is discussed.
Effects of superoxide dismutase mimetics on the activity of nitric oxide in rat aorta (1999)

A number of structurally distinct superoxide dismutase (SOD) mimetics were examined to determine if they shared the ability of authentic Cu/Zn SOD to produce endothelium-dependent relaxation of rings of rat aorta by protecting basal nitric oxide from destruction by endogenously produced superoxide anion. MnCl2 (10 nM-100 microM), CuSO4 (100 nM-1 mM) and CuDIPS (Cu [II]-[diisopropylsalicylate]2; 100 nM-30 microM) each mimicked the ability of Cu/Zn SOD (0.1-300 u ml(-1)) to produce relaxation of phenylephrine-precontracted aortic rings in a manner inhibited by endothelial removal or treatment with N(G)-nitro-L-arginine methyl ester (L-NAME, 100 microM). In contrast, MnTMPyP (Mn [III] tetrakis [1-methyl-4-pyridyl] porphyrin; 10 nM-30 microM) augmented phenylephrine-induced contraction and this was blocked by endothelial removal or treatment with L-NAME (100 microM), consistent with destruction rather than protection of basal nitric oxide activity. Pretreatment with Cu/Zn SOD (250 u ml(-1)) blocked this augmentation suggesting that it arose paradoxically through destruction of nitric oxide by superoxide anion. The spin trap agents tiron (100 nM-1 mM), tempol (100 nM-1 mM) and PTIYO (4-phenyl-2,2,5,5-tetramethyl imidazolin-1-yloxy-5-oxide; 100 nM-300 microM) all failed to promote endothelium-dependent relaxation. In fact, the last two augmented phenylephrine-induced tone and this was blocked by endothelial removal or treatment with L-NAME (100 microM), consistent with destruction of basal nitric oxide activity. This destruction was unaffected by pretreatment with Cu/Zn SOD (250 u ml(-1)) and probably reflected the direct ability of tempol and PTIYO to destroy nitric oxide. Thus, the ideal SOD mimetic for protection of nitric oxide activity in conditions of oxidant stress still awaits development.
Sensing and characterization of explosive vapors near 700 cm<sup>-1</sup> (2007)

One of the technological challenges associated with trace vapor detection of explosive materials are the relatively low vapor pressures exhibited by most energetic materials under ambient conditions. For example, the vapor pressure for TNT is ~10 ppbv at room temperature, a concentration near the Limit of Detection for many of the technologies currently being deployed. In the case of improvised explosive devices, the clandestine nature of the device further serves to exacerbate the vapor pressure issue. Interestingly, the gold standard in explosives detection remains the trained canine nose. While there is still some debate as to what the dog actually <i>smells</i>, recent studies have indicated the alert response is triggered, not by the vapor presence of a specific explosive compound but, by a characteristic bouquet of odors from chemical impurities used to manufacture and process the explosives. Here we present high resolution infrared data for several of these volatile organic compounds in the 700 cm<sup>-1</sup> region required for real time optical sensing of energetic materials.
A Modular Software System to Assist Interpretation of Medical Images—Application to Vascular Ultrasound Images (2006)

Improvements in medical imaging technology have greatly contributed to early disease detection and diagnosis. However, the accuracy of an examination depends on both the quality of the images and the ability of the physician to interpret those images. Use of output from computerized analysis of an image may facilitate the diagnostic tasks and, potentially improve the overall interpretation of images and the subsequent patient care. In this paper, Analysis, a modular software system designed to assist interpretation of medical images, is described in detail. Analysis allows texture and motion estimation of selected regions of interest (ROIs). Texture features can be estimated using first-order statistics, second-order statistics, Laws' texture energy, neighborhood gray-tone difference matrix, gray level difference statistics, and the fractal dimension. Motion can be estimated from temporal image sequences using block matching or optical flow. Image preprocessing, manual and automatic definition of ROIs, and dimensionality reduction and clustering using fuzzy c-means, are also possible within Analysis. An important feature of Analysis is the possibility for online telecollaboration between health care professionals under a secure framework. To demonstrate the applicability and usefulness of the system in clinical practice, Analysis was applied to B-mode ultrasound images of the carotid artery. Diagnostic tasks included automatic segmentation of the arterial wall in transverse sections, selection of wall and plaque ROIs in longitudinal sections, estimation of texture features in different image areas, motion analysis of tissue ROIs, and clustering of the extracted features. It is concluded that Analysis can provide a useful platform for computerized analysis of medical images and support of diagnosis
Adaptive Directional Lifting-Based Wavelet Transform for Image Coding (2007)

We present a novel 2-D wavelet transform scheme of adaptive directional lifting (ADL) in image coding. Instead of alternately applying horizontal and vertical lifting, as in present practice, ADL performs lifting-based prediction in local windows in the direction of high pixel correlation. Hence, it adapts far better to the image orientation features in local windows. The ADL transform is achieved by existing 1-D wavelets and is seamlessly integrated into the global wavelet transform. The predicting and updating signals of ADL can be derived even at the fractional pixel precision level to achieve high directional resolution, while still maintaining perfect reconstruction. To enhance the ADL performance, a rate-distortion optimized directional segmentation scheme is also proposed to form and code a hierarchical image partition adapting to local features. Experimental results show that the proposed ADL-based image coding technique outperforms JPEG 2000 in both PSNR and visual quality, with the improvement up to 2.0 dB on images with rich orientation features.
Sterol 14alpha-Demethylase (CYP51) as a Therapeutic Target for Human Trypanosomiasis and Leishmaniasis (2011)

Pathogenic protozoa threaten lives of several hundred million people throughout the world and are responsible for large numbers of deaths globally. The parasites are transmitted to humans by insect vectors, more than a hundred of infected mammalian species forming reservoir. With human migrations, HIV-coinfections, and blood bank contamination the diseases are now spreading beyond the endemic tropical countries, being found in all parts of the world including the USA, Canada and Europe. In spite of the widely appreciated magnitude of this health problem, current treatment for sleeping sickness (Trypanosoma brucei), Chagas disease (Trypanosoma cruzi) and leishmaniasis (Leishmania spp.) remains unsatisfactory. The drugs are decades old, their efficacy and safety profiles are unacceptable. This review describes sterol 14α-demethylase, an essential enzyme in sterol biosynthesis in eukaryotes and clinical target for antifungal azoles, as a promising target for antiprotozoan chemotherapy. While several antifungal azoles have been proven active against Trypanosomatidae and are under consideration as antiprotozoan agents, crystal structures of sterol 14α-demethylases from three protozoan pathogens, Trypanosoma brucei, Trypanosoma cruzi and Leishmania infantum provide the basis for the development of new, highly potent and pathogen-specific drugs with rationally optimized pharmacological properties.
Observations On the Curation of Plant and Soil Nematodes (1986)

Observations are made on the curation of plant and soil nematodes by reference to the extensive collection of microscope slides and specimens in the Nematology Department, Rothamsted Experimental Station. Better packaging of specimens in transit is required. The addition of 2 % glycerol to fixatives/preservatives to prevent drying out and aid in the processing of specimens to glycerol is recommended. The cuticles of some nematodes degenerate in TAF fixative which should not be used for long term storage. The metal Cobb-type double cover glass slides are more convenient for transport and storage; a longer base cover glass improves clearance for microscope objectives. Cover glass supports need to be much more extensive than in the past to avoid the eventual flattening of specimens. The wax ring seal/support system is quite effective but a secondary seal and cover glass support are recommended. Immersion oil damages some seals and should be removed immediately after use. The drying out of slide mounts is a problem; specimens keep better in glycerol in vials than on slides. Slide mounts should be adequately and clearly labelled in water/oil-proof ink; type slides should be clearly indicated.
Stabilized Lasers and Precision Measurements (1978)

This article traces the development of stabilized lasers from the Massachusetts Institute of Technology passive-stabilization experiments of the early 1960's up through the current epoch of highly stabilized helium-neon and carbon dioxide and continuous wave dye lasers. The utility, present performance, and limitations of stabilized lasers as standards of length or frequency for precision measurements are discussed. Examples considered of laser applications to physical measurements of outstanding scientific interest include determination of the speed of light, redefinition of the meter, resolution of the photon recoil-induced spectral doubling, use of optical "Ramsey" interference fringes from ultrahigh-resolution spectroscopy, and two improved tests of special relativity.
The application of thermography in the study of coronary blood flow. (1978)

Conjugated copolymer derivatives of poly[2-methoxy-5-(3',7'-dimethyloctyloxy)-1,4-phenylenevinylene] (MDMO-PPV) and poly(3-hexylthiophene) (P3HT) containing 10% of alkyne functionalities in the side chains have been prepared using the sulfinyl precursor route and the Rieke method, respectively. With the aim of expanding the absorption range of these conjugated polymers for their use in bulk heterojunction (BHJ) polymer:fullerene solar cells, appropriate phthalocyanine (Pc) molecules have been covalently bound through a post-polymerization "click chemistry" reaction between the alkyne functionalities in the side chains of the copolymers and a Pc functionalized with an azide moiety. The resulting poly(p-phenylenevinylene)-Pc (PPV-Pc) material holds a 9 mol% content of Pcs, while the polythiophene-Pc material (PT-Pc) contains a 8 mol% of Pc-functionalization in the side chains. As expected, the presence of the Pc contributes to the extension of the absorption up to 700 nm. BHJ solar cells have been prepared using PPV-Pc and PT-Pc materials in combination with PCBM. Although the Pc absorption contributes to the generation of photocurrent, the overall power conversion efficiencies (PCE) obtained from these cells are lower than those obtained with BHJ P3HT:PCBM (1:1) and MDMO-PPV:PCBM (1:4) solar cells. A plausible explanation could be the moderate solubility of the PPV-Pc and PT-Pc materials that limits the processing into thin films.
The Subventricular Zone Is Able to Respond to a Demyelinating Lesion After Localized Radiation (2013)

Radiation is a common tool in the treatment of brain tumors that induces neurological deficits as a side effect. Some of these deficits appear to be related to the impact of radiation on the neurogenic niches, producing a drastic decrease in the proliferative capacity of these regions. In the adult mammalian brain, the subventricular zone (SVZ) of the lateral ventricles is the main neurogenic niche. Neural stem/precursor cells (NSCs) within the SVZ play an important role in brain repair following injuries. However, the irradiated NSCs' ability to respond to damage has not been previously elucidated. In this study, we evaluated the effects of localized radiation on the SVZ ability to respond to a lysolecithin-induced demyelination of the striatum. We demonstrated that the proliferation rate of the irradiated SVZ was increased after brain damage and that residual NSCs were reactivated. The irradiated SVZ had an expansion of doublecortin positive cells that appeared to migrate from the lateral ventricles toward the demyelinated striatum, where newly generated oligodendrocytes were found. In addition, in the absence of demyelinating damage, remaining cells in the irradiated SVZ appeared to repopulate the neurogenic niche a year post-radiation. These findings support the hypothesis that NSCs are radioresistant and can respond to a brain injury, recovering the neurogenic niche. A more complete understanding of the effects that localized radiation has on the SVZ may lead to improvement of the current protocols used in the radiotherapy of cancer.