gebhart/patrepeval huggingface dataset:
Correction of Genetic Blood Defects by Gene Transfer (2007)

Gene therapy has been proposed as an appealing tool for introducing a normal gene into affected hematopoietic stem cells to correct their inherited defect. Theoretically, in the absence of a related human leukocyte antigen identical donor, gene therapy could be an alternative given the accessibility and the information available on the hematopoietic stem cell biology. This chapter describes the progress and limits of the gene therapy approach applied to some genetic blood defects that appear to be good targets for this strategy.
Sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan. (2001)

Strain EDIVT, an exopolysaccharide-producing bacterium, was subjected to polyphasic characterization. The bacterium produced copious amounts of an extracellular polysaccharide, forming slimy, viscous, intensely yellow-pigmented colonies on Czapek-Dox (CZD) agar. The culture fluids of the liquid version of CZD medium were highly viscous after cultivation for 5 d. Cells of strain EDIVT were Gram-negative, catalase-positive, oxidase-negative, nonspore-forming, rod-shaped and motile. Comparisons of 16S rDNA gene sequences demonstrated that EDIVT clusters phylogenetically with the species of the genus Sphingomonas sensu stricto. The G+C content of the DNA (64.5 mol%), the presence of ubiquinone Q-10, the presence of 2-hydroxymyristic acid (14:0 2-OH) as the major hydroxylated fatty acid, the absence of 3-hydroxy fatty acids and the detection of sym-homospermidine as the major component in the polyamine pattern, together with the presence of sphingoglycolipid, supported this delineation. 16S rDNA sequence analysis indicated that strain EDIVT is most closely related (99.4% similarity) to Sphingomonas trueperi LMG 2142T. DNA-DNA hybridization showed that the level of relatedness to S. trueperi is only 45.5%. Further differences were apparent in the cellular fatty acid profile, the polar lipid pattern, the Fourier-transform infrared spectrum and whole-cell proteins and in a number of biochemical characteristics. On the basis of the estimated phylogenetic position derived from 16S rDNA sequence data, DNA-DNA reassociation and phenotypic differences, strain EDIVT (= CIP 106154T = DSM 13101T) was recognized as a new species of Sphingomonas, for which the name Sphingomonas pituitosa sp. nov. is proposed. A component analysis of the exopolysaccharide (named PS-EDIV) suggested that it represents a novel type of sphingan composed of glucose, rhamnose and an unidentified sugar. Glucuronic acid, which is commonly found in sphingans, was absent. The mean molecular mass of PS-EDIV was approximately 3 x 10(6) Da.
Fabrication, characterization, and analysis of mass-transported GaInAsP/InP buried-heterostructure lasers (1984)

The mass-transported buried-heterostructure lasers have been investigated in detail. Techniques have been developed for fabrication control and wafer characterization. High yield of low-threshold lasers was obtained with the lowest threshold current being 5.5 mA. Differential quantum efficiencies as high as 28 percent per facet and smooth far-field patterns were also obtained. Deep Zn-diffusion and higher p-doping have been used to improve the linearity of the light-current characteristics. Linear light output to greater than 13 mW per facet and well-behaved threshold-temperature dependence were achieved. A conformal mapping technique has been used to calculate the voltage distribution in the laser mesa. The forward-bias voltage thus obtained for the InP pn homojunctions in the transported regions is shown to be capable of resulting in the sublinear dependence of light output on current observed in lasers with lightly p-doped cap layers. The current limit within which the laser can be operated without leakage through the homojunctions has been calculated for various device geometries and doping levels.
GRID-BASED INVERSION OF PRESSURE TRANSIENT TEST DATA WITH STOCHASTIC GRADIENT TECHNIQUES (2012)

In any subsurface exploration and development, indirect information and measurements, such as detailed geological description, outcrop studies, and direct measurements (such as seismic, cores, logs, and fluid samples), provide useful data and information for static reservoir characterization, simulation, and forecasting. However, core and log data delineate rock properties only in the vicinity of the wellbore, while geological and seismic data are usually not directly related to formation permeability. Pressure transient test (PTT) data provide dynamic information about the reservoir and can be used to estimate rock properties, fluid samples for well productivity, and dynamic reservoir description. Therefore, PTT data are essential in the industry for the general purposes of production and reservoir engineering as well as commonly used for exploration environments. With the need for improved spatial resolution of the reservoir parameters, grid-based techniques have been developed in which the reservoir properties are discretized over a fine grid and characterization of the probable state of the reservoir is sought using the Bayesian framework. Unfortunately, for the exploration of hydrocarbon-bearing formations, the available prior information is often limited: in particular, unexpected geological features, such as fracture and faults, may be present. There are two groups of recent methods for dynamic characterization of the reservoir: (i) data assimilation techniques, e.g., ensemble Kalman filter (EnKF) and (ii) maximum-likelihood techniques, such as gradient-based methods. The EnKF is designed to produce a set of realizations of the reservoir properties that fit the PTT data; however, the method often fails to honor the data when unexpected features are not captured by the prior model. The alternative gradient-based methods do provide a good fit to the PTT data. They can also be made efficient for high-dimensional problems by using an adjoint scheme for determining the gradient of the log-likelihood function. However, as a maximum likelihood technique, this method only yields a single realization of the reservoir. It is important to maintain a model of the uncertainty of the reservoir characterization after PTT data assimilation, so that the risk associated with future decisions is understood. We therefore present and investigate a stochastic, gradient-based method that allows for proper sampling of realizations of the reservoir parameters that preserve the fit with the PTT data. The results indicate that our proposed method is quite encouraging for efficiently generating realizations of rock property distributions conditioned to PTT data sets and a given prior geostatistical model.
Band 3 Peptides Block the Adherence of Sickle Cells to Endothelial Cells In Vitro (1997)

Malaria-parasitized erythrocytes have increased endothelial adherence due to exposure of previously buried intramembranous sites of band 3. Because sickle erythrocytes also show increased adhesiveness and because the membrane portion of band 3 is aggregated in both types of cells, we examined the role of band 3 in sickle cell adhesiveness. Synthetic peptides derived from the second and third exofacial, interhelical regions of band 3 completely inhibited the abnormal adherence of sickle cells to an endothelial monolayer in a static assay. This effect was observed independently of plasma factors, required micromolar levels of peptide, was sequence-specific, and was found with both L- and D-isomers. The active peptides also inhibited the increased adherence induced by low-dose calcium loading of normal red blood cells. Finally, a monoclonal antibody against an active peptide specifically immunostained a fraction of sickle cells. These findings implicate a role for band 3 in at least one type of sickle cell adhesiveness via the exposure of normally cryptic membrane sites.
Cytotoxic Withanolide Constituents of <i>Physalis longifolia</i> (2011)

Fourteen new withanolides, 1-14, named withalongolides A-N, respectively, were isolated from the aerial parts of Physalis longifolia together with eight known compounds (15-22). The structures of compounds 1-14 were elucidated through spectroscopic techniques and chemical methods. In addition, the structures of withanolides 1, 2, 3, and 6 were confirmed by X-ray crystallographic analysis. Using a MTS viability assay, eight withanolides (1, 2, 3, 7, 8, 15, 16, and 19) and four acetylated derivatives (1a, 1b, 2a, and 2b) showed potent cytotoxicity against human head and neck squamous cell carcinoma (JMAR and MDA-1986), melanoma (B16F10 and SKMEL-28), and normal fetal fibroblast (MRC-5) cells with IC₅₀ values in the range between 0.067 and 9.3 μM.
Transforming Growth Factor-β Isoforms and the Induction of Bone Formation (2009)

Craniofacial skeletal reconstruction remains a challenging problem despite major molecular and surgical developments in the understanding of bone formation by induction. The induction of bone formation has been a critical topic of research across the planet. The bone induction principle identified important cues for tissue engineering of bone, namely, osteogenic soluble molecular signals, the bone morphogenetic and osteogenic proteins, and insoluble signals or substrata including biomimetic bioactive matrices and responding stem cells. In primates, and in primates only, the osteogenic soluble molecular signals that initiate the induction of bone formation additionally include the 3 mammalian transforming growth factor-beta (TGF-beta) isoforms, members of the TGF-beta supergene family. The mammalian TGF-beta isoforms, when implanted in the rectus abdominis muscle of the nonhuman primate Papio ursinus, induce rapid and substantial endochondral bone formation resulting in large corticalized ossicles by day 30 after heterotopic implantation; in calvarial defects of the same nonhuman primates, identical or higher doses of the TGF-beta protein do not induce bone formation because of the overexpression of Smad-6 and Smad-7, gene product inhibitors of the TGF-beta signaling pathway. The addition of minced fragments of autogenous rectus abdominis muscle partially restores the osteoinductive activity of the human TGF-beta3 isoform resulting in the induction of bone formation in the treated calvarial defects. Recombinant human TGF-beta3 delivered by Matrigel matrix and implanted in class II and III furcation defects of mandibular molars of P. ursinus induce periodontal tissue regeneration. The addition of minced fragments of autogenous rectus abdominis muscle significantly enhances cementogenesis. This review highlights the induction of bone formation by the osteogenic proteins of the TGF-beta superfamily in the nonhuman primate P. ursinus and reviews combinatorial applications of myoblastic/myogenic stem cell-based therapeutics for bone induction and morphogenesis. The recruitment of myoendothelial cells is also discussed in the light of the intrinsic and spontaneous induction of bone formation by smart biomaterial matrices that induce bone differentiation in heterotopic extraskeletal sites of P. ursinus without the exogenous application of the osteogenic soluble molecular signals of the TGF-beta superfamily.
Rex: Symbolic Regular Expression Explorer (2010)

Constraints in form regular expressions over strings are ubiquitous. They occur often in programming languages like Perl and C#, in SQL in form of LIKE expressions, and in web applications. Providing support for regular expression constraints in program analysis and testing has several useful applications. We introduce a method and a tool called Rex, for symbolically expressing and analyzing regular expression constraints. Rex is implemented using the SMT solver Z3, and we provide experimental evaluation of Rex.
Error Bounds for FDD Massive MIMO Channel Covariance Conversion with Set-Theoretic Methods (2018)

We derive novel bounds for the performance of algorithms that estimate the downlink covariance matrix from the uplink covariance matrix in frequency division duplex (FDD) massive multiple-input multiple-output (MIMO) systems. The focus is on algorithms that use estimates of the angular power spectrum as an intermediate step. Unlike previous results, the proposed bounds follow from simple arguments in possibly infinite dimensional Hilbert spaces, and they do not require strong assumptions on the array geometry or on the propagation model. Furthermore, they are suitable for the analysis of set-theoretic methods that can efficiently incorporate side information about the angular power spectrum. This last feature enables us to derive simple techniques to enhance set-theoretic methods without any heuristic arguments. In particular, we show that the performance of a simple algorithm that requires only a simple matrix-vector multiplication cannot be improved significantly in some practical scenarios, especially if coarse information about the support of the angular power spectrum is available.
Differentiation Between Analyte Adsorption and Homogenous Index Sensing in WGM Biodetection (2012)

We propose new parameters to characterize a whispering gallery mode spectrum, which can be regarded as reliable independent biodetection indicators for an instantaneous microsphere's spectrum. With these parameters, since there is no need for spectral comparison to an analyte-free reference, three-dimensional stirring of fluorescent microspheres in fluidic setup is allowed. Through an analysis of fluorescent microspheres in the presence of bacterial spores, we found five insightful quantitative independent parameters for biodetection. Unveiled by this analysis, we demonstrate the possibility to discriminate between analyte presence and homogeneous variation of the solution's refractive index.
Fast Dynamic Voronoi Treemaps (2010)

The Voronoi Treemap is a space-filling treemap technique that relaxes the constraints of rectangular nodes. Its organic shapes maintain a one-to-one aspect ratio, are flexible with their placement, allowing stable zooming and dynamic data values. In this paper, we present algorithms for efficient computation and dynamic update of Voronoi Treemaps. Our GPGPU-based technique allows for rapid computation of centroidal Voronoi Diagrams, providing almost two orders of magnitude speedup over previous work. In addition, we present a hierarchical algorithm for stable updates. Finally, we demonstrate the application of Voronoi treemaps to real-world dynamic datasets, including interactive navigation.
ChemInform Abstract: High‐Yielding Staudinger Ligation of a Phosphinothioester and Azide to Form a Peptide. (2001)

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.
Enantioselective Synthesis of Acyclic α‐Quaternary Carboxylic Acid Derivatives through Iridium‐Catalyzed Allylic Alkylation (2017)

Abstract The first highly enantioselective iridium‐catalyzed allylic alkylation that provides access to products bearing an allylic all‐carbon quaternary stereogenic center has been developed. The reaction utilizes a masked acyl cyanide (MAC) reagent, which enables the one‐pot preparation of α‐quaternary carboxylic acids, esters, and amides with a high degree of enantioselectivity. The utility of these products is further explored through a series of diverse product transformations.
Purification, Cloning, and Characterization of XendoU, a Novel Endoribonuclease Involved in Processing of Intron-encoded Small Nucleolar RNAs in Xenopus laevis (2003)

Here we report the purification, from Xenopus laevis oocyte nuclear extracts, of a new endoribonuclease, XendoU, that is involved in the processing of the intron-encoded box C/D U16 small nucleolar RNA (snoRNA) from its host pre-mRNA. Such an activity has never been reported before and has several uncommon features that make it quite a novel enzyme: it is poly(U)-specific, it requires Mn(2+) ions, and it produces molecules with 2'-3'-cyclic phosphate termini. Even if XendoU cleaves U-stretches, it displays some preferential cleavage on snoRNA precursor molecules. XendoU also participates in the biosynthesis of another intron-encoded snoRNA, U86, which is contained in the NOP56 gene of Xenopus laevis. A common feature of these snoRNAs is that their production is alternative to that of the mRNA, suggesting an important regulatory role for all the factors involved in the processing reaction.
Inhibition of UV‐lnduced Immune Suppression and lnterleukin‐10 Production by Plant Oligosaccharides and Polysaccharides (1999)

Application of Aloe barbadensis poly/oligosaccharides to UV-irradiated skin prevents photosuppression of delayed-type hypersensitivity (DTH) responses in mice. We tested the hypothesis that these carbohydrates belong to a family of biologically active, plant-derived polysaccharides that can regulate responses to injury in animal tissues. C3H mice were exposed to 5 kJ/m2 UVB from unfiltered FS40 sunlamps and treated with between 1 pg and 10 micrograms tamarind xyloglucans or control polysaccharides methylcellulose or dextran in saline. The mice were sensitized 3 days later with Candida albicans. Tamarind xyloglucans and purified Aloe poly/oligosaccharides prevented suppression of DTH responses in vivo and reduced the amount of interleukin (IL)-10 observed in UV-irradiated murine epidermis. Tamarind xyloglucans were immunoprotective at low picogram doses. In contrast, the control polysaccharides methylcellulose and dextran had no effect on immune suppression or cutaneous IL-10 at any dose. Tamarind xyloglucans and Aloe poly/oligosaccharides also prevented suppression of immune responses to alloantigen in mice exposed to 30 kJ/m2 UVB radiation. To assess the effect of the carbohydrates on keratinocytes, murine Pam212 cells were exposed to 300 J/m2 UVB radiation and treated for 1 h with tamarind xyloglucans or Aloe poly/oligosaccharides. Treatment of keratinocytes with immunoprotective carbohydrates reduced IL-10 production by approximately 50% compared with the cells treated with UV radiation alone and completely blocked suppressive activity of the culture supernatants in vivo. The tamarind xyloglucans also blocked UV-activated phosphorylation of SAPK/JNK protein but had no effect on p38 phosphorylation. These results indicate that animals, like plants, may use carbohydrates to regulate responses to environmental stimuli.
Column-anchored zeroforcing blind equalization for multiuser wireless FIR channels (1999)

We propose a direct blind zeroforcing approach to cancel intersymbol interference (ISI) in multiple user finite impulse response (FIR) channels. By selectively anchoring columns of the channel convolution matrix, we present two column-anchored zeroforcing equalizers (CAZE), one without output delay and one with a chosen delay. Unlike many known blind identification algorithms, these equalizers do not need an accurate estimate of the channel orders. Exploiting second-order statistics (SOS) of the received signals, they can retain preselected d columns in the channel convolution matrix (d is the number of users) and force the remaining columns to zero. CAZE can effectively equalize single-input-multiple-output (SIMO) systems and can reduce dynamic multiple-input-multiple-output (MIMO) systems into a memoryless signal mixing system for source separation. Simulation results show that the CAZE is not only effective for blind equalization of linear quadrature amplitude modulation (QAM) systems, but it is also applicable to the nonlinear GMSK modulation in the popular wireless GSM systems when computational cost severely limits the use of nonlinear methods such as the Viterbi algorithm.
Elucidating Novel Serum Biomarkers Associated with Pulmonary Tuberculosis Treatment (2013)

In an unbiased approach to biomarker discovery, we applied a highly multiplexed proteomic technology (SOMAscan, SomaLogic, Inc, Boulder, CO) to understand changes in proteins from paired serum samples at enrollment and after 8 weeks of TB treatment from 39 patients with pulmonary TB from Kampala, Uganda enrolled in the Center for Disease Control and Prevention's Tuberculosis Trials Consortium (TBTC) Study 29. This work represents the first large-scale proteomic analysis employing modified DNA aptamers in a study of active tuberculosis (TB). We identified multiple proteins that exhibit significant expression differences during the intensive phase of TB therapy. There was enrichment for proteins in conserved networks of biological processes and function including antimicrobial defense, tissue healing and remodeling, acute phase response, pattern recognition, protease/anti-proteases, complement and coagulation cascade, apoptosis, immunity and inflammation pathways. Members of cytokine pathways such as interferon-gamma, while present, were not as highly represented as might have been predicted. The top proteins that changed between baseline and 8 weeks of therapy were TSP4, TIMP-2, SEPR, MRC-2, Antithrombin III, SAA, CRP, NPS-PLA2, LEAP-1, and LBP. The novel proteins elucidated in this work may provide new insights for understanding TB disease, its treatment and subsequent healing processes that occur in response to effective therapy.
Synthesis and properties of a nonexchangeable radioiodinated phospholipid (1982)

An efficient method for the synthesis and purification of N-[3-(3-[125I]iodo-4-hydroxybenzyl)propionyl]- phosphatidylethanolamine (125I-phenylpropionyl-PE), a nonexchangeable iodinated lipid of high specific radioactivity, is described. The technique involves acylation of phosphatidylethanolamine with N-succinimidyl 3-(3-[125I]iodo-4-hydroxyphenyl)propionate (monoiodinated Bolton-Hunter reagent) and purification by thin-layer chromatography. Quantitative incorporation of the iodinated lipid into vesicles prepared by a variety of techniques was observed to occur. With these vesicles, no transfer of the labeled lipid to other vesicles or cells occurred, irrespective of vesicle composition or the presence of other transferable lipids in the same bilayer membranes. This, 125I-phenylpropionyl-PE appears to be an accurate liposome tracer and can be used in a variety of in vitro and in vivo assays that require high levels of sensitivity unobtainable with most other lipid-labeling techniques.
Particle Conformation Regulates Antibody Access to a Conserved GII.4 Norovirus Blockade Epitope (2014)

In this study, we explored the factors that govern norovirus (NoV) cross-strain antibody blockade. We found that access to the conserved GII.4 blockade epitope is regulated by temperature and distal residues outside the antibody binding site. These data are most consistent with a model of NoV particle conformation plasticity that regulates antibody binding to a distally conserved blockade epitope. Further, antibody "locking" of the particle into an epitope-accessible conformation prevents ligand binding, providing a potential target for broadly effective drugs. These observations open lines of inquiry into the mechanisms of human NoV entry and uncoating, fundamental biological questions that are currently unanswerable for these noncultivatable pathogens.