gebhart/patrepeval huggingface dataset:
Investigation of cell culture media infected with viruses by pyrolysis mass spectrometry: Implications for bioaerosol detection (1999)

Mass spectrometry coupled with a pyrolysis inlet system was used to investigate media from cell cultures infected with viruses. Cell culture media is an intricate mixture of numerous chemical constituents and cells that collectively produce complicated mass spectra. Cholesterol and free fatty acids were identified and attributed to lipid sources in the media (blood serum supplement and plasma membranes of host cells). These lipid moieties could be utilized as signature markers for rapidly detecting the cell culture media. Viruses are intracellular parasites and are dependent upon host cells in order to exist. Therefore, it is highly probable that significant quantities of media needed to grow and maintain viable host cells would be present if a viral agent were disseminated as an aerosol into the environment. Cholesterol was also detected from a purified virus sample, further substantiating its use as a target compound for detection. Implications of this research for detection of viral bioaerosols, using a field-portable pyrolysis mass spectrometer, is described.
The Biology of Natural Killer Cells and Implications for Therapy of Human Disease (2001)

Natural killer (NK) cells are unique lymphocytes capable of lysing target cells without prior immunization. NK cells activated with cytokines, like interleukin-2 (IL-2), have been used since the 1980s as adoptive immunotherapy against metastatic solid tumors, but their effectiveness has been limited. The mechanisms by which NK cells recognize their targets are complex, including newly identified receptors that recognize class I MHC molecules. Understanding these mechanisms may support the use of NK cells as clinical therapy against infectious diseases and cancer. We have been interested in the use of NK cells clinically for their potential to eradicate minimal residual disease and prevent relapses after autologous stem cell transplantation. Several strategies are discussed to increase the specificity and efficacy of NK cell therapy. One method is to increase the targeting of NK cells by the use of monoclonal antibodies. Another approach uses allogeneic NK cells to overcome the inhibitory receptor mechanisms that may block target cell lysis by recognition of class I molecules. These and other novel strategies may prove to be attractive and effective immunotherapeutic tools to manipulate NK cells to fight human disease.
Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1 (2006)

Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 A, alpha = 62.3 degrees) and shown to diffract X-rays to at least 2.5 A resolution. The diffraction data were subsequently processed and reduced with an overall R(sym) of 12.3% and a completeness of 89.0%. Based on the unit-cell volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 A resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.
Cloning and Characterization of A-kinase Anchor Protein 100 (AKAP100) (1995)

Differential localization of the type II cAMP-dependent protein kinase (PKA) is achieved by interaction of the regulatory subunit (RII) with A-kinase anchor proteins (AKAPs). Anchoring is a likely means to adapt PKA for regulation of cAMP-responsive events through colocalization of the kinase with preferred substrates. Using an interaction cloning strategy with an RII alpha protein probe, we have identified a 655-amino acid protein (named AKAP100). Recombinant AKAP100, expressed in Escherichia coli, binds RII alpha in a solid-phase overlay assay. The cellular and subcellular distribution of AKAP100 was analyzed by various methods. Northern blot analysis with the AKAP100 cDNA as a probe detected an 8-kilobase message in some human tissues including various brain regions; however, the message was predominately expressed in cardiac and skeletal muscle. Anti-AKAP100 antibodies confirmed expression in the rat cardiac and skeletal muscle cell lines, H9c2 and L6P, whereas immunohistochemical analysis revealed that AKAP100 was localized to the sarcoplasmic reticulum of both cell types. RII was also detected in these regions. AKAP100 was detected in preparations of RII purified from L6P cell extracts by cAMP-agarose affinity chromatography. Collectively, these results suggest that AKAP100 functions to maintain the type II PKA at the sarcoplasmic reticulum.
Guaranteed Internet bandwidth (2002)

As Internet services, such as the World Wide Web, become basic information tools for businesses and individuals, its users are becoming less patient with long delays and unpredictable performance. In addition, sites offering multimedia streams are rapidly emerging, adding significant strain on an already heavily loaded Internet, whose current transport protocols were designed to offer "best effort" service without performance guarantees. This article describes guaranteed Internet bandwidth (GIB), a new technology that provides predictable performance by enabling end-user applications to establish end-to-end, on-demand, ISDN or ATM circuits and redirect selected Internet Protocol (IP) traffic through them. The GIB is easy to deploy in the short term, does not require changes in existing Internet routers, and includes simple and effective handling of payment agreement and billing.
Therapeutic potential of bone morphogenetic proteins (2001)

Recently, there has been substantial progress in the area of bone morphogenetic protein (BMP) research. This review serves as an up-to-date summary of the history of BMPs, the mechanisms of BMP signalling and the role of BMPs in adipose, kidney, liver, bone and nervous system. The potential of BMPs as therapeutic agents will also be discussed.
Selective gene expression in failing human heart. Quantification of steady-state levels of messenger RNA in endomyocardial biopsies using the polymerase chain reaction. (1991)

Alterations in gene expression in the failing human heart appear to be selective. In addition, the present study suggests that PCR provides a rapid and economical way to quantify the expression of multiple genes of interest in endomyocardial biopsy specimens and may therefore be used to advance our understanding of heart muscle disease.
System level power allocation algorithm for mobile devices for full playback guarantee (2011)

We propose a system level power allocation algorithm for mobile devices for guaranteed playback duration. The algorithm takes as input the media playback duration and current battery charge available on the device. It calculates energy budget based on this. It finds a set of feasible operating points based on maximization of a joint quality function while meeting energy budget constraint. The joint quality function consists of contributions from backlight and playback frame rate quality functions. A side-by-side comparison of our algorithm with state-of-the-art native video player application on the smartphone shows similar audio-visual experience while providing 19% system level energy savings.
Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures (2011)

The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120). The design of soluble versions of trimeric Env that display structural and functional properties similar to those observed on intact viruses is highly desirable from the viewpoint of designing immunogens that could be effective as vaccines against HIV/AIDS. Using cryoelectron tomography combined with subvolume averaging, we have analyzed the structure of SOSIP gp140 trimers, which are cleaved, solubilized versions of the ectodomain of trimeric HIV-1 Env. We show that unliganded gp140 trimers adopt a quaternary arrangement similar to that displayed by native unliganded trimers on the surface of intact HIV-1 virions. When complexed with soluble CD4, Fab 17b, which binds to gp120 at its chemokine coreceptor binding site, or both soluble CD4 and 17b Fab, gp140 trimers display an open conformation in which there is an outward rotation and displacement of each gp120 protomer. We demonstrate that the molecular arrangements of gp120 trimers in the closed and open conformations of the soluble trimer are the same as those observed for the closed and open states, respectively, of trimeric gp120 on intact HIV-1 BaL virions, establishing that soluble gp140 trimers can be designed to mimic the quaternary structural transitions displayed by native trimeric Env.
Recognition of AvrBs3-Like Proteins Is Mediated by Specific Binding to Promoters of Matching Pepper Bs3 Alleles (2009)

The pepper (Capsicum annuum) bacterial spot (Bs) resistance gene Bs3 and its allelic variant Bs3-E mediate recognition of the Xanthomonas campestris pv vesicatoria type III effector protein AvrBs3 and its deletion derivative AvrBs3Deltarep16. Recognition specificity resides in the Bs3 and Bs3-E promoters and is determined by a defined promoter region, the UPA (for up-regulated by AvrBs3) box. Using site-directed mutagenesis, we defined the exact boundaries of the UPA(AvrBs3) box of the Bs3 promoter and the UPA(AvrBs3Deltarep16) box of the Bs3-E promoter and show that both boxes overlap by at least 11 nucleotides. Despite partial sequence identity, the UPA(AvrBs3) box and the UPA(AvrBs3Deltarep16) box were bound specifically by the corresponding AvrBs3 and AvrBs3Deltarep16 proteins, respectively, suggesting that selective promoter binding of AvrBs3-like proteins is the basis for promoter activation specificity. We also demonstrate that the UPA(AvrBs3) box retains its functionality at different positions within the pepper Bs3 promoter and confers AvrBs3 inducibility in a novel promoter context. Notably, the transfer of the UPA(AvrBs3) box to different promoter locations is always correlated with a new transcriptional start site. The analysis of naturally occurring Bs3 alleles revealed many pepper accessions that encode a nonfunctional Bs3 variant. These accessions showed no apparent abnormalities, supporting the supposition that Bs3 functions only in disease resistance and not in other developmental or physiological processes.
Isothiazoles I: 4‐isothiazolin‐3‐ones. A general synthesis from 3,3′‐dithiodipropionamides (1971)

Abstract The syntheses of 3‐hydroxyisothiazole, 4‐methyl‐3‐hydroxyisothiazole, and a eomprehensive series of the respective 2‐substituted‐4‐isothiazoIin‐3‐ones have been achieved by the one‐step chlorination‐cyclization of the corresponding 3,3 ‐dithiodipropionamides. In several instances, 5‐chloro‐4‐isothiazolin‐3‐ones were isolated as side products; however, no 4‐chloro‐4‐isothiazo‐lin‐3‐ones were evident in the reaction mixtures. These observations, coupled with the exclusive 4‐ or 4,5‐halogenation of several preformed 4‐isothiazoIin‐3‐ones, support a proposed reaction pathway involving introduction of chlorine α to the sulfur atom in intermediate reaction products.
Culture-proved disseminated cat-scratch disease in acquired immunodeficiency syndrome (1989)

• A male homosexual (positive for the human immunodeficiency virus) with a recent cat scratch developed fever, epitrochlear and axillary lymphadenopathy, and retinitis. Subsequently, he developed skin (epithelioid hemangioma) and mucosal lesions (Kaposi's sarcoma), multiple liver abscesses, and pleural effusion. Warthin-Starry stains and/or electron micrographs of lymph nodes and skin lesions demonstrated bacilli characteristic of those associated with cat-scratch disease. Cultures of lymph node, pleural fluid, and liver abscess specimens yielded organisms believed to be the causative agent of cat-scratch disease. We believe that disseminated cat-scratch disease may become an indicator of opportunistic infection signaling acquired immunodeficiency syndrome in a patient who is positive for the human immunodeficiency virus. (<i>Arch Intern Med</i>. 1989;149:1437-1439)
Ulcerative Colitis and Colorectal Cancer (1990)

Close surveillance and perhaps even prophylactic proctocolectomy should be recommended for patients given a diagnosis of pancolitis, especially those who are less than 15 years of age at diagnosis.
A novel type I factor X variant (factor X Cys350Phe) due to loss of a disulfide bond in the catalytic domain (2003)

We report a novel mutation within the coagulation factor X (FX) that we have designated FX Padua 4. The phenotype and genotype of the proband and family members were studied. The proband was a child affected by a complex neurological syndrome who, after birth, experienced severe bleeding. The proband showed a laboratory pattern characterized by a severe reduction of FX activity and FX antigen, suggesting a true deficiency. Molecular analysis disclosed a new FX mutation localized in the catalytic domain responsible for a Cys350Phe substitution. The proband was homozygous for this mutation. The proband's mother and father showed a heterozygous pattern and had approximately one-half the normal FX activity and FX antigen. Residual purified FX Cys350Phe had an identical behavior to normal FX as showed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Molecular modeling confirms that the mutation leads to the disruption of a disulfide bridge in the catalytic region of FX. Comparison with other topologically equivalent mutations in other vitamin K-dependent proteins suggests that this disruption could adversely affect protein folding/stability, accounting for the cross-reactive material negative phenotype.
Supraorbital transcutaneous neurostimulation has sedative effects in healthy subjects (2011)

Supraorbital high frequency TNS applied with the Cefaly® device decreases vigilance in healthy volunteers. Additional studies are needed to determine the duration of this effect, the underlying mechanisms and the possible relation with the stimulation parameters. Meanwhile, this effect opens interesting perspectives for the treatment of hyperarousal states and, possibly, insomnia.
Pathways of macromolecular tracer transport across venules and small veins. Structural basis for the hyperpermeability of tumor blood vessels. (1992)

VVO are prominent structures in both tumor-supplying and control vessel endothelial cells and provide the primary pathway for macromolecular extravasation. The large increase in permeability characteristic of tumor vessels is likely attributable to upregulation of VVO function.
Bactericidal effect of laser light and its potential use in the treatment of plaque-related diseases. (1994)

Chemical antibacterial agents are increasingly being used in prophylactic and therapeutic regimes for plaque-related diseases. As these agents can be rendered ineffective by the development of resistance in the target organisms there is a need to develop alternative antimicrobial approaches. Light from high-power lasers is known to be bactericidal and investigations have shown that it is effective against organisms implicated in caries and inflammatory periodontal diseases. However, the adverse effects of such light on dental hard tissues argue against its use solely as an antibacterial agent. Although light from low-power lasers has no adverse effect on bacterial viability, bacteria can be sensitised to killing by such light by prior treatment with a chemical photosensitising agent. Lethal photosensitisation of a wide range of cariogenic and periodontopathogenic bacteria has been demonstrated using light from a helium/neon or gallium aluminium arsenide laser in conjunction with a dye such as toluidine blue or aluminium disulphonated phthalocyanine as a photosensitiser. The advantages of the technique are that killing is achieved in very short periods of time (< 60 s), resistance development in the target bacteria would be unlikely and damage to adjacent host tissues can be avoided. This approach may be a useful alternative to antibiotics and antiseptics in eliminating cariogenic and periodontopathogenic bacteria from disease lesions.
An Image-Based Approach to Three-Dimensional Computer Graphics (1997)

The conventional approach to three-dimensional computer graphics produces images from geometric scene descriptions by simulating the interaction of light with matter. My research explores an alternative approach that replaces the geometric scene description with perspective images and replaces the simulation process with data interpolation. I derive an image-warping equation that maps the visible points in a reference image to their correct positions in any desired view. This mapping from reference image to desired image is determined by the center-of-projection and pinhole-camera model of the two images and by a generalized disparity value associated with each point in the reference image. This generalized disparity value, which represents the structure of the scene, can be determined from point correspondences between multiple reference images. The image-warping equation alone is insufficient to synthesize desired images because multiple reference-image points may map to a single point. I derive a new visibility algorithm that determines a drawing order for the image warp. This algorithm results in correct visibility for the desired image independent of the reference image’s contents. The utility of the image-based approach can be enhanced with a more general pinholecamera
Detecting large-scale system problems by mining console logs (2009)

Surprisingly, console logs rarely help operators detect problems in large-scale datacenter services, for they often consist of the voluminous intermixing of messages from many software components written by independent developers. We propose a general methodology to mine this rich source of information to automatically detect system runtime problems. We first parse console logs by combining source code analysis with information retrieval to create composite features. We then analyze these features using machine learning to detect operational problems. We show that our method enables analyses that are impossible with previous methods because of its superior ability to create sophisticated features. We also show how to distill the results of our analysis to an operator-friendly one-page decision tree showing the critical messages associated with the detected problems. We validate our approach using the Darkstar online game server and the Hadoop File System, where we detect numerous real problems with high accuracy and few false positives. In the Hadoop case, we are able to analyze 24 million lines of console logs in 3 minutes. Our methodology works on textual console logs of any size and requires no changes to the service software, no human input, and no knowledge of the software's internals.
Sol-gel processing of alkoxysilyl-substituted nickel complexes for the preparation of highly dispersed nickel in silicaElectronic supplementary information (ESI) available: Tables S1–S5 giving additional analytical data as described in the text and the exact quantities for the syntheses. See http://www.rsc.org/suppdata/nj/b1/b110612k/ (2002)

Nanocomposites containing nickel nanoparticles in silica were obtained by sol-gel processing of Ni(NO3)2, Ni(OAc)2 (OAc = acetate), NiCl2, or Ni(acac)2 (acac = acetylacetonate), a complexing silane [(EtO)3Si(CH2)3NHCH2CH2NH2, (EtO)3Si(CH2)3NH2 or (RO)3Si(CH2)3NHCH2CH2NHCH2CH2NH2] and Si(OEt)4, followed by calcination of the metal-complex-containing xerogels in air and reduction in hydrogen. Two types of nanocomposite materials were prepared, both containing about 8–8.5 wt % of elemental nickel: (i) Ni/SiO2 nanocomposite powders in which the silica matrix is mainly formed from Si(OR)4, and (ii) Ni particles on pre-formed silica spheres. The latter were prepared by impregnating silica spheres with sols from the particular complexing silane–nickel salt combination followed by calcination and reduction. In both types of materials, the average nickel particle size is influenced by the composition of the precursor mixture, particularly the counter-ion of the employed nickel salt. The smallest particles (diameter below 3 nm) were obtained from Ni(NO3)2 [and Ni(OAc)2 for the powders], while the use of Ni(acac)2 and NiCl2 resulted in larger nickel particles. The variation of the nickel particle diameters was much larger for the powders than for the impregnated spheres.
PCR-Based Site-Directed Mutagenesis (2003)

Protocols for site-directed mutagenesis are widely used in molecular biology and include many polymerase chain reaction (PCR)-based methods that have been developed in order to achieve efficient mutagenesis of a target DNA sequence (, , , ). However, some of these methods described require two or more specific-oligonucleotides for each round of mutagenesis, making the cost of such procedures expensive. This chapter describes an efficient and economic PCR-based site-directed mutagenesis method, which is designed to introduce a series of mutations into DNA cloned into pUC vectors (pUC 18, 19, 118, 119). The protocol uses a combination of a primer designed for introducing a mutation at the target sequence, with primers that may be reused for each mutagenesis reaction (Fig. 1). By using this method, a series of site-directed mutations may be undertaken that only require a single primer for each desired change, and furthermore, no reiterative transformation steps are necessary. Open image in new window Fig. 1. Principle of PCR in vitro mutagenesis. [1] First round PCR of target DNA following cloning of sequence into multicloning site of one of the pUC series of vectors. One of the MUT primers is chosen to destroy a restriction site, based on both the direction of R1 primer (primer for introducing a mutation) and the restriction site used for cloning the target DNA sequence. The first round PCR is carried out by the combination of R1 primer and M13 primer RV (or M13 primer M4), MUT primer, and M13 primer M4 (or M13 primer RV) separately in two tubes. [2] After DNA purification to remove excess primers, the amplified products are mixed, heat denatured, and annealed. [3] Taq DNA polymerase is added to complete the DNA heteroduplex. [4] The second round PCR is performed using M13 primer M4 and M13 primer RV flanking oligonucleotides, which will result in two types of amplified products, (a) and (b). [5] The amplified products are digested with two restriction enzymes, one of which shall recognize the site (X) that had been destroyed by the MUT primer and the other which recognizes the appropriate site (Y) within the multicloning site. [6] Reclone the digested fragment into the vector digested with the same two restriction enzymes. Only the fragment (a) that contains the mutation introduced by R1 primer sequence will be recloned.