gebhart/patrepeval huggingface dataset:
Impact of Global Transcriptional Regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on Glucose Catabolism in Escherichia coli (2005)

Even though transcriptional regulation plays a key role in establishing the metabolic network, the extent to which it actually controls the in vivo distribution of metabolic fluxes through different pathways is essentially unknown. Based on metabolism-wide quantification of intracellular fluxes, we systematically elucidated the relevance of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc for aerobic glucose catabolism in batch cultures of Escherichia coli. Knockouts of ArcB, Cra, Fnr, and Mlc were phenotypically silent, while deletion of the catabolite repression regulators Crp and Cya resulted in a pronounced slow-growth phenotype but had only a nonspecific effect on the actual flux distribution. Knockout of ArcA-dependent redox regulation, however, increased the aerobic tricarboxylic acid (TCA) cycle activity by over 60%. Like aerobic conditions, anaerobic derepression of TCA cycle enzymes in an ArcA mutant significantly increased the in vivo TCA flux when nitrate was present as an electron acceptor. The in vivo and in vitro data demonstrate that ArcA-dependent transcriptional regulation directly or indirectly controls TCA cycle flux in both aerobic and anaerobic glucose batch cultures of E. coli. This control goes well beyond the previously known ArcA-dependent regulation of the TCA cycle during microaerobiosis.
Fecal Microbiota Transplantation for Clostridium Difficile Infection in Immunocompromised Hosts: “One Easy Strategy, One Giant Success”. (2014)

Introduction: Fecal microbiota transplantation (FMT) is highly efficacious and a safe procedure to treat recurrent/refractory Clostridium difficile infection (CDI). Immunocompromised hosts (IH) including organ transplant recipients have a higher incidence rate of CDI but only rare case reports describe the use of FMT in these patients. We sought to assess the efficacy and safety of FMT for the treatment of CDI in IH at our center. Methods: A retrospective single-center study was performed in a 900 bed urban medical center in Detroit, Michigan from May 2010 to December 2013. All patients with CDI including primary or recurrent, of moderate to severe intensity or not responding to conventional antibiotic therapy were evaluated by Infectious Diseases and referred for FMT. Data abstracted include demographics, co-morbidites, anti-microbial use, immune suppression, severity and number of CDI episodes. Healthy donors were screened for communicable diseases and using fresh stools from the day of procedure, FMT was performed using nasogastric (NGT) or enema route. All patients were followed for at least 100 days post-FMT. Results: The data from the first 200 patients in the study period were analyzed. Of the 200 recipients of FMT, 22 were considered to be immunocompromised (solid organ transplant recipients 7, stem cell transplant 3, advanced HIV 1 and patients on active immune suppressants 11). Mean age of the subjects was 58 years. Primary refractory CDI was seen in 23% of subjects and severe disease was seen in 64%. Naso-gastric route was used to perform FMT in 95% and enema in the remainder. Resolution of CDI was seen in 91% of subjects within 7 days of FMT. Of those patients who had resolution, 15% had recurrence of CDI within 100 days post-FMT. The 30-day all-cause mortality was 5% and was seen in patients with severe disease. None of the patients died from CDI or FMT. No major adverse effect was attributable to FMT. Conclusion: Immune suppression does not preclude the use of FMT for treatment of recurrent or refractory CDI and can be safely performed in both inpatient and outpatient setting.
Molecular and biochemical characterization of a novel gamma-interferon-inducible protein. (1988)

A cDNA clone has been isolated from mRNA derived from the monocytic cell line U937, which detects an mRNA that is present and inducible by gamma-interferon (IFN gamma) in cells of the hematopoietic lineage and absent but inducible in non-hematopoietic cells. Following recombinant IFN gamma (rIFN gamma) treatment, mRNA accumulation can be detected within 30 min, plateaus at 24 h, and remains elevated for several days. This mRNA accumulation is due, at least in part, to increased transcription and is not inhibited by cycloheximide, although cycloheximide alone induces both mRNA accumulation and transcription of this gene. rIFN gamma is a more potent inducing agent than either rIFN alpha or rIFN beta. Polyclonal monospecific antiserum raised to the longest open reading frame expressed in Escherichia coli immunoprecipitates multiple polypeptides that are inducible by rIFN gamma in human monocytes, fibroblasts, endothelial cells, and keratinocytes. In pulse-chase experiments analyzed under reducing conditions, a 30-kDa polypeptide (referred to as IP-30) is either secreted or converted intracellularly into a 25-kDa protein; when analyzed under nonreducing conditions, the two intracellular forms have apparent molecular masses of 25 and 20 kDa, and the extracellular protein is found in two forms of apparent molecular mass 50 and 25 kDa. These data suggest that the intracellular form contains intrachain disulfide bonds, and the extracellular form is involved in both intrachain and interchain disulfide bonding. Indirect immunofluorescence microscopy reveals a punctate fluorescence pattern in monocytes consistent with a vesicular subcellular location. These data are consistent with IP-30 being a novel IFN gamma-inducible protein which may be lysosomal in location.
Hyperproduction of Recombinant Ferredoxins in Escherichia coli by Coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 Gene Cluster (1999)

Fe-S proteins acquire Fe-S clusters by an unknown post-translational mechanism. To study the in vivo synthesis of the Fe-S clusters, we constructed an experimental system to monitor the expressed ferredoxin (Fd) as a reporter of protein-bound Fe-S clusters assembled in Escherichia coli. Overexpression of five Fds in a T7 polymerase-based system led to the formation of soluble apoFds and mature holoFds, indicating that assembly of the Fe-S cluster into apoFd polypeptides is a rate-limiting step. We examined the coexpression of the E. coli ORF1-ORF2-iscS-iscU-iscA-hscB-hsc A-fdx-ORF3 gene cluster, which has recently been suggested to be involved in the formation or repair of Fe-S protein [Zheng, L., Cash, V.L., Flint, D.H., and Dean, D.R. (1998) J. Biol. Chem. 273, 13264-13272], with reporter Fds using compatible plasmids. The production of all five reporter holoFds examined was dramatically increased by the coexpression of the gene cluster, and apparent specificity to the polypeptides or to the type of Fe-S clusters was not observed. The increase in holoFd production was observed under the coexpression conditions in all culture media examined, with either 2 x YT medium or Terrific broth, and with or without supplemental cysteine or iron. These results indicate that the proteins encoded by the gene cluster are involved in the assembly of the Fe-S clusters in a wide variety of Fe-S proteins.
Copolymer Approach to Design of Sensitive Deep-UV Resist Systems with High Thermal Stability and Dry Etch Resistance (1989)

A sensitive deep UV resist was designed by copolymerizing α,α-dimethylbenzyl methacrylate with α-methylstyrene by radical initiation. The electron-rich α-methylstyrene lacks self-propagation and tends to undergo alternating copolymerization with electron-poor monomers such as methacrylates, especially at high feed ratios. Intramolecular anhydride formation that occurs upon heating of certain polymethacrylates and poly(methacrylic acid) is suppressed in such alternating copolymers. Thus, a high glass transition temperature of 210°C is observed for the 1:1 copolymer after deesterification. When mixed with an "onium salt" photochemical acid generator, the dimethylbenzyl ester moiety provides a high resist sensitivity and acid-catalyzed polarity changes. The methacrylate units incorporated in the polymer chain give excellent UV transmission, while the α-methylstyrene units provide good dry etch resistance and high thermal stability.
Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores (2017)

Nucleic acid nanoparticles (NANPs) are an emerging class of programmable structures with tunable shape and function. Their promise as tools for fundamental biophysics studies, molecular sensing, and therapeutic applications necessitates methods for their detection and characterization at the single-particle level. In this work, we study electrophoretic transport of individual ring-shaped and cube-shaped NANPs through solid-state nanopores. In the optimal nanopore size range, the particles must deform to pass through, which considerably increases their residence time within the pore. Such anomalously long residence times permit detection of picomolar amounts of NANPs when nanopore measurements are carried out at a high transmembrane bias. In the case of a NANP mixture, the type of individual particle passing through nanopores can be efficiently determined from analysis of a single electrical pulse. Molecular dynamics simulations provide insight into the mechanical barrier to transport of the NANPs and corroborate the difference in the signal amplitudes observed for the two types of particles. Our study serves as a basis for label-free analysis of soft programmable-shape nanoparticles.
Room-temperature microparticle-based persistent spectral hole burning memory (1991)

We show both theoretically and experimentally that a random distribution of spherical microparticles may be used as a spectral hole burning memory. This microparticle hole burning memory, which can be both written and read at room temperature, is a direct consequence of the properties of morphology-dependent resonances of microparticles.
Direct Profiling of Proteins in Biological Tissue Sections by MALDI Mass Spectrometry (1999)

The direct profiling of proteins present in tissue sections for several organs of the mouse has been accomplished using matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). Fresh tissue was sectioned and blotted on a conductive polyethylene membrane. The dried membrane blot was coated with matrix, typically sinapinic acid, and directly analyzed in the mass spectrometer. Generally, well over 100 peptide/protein signals in the 2000-30,000 Da range were observed, with 30-50 having relatively high signal intensities. Analysis of different areas of the same tissue gave remarkably similar mass spectra with greater than 90% homology. However, different parts of a segmented tissue, such as the proximal, intermediate, and distal colon, gave some unique protein signals. After treatment of the tissue blot with protease and subsequent MALDI MS analysis using postsource decay methods for peptide sequencing, some of the proteins were identified. The unique protein profiles measured from these tissue blots also showed differences from strain to strain of the mouse, with genetically similar strains having very similar patterns.
A new criterion in selection and discretization of attributes for the generation of decision trees (1997)

It is important to use a better criterion in selection and discretization of attributes for the generation of decision trees to construct a better classifier in the area of pattern recognition in order to intelligently access huge amount of data efficiently. Two well-known criteria are gain and gain ratio, both based on the entropy of partitions. We propose in this paper a new criterion based also on entropy, and use both theoretical analysis and computer simulation to demonstrate that it works better than gain or gain ratio in a wide variety of situations. We use the usual entropy calculation where the base of the logarithm is not two but the number of successors to the node. Our theoretical analysis leads some specific situations in which the new criterion works always better than gain or gain ratio, and the simulation result may implicitly cover all the other situations not covered by the analysis.
Modeling of moving objects in a video database (1997)

We introduce an innovative way to represent the trajectory of a single moving object and the relative spatio-temporal relations between multiple moving objects. The representation supports a rich set of spatial topological and directional relations. It also supports both quantitative and qualitative user queries about moving objects. Algorithms for matching trajectories and spatio-temporal relations of moving objects are designed to facilitate query processing. These algorithms can handle both exact and similarity matches. We also discuss the integration of our moving object model, based on a video model, in an object oriented system.
Fast Poisson blending using multi-splines (2011)

We present a technique for fast Poisson blending and gradient domain compositing. Instead of using a single piecewise-smooth offset map to perform the blending, we associate a separate map with each input source image. Each individual offset map is itself smoothly varying and can therefore be represented using a low-dimensional spline. The resulting linear system is much smaller than either the original Poisson system or the quadtree spline approximation of a single (unified) offset map. We demonstrate the speed and memory improvements available with our system and apply it to large panoramas. We also show how robustly modeling the multiplicative gain rather than the offset between overlapping images leads to improved results, and how adding a small amount of Laplacian pyramid blending improves the results in areas of inconsistent texture.
The Effects of Adding Mass to the Legs on the Energetics and Biomechanics of Walking (2007)

Distal leg loads increase the metabolic rate required for swinging the leg. The increase in metabolic rate with more proximal loads may be attributable to a combination of supporting (via hip abduction muscles) and propagating the swing leg.
A New and Efficient Solid Phase Synthesis of Hydroxamic Acids (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA New and Efficient Solid Phase Synthesis of Hydroxamic AcidsKhehyong Ngu and Dinesh V. PatelView Author Information Versicor Inc., 34790 Ardentech Court, Fremont, California 94555 Cite this: J. Org. Chem. 1997, 62, 21, 7088–7089Publication Date (Web):October 17, 1997Publication History Received14 July 1997Published online17 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/jo971274ghttps://doi.org/10.1021/jo971274grapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1050Altmetric-Citations61LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Crystal cleavage,Inhibitors,Organic polymers,Peptides and proteins Get e-Alerts
Intermolecular Interactions of IgG1 Monoclonal Antibodies at High Concentrations Characterized by Light Scattering (2010)

Light scattering intensity measurements of solutions of two purified monoclonal antibodies were performed over a wide range of concentrations (0.5-275 mg/mL) and ionic strengths (0.02 to 0.6 M). Despite extensive sequence homology between these mAbs, alteration of ∼20 amino acids in the complementarity determining regions resulted in different net intermolecular interactions and responses to solution ionic strength. The concentration dependence of scattering was analyzed by comparison with the predictions of three models, allowing for intermolecular interaction of various types. In order of increasing complexity, the three models account for: (1) steric repulsions (simple hard-sphere model), (2) steric repulsion with short-ranged attractive interactions of varying magnitude (adhesive hard-sphere model), and (3) steric and nonsteric repulsive interactions between several species whose relative concentrations may change as a function of total protein concentration as dictated by equilibrium self-association (effective hard-sphere mixture model). Simple scattering models of noninteracting and adhesive hard-sphere species permitted qualitative interpretation of contributions from excluded volume, electrostatic, and van der Waals interactions on net mAb interactions at high concentration as a function of ionic strength. mAb2 electrostatic interactions were repulsive, whereas mAb1 interactions were net attractive at low ionic strengths, attributed to an anisotropic distribution of molecular charge. The effective hard-sphere mixture model can account quantitatively for the dependence of scattering for both antibodies over the entire concentration range and at salt concentrations exceeding 40 mM. This analysis showed that at high ionic strength both mAbs self-associate weakly to form dimer with an affinity that varies little with salt concentration at concentrations exceeding 75 mM. In addition, mAb1 appears to self-associate further to form oligomers with stoichiometry of 4-6 and an affinity that declines substantially with increasing ionic strength. All three models lead to the conclusion that at high concentrations repulsive interactions are predominantly due to excluded volume, whereas additional features are salt-dependent and reflect a substantial electrostatic contribution to intermolecular interactions of both mAbs.
Molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-Å resolution (1975)

The structure of the variable portions of a K-type Bence-Jones protein REI forming a dimer has been determined by X-ray diffraction to a resolution of 2.0 A. The structure has been refined using a constrained crystallographic refinement procedure. The final R value is 0.24 for 15000 significantly measured reflections; the estimated standard deviation of atomic positions is 0.09 A. A more objective assessment of the error in the atomic positions is possible by comparing the two independently refined monomers. The mean deviation of main-chain atoms of the two chains in internal segments in 0.22 A, of main-chain dihedral angles 6.3 degrees for these segments. The unrefined molecular structure of the VREI dimer has been published (Epp, O., Colman, P., Fehlhammer, H., Bode, W., Schiffer, M., Huber, R., and Palm, W. (1974), Eur. J. Biochem. 45, 513). Now a detailed analysis is presented in terms of hydrogen bonds and conformational angles. Secondary structural elements (antiparallel beta structure, reverse turns) are defined. A more precise atomic arrangement of the amino acid residues forming the contact region and the hapten binding site is given as well as the localization of solvent molecules. Two cis-prolines (Pro-8 and Pro-95) were detected. The intrachain disulfide bridge (Cys-23-Cys-88) occurs statistically in two alternative conformations. The structure suggests reasons for strong conservation of several amino acid residues. The knowledge of the refined molecular structure enables crystal structure analyses of related molecules to be made by Patterson search techniques. The calculated phases based on the refined structure are much improved compared to isomorphous phases. Therefore the effects of hapten binding on the molecular structure can be analyzed by the difference Fourier technique with more reliability. Hapten binding studies have been started.
Amphiphilic Cationic [Dendritic poly(L‐lysine)]‐block‐poly(L‐lactide)‐block‐[dendritic poly(L‐lysine)]s in Aqueous Solution: Self‐Aggregation and Interaction with DNA as Gene Delivery Carriers (2010)

A new series of triblock [dendritic poly(L-lysine)]-block-PLLA-block-[dendritic poly(L-lysine)]s (DL(2) -PLLA-DL(2) ) with PLLA block lengths of 11.5-26.5 and double 2-generation PLL dendrons DL(2) as model cationic amphiphiles were synthesized and characterized. Their CAC, self-aggregation and plasmid DNA binding affinities in pure water and PBS were studied. The PLLA block length dependence of particle size, morphology and ξ potential for organized pDNA/amphiphile polyplex aggregates were examined. Finally, toxicities of these DL(2) -PLLA-DL(2) amphiphiles and their polyplexes were assayed by MTT with HeLa, SMMC-7721 and COS-7 cells, and COS-7 cell luciferase and eGFP gene transfection efficacies with these amphiphiles as the delivery carriers were investigated.
Formation of Wild-Type and Chimeric Influenza Virus-Like Particles following Simultaneous Expression of Only Four Structural Proteins (2001)

We are studying the structural proteins and molecular interactions required for formation and release of influenza virus-like particles (VLPs) from the cell surface. To investigate these events, we generated a quadruple baculovirus recombinant that simultaneously expresses in Sf9 cells the hemagglutinin (HA), neuraminidase (NA), matrix (M1), and M2 proteins of influenza virus A/Udorn/72 (H3N2). Using this quadruple recombinant, we have been able to demonstrate by double-labeling immunofluorescence that matrix protein (M1) localizes in nuclei as well as at discrete areas of the plasma membrane where HA and NA colocalize at the cell surface. Western blot analysis of cell supernatant showed that M1, HA, and NA were secreted into the culture medium. Furthermore, these proteins comigrated in similar fractions when concentrated supernatant was subjected to differential centrifugation. Electron microscopic examination (EM) of these fractions revealed influenza VLPs bearing surface projections that closely resemble those of wild-type influenza virus. Immunogold labeling and EM demonstrated that the HA and NA were present on the surface of the VLPs. We further investigated the minimal number of structural proteins necessary for VLP assembly and release using single-gene baculovirus recombinants. Expression of M1 protein alone led to the release of vesicular particles, which in gradient centrifugation analysis migrated in a similar pattern to that of the VLPs. Immunoprecipitation of M1 protein from purified M1 vesicles, VLPs, or influenza virus showed that the relative amount of M1 protein associated with M1 vesicles or VLPs was higher than that associated with virions, suggesting that particle formation and budding is a very frequent event. Finally, the HA gene within the quadruple recombinant was replaced either by a gene encoding the G protein of vesicular stomatitis virus or by a hybrid gene containing the cytoplasmic tail and transmembrane domain of the HA and the ectodomain of the G protein. Each of these constructs was able to drive the assembly and release of VLPs, although enhanced recruitment of the G glycoprotein onto the surface of the particle was observed with the recombinant carrying a G/HA chimeric gene. The described approach to assembly of wild-type and chimeric influenza VLPs may provide a valuable tool for further investigation of viral morphogenesis and genome packaging as well as for the development of novel vaccines.
ChemInform Abstract: AN UNEXPECTED PRODUCT FROM THE REACTION OF IMIDAZOLE WITH ETHYL 3‐ETHOXY‐2‐NITROPROPENOATE (1985)

Abstract Aus dem Nitro‐olefin (I) entstehen mit nucleophilen Reagentien (II) die Substitutionsprodukte (III).