gebhart/patrepeval huggingface dataset:
Targeted translational regulation using the PUF protein family scaffold (2011)

Regulatory complexes formed on mRNAs control translation, stability, and localization. These complexes possess two activities: one that binds RNA and another--the effector--that elicits a biological function. The Pumilio and FBF (PUF) protein family of RNA binding proteins provides a versatile scaffold to design and select proteins with new specificities. Here, the PUF scaffold is used to target translational activation and repression of specific mRNAs, and to induce specific poly(A) addition and removal. To do so, we linked PUF scaffold proteins to a translational activator, GLD2, or a translational repressor, CAF1. The chimeric proteins activate or repress the targeted mRNAs in Xenopus oocytes, and elicit poly(A) addition or removal. The magnitude of translational control relates directly to the affinity of the RNA-protein complex over a 100-fold range of K(d). The chimeric proteins act on both reporter and endogenous mRNAs: an mRNA that normally is deadenylated during oocyte maturation instead receives poly(A) in the presence of an appropriate chimera. The PUF-effector strategy enables the design of proteins that affect translation and stability of specific mRNAs in vivo.
Computer Manipulation of DNA and Protein Sequences (1995)

This unit outlines a variety of methods by which DNA sequences can be manipulated by computers. Procedures for entering sequence data into the computer and assembling raw sequence data into a contiguous sequence are described first, followed by a description of methods of analyzing and manipulating sequences--e.g., verifying sequences, constructing restriction maps, designing oligonucleotides, identifying protein-coding regions, and predicting secondary structures. This unit also provides information on the large amount of software available for sequence analysis. The appendix to this unit lists some of the commercial software, shareware, and free software related to DNA sequence manipulation. The goal of this unit is to serve as a starting point for researchers interested in utilizing the tremendous sequencing resources available to the computer-knowledgeable molecular biology laboratory.
An Introduction to Propensity Score Methods for Reducing the Effects of Confounding in Observational Studies (2011)

The propensity score is the probability of treatment assignment conditional on observed baseline characteristics. The propensity score allows one to design and analyze an observational (nonrandomized) study so that it mimics some of the particular characteristics of a randomized controlled trial. In particular, the propensity score is a balancing score: conditional on the propensity score, the distribution of observed baseline covariates will be similar between treated and untreated subjects. I describe 4 different propensity score methods: matching on the propensity score, stratification on the propensity score, inverse probability of treatment weighting using the propensity score, and covariate adjustment using the propensity score. I describe balance diagnostics for examining whether the propensity score model has been adequately specified. Furthermore, I discuss differences between regression-based methods and propensity score-based methods for the analysis of observational data. I describe different causal average treatment effects and their relationship with propensity score analyses.
Biology and clinical applications of mesenchymal stem cells (2003)

Stem cell populations are found in most adult tissues and, in general, their differentiation potential may reflect the local cell population. Hematopoietic, epidermal, mesenchymal, neural and hepatic stem cells have been described. It may be that, in the adult, these cells are the reservoirs of reparative cells that are mobilized following injury and migrate to the wound site where, in cooperation with local cells, they participate in the repair response. Mesenchymal stem cells, isolated from the bone marrow, have the capacity to differentiate into cells of connective tissues. Some striking examples of the therapeutic use of MSCs have been reported recently in applications such as coronary artery disease, spinal cord injury, Parkinson's Disease, and liver regeneration. In orthopaedic medicine, MSC therapy has been applied in bone and cartilage repair and in the treatment of osteoarthritis. The question of the host response to implanted MSCs is critical as these cells are being evaluated in clinical applications. There are several aspects to the implanted cell-host interaction that need to be addressed as we attempt to understand the mechanisms underlying stem cell therapies. These are (1) the host immune response to implanted cells, (2) the homing mechanisms that guide delivered cells to a site of injury, and (3) differentiation of implanted cells under the influence of local signals.
Synthesis and synthetic utility of 1-acyl-5-(trialkylsilyl)-1,2-dihydropyridines. A synthesis of (.+-.)-elaeokanine A (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and synthetic utility of 1-acyl-5-(trialkylsilyl)-1,2-dihydropyridines. A synthesis of (.+-.)-elaeokanine ADaniel L. Comins and Young Chan MyoungCite this: J. Org. Chem. 1990, 55, 1, 292–298Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/jo00288a049https://doi.org/10.1021/jo00288a049research-articleACS PublicationsRequest reuse permissionsArticle Views808Altmetric-Citations66LEARN 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-Alertsclose Get e-Alerts
Glycan-functionalized diamond nanoparticles as potent E. coli anti-adhesives (2013)

Bacterial attachment and subsequent biofilm formation on biotic surfaces or medical devices is an increasing source of infections in clinical settings. A large proportion of these biofilm-related infections are caused by Escherichia coli, a major nosocomial pathogen, in which the major adhesion factor is the FimH adhesin located at the tip of type 1 fimbriae. Inhibition of FimH-mediated adhesion has been identified as an efficient antibiotic-alternative strategy to potentially reduce E. coli-related infections. In this article we demonstrate that nanodiamond particles, covently modified with mannose moieties by a "click" chemistry approach, are able to efficiently inhibit E. coli type 1 fimbriae-mediated adhesion to eukaryotic cells with relative inhibitory potency (RIP) of as high as 9259 (bladder cell adhesion assay), which is unprecedented when compared with RIP values previously reported for alternate multivalent mannose-functionalized nanostructures designed to inhibit E. coli adhesion. Also remarkable is that these novel mannose-modified NDs reduce E. coli biofilm formation, a property previously not observed for multivalent glyco-nanoparticles and rarely demonstrated for other multivalent or monovalent mannose glycans. This work sets the stage for the further evaluation of these novel NDs as an anti-adhesive therapeutic strategy against E. coli-derived infections.
Autograft bone‐patella tendon‐bone plug comminution with loss of ligament fixation and stability (1996)

Two cases are described in which bone plug comminution caused a loss of femoral fixation after endoscopic bone-patellar tendon-bone, anterior cruciate ligament autograft reconstruction. Clinically there was loss of knee joint stability, and radiographically the bone graft had dislodged. One case was salvaged by graft inversion, with femoral interference screw and tibial traction suture fixation. The second case required graft replacement with a patella bone-quadriceps tendon autograft.
The effect of nonionic detergent on dengue and Japanese encephalitis virus antigens in antigen detection ELISA and IgM-capture ELISA. (1997)

In order to simplify dengue and Japanese encephalitis (JE) IgM-ELISA, we have been trying to produce antigens as infected C6/36 cell culture fluid. In this study, we examined the effect of nonionic detergents, which were used to inactivate viral infectivity, on dengue and JE antigen titers as well as the results in an IgM-capture ELISA. In the antigen detection ELISA, antigen titers were not significantly reduced after treatment with nonionic detergents (Nonidet P-40 or Triton X-100, at 0.01 to 0.1% final concentration). In contrast, in the IgM-capture ELISA, the color development was significantly reduced when the antigens were pretreated with nonionic detergents. The results suggest that certain epitopes which react with anti-viral IgM antibodies, but not IgG antibodies, have been destroyed by treatment with nonionic detergents. The results indicate that we cannot use nonionic detergents to inactivate the infectivity of assay antigens.
Diffraction Theory (1954)

A critical review is presented of recent progress in classical diffraction theory. Both scalar and electromagnetic problems are discussed. The report may serve as an introduction to general diffraction theory although the main emphasis is on diffraction by plane obstacles. Various modifications of the Kirchhoff and Kottler theories are presented. Diffraction by obstacles small compared with the wavelength is discussed in some detail. Other topics included are: variational formulation of diffraction problems, the Wiener-Hopf technique of solving integral equations of diffraction theory, the rigorous formulation of Babinet's principle, the nature of field singularities at sharp edges, the application of Mathieu functions and spheroidal wave functions to diffraction theory. Reference is made to more than 500 papers published since 1940.
Parenteral Monoacetoacetin and Liver Regeneration Interaction After Partial Hepatectomy in the Rat (1994)

Parenteral nutrients can be used to manipulate cell proliferation after partial hepatectomy. The relationship among macronutrients--glucose, monoacetoacetin, amino acids--and liver regeneration after partial hepatectomy was investigated. Male rats were anesthetized, received a 70% hepatectomy, and received a low-dose infusion of (1) glucose or (2) monoacetoacetin and a high-dose infusion of (3) glucose, (4) glycerol-glucose, or (5) monoacetoacetin-glucose beginning 6 hours after surgery. The five nonprotein nutrient combinations were infused with and without amino acids. Rats were killed 48 hours after partial hepatectomy, and the label and mitotic indices were determined. Each of the five treatments had a higher label index with amino acids present than with amino acids absent. Low-dose glucose and monoacetoacetin as well as high-dose glucose and glucose-glycerol had higher mitotic indices with amino acids than without amino acids. High-dose monoacetoacetin-glucose was associated with a greater mitotic index than was any other nonprotein substrate treatment, and this response was independent of amino acids being present or absent. In summary, (1) amino acids were needed for maximal cell proliferation rate; (2) the absence of amino acids and not the presence of glucose resulted in reduction of the label and mitotic indices for regenerating liver; (3) high-dose monoacetoacetin increased mitosis with or without amino acids; and (4) monoacetoacetin activity was dose dependent. The results indicate that the best nutrient for treatment of patients with liver injury is acetoacetate. The second best nutrient would be the combination of high-dose glucose and amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)
Chemistry of phosgene (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleChemistry of phosgeneHarry Babad and Andrew G. ZeilerCite this: Chem. Rev. 1973, 73, 1, 75–91Publication Date (Print):February 1, 1973Publication History Published online1 May 2002Published inissue 1 February 1973https://pubs.acs.org/doi/10.1021/cr60281a005https://doi.org/10.1021/cr60281a005research-articleACS PublicationsRequest reuse permissionsArticle Views4874Altmetric-Citations335LEARN 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-Alertsclose Get e-Alerts
In vitro antioxidant capacity and antiproliferative effects of different parts and extractions from Ajuga bracteosa on HepG2 cell line (2012)

The aim of this study was to investigate phenolic content, antioxidant activity and antiproliferative of Ajuga bracteosa extracts. These results revealed that A. bracteosa flower in water extract contained high amount of phenolic, flavonoids and tannin at 34.23 µg/ml (GAE), 14.23 µg/ml (QE) and 1.606 µg/ml (TE), respectively. Compared to positive control, A. bracteosa showed highest result in DPPH radical scavenging activity while lowest result in TEAC assays (ABTS radical scavenging activity) and reducing power. Leaf in water extract of A. bracteosa presented the highest activity in DPPH radical scavenging activity, while water, ethanol and methanol extracts of A. bracteosa flower showed highest antioxidant activity in TEAC assay compared to other parts. A. bracteosa from water extraction and flower part revealed highest activity in antiproliferative effect. From correlation analysis, radical scavenging activity of A. bracteosa may be influenced by all phenolic content, while antiproliferative effect may due to flavonoid content. In conclusion, water extract from flower A. bracteosa might be used as a potential source of natural antioxidants and antitumor agents.
Islet pathology of non-insulin-dependent diabetes mellitus (NIDDM). (1996)

Islet amyloid polypeptide (IAPP) gives rise to islet amyloid fibrils in NIDDM. Islet amyloid tends to replace islet cells, especially beta-cells and may act as a diffusion barrier. It has also been proposed that IAPP amyloid fibrils are beta-cell cytotoxic. The pathogenesis of islet amyloid is not clear and several factors are probably necessary for amyloid formation. One factor is an amyloidogenic amino acid sequence of IAPP and a second is probably a high local concentration of IAPP. Islet amyloid is not seen in the normal human pancreas and has not been described in the pancreata of transgenic mice over-expressing human IAPP. However, islet amyloid is rapidly deposited in in vitro cultivated islets from these transgenic animals and in isolated normal human islets transplanted into nude mice. Consequently, besides an amyloidogenic structure and high production of IAPP, further factors are necessary for islet amyloid formation in NIDDM.
Linked strategy for the production of fuels via formose reaction (2013)

Formose reaction converts formaldehyde to carbohydrates. We found that formose reaction can be used linking the biomass gasification with the aqueous-phase processing (APP) to produce liquid transportation fuel in three steps. First, formaldehyde from syn-gas was converted to triose. This was followed by aldol condensation and dehydration to 4-hydroxymethylfurfural (4-HMF). Finally, 4-HMF was hydrogenated to produce 2,4-dimethylfuran (2,4-DMF) or C(9)-C(15) branched-chain alkanes as liquid transportation fuels. In the linked strategy, high energy-consuming pretreatment as well as expensive and polluting hydrolysis of biomass were omitted, but the high energy recovery of APP was inherited. In addition, the hexoketoses via formose reaction could be converted to HMFs directly without isomerization. A potential platform molecule 4-HMF was formed simultaneously in APP.
CRISPR genome engineering and viral gene delivery: A case of mutual attraction (2015)

Abstract The adaptation of the CRISPR/Cas9 DNA engineering machinery for mammalian cells has revolutionized our approaches to low‐ or high‐throughput genome annotation and paved the way for conceptually novel therapeutic strategies. A large part of the attraction of CRISPR stems from the small size of its two core components – Cas9 and gRNA – and hence its compatibility with virtually any available viral vector delivery system. As a result, over the past two years, four major classes of viral vectors have already been engineered and applied as CRISPR delivery tools – retroviruses, lentiviruses, adenoviruses, and adeno‐associated viruses (AAVs). The juxtaposition of these two technologies reflects a case of tremendous mutual attraction and holds unprecedented promises for biology and medicine. Here, we provide an overview of the state‐of‐the‐art of this rapidly emerging field, from a comparative description of the principal vector designs, to a synopsis of some of the most exciting applications that were reported to date, including the use of viral CRISPR vectors for genome‐wide loss‐of‐function screens, multiplexed gene editing or disease modeling in animals. Once specificity and safety have been improved further, viral vector‐mediated in vitro/in vivo CRISPR delivery and expression promise to radically transform basic and applied biomedical research.
B-Lymphocyte Deficiency Increases Atherosclerosis in LDL Receptor–Null Mice (2002)

Collectively, these data demonstrate that B cells and/or antibodies are protective against atherosclerosis and that this protection may be conferred by B cell-mediated immune regulation.
Capacitance Planar Array Sensor for Fast Multiphase Flow Imaging (2009)

In this paper, we introduce a novel planar array sensor based on electrical capacitance (permittivity) measurements to visualize flows of multiphase mixtures along the surface of objects. The prototype sensor is formed by 32 times 32 interdigital sensing structures. It can be mounted onto the wall of pipes or vessels and thus has minimal influence on the flow. An associated electronics measures the capacitance of the fluid at each sensing structure in a multiplexed manner at high sampling rate. This way, images of the fluid distribution are produced. The electronics is able to generate up to 15 000 images/s. Results of system evaluation and results of two exemplary flow experiments are presented and discussed.
Applicability of a “Speed” Congenic Strategy to Dissect Blood Pressure Quantitative Trait Loci on Rat Chromosome 2 (2000)

The identification of any quantitative trait locus (QTL) via a genome scan is only the first step toward the ultimate goal of gene identification. The next step is the production of congenic strains by which the existence of a QTL may be verified and the implicated chromosomal region be reduced to a size applicable to positional cloning of the causal gene. We used a speed congenic breeding protocol previously verified in mice for 2 blood pressure QTLs on rat chromosome 2. Four congenic strains were produced through introgression of various segments of chromosome 2 from Wistar-Kyoto rats from Glasgow colonies [WKY((Gla)) rats] into the recipient stroke-prone spontaneously hypertensive rats from Glasgow colonies [SHRSP((Gla))], and vice versa. The number of backcross generations required for each strain to achieve complete homozygosity at 83 background genetic markers in a "best" male varied between 3 and 4. Transfer of the region of rat chromosome 2 containing both QTLs from WKY((Gla)) into an SHRSP((Gla)) genetic background lowered both baseline and salt-loaded systolic blood pressure by approximately 20 and approximately 40 mm Hg in male congenic rats compared with the SHRSP parental strain (F=53.4, P<0.005; F=28.0, P< 0.0005, respectively). In contrast, control animals for stowaway heterozygosity presented no deviation from the blood pressure values recorded for the SHRSP((Gla)), indicating that if such heterozygosity exists, its effect on blood pressure is negligible. A reciprocal strategy in which 1 or both QTLs on rat chromosome 2 were transferred from SHRSP((Gla)) into a WKY((Gla)) genetic background resulted in statistically significant but smaller blood pressure increases for 1 of these QTLs. These results confirm the existence of blood pressure QTLs on rat chromosome 2 and demonstrate the applicability of a speed congenic strategy in the rat and emphasize the important role of the genetic background.
Control of sensor information in distributed multisensor systems (1999)

Provides an analysis of error covariance control techniques for allocating sensing resources in distributed, multiprocessor, multisensor systems. We present two algorithms for allocating sensing resources that manage the rates and resolutions at which sensor information from various nodes is processed. An elliptical annulus described by two covariance matrices is used to control the prediction and update covariances in the decentralized Kalman filter. These algorithms allow for nodal autonomy by letting each node control the usage of its own suite of sensors. With a single state filter, these sensor management techniques are shown to result in a discrete periodic Riccati equation.