gebhart/patrepeval huggingface dataset:
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts (2011)

Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.
Maladaptive Remodeling of Cardiac Myocyte Shape Begins Long Before Failure in Hypertension (1998)

Progression to failure in hypertension is associated with ventricular dilation, excessive myocyte lengthening, and an increase in myocyte length/width ratio. The temporal development of these changes in relation to impaired pump performance is unknown. We examined isolated myocytes from 1- to 12-month-old spontaneously hypertensive heart failure (SHHF) rats who develop heart failure at approximately 24 months of age. Left ventricular myocyte cross-sectional area reached a maximum of approximately 350 to 400 microm2 at 3 months of age and did not change significantly thereafter. Nonetheless, LV systolic wall stress, a known stimulus for myocyte transverse growth, increased progressively between 3 and 12 months of age. Unlike the situation in normally aging rats with stable body mass, myocyte length in SHHF rats continued to increase with aging (P<0.05 from 9 to 12 months of age). In summary, (1) left ventricular myocyte transverse growth reaches an upper limit by 3 months of age although systolic wall stress continues to rise; and (2) cell length is significantly increased by 12 months of age. This study suggests that maladaptive remodeling of cardiac myocyte shape begins long before pump failure in hypertension. Additionally, it appears that the left ventricle may be robbed of an important adaptive mechanism to normalize wall stress (eg, myocyte transverse growth) early in the progression to failure.
Risk factors for symptomatic knee osteoarthritis fifteen to twenty‐two years after meniscectomy (2004)

Contributing risk factors for OA development after meniscal resection are similar to risk factors for common knee OA. Systemic factors and local biomechanical factors interact. Obesity, female sex, and preexisting early-stage OA are features associated with poor self-reported and radiographic outcome. Partial meniscal resection is associated with less radiographic OA over time than is total meniscectomy.
Protection against Fas/APO-1- and tumor necrosis factor-mediated cell death by a novel protein, sentrin (1996)

Fas/APO-1 and TNF receptor 1 share a common signaling motif in their cytoplasmic tail called the "death domain." Using the death domain as bait in the yeast two-hybrid system, several death domain-containing proteins that participate in cell death signaling have been identified. Here we report the isolation of a novel protein, sentrin, which interacts with Fas/APO-1 and TNF receptor 1 but not with FADD/MORT1 or CD40. Two-hybrid interaction assays reveal that sentrin associates only with the signal-competent forms of Fas/APO-1 or TNF receptor 1 death domains. Sentrin is a novel protein of 101 amino acids with homology to ubiquitin, Nedd8, and a Saccharomyces cerevisiae protein, Smt3. When overexpressed, sentrin provides protection against both anti-Fas/APO-1 and TNF-induced cell death.
Solution structure of epiregulin and the effect of its C‐terminal domain for receptor binding affinity (2003)

Epiregulin (EPR), a novel member of epidermal growth factor (EGF) family, is a ligand for ErbB-1 and ErbB-4 receptors. The binding affinity of EPR for the receptors is lower than those of other EGF-family ligands. The solution structure of EPR was determined using two-dimensional nuclear magnetic resonance spectroscopy. The secondary structure in the C-terminal domain of EPR is different from other EGF-family ligands because of the lack of hydrogen bonds. The structural difference in the C-terminal domain may provide an explanation for the reduced binding affinity of EPR to the ErbB receptors.
Conversions of Formaldehyde-modified 2′-Deoxyadenosine 5′-Monophosphate in Conditions Modeling Formalin-fixed Tissue Dehydration (2005)

Formalin-fixed, paraffin-embedded specimens typically provide molecular biologists with low yields of extractable nucleic acids that exhibit extensive strand cleavage and covalent modification of nucleic acid bases. This study supports the idea that these deleterious effects are promoted by the first step in formalin-fixed tissue processing--i.e., tissue dehydration with a graded series of alcohols. We analyzed the conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate (dAMP) by reverse-phase ion-pair, high-performance liquid chromatography and found that dehydration does not stabilize N-methylol groups in the modified nucleotide. Furthermore, spontaneous demodification in a dry state or in anhydrous ethanol can be as fast as it is in aqueous solutions if the preparation is contaminated with salts of orthophosphoric acid. In ethanol, orthophosphates also catalyze formation of abundant N6-ethoxymethyl-dAMP, as well as cross-linking and depurination of nucleotides present in the mixture. Identification of the products was performed using ultraviolet absorbance spectroscopy and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry. Alternatives to the traditional processing of formalin-fixed tissues are discussed.
Mixture model based label association techniques for web accessibility (2010)

An important aspect of making the Web accessible to blind users is ensuring that all important web page elements such as links, clickable buttons, and form fields have explicitly assigned labels. Properly labeled content is then correctly read out by screen readers, a dominant assistive technology used by blind users. In particular, improperly labeled form fields can critically impede online transactions such as shopping, paying bills, etc. with screen readers. Very often labels are not associated with form fields or are missing altogether, making form filling a challenge for blind users. Algorithms for associating a form element with one of several candidate labels in its vicinity must cope with the variability of the element's features including label's location relative to the element, distance to the element, etc. Probabilistic models provide a natural machinery to reason with such uncertainties. In this paper we present a Finite Mixture Model (FMM) formulation of the label association problem. The variability of feature values are captured in the FMM by a mixture of random variables that are drawn from parameterized distributions. Then, the most likely label to be paired with a form element is computed by maximizing the log-likelihood of the feature data using the Expectation-Maximization algorithm. We also adapt the FMM approach for two related problems: assigning labels (from an external Knowledge Base) to form elements that have no candidate labels in their vicinity and for quickly identifying clickable elements such as add-to-cart, checkout, etc., used in online transactions even when these elements do not have textual captions (e.g., image buttons w/o alternative text). We provide a quantitative evaluation of our techniques, as well as a user study with two blind subjects who used an aural web browser implementing our approach.
The healing process at polymer–polymer interfaces (1981)

When two pieces of the same amorphous polymer are brought into contact at a temperature above the glass transition, the junction surface gradually heals until, at very long contact times, it is indistinguishable from bulk polymer. We have developed an analysis of this welding process based on the reptation picture of polymer dynamics due to de Gennes. The theory predicts the number of bridges (pieces of polymer chain) per unit area spanning the original junction surface as a function of time. At fixed time the number of bridges (σ) also depends on the molecular weight (M) of the chains. If the initial contact is between surfaces which have been equilibrated against a gas phase, we find that σ∼t1/2M−3/2. Alternatively, if the contacting surfaces contain many chain ends, such as may be found at brittle fracture surfaces in glassy polymers, we find that σ∼t1/4M−1/4 at short times. The theory may be compared to available measurements on strength development in healing interfaces leading to the conclusion that the model reproduces several aspects of the observed phenomenon.
Experimental Yersinia enterocolitica infection in mice: Kinetics of growth (1974)

Infection of several strains of laboratory mice with a virulent strain of Yersinia enterocolitica was followed by performing viable bacterial counts on homogenates of selected tissues at intervals after intragastric, aerogenic, or intravenous infection. It is observed that CD-1 mice are more susceptible to Y. enterocolitica infection than either the C(57)B1/6 or B6D2 strains. Development of an enteric infection is dose dependent; less than 5 x 10(7) organisms by mouth yields sporadic, low levels of systemic infection, with many of the animals showing no apparent infection. Increasing the challenge inoculum by a factor of 10 eliminates the variability among the animals, giving rise to an enteric infection in all of the mice that moves quickly to the mesenteric lymph node. The bacterial population in the lymph node multiplies rapidly, and the infection is disseminated to the spleen, liver, and lungs, ultimately killing most of the animals. Exposure to an aerogenic challenge of less than 1,000 organisms resulted in a fulminating pneumonitis with an invariably fatal outcome. Intravenous challenge with 500 organisms caused a rapidly fatal, systemic infection. The growth of the bacteria in the intravenously infected mouse depends upon the temperature at which the challenge inoculum had been grown in vitro. At temperatures below 26 C, the bacteria are cleared from the blood at a slower rate and are more resistant to intracellular killing, as compared to organisms grown at 37 C. This effect results in the inoculum increasing to greater numbers in the tissues in a shorter period of time.
Lymphoid and myeloid differentiation of single human CD34+, HLA-DR+, CD38- hematopoietic stem cells (1994)

Multilineage differentiation of human fetal bone marrow CD34+ cell subsets was examined using a single-cell liquid culture assay. Four CD34+ cell populations, ie, (1) CD38-, HLA-DR+, (2) CD38-, HLA-DR-, (3) CD38+, HLA-DR-, and (4) CD38+, HLA-DR+ cells, were sorted as single cells into 96-well flat-bottom culture plates containing long-term culture medium supplemented with interleukin-3, interleukin-6, stem cell factor (SCF), granulocyte-macrophage colony-stimulating factor, erythropoietin, basic fibroblast growth factor (bFGF), and insulin-like growth factor-1 (IGF-1). Single CD34+, CD38-, HLA-DR+ cells had the highest replating efficiency as well as the highest replating efficiency. The cellular composition of the single-cell progeny was studied by morphologic and/or flow cytometric examination. Only the progeny of single CD34+ cells that lacked CD38 could give rise to each of the hematopoietic cell lineages. The expansion of the progeny of single CD34+, CD38-, HLA-DR+ cells was examined in more detail and showed three clearly distinguishable growth patterns: 28% (SD, +/- 10%; n = 14) of the single cells formed cell clusters/colonies; 9% (SD, +/- 4%; n = 14) formed dispersed cells; and 11% (SD, +/- 6%; n = 14) gave rise to a mixture of cell clusters and dispersed cells. The dispersed cell growth pattern was reduced when SCF or bFGF and IGF-1 was absent in the growth factor cocktail. The replating ability of the dispersed cells was considerably larger than that of cells with other growth patterns, in that 76% of the cells that gave rise to dispersed cells and 54% of the cells that gave rise to dispersed cells as well as cell clusters gave rise to a second generation, but only 7% of the cells that gave rise to cell clusters gave rise to a second generation. The second generation of cells continued to produce third and fourth generations after repetitive replating, except for the replated cells from cell clusters. In contrast with the first-generation progeny, SCF did not have an influence on the replating ability of the cells. Only in the progeny of single CD34+, CD38-, HLA-DR+ cells that gave rise to dispersed cells was each of the hematopoietic cell lineages found, ie, B lymphocytes, neutrophils, monocytes, macrophages, osteoclasts, basophils/mast cells, eosinophils, erythrocytes, megakaryocytes, and platelets.(ABSTRACT TRUNCATED AT 400 WORDS)
Oxidative Addition Reactions of Organoplatinum(II) Complexes with Nitrogen-Donor Ligands (1997)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTOxidative Addition Reactions of Organoplatinum(II) Complexes with Nitrogen-Donor LigandsLouis M. Rendina and Richard J. PuddephattView Author Information Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia, and Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, CanadaCite this: Chem. Rev. 1997, 97, 6, 1735–1754Publication Date (Web):October 1, 1997Publication History Received5 March 1997Revised20 May 1997Published online1 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/cr9704671https://doi.org/10.1021/cr9704671research-articleACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views3375Altmetric-Citations314LEARN 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 SUBJECTS:Addition reactions,Ligands,Metals,Oxidation reactions,Oxidative addition Get e-Alerts
Reduction in Stent and Vascular Graft Thrombosis and Enhancement of Thrombolysis by Recombinant Lys-Plasminogen in Nonhuman Primates (1997)

Elective bolus injections of r-LysPgn before stent deployment decrease the amount of thrombus formed without compromising hemostasis by facilitating endogenous TPA thrombolysis. r-LysPgn may provide effective and safe antithrombotic therapy for interventional vascular procedures.
Transfection by Electroporation (2003)

Electroporation--the use of high-voltage electric shocks to introduce DNA into cells--can be used with most cell types, yields a high frequency of both stable transformation and transient gene expression, and, because it requires fewer steps, can be easier than alternate techniques. In this unit, the describes the electroporation of mammalian cells and an outlines modifications for preparation and transfection of plant protoplasts.
Effect of Nonuniform Implosion on High-Gain Intertial Confinement Fusion Targets (1993)

High-gain target design and gain sensitivity to nonuniform implosion dynamics have been studied numerically. First of all, sensitivity of the pellet gain to the tailored pulse shape has been studied using the laser implosin code ILESTA-1D, and the gain scaling law has been obtained through an optimization of target and laser parameters. Then, the two-dimensional code, ILESTA-2D, was used to study the sensitivity of the pellet gain to the nonuniformity in target implosion. It is found that the fire-polishing effect by alpha-particle heating drastically smooths the spark structure. The implosion mode optimized with the ILESTA-1D code is relatively sensitive to nonuniformity and, therefore, higher implosion velocity modes are recommended from stability.
Cyclobenzaprine ER for muscle spasm associated with low back and neck pain: two randomized, double-blind, placebo-controlled studies of identical design (2009)

Once-daily CER 15 mg (study 2) and CER 30 mg (study 1) were effective in treating muscle spasm associated with painful musculoskeletal conditions after 4 days of treatment. Differences between CER and placebo groups did not reach statistical significance on all efficacy measures, and the protocols were not powered to detect differences between active treatment arms. CER was generally safe and well tolerated, with low rates of somnolence.
Synthesis and phosphodiesterase activity of carboxylic acid mimetics of cyclic guanosine 3',5'-monophosphate (1993)

Synthetic analogs of the natural product griseolic acid in which a guanine base is substituted for the adenine have been prepared. The best of these compounds inhibits a cyclic guanosine 3',5'-monophosphate (cGMP) phosphodiesterase preparation with an IC50 of 0.34 microM but is a very weak inhibitor of a cyclic adenosine 3',5'-monophosphate (cAMP) phosphodiesterase. An exploration of stereochemistry indicates that the configuration of the carboxylic acids and the ring fusion in the inhibitors is important for potent cGMP PDE inhibition. PDE inhibition is not sensitive to the presence of the 2' or 4' oxygen atoms in the ribose, but inhibition is decreased when the 3' oxygen is removed. A selected group of analogs in which a monocarboxylic acid is present are poor inhibitors. The structure-activity relationship is consistent with the carboxylic acid functionality acting as a mimetic for the phosphate anion in cGMP. This concept is supported by a conformational analysis of two of the inhibitors.
The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis. (1993)

eIF-4A is a eukaryotic translation initiation factor that is required for mRNA binding to ribosomes. It exhibits single-stranded RNA-dependent ATPase activity, and in combination with a second initiation factor, eIF-4B, it exhibits duplex RNA helicase activity. eIF-4A is the prototype of a large family of proteins termed the DEAD box protein family, whose members share nine highly conserved amino acid regions. The functions of several of these conserved regions in eIF-4A have previously been assigned to ATP binding, ATPase, and helicase activities. To define the RNA-binding region of eIF-4A, a UV-induced cross-linking assay was used to analyze binding of mutant eIF-4A proteins to RNA. Mutants carrying mutations in the ATP-binding region (AXXXXGKT), ATPase region (DEAD), helicase region (SAT), and the most carboxy-terminal conserved region of the DEAD family, HRIGRXXR, were tested for RNA cross-linking. We show that mutations, either conservative or not, in any one of the three arginines in the HRIGRXXR sequence drastically reduced eIF-4A cross-linking to RNA. In addition, all the mutations in the HRIGRXXR region abrogate RNA helicase activity. Some but not all of these mutations affect ATP binding and ATPase activity. This is consistent with the hypothesis that the HRIGRXXR region is involved in the ATP hydrolysis reaction and would explain the coupling of ATPase and RNA-binding/helicase activities. Our results show that the HRIGRXXR region, which is QRXGRXXR or QXXGRXXR in the RNA and DNA helicases of the helicase superfamily II, is involved in ATP hydrolysis-dependent RNA interaction during unwinding. We also show that mutations in other regions of eIF-4A that abolish ATPase activity sharply decrease eIF-4A cross-linking to RNA. A model is proposed in which eIF-4A first binds ATP, resulting in a change in eIF-4A conformation which allows RNA binding that is dependent on the HRIGRXXR region. Binding of RNA induces ATP hydrolysis, leading to a more stable interaction with RNA. This process is then linked to unwinding of duplex RNA in the presence of eIF-4B.
Benefits and Harms of Prostate-Specific Antigen Screening for Prostate Cancer: An Evidence Update for the U.S. Preventive Services Task Force (2008)

Prostate-specific antigen screening is associated with psychological harms, and its potential benefits remain uncertain.
Expansion of human NOD/SCID-repopulating cells by stem cell factor, Flk2/Flt3 ligand, thrombopoietin, IL-6, and soluble IL-6 receptor (2000)

Here, we demonstrate a significant ex vivo expansion of human hematopoietic stem cells capable of repopulating in NOD/SCID mice. Using a combination of stem cell factor (SCF), Flk2/Flt3 ligand (FL), thrombopoietin (TPO), and a complex of IL-6 and soluble IL-6 receptor (IL-6/sIL-6R), we cultured cord blood CD34(+) cells for 7 days and transplanted these cells into NOD/SCID mice. Bone marrow engraftment was judged successful when recipient animals contained measurable numbers of human CD45(+) cells 10-12 weeks after transplantation. When cells were cultured with SCF+FL+TPO+IL-6/sIL-6R, 13 of 16 recipients were successfully engrafted, and CD45(+) cells represented 11.5% of bone marrow cells in engrafted recipients. Cells cultured with a subset of these factors were less efficiently engrafted, both as measured by frequency of successful transplantations and prevalence of CD45(+) cells. In animals receiving cells cultured with all 4 factors, human CD45(+) cells represented various lineages, including a large number of CD34(+) cells. The proportion of CD45(+) cells in recipient marrow was 10 times higher in animals receiving these cultured cells than in those receiving comparable numbers of fresh CD34(+) cells, and the expansion rate was estimated at 4.2-fold by a limiting dilution method. Addition of IL-3 to the cytokine combination abrogated the repopulating ability of the expanded cells. The present study may provide a novel culture method for the expansion of human transplantable hematopoietic stem cells suitable for clinical applications.