gebhart/patrepeval huggingface dataset:
Pincer-type Pyridine-Based N-Heterocyclic Carbene Amine Ru(II) Complexes as Efficient Catalysts for Hydrogen Transfer Reactions (2011)

Stable well-defined pincer-type N-heterocyclic carbene−ruthenium complexes were developed as an alternative to phosphine complexes. These highly stable phosphine-free complexes were found to be efficient catalysts for transfer hydrogen reactions: the conversion of primary alcohols to esters and the reduction of carbonyl compounds. We also describe one approach toward immobilization through covalent bonding to silica via a pendant alkoxysilane group.
X-Pro dipeptidyl-peptidase (1998)

Part. S: CLAN SC-S15, nø136
An introduction to high speed photography and photonics (2009)

(2009). An introduction to high speed photography and photonics. The Imaging Science Journal: Vol. 57, High Speed Photography and Photonics, pp. 293-302.
A Ruler Protein in a Complex for Antiviral Defense Determines the Length of Small Interfering CRISPR RNAs (2013)

Small RNAs undergo maturation events that precisely determine the length and structure required for their function. CRISPRs (clustered regularly interspaced short palindromic repeats) encode small RNAs (crRNAs) that together with CRISPR-associated (cas) genes constitute a sequence-specific prokaryotic immune system for anti-viral and anti-plasmid defense. crRNAs are subject to multiple processing events during their biogenesis, and little is known about the mechanism of the final maturation step. We show that in the Staphylococcus epidermidis type III CRISPR-Cas system, mature crRNAs are measured in a Cas10·Csm ribonucleoprotein complex to yield discrete lengths that differ by 6-nucleotide increments. We looked for mutants that impact this crRNA size pattern and found that an alanine substitution of a conserved aspartate residue of Csm3 eliminates the 6-nucleotide increments in the length of crRNAs. In vitro, recombinant Csm3 binds RNA molecules at multiple sites, producing gel-shift patterns that suggest that each protein binds 6 nucleotides of substrate. In vivo, changes in the levels of Csm3 modulate the crRNA size distribution without disrupting the 6-nucleotide periodicity. Our data support a model in which multiple Csm3 molecules within the Cas10·Csm complex bind the crRNA with a 6-nucleotide periodicity to function as a ruler that measures the extent of crRNA maturation.
Impact of blood pressure and insulin on the relationship between body fat and left ventricular structure (2003)

Both total adipose tissue and lean body mass predict an increase in myocardial mass, while adipose tissue alone is related to a rise in relative wall thickness. The concentric left ventricular geometry associated with body fat accumulation appears to be mediated, at least in part, by blood pressure and insulin levels.
Ask Me Anything: Dynamic Memory Networks for Natural Language Processing (2015)

Most tasks in natural language processing can be cast into question answering (QA) problems over language input. We introduce the dynamic memory network (DMN), a neural network architecture which processes input sequences and questions, forms episodic memories, and generates relevant answers. Questions trigger an iterative attention process which allows the model to condition its attention on the inputs and the result of previous iterations. These results are then reasoned over in a hierarchical recurrent sequence model to generate answers. The DMN can be trained end-to-end and obtains state-of-the-art results on several types of tasks and datasets: question answering (Facebook's bAbI dataset), text classification for sentiment analysis (Stanford Sentiment Treebank) and sequence modeling for part-of-speech tagging (WSJ-PTB). The training for these different tasks relies exclusively on trained word vector representations and input-question-answer triplets.
Identification of a p28 Gene in Ehrlichia ewingii : Evaluation of Gene for Use as a Target for a Species-Specific PCR Diagnostic Assay (2001)

PCR was used to amplify a 537-bp region of an Ehrlichia ewingii gene encoding a homologue of the 28-kDa major antigenic protein (P28) of Ehrlichia chaffeensis. The E. ewingii p28 gene homologue was amplified from DNA extracted from whole blood obtained from four humans and one canine with confirmed cases of infection. Sequencing of the PCR products (505 bp) revealed a partial gene with homology to outer membrane protein genes from Ehrlichia and Cowdria spp.: p30 of Ehrlichia canis (< or =71.3%), p28 of E. chaffeensis (< or =68.3%), and map1 of Cowdria ruminantium (67.3%). The peptide sequence of the E. ewingii partial gene product was deduced (168 amino acids) and the antigenicity profile was analyzed, revealing a hydrophilic protein with < or =69.1% identity to P28 of E. chaffeensis, < or =67.3% identity to P30 of E. canis, and < or =63.1% identity to MAP1 of C. ruminantium. Primers were selected from the E. ewingii p28 sequence and used to develop a species-specific PCR diagnostic assay. The p28 PCR assay amplified the expected 215-bp product from DNA that was extracted from EDTA-treated blood from each of the confirmed E. ewingii infections that were available. The assay did not produce PCR products with DNA extracted from E. chaffeensis-, E. canis-, or E. phagocytophila-infected samples, confirming the specificity of the p28 assay for E. ewingii. The sensitivity of the E. ewingii-specific PCR assay was evaluated and determined to detect as few as 38 copies of the p28 gene.
Glial cell line-derived neurotrophic factor (GDNF), a new neurotrophic factor for motoneurones (1994)

Glial cell line-derived neurotrophic factor (GDNF) has been postulated to be a specific dopaminergic neurotrophic factor since it selectively enhances the survival of dopaminergic neurones in vitro. We report here that GDNF can also act as a neurotrophic factor for motoneurones. GDNF released by GDNF-transfected BHK cells increases the activity of choline acetyltransferase (ChAT) in cultures from embryonic rat ventral mesencephalon containing cholinergic neurones from cranial motor nuclei and in cultured spinal motoneurones. Furthermore, local application of polymer-encapsulated BHK cells releasing GDNF to transected facial nerve in newborn rats diminishes the death of motoneurones normally occurring after axotomy in the neonatal period. The present results indicate that GDNF may have a therapeutic potential in human motoneurone diseases such as amyotrophic lateral sclerosis.
Reactive Arthritis. Reaktive Arthritis (1999)

The clinical picture or reactive arthritis is characterized by an asymmetric oligoarthritis of the lower limbs and a preceding infection in the gut or the urethra. Diagnostic criteria for reactive arthritis rely mainly on such clinical features but one should try to identify the causative microbe. Stool cultures are rarely positive but urethral smears and urine examinations by PCR can be helpful. Serology is mostly too nonspecific and partly not sensitive enough. The microbiological results have to be carefully interpreted -especially since there is no indication that a positive result should have therapeutical consequences such as antibiotic therapy. Studying the immunologic mechanisms that cause reactive arthritis is essential also for the pathogenesis of other spondyloarthropathies such as ankylosing spondylitis. The details of the interplay between bacterial antigens and HLA-B27 have become somewhat clearer in recent years. There is some evidence for longer bacterial persistence in the joints and there is a local antigen-specific immune response in which CD4+ and CD8 + T cells seem to play a role, immunodominant antigens and peptides have been identified. Furthermore, there seems to be a distinct cytokine pattern in reactive arthritis which is more TH2 like . The prognosis of reactive arthritis patients is influenced by the ability of the patients to secrete TNF-. There seems to be a link between TNF polymorphisms and HLA-B27.
Computing kernels implemented with a wormhole RTR CCM (2002)

The wormhole run-time reconfiguration (RTR) computing paradigm is a method for creating high performance computational pipelines. The scalability, distributed control and data flow features of the paradigm allow it to fit neatly into the configurable computing machine (CCM) domain. To date, the field has been dominated by large bit-oriented devices whose flexibility can lead to lowered silicon utilization efficiencies. In an effort to raise this efficiency, the Colt CCM has been created based on the wormhole RTR paradigm. This paper outlines methods of implementation and performance for several common operations using these concepts. They serve as indicators of the diversity of algorithms that can be instantiated through the high-speed run-time reconfiguration that these devices make possible. Particular attention is paid to floating point multiplication. Also discussed is the topic of data dependent computation which would seem to be counter intuitive to the wormhole RTR paradigm. The paper concludes with a summary of performance of the three computations.
Two-step total gene synthesis method (2004)

In the post-genomic era, the ability to synthesize any arbitrary DNA sequence is increasingly in demand. A bottleneck in current gene synthesis technologies is the associated cost, due primarily to the high cost of oligonucleotides synthesis and post-synthesis sequencing. In the present paper, an improved method for low-cost gene synthesis that combines dual asymmetrical PCR and overlap extension PCR is presented, which enables any DNA sequence to be synthesized error free. Additionally, the method is easily amenable to automation.
Phosphatidylinositol Phosphate Kinases, a Multifaceted Family of Signaling Enzymes (1999)

The importance of phosphoinositides as lipid signaling molecules in eucaryotic cells was first recognized by Lowell and Mabel Hokin in the 1950s (who also discovered the enzyme activities that phosphorylate phosphatidylinositol (PI) 1 ) (1-5). Since those early years, PI signaling pathways have expanded both in importance and complexity. The classical pathway transforms PI to PI-4,5-P 2 by the successive actions of PI 4-kinases and PI-4-P 5-kinases. PI-4,5-P 2 is the precursor for second messengers and also acts directly to modify effectors, for example actin-binding proteins (6 -9). Significant roles for other phosphoinositide lipid products in signaling, combined with recently identified lipid kinase activities, are illuminating the many mechanisms by which cells use lipid messengers (10 -13). This review will focus on the phosphatidylinositolphosphate kinase (PIPK) family, which has the ability to synthesize all known PIP 2 isomers and PIP 3 .
A line electron lens (1985)

An electron lens, designed for simultaneous exposure of the entire length of a line, has been developed. Two versions have been built and tested. The focal properties of the lenses for both paraxial and far-off-axis trajectories have been computed with a short (two page) fortran program. It is expected that a more carefully made version of this lens should be capable of producing lines less than 0.025 μm wide, and as smooth as the capability of the resist which will be exposed. Furthermore, it is expected that the lines can be made straight to substantially better than 0.025 μm. It is also expected that it will be possible to position lines parallel to one another to an accuracy commensurate with their straightness. The lens is electrostatic, and focal conditions can be adjusted so that the lens is afocal to first order with respect to changes in the lens-to-workpiece spacing. It is also possible to mask segments of the line, although the axial resolution will probably be good only to a few micrometers. The structure and mathematics which permit its characteristics to be so easily obtained are described.
Postsynthetic Metal and Ligand Exchange in MFU‐4l: A Screening Approach toward Functional Metal–Organic Frameworks Comprising Single‐Site Active Centers (2015)

The isomorphous partial substitution of Zn(2+) ions in the secondary building unit (SBU) of MFU-4l leads to frameworks with the general formula [M(x)Zn(5-x)Cl4(BTDD)3], in which x≈2, M = Mn(II), Fe(II), Co(II), Ni(II), or Cu(II), and BTDD = bis(1,2,3-triazolato-[4,5-b],[4',5'-i])dibenzo-[1,4]-dioxin. Subsequent exchange of chloride ligands by nitrite, nitrate, triflate, azide, isocyanate, formate, acetate, or fluoride leads to a variety of MFU-4l derivatives, which have been characterized by using XRPD, EDX, IR, UV/Vis-NIR, TGA, and gas sorption measurements. Several MFU-4l derivatives show high catalytic activity in a liquid-phase oxidation of ethylbenzene to acetophenone with air under mild conditions, among which Co- and Cu derivatives with chloride side-ligands are the most active catalysts. Upon thermal treatment, several side-ligands can be transformed selectively into reactive intermediates without destroying the framework. Thus, at 300 °C, Co(II)-azide units in the SBU of Co-MFU-4l are converted into Co(II)-isocyanate under continuous CO gas flow, involving the formation of a nitrene intermediate. The reaction of Cu(II)-fluoride units with H2 at 240 °C leads to Cu(I) and proceeds through the heterolytic cleavage of the H2 molecule.
Integral dose conservation in radiotherapy (2009)

Treatment planners frequently modify beam arrangements and use IMRT to improve target dose coverage while satisfying dose constraints on normal tissues. The authors herein analyze the limitations of these strategies and quantitatively assess the extent to which dose can be redistributed within the patient volume. Specifically, the authors hypothesize that (1) the normalized integral dose is constant across concentric shells of normal tissue surrounding the target (normalized to the average integral shell dose), (2) the normalized integral shell dose is constant across plans with different numbers and orientations of beams, and (3) the normalized integral shell dose is constant across plans when reducing the dose to a critical structure. Using the images of seven patients previously irradiated for cancer of brain or prostate cancer and one idealized scenario, competing three-dimensional conformal and IMRT plans were generated using different beam configurations. Within a given plan and for competing plans with a constant mean target dose, the normalized integral doses within concentric "shells" of surrounding normal tissue were quantitatively compared. Within each patient, the normalized integral dose to shells of normal tissue surrounding the target was relatively constant (1). Similarly, for each clinical scenario, the normalized integral dose for a given shell was also relatively constant regardless of the number and orientation of beams (2) or degree of sparing of a critical structure (3). 3D and IMRT planning tools can redistribute, rather than eliminate dose to the surrounding normal tissues (intuitively known by planners). More specifically, dose cannot be moved between shells surrounding the target but only within a shell. This implies that there are limitations in the extent to which a critical structure can be spared based on the location and geometry of the critical structure relative to the target.
Intermolecular interactions between the A and B subunits of heat-labile enterotoxin from Escherichia coli promote holotoxin assembly and stability in vivo. (1992)

Cholera toxin and the related heat-labile enterotoxin (LT) produced by Escherichia coli consist of a holotoxin of one A subunit and five B subunits (AB5). Here we investigate the domains of the A subunit (EtxA) of E. coli LT which influence the events of B-subunit (EtxB) oligomerization and the formation of a stable AB5 holotoxin complex. We show that the C-terminal 14 amino acids of the A subunit comprise two functional domains that differentially affect oligomerization and holotoxin stability. Deletion of the last 14 amino acids (-14) from the A subunit resulted in a molecule that was significantly impaired in its capacity to promote the assembly of a mutant B subunit, EtxB191.5. In contrast, deletion of the last four amino acids (-4) from the A subunit gave a molecule that retained such a capacity. This suggests that C-terminal residues within the -14 to -4 region of the A subunit are important for promoting the oligomerization of EtxB. In addition, we demonstrate that the truncated A subunit lacking the last 4 amino acids was unable to form a stable AB5 holotoxin complex even though it promoted B-subunit oligomerization. This suggests that the last 4 residues of the A subunit function as an "anchoring" sequence responsible for maintaining the stability of A/B subunit interaction during holotoxin assembly. These data represent an important example of how intermolecular interactions between polypeptides in vivo can modulate the folding and assembly of a macromolecular complex.
Robust in vivo gene transfer into adult mammalian neural stem cells by lentiviral vectors (2004)

Stable genetic modification of adult stem cells is fundamental for both developmental studies and therapeutic purposes. Using in vivo marking studies, we showed that injection of lentiviral vectors (LVs) into the subventricular zone of the adult mouse brain enables efficient gene transfer into long-term self-renewing neural precursors and steady, robust vector expression in their neuronal progeny throughout the subventricular zone and its rostral extension, up to the olfactory bulb. By clonal and population analysis in culture, we proved that in vivo-marked neural precursors display self-renewal and multipotency, two essential characteristics of neural stem cells (NSCs). Thus, LVs efficiently target long-term repopulating adult NSCs, and the effect of the initial transduction is amplified by the continuous generation of NSC-derived, transduced progeny. LVs may thus allow novel studies on NSCs' physiology in vivo, and introduction of therapeutic genes into NSCs may allow the development of novel approaches for untreatable CNS diseases.
Interaction of mumps virus V protein variants with STAT1-STAT2 heterodimer: experimental and theoretical studies (2010)

Our results suggest that VWT protein of Urabe AM9 strain of mumps virus may be more efficient than VGly to inactivate both the IFN signaling pathway and antiviral response due to differences in their finest molecular interaction with STAT proteins.
Tumor-Expressed B7-H1 and B7-DC in Relation to PD-1+ T-Cell Infiltration and Survival of Patients with Cervical Carcinoma (2009)

B7-H1 is expressed on only a minority of cervical cancers and does not influence the survival of patients with cervical cancer. PD-1 is expressed by a vast number of infiltrating CD8 T cells, suggesting that blocking of PD-1 could have therapeutic potential in cervical cancer patients.
Early Detection of Lung Cancer Using Serum RNA or DNA Markers: Ready for “Prime Time” or for Validation? (2003)

Article Tools EDITORIALS Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.2003.07.976 Journal of Clinical Oncology - published online before print September 21, 2016 PMID: 14507944 Early Detection of Lung Cancer Using Serum RNA or DNA Markers: Ready for “Prime Time” or for Validation? Paul A. Bunn JrxPaul A. Bunn JrSearch for articles by this author Show More University of Colorado Cancer Center, Denver, CO https://doi.org/10.1200/JCO.2003.07.976 First Page Full Text PDF Figures and Tables © 2003 by American Society of Clinical Oncology
Evaluation of a New Reagent for Preserving Fresh Blood Samples and Its Potential Usefulness for Internal Quality Controls of Multichannel Hematology Analyzers (1999)

We describe a new, easy-to-use reagent, Cyto-Chex (Streck Laboratories, Omaha, Neb), that preserves fresh whole blood in a non-cross-linking, nonformalin manner. Target values assigned to fresh blood were essentially met after preservation and storage of up to 31 days. Respective mean analytic inaccuracies and short-term intra-assay coefficients of variation (n = 30) were as follows: WBCs, 6.7% and 1.99%; RBCs, 0.7% and 0.76%; hemoglobin, -1.8% and 0.79%; hematocrit, -0.3% and 0.75%; mean corpuscular volume, -1.0% and 0.78%; and platelets, 6.9% and 3.12%. Linearity of dilution-sensitive analytes was satisfactory over a wide range of dilutions after preservation of blood samples. Ten independent laboratories using 10 different instruments determined day-to-day interassay imprecision during four 7-day periods after blood preservation. Mean interassay coefficients of variation for participating laboratories were WBC, 1.92%; RBC, 1.00%; hemoglobin, 1.29%; hematocrit, 2.00%; and platelets 3.29%. Cyto-Chex enables long-term monitoring of instrument accuracy and precision with retained blood specimens of healthy persons. Blood from patient cohorts with various hematologic disorders and with a wide range of numeric abnormalities and/or parameter aberrations can be preserved satisfactorily with this reagent. The reanalysis of preserved patient blood samples is an important adjunct to the use of commercial control material in quality control programs of multichannel hematology analyzers.
An Optimized Method for the Functional Analysis of Human Regulatory T Cells (2006)

Naturally occurring regulatory T cells (Treg) suppress the activation of antigen-responsive T cells in a cell contact-dependent manner. In order to investigate the impact of soluble mediators and receptor-ligand interactions on the interplay between naive T cells and Treg, a reproducible suppressor cell assay which functions in the absence of additional feeder cells or antigen-presenting cells is mandatory. Here, we describe such a method which is suited to study the modulation of responder T cell/Treg interactions in vitro. Treg were isolated from negatively purified total human CD4+ T cells by positive selection using anti-CD25 monoclonal antibody (MoAb)-coated Dynabeads followed by a detachment step. The remaining CD4+ CD25- responder T cells were cocultured with CD4+ CD25+ Treg in the presence of T-cell Activation/Expansion Beads from Miltenyi Biotec pre-coated with anti-CD3 plus anti-CD28 monoclonal antibody (MoAb). The optimal concentration for coating was 5 microg/ml for both MoAb. At this concentration, strong proliferation of responder T cells was elicited which was almost completely suppressed by Treg at 1:1 cell ratios. When higher concentrations of anti-CD3/anti-CD28 MoAb were used for coating, Treg also showed some degree of proliferation. The optimized suppressor assay proved to be highly reproducible and was used here to confirm the partial or complete reversal of Treg-mediated T-cell suppression by some cytokines (IL-2, IL-15), soluble IL-6 receptor/IL-6 fusion protein and recombinant GITR-ligand. Furthermore, our data confirm that Treg do not need other cell types to suppress proliferation of CD4+ CD25- responder T cells.
Cefazolin versus Cefazolin plus Metronidazole for Antibiotic Prophylaxis at Cesarean Section (2003)

Antibiotic prophylaxis with metronidazole and cefazolin results in fewer postoperative infections, decreased duration of hospitalization, and lower medication cost than cefazolin alone.
High-Yield Selective Placement of Carbon Nanotubes on Pre-Patterned Electrodes (2002)

Practical utilization of carbon nanotubes (CNTs) in nanoscale devices requires their directed placement on a substrate. Controlled placement has been achieved by a combination of the highly selective adsorption of single walled CNTs (SWNTs) onto open regions of amino-functionalized SiO2 in a polymeric resist, followed by liftoff. Careful selection of the surfactant used to suspend the SWNTs as well as other processing parameters allow controlled placement in high yield. This technique may provide a path for the large-scale fabrication of CNT-based devices and circuits.