gebhart/patrepeval huggingface dataset:
Ring-opening metathesis polymerization (ROMP) of norbornene by a Group VIII carbene complex in protic media (1992)

During the past two decades, intense research efforts have enabled an in-depth understanding of the olefin metathesis reaction as catalyzed by early transition metal complexes. In contrast, the nature of the intermediates and the reaction mechanism for group VIII transition metal metathesis catalysts remain elusive. Such knowledge is important in view of the promise group VIII metals show in polymerizing a wide variety of functionalized cyclic olefins in protic solvents. Highly active late transition metal catalysts should also open the way to the metathesis of functionalized acyclic olefins. Previous studies in our group have focused on the chemistry of highly active, functional-group-tolerant catalysts prepared from aquoruthenium(II) olefin complexes. In these systems, characterization of the catalytic intermediates is difficult due to their very low concentrations and high activity in the reaction mixtures. Although it is reasonable to assume that the active species are ruthenacyclobutanes and ruthenium carbenes (ruthenaolefins), the oxidation state and ligation of these intermediates are not known. Furthermore, the discrete ruthenium carbene complexes that have been isolated to date do not exhibit both metathesis activity and stability to protic/aqueous solvents. We report here the reaction of an Ru(II) complex with a strained olefin to produce a carbene species that polymerizes norbornene in organic media both in the absence and presence of protic/aqueous solvents. In both solvent systems, a stable propagating carbene complex can be observed throughout the course of the polymerization, as has been previously found with titanium, tantalum, tungsten, molybdenum, and ruthenium complexes.
Prolonged half-life and preserved enzymatic properties of factor IX selectively PEGylated on native N-glycans in the activation peptide (2011)

Current management of hemophilia B entails multiple weekly infusions of factor IX (FIX) to prevent bleeding episodes. In an attempt to make a longer acting recombinant FIX (rFIX), we have explored a new releasable protraction concept using the native N-glycans in the activation peptide as sites for attachment of polyethylene glycol (PEG). Release of the activation peptide by physiologic activators converted glycoPEGylated rFIX (N9-GP) to native rFIXa and proceeded with normal kinetics for FXIa, while the K(m) for activation by FVIIa-tissue factor (TF) was increased by 2-fold. Consistent with minimal perturbation of rFIX by the attached PEG, N9-GP retained 73%-100% specific activity in plasma and whole-blood-based assays and showed efficacy comparable with rFIX in stopping acute bleeds in hemophilia B mice. In animal models N9-GP exhibited up to 2-fold increased in vivo recovery and a markedly prolonged half-life in mini-pig (76 hours) and hemophilia B dog (113 hours) compared with rFIX (16 hours). The extended circulation time of N9-GP was reflected in prolonged correction of coagulation parameters in hemophilia B dog and duration of effect in hemophilia B mice. Collectively, these results suggest that N9-GP has the potential to offer efficacious prophylactic and acute treatment of hemophilia B patients at a reduced dosing frequency.
Antisense oligonucleotide binding to U5 snRNP induces a conformational change that exposes the conserved loop of U5 snRNA (1997)

Conformational rearrangements of the spliceosomal small nuclear RNAs (U snRNAs) are essential for proper assembly of the active site prior to the first catalytic step of splicing. We have previously shown that conformational changes caused by binding of an antisense 2'-O-methyl RNA oligonucleotide (BU5Ae) to U5 snRNA nt 68-88 disrupted the U4/U5/U6 complex and induced formation of the U1/U4/U5 and U2/U6 complexes. Here we show that the conformational change induced by BU5Ae exposes the invariant loop of U5 that binds the 5'exon and also reorganizes internal loop 1 (IL1) and the top of stem 2. Interestingly, we have also previously found that the U1/U4/U5 complex induced by BU5Ae brings the invariant loop of U5 into close proximity with the 5'-end of U1. Taken together, these data suggest that U1 and U5 may both contribute to the ability of the U1/U4/U5 complex to bind the 5' splice site.
The Arabidopsis HY2 Gene Encodes Phytochromobilin Synthase, a Ferredoxin-Dependent Biliverdin Reductase (2001)

Light perception by the plant photoreceptor phytochrome requires the tetrapyrrole chromophore phytochromobilin (P Phi B), which is covalently attached to a large apoprotein. Arabidopsis mutants hy1 and hy2, which are defective in P Phi B biosynthesis, display altered responses to light due to a deficiency in photoactive phytochrome. Here, we describe the isolation of the HY2 gene by map-based cloning. hy2 mutant alleles possess alterations within this locus, some of which affect the expression of the HY2 transcript. HY2 encodes a soluble protein precursor of 38 kD with a putative N-terminal plastid transit peptide. The HY2 transit peptide is sufficient to localize the reporter green fluorescent protein to plastids. Purified mature recombinant HY2 protein exhibits P Phi B synthase activity (i.e., ferredoxin-dependent reduction of biliverdin IX alpha to P Phi B), as confirmed by HPLC and by the ability of the bilin reaction products to combine with apophytochrome to yield photoactive holophytochrome. Database searches and hybridization studies suggest that HY2 is a unique gene in the Arabidopsis genome that is related to a family of proteins found in oxygenic photosynthetic bacteria.
16 × 16 non-blocking silicon optical switch based on electro-optic Mach-Zehnder interferometers (2016)

We experimentally demonstrate a 16 × 16 non-blocking optical switch fabric with a footprint of 10.7 × 4.4 mm<sup>2</sup>. The switch fabric is composed of 56 2 × 2 silicon Mach-Zehnder interferometers (MZIs), with each integrated with a pair of TiN resistive micro-heaters and a p-i-n diode. The average on-chip insertion loss at 1560 nm wavelength is ~6.7 dB and ~14 dB for the "all-cross" and "all-bar" states, respectively, with a loss variation of ± 1 dB over all routing paths. The measured rise/fall time of the switch upon electrical tuning is 3.2/2.5 ns. The switching functionality is verified by transmission of 20 Gb/s on-off keying (OOK) and 50 Gb/s quadrature phase-shift keying (QPSK) optical signals.
ACCURACY OF MOTOR AXON REGENERATION ACROSS AUTOGRAFT, SINGLE-LUMEN, AND MULTICHANNEL POLY(LACTIC-CO-GLYCOLIC ACID) NERVE TUBES (2008)

Retrograde tracing techniques provide new insights into the process of regeneration across nerve tubes. The methods and data presented in this study can be used as a basis for the development of a nerve tube for motor nerve repair.
Acylation of Indole under Friedel−Crafts ConditionsAn Improved Method To Obtain 3-Acylindoles Regioselectively (2001)

[reaction: see text]. The reaction of unsubstituted indole with different acylating agents such as acid chlorides, anhydrides, nitriles, and amino acid derivatives in the presence of Lewis acid is reported.
Specific termination of RNA polymerase synthesis as a method of RNA and DNA sequencing (1978)

Termination of RNA synthesis with 3'-O-Methylnucleoside 5'-triphosphates have been studied using E. coli RNA polymerase holoenzyme and poly [d(A-T)] as well as unfractionated T7 D delta III DNA as templates. It was shown that the termination can be used for DNA sequencing. A sequence of a part of RNA synthesized from AI promoter of the DNA have been determined. Syntheses of four 3'-O-Methylnucleoside 5'-triphosphates are described.
Dyke-Davidoff-Masson sendromunda manyetik rezonans görüntüleme bulguları (2001)

Purpose: To define the extent of cerebral parenchymal involvement in Davidoff Dyke-Masson syndrome by magnetic resonance imaging. Material and method: T1 and T2 weighted axial and coronal images were obtained to evaluate brain parenchyma of three patients with MRI. Findings: Right cerebral hemiatrophy were seen in two of the cases while left cerebral hemiatrophy was observed in one case. Ipsilateral atrophy in basal ganglia, loss in white and gray ma tter and hypoplasia of cerebral peduncles were seen. The etiology of the syndrome included meneng itis in two patients and traumatic delivery in one patient. Results: Magnetic resonance imaging is the procedure of choice with respect t o the assesment of the etiology and extent of cerebral parenchymal involvement in Davidoff Dyke -Masson syndrome. Key words: Dyke-Davidoff-Masson syndrome, magnetic resonance imaging, unilateral cerebral atrophy.
A physical model for planar spiral inductors on silicon (2002)

This paper presents a physical model for planar spiral inductors on silicon. The model has been confirmed with measured and published data of inductors having different geometric and process parameters. This model is scalable with inductor geometry, allowing designers to predict and optimize the quality factor.
Design Of New Holographic Gratings For A High S/N Ratio Flat Field Spectrograph (1986)

The rapidly growing use of multichannel detectors in the design of analytical instruments has lead to the development of concave holographic gratings which produce a flat spectrum. These gratings are corrected from aberrations, mainly astigmatism, and are blazed for improving the signal. Spectroscopic instruments are subject to two forms of stray-light - diffuse scatter from the grating, a problem that can be significantly reduced by using holographic gratings and multireflections that may include the grating. This problem may be solved by calculating an aberration corrected grating that operates &quot;off plane&quot; and is, in fact, tilted. This paper describes the effect of these improvements for optimizing signal to noise ratio of flat field spectrographs.
Comparison of two coprological methods for the veterinary diagnosis of fasciolosis (2005)

The sensitivity and utility of a standard faecal sedimentation method (FSM) and a modified stool sieving staining method (FSSM), both currently employed for the diagnosis of Fasciola hepatica infection were compared. Faecal samples were obtained from 51 bovines of an endemic area for fasciolosis in Southwestern Argentina. Each sample was placed in a recipient containing 5% formalin. Eight millilitres of the suspension, equivalent to 2g of faeces, were used for each of the two methods tested. The number of eggs found per sample was recorded. The proportion of positive samples obtained by the FSSM (27/51) was significantly higher than that by the FSM (11/51) (P&lt;0.05). The percent of agreement between methods was 41%. Over a total of 27 positive samples detected by the FSSM, the FSM missed 16, yielding 60% false negative samples. The FSSM enhanced 2.5 times the sensitivity of diagnosis. The complexity of the FSM may decrease its sensitivity through missing and loss of eggs during sample processing. These results confirmed that the commonly used FSM underestimates the prevalence and the egg output in cattle and that the FSSM is a more reliable diagnostic method.
'Playing Chicken' Over Gene Markers (1997)

HUMAN GENOME PROJECTThe U.S. government is getting set to launch a big addition to its human genome project this winter. Details of the venture--which involves sequencing snippets of DNA from hundreds of individuals of different racial backgrounds and putting them in a public repository--were discussed at a meeting at the National Institutes of Health last week, and a funding announcement could be issued within a month. The variations could serve as landmarks in a fine-scale map of the genome.
Automatic Labelling Of Coronary Arteries (2009)

Publication in the conference proceedings of EUSIPCO, Glasgow, Scotland, 2009
Differential effects of rapamycin on mammalian target of rapamycin signaling functions in mammalian cells. (2003)

Rapamycin and its analogues have shown promising anticancer activities in preclinical and clinical studies. However, the mechanism whereby rapamycin inhibits signaling through the mammalian target of rapamycin (mTOR) remains poorly understood. Here, we show that the FKBP12/rapamycin complex is an essentially irreversible inhibitor of mTOR kinase activity in vitro. However, we observe no suppression of mTOR catalytic activity after immunoprecipitation from rapamycin-treated cells. These results suggest either that rapamycin acts as a reversible kinase inhibitor in intact cells or that the cellular effects of rapamycin are not mediated through global suppression in mTOR kinase activity. To better understand the cellular pharmacology of rapamycin, we compared the individual and combined effects of rapamycin and kinase-inactive mTOR expression on a panel of mTOR-dependent cellular responses. These studies identified glycolytic activity, amino acid transporter trafficking, and Akt kinase activity as novel, mTOR-modulated functions in mammalian cells. Whereas kinase-inactive mTOR did not enhance the decreases in cell size and glycolysis induced by rapamycin, expression of this mTOR mutant significantly enhanced the inhibitory effects of rapamycin on cell proliferation, 4EBP1 phosphorylation, and Akt activity. Unexpectedly, amino acid transporter trafficking was perturbed by kinase-inactive mTOR but not by rapamycin, indicating that this process is rapamycin insensitive. These results indicate that rapamycin exerts variable inhibitory actions on mTOR signaling functions and suggest that direct inhibitors of the mTOR kinase domain will display substantially broader anticancer activities than rapamycin.
Long-Term Treatment of Primary Pulmonary Hypertension with Aerosolized Iloprost, a Prostacyclin Analogue (2000)

Long-term treatment with aerosolized iloprost is safe and has sustained effects on exercise capacity and pulmonary hemodynamics in patients with primary pulmonary hypertension.
“Not a Feminist, But...”: The Political Career of Ellen Louks Fairclough,Canada’s First Female Federal Cabinet Minister (1996)

This paper traces the life course of Ellen Louks Fairclough, Canada’s first federal female cabinet minister (1957-63), discusses the factors that contributed to her success in civic and federal elections in Hamilton between 1946 and 1963, and assesses her achievements as the lone woman in the Progressive Conservative cabinet led by John Diefenbaker. While Fairclough claims not to be a feminist, it is argued here that her public and private choices were shaped by middle class feminist goals as they were defined in North America in the interwar years and Shat these goals had a significant impact on the policies adopted by both Fairclough and the party she represented in the 1940s and l950s.
State-of-the-Art and Trends in Scalable Video Compression With Wavelet-Based Approaches (2007)

Scalable video coding (SVC) differs form traditional single point approaches mainly because it allows to encode in a unique bit stream several working points corresponding to different quality, picture size and frame rate. This work describes the current state-of-the-art in SVC, focusing on wavelet based motion-compensated approaches (WSVC). It reviews individual components that have been designed to address the problem over the years and how such components are typically combined to achieve meaningful WSVC architectures. Coding schemes which mainly differ from the space-time order in which the wavelet transforms operate are here compared, discussing strengths and weaknesses of the resulting implementations. An evaluation of the achievable coding performances is provided considering the reference architectures studied and developed by ISO/MPEG in its exploration on WSVC. The paper also attempts to draw a list of major differences between wavelet based solutions and the SVC standard jointly targeted by ITU and ISO/MPEG. A major emphasis is devoted to a promising WSVC solution, named STP-tool, which presents architectural similarities with respect to the SVC standard. The paper ends drawing some evolution trends for WSVC systems and giving insights on video coding applications which could benefit by a wavelet based approach.
An approach to genomewide screens of expressed small interfering RNAs in mammalian cells (2003)

To facilitate the construction of large genomewide libraries of small interfering RNAs (siRNAs), we have developed a dual promoter system (pDual) in which a synthetic DNA encoding a gene-specific siRNA sequence is inserted between two different opposing polymerase III promoters, the mouse U6 and human H1 promoters. Upon transfection into mammalian cells, the sense and antisense strands of the duplex are transcribed by these two opposing promoters from the same template, resulting in a siRNA duplex with a uridine overhang on each 3' terminus. A single-step PCR protocol has been developed by using this dual promoter system that allows the production of siRNA expression cassettes in a high-throughput manner. We have shown that siRNAs transcribed by either the dual promoter vector or siRNA expression cassettes can induce strong and gene-specific suppression of both endogenous genes and ectopically expressed genes in mammalian cells. Furthermore, we have constructed an arrayed siRNA expression cassette library that targets >8000 genes with two siRNA sequences per gene. A high-throughput screen of this library has revealed both known and unique genes involved in the NF-kappaB signaling pathway.
SK2 encodes the apamin‐sensitive Ca2+‐activated K+ channels in the human leukemic T cell line, Jurkat (2000)

T cells express two different types of voltage-independent Ca(2+)-activated K(+) channels with small (SK) and intermediate (IK) conductance that serve important roles in the activation of T lymphocytes. In contrast to the IK channels from T lymphocytes which are upregulated upon mitogen stimulation, SK channels of Jurkat T cells, a human leukemic T cell line, are constitutively expressed even in the absence of mitogenic stimulation. We have used patch-clamp recordings from transfected or injected mammalian cells to show that the cloned SK2 channel demonstrates the biophysical and pharmacological properties of the majority of K(Ca) channels in Jurkat T cells. The cloned and native channels are voltage-independent, Ca(2+)-activated, apamin-sensitive, show an equivalent voltage-dependent Ba(2+) block and possess a similar ion selectivity. In addition, we used the polymerase chain reaction to demonstrate the presence of SK2 mRNA in Jurkat T cells, whereas SK3 transcripts encoding the other cloned apamin-sensitive SK channel were not detected. These data suggest that the voltage-independent apamin-sensitive K(Ca) channel in Jurkat T cells represents the recently cloned SK2 channel.
Reaction Between Methanol and Commercial Seed Oils Under Microwave Irradiation (1999)

The transformation of triglycerides, contained in a commercial seed oil into methyl esters, was studied in the presence of microwave irradiation and the results were compared with those obtained using traditional methods. This reaction is quite rapid using conventional and microwave heating; shorter reaction times were observed under microwaves in the presence of a variety of catalysts and the reaction was found practically complete in less than 2 minutes in most cases. Longer irradiation times in the absence of catalysts yielded increasing amounts offree acids, as detected by gas chromatography. The catalytic be of sodium methylate, sodium hydroxide, sodium carbonate, sulfuric acid, benzensulfonic acid and boron carbide was briefly discussed. The carbide provides an effective catalysis of the trans-estenfication in the presence of microwaves, without leaving traces of acidic or basic by-products. A lab scale plant for a continuous transestenfication process was also described.
A plug-in program to perform Hanawalt or Fink search-indexing using organics entries in the ICDD PDF-4/organics 2003 database (2004)

In an attempt to fill a gap between fully automatic search/match programs and purely manual methods based on paper products, a relational database plug-in has been developed that functions as a PC-based Search/Index program for extracting information from PDF-4 powder diffraction databases. The plug-in provides an adjustable search window and match window to account for experimental errors. Both Hanawalt and Fink search methods are incorporated. In this paper, we report search-indexing results obtained with the new PDF-4 plug-in applied to a new relational database, the PDF-4/Organics 2003. This database has 24 385 experimental entries and 122 816 calculated patterns derived from the Cambridge Crystallographic Database. We introduce a goodness of match (GOM) parameter to describe the relative agreement between the experimental input data and selected reference patterns from the PDF-4/Organics 2003. The relevance of the GOM is illustrated in several example problems. Multiphase samples can be treated on a phase-by-phase basis.
Physicochemical characterization and biological activity of a glycoglycerolipid from Mycoplasma fermentans (2003)

We report a comprehensive physicochemical characterization of a glycoglycerolipid from Mycoplasma fermentans, MfGl-II, in relation to its bioactivity and compared this with the respective behaviors of phosphatidylcholine (PC) and a bacterial glycolipid, lipopolysaccharide (LPS) from deep rough mutant Salmonella minnesota strain R595. The beta left arrow over right arrow alpha gel-to-liquid crystalline phase transition behavior of the hydrocarbon chains with Tc = 30 degrees C for MfGl-II as well as for LPS exhibits high similarity between the two glycolipids. A lipopolysaccharide-binding protein (LBP)-mediated incorporation into negatively charged liposomes is observed for both glycolipids. The determination of the supramolecular aggregate structure confirms the existence of a mixed unilamellar/cubic structure for MfGl-II, similar to that observed for the lipid A moiety of LPS. The biological data clearly show that MfGl-II is able to induce cytokines such as tumor necrosis factor-alpha (TNF-alpha) in human mononuclear cells, although to a significantly lower degree than LPS. In contrast, in the Limulus amebocyte lysate test, MfGl-II is completely inactive, and in the CHO reporter cell line it does not indicate any reactivity with the Toll-like receptors TLR-2 and -4, in contrast to control lipopeptides and LPS. These data confirm the applicability of our conformational concept of endotoxicity to nonlipid A structures: an amphiphilic molecule with a nonlamellar cubic aggregate structure corresponding to a conical conformation of the single molecules and a sufficiently high negative charge density in the backbone.
Macrophage activation syndrome in patients with systemic juvenile idiopathic arthritis is associated with MUNC13‐4 polymorphisms (2008)

The data suggest an association between MUNC13-4 polymorphisms and macrophage activation syndrome in patients with systemic JIA.
Haploview: analysis and visualization of LD and haplotype maps (2004)

jcbarret@broad.mit.edu
Transperineal 125 Iodine Seed Implantation in Prostatic Cancer Guided by Transrectal Ultrasonography (1983)

A new method is described for precise transperineal insertion of radioactive 125iodine seeds in patients with prostatic cancer. The procedure is done under transrectal ultrasonography guidance using a special multichannel puncture attachment and a simple, efficient insertion technique. The advantages of the method are 1) the patients are spared the inconvenience and risk of an operation, 2) improved dose calculations are possible, and 3) seed application is easy and more precise than by the conventional operative free-hand technique.