gebhart/patrepeval huggingface dataset:
Total Synthesis of the Serine/Threonine-Specific Protein Phosphatase Inhibitor Tautomycin1 (1997)

A convergent, asymmetric synthesis of the protein phosphatase inhibitor, tautomycin, is described. The natural product was constructed by joining two major fragments of comparable complexity at the C21-C22 bond. Absolute stereochemistry of the C1-C21 ketone originates from (S)-citronellene and (2R,3S)-geraniol epoxide. The anti stereochemical relationships at C6-C7 and C18-C19 were introduced with Duthaler's chiral titanium propionic enolate. Syn stereochemical relationships at C13-C14 and C23-C24 were established using an Evan's oxazolidinone chiral auxiliary. The spiroketal was efficiently constructed via a one-pot double-alkylation-spirocyclization sequence with acetone N,N-dimethylhydrazone serving as the central linchpin. Final coupling of the two halves using a chelation-controlled Mukaiyama aldol addition followed by deprotection yielded synthetic tautomycin that is identical to the natural product.
Interactions among members of the Bcl-2 protein family analyzed with a yeast two-hybrid system. (1994)

Interactions of the Bcl-2 protein with itself and other members of the Bcl-2 family, including Bcl-X-L, Bcl-X-S, Mcl-1, and Bax, were explored with a yeast two-hybrid system. Fusion proteins were created by linking Bcl-2 family proteins to a LexA DNA-binding domain or a B42 trans-activation domain. Protein-protein interactions were examined by expression of these fusion proteins in Saccharomyces cerevisiae having a lacZ (beta-galactosidase) gene under control of a LexA-dependent operator. This approach gave evidence for Bcl-2 protein homodimerization. Bcl-2 also interacted with Bcl-X-L and Mcl-1 and with the dominant inhibitors Bax and Bcl-X-S. Bcl-X-L displayed the same pattern of combinatorial interactions with Bcl-2 family proteins as Bcl-2. Use of deletion mutants of Bcl-2 suggested that Bcl-2 homodimerization involves interactions between two distinct regions within the Bcl-2 protein, since a LexA protein containing Bcl-2 amino acids 83-218 mediated functional interactions with a B42 fusion protein containing Bcl-2 amino acids 1-81 but did not complement a B42 fusion protein containing Bcl-2 amino acids 83-218. In contrast to LexA/Bcl-2 fusion proteins, expression of a LexA/Bax protein was lethal to yeast. This cytotoxicity could be abrogated by B42 fusion proteins containing Bcl-2, Bcl-X-L, or Mcl-1 but not those containing Bcl-X-S (an alternatively spliced form of Bcl-X that lacks a well-conserved 63-amino acid region). The findings suggest a model whereby Bax and Bcl-X-S differentially regulate Bcl-2 function, and indicate that requirements for Bcl-2/Bax heterodimerization may be different from those for Bcl-2/Bcl-2 homodimerization.
Celiac Plexus Block (1981)

Techniques for blocking the celiac plexus were evaluated by conventional posteroanterior and lateral x-rays and computed tomography (CT) in 20 patients with intractable pain due to carcinoma of the pancreas and by determining spread of injected dye at the time of autopsy in three corpses. The results showed that (a) the site for insertion of the needles should not be more than 7.5 cm lateral to the spinous process of a lumbar vertebra, (b) needles should be placed bilaterally, (c) the depth to which needles are inserted is greater than previously recommended, and (d) at least 25 ml of solution should be injected through each needle.
The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. (1992)

A conditional block to transcriptional elongation is an important mechanism for regulating c-myc gene expression. This elongation block within the first c-myc exon was defined originally in mammalian cells by nuclear run-on transcription analyses. Subsequent oocyte injection and in vitro transcription analyses suggested that sequences near the end of the first c-myc exon are sites of attenuation and/or premature termination. We report here that the mapping of single stranded DNA in vivo with potassium permanganate (KMnO4) and nuclear run-on transcription assays reveal that polymerase is paused near position +30 relative to the major c-myc transcription initiation site. Deletion of 350 bp, including the sites of 3'-end formation and intrinsic termination defined in oocyte injection and in vitro transcription assays does not affect-the pausing of polymerase in the promoter-proximal region. In addition, sequences upstream of +47 are sufficient to confer the promoter-proximal pausing of polymerases and to generate the polarity of transcription farther downstream. Thus, the promoter-proximal pausing of RNA polymerase II complexes accounts for the block to elongation within the c-myc gene in mammalian cells. We speculate that modification of polymerase complexes at the promoter-proximal pause site may determine whether polymerases can read through intrinsic sites of termination farther downstream.
Asymptomatic Chlamydia trachomatis Infections Among Sexually Active Men (1986)

Journal Article Asymptomatic Chlamydia trachomatis Infections Among Sexually Active Men Get access George H. Karam, George H. Karam Louisiana State University School of Medicine, New Orleans, Louisiana Please address requests for reprints to Dr. George H. Karam, Louisiana State University, School of Medicine, Department of Medicine, 1542 Tulane Avenue, Room 408, New Orleans, Louisiana 70112. Search for other works by this author on: Oxford Academic PubMed Google Scholar David H. Martin, David H. Martin Louisiana State University School of Medicine, New Orleans, Louisiana Search for other works by this author on: Oxford Academic PubMed Google Scholar Terence R. Flotte, Terence R. Flotte Louisiana State University School of Medicine, New Orleans, Louisiana Search for other works by this author on: Oxford Academic PubMed Google Scholar Frank O. Bonnarens, Frank O. Bonnarens Louisiana State University School of Medicine, New Orleans, Louisiana Search for other works by this author on: Oxford Academic PubMed Google Scholar John R. Joseph, John R. Joseph Louisiana State University School of Medicine, New Orleans, Louisiana Search for other works by this author on: Oxford Academic PubMed Google Scholar Tomasz F. Mroczkowski, Tomasz F. Mroczkowski Louisiana State University School of Medicine, New Orleans, Louisiana Search for other works by this author on: Oxford Academic PubMed Google Scholar William D. Johnson William D. Johnson Louisiana State University School of Medicine, New Orleans, Louisiana Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 154, Issue 5, November 1986, Pages 900–903, https://doi.org/10.1093/infdis/154.5.900 Published: 01 November 1986 Article history Received: 07 February 1986 Revision received: 30 May 1986 Published: 01 November 1986
Anti-HLA-DR/anti-DOTA Diabody Construction in a Modular Gene Design Platform: Bispecific Antibodies for Pretargeted Radioimmunotherapy (2001)

Recombinant immunoglobulin libraries of single chain molecules (sc) from the variable domains of antibody light and heavy chains (Fv), have great promise for new approaches to radioimmunotherapy (RIT). However, creating and evaluating scFv from diverse sources is time consuming and differences in molecular format can influence in vitro and in vivo characteristics. Furthermore, scFv do not have optimal characteristics for targeting therapy to tumor because of their small size and univalent binding. Diabody molecules at least twice the size of scFv are better for RIT because bivalent and bispecific molecules can be constructed. A polymerase chain reaction (PCR) based primer system was created to easily convert scFv genes into a diabody gene format, once they have been placed into pCANTAB 5E, a readily available vector. The primer system for this diabody gene platform was developed and tested by constructing an anti-lymphoma/anti-chelate, bispecific diabody (anti-HLA-DR/anti-DOTA). Two mouse scFv libraries were screened for reactive clones using recombinant phage display techniques. Selected mouse anti-HLA-DR and anti-DOTA scFv genes were combined, ligated into the pCANTAB 5E vector that co-expressed these self-assembling scFv in E. coli as two mismatched nonlinked pairs (VHA-link-VLB; VHB-link-VLA). The diabody protein that was purified from periplasm had the expected molecular characteristics when analyzed by sequencing, chromatography, electrophoresis and Western blot. This modular gene design platform provides methodology for easy and rapid creation of diabody molecules from diverse scFv libraries. Diabodies from various scFv can easily be produced, thereby facilitating comparative preclinical studies en route to development of new tumor targeting molecules.
Architectural Semantics for Practical Transactional Memory (2006)

Transactional Memory (TM) simplifies parallel programming by allowing for parallel execution of atomic tasks. Thus far, TM systems have focused on implementing transactional state buffering and conflict resolution. Missing is a robust hardware/software interface, not limited to simplistic instructions defining transaction boundaries. Without rich semantics, current TM systems cannot support basic features of modern programming languages and operating systems such as transparent library calls, conditional synchronization, system calls, I/O, and runtime exceptions. This paper presents a comprehensive instruction set architecture (ISA) for TM systems. Our proposal introduces three key mechanisms: two-phase commit; support for software handlers on commit, violation, and abort; and full support for open- and closed-nested transactions with independent rollback. These mechanisms provide a flexible interface to implement programming language and operating system functionality. We also show that these mechanisms are practical to implement at the ISA and microarchitecture level for various TM systems. Using an execution-driven simulation, we demonstrate both the functionality (e.g., I/O and conditional scheduling within transactions) and performance potential (2.2× improvement for SPECjbb2000) of the proposed mechanisms. Overall, this paper establishes a rich and efficient interface to foster both hardware and software research on transactional memory.
Interferons in melanoma (1996)

The interferons are complex proteins that have been widely tested as therapy for neoplastic diseases. Interferon (IFN)-alpha has been the most extensively studied in melanoma. It produces responses in about 16% of metastatic melanomas, about one third of which are complete. It has been combined with chemotherapy and biologic therapy in an attempt to improve on this response rate, but despite encouraging reports from single-institution trials, firm evidence for improved efficacy is still forthcoming. Randomized trials of sequenced biochemotherapies should shed further light on this issue. The outlook in the adjuvant setting is much brighter with the recently reported positive results of the European Cooperative Oncology Group trial E1684 that showed improved overall and disease-free survival for high-risk patients treated with IFN-alpha. The lack of efficacy of lower dosages and different schedules of administration argues for the use of maximally tolerated doses. IFN-gamma has proved disappointing in cases of both metastatic and high risk for relapse melanoma, but has been effective in locoregional disease, particularly in combination with tumor necrosis factor-alpha and melphalan. Further research will need to focus on sequencing, improved methods of administration, and efforts to reduce toxicity.
Inhibition of hepatic endothelial E-selectin expression by C-raf antisense oligonucleotides blocks colorectal carcinoma liver metastasis. (2002)

Cytokine-dependent induction of E-selectin expression is mediated through cooperative signaling involving the Ras/Raf/mitogen-activated protein kinase pathway. We previously reported that metastatic tumor cells entering the hepaticcirculation rapidly induce a cytokine cascade leading to E-selectin induction (A-M. Khatib, et al., Cancer Res., 59:1356-1361, 1999).Here, we investigated the effect of a blockade of E-selectin induction on colorectal carcinoma metastasis using rodent (host)-specific C-raf antisense oligonucleotides and human colorectal carcinoma CX-1 cells. Pretreatment of hepatic endothelial cells in vitro with the antisense oligonucleotides abrogated E-selectin-dependent CX-1 adhesion. In vivo, pretreatment of nude mice with these oligonucleotides abrogated E-selectin induction in response to intrasplenic/portal inoculation of CX-1 cells, and this reduced the number of liver metastases by 86% relative to controls. The results suggest that the inhibition of tumor-induced, hepatic microvessel E-selectin expression may provide a useful strategy for the prevention of hepatic metastasis.
Synthesis and Separation Performance of SSZ-13 Zeolite Membranes on Tubular Supports (2002)

SSZ-13 zeolite membranes were synthesized on the inside surface of porous stainless steel tubes. In parallel with zeolite pores, the membranes had nonzeolite pores that were larger than the 0.38-nm zeolite pore diameter, but single-gas permeances of H2, N2, CH4, and n-C4H10 decreased with increasing kinetic diameter at 298 K. The CO2/CH4, H2/CH4 and H2/n-C4H10 ideal selectivities were 11, 9.0, and 63, respectively, at 298 K, and the separation selectivities for the mixtures of the same gas pairs were 12, 8.2, and 5.7 at 298 K. The SSZ-13 membranes selectively removed H2O from HNO3/H2O liquid mixtures by pervaporation to break the azeotrope at 69.5 wt % HNO3. The permeate concentration was 38.3% HNO3, and the total flux was 0.12 kg/m2·h at 298 K.
Radical performance enhancements for combinatorial optimization algorithms based on the dead‐end elimination theorem (1998)

Recent advances in protein design have demonstrated the effectiveness of optimization algorithms based on the dead-end elimination theorem. The algorithms solve the combinatorial problem of finding the optimal placement of side chains for a set of backbone coordinates. Although they are powerful tools, these algorithms have severe limitations when the number of side chain rotamers is large. This is due to the high-order time dependence of the aspect of the calculation that deals with rotamer doubles. We present three independent algorithmic enhancements that significantly increase the speed of the doubles computation. These methods work by using quantities that are inexpensive to compute as a basis for forecasting which expensive calculations are worthwhile. One of the methods, the comparison of extrema, is derived from analytical considerations, and the remaining two, the “magic-bullet” and the “qrs” and “quv” metrics, are based on empirical observation of the distribution of energies in the system. When used together, these methods effect an overall speed improvement of as much as a factor of 47, and for the doubles aspect of the calculation, a factor of 95. Together, these enhancements extend the envelope of inverse folding to larger proteins by making formerly intractable calculations attainable in reasonable computer time. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1505–1514, 1998
Retrieving hierarchical text structure from typeset scientific articles - a prerequisite for e-science text mining (2005)

Despite the growth and development of the web in scientific publishing, there remain significant obstacles to the application of computer based text processing technologies. One obvious obstacle is the relative paucity of freely and publicly available full-text articles. Such obstacles have resulted in a large concentration of text processing research on the relatively small amount of suitable material that is currently available, notably MedLine abstracts. In this paper, we discuss a processing framework (PTX) for scientific documents guided by two main principles. We start from the de facto position that most published material is available in PDF, a layout or document appearance format. For text processing, the (hierarchical) structure of the text is required. Secondly, we believe that the most likely users of scientific text processing will be scientists exploring literature within a particular specialism. Consequently, the framework can and should exploit (in a modular fashion) knowledge about that specific literature. The framework is being developed in the context of two E-Science projects: FlySlip and CitRAZ. The former is developing tools to aid human database curation of Drosophila genetics literature. The latter is combining Argumentative Zoning with citation information in order to help improve both citation indexing and text summarisation. 1.
A unique antigen on mature B cells defined by a monoclonal antibody. (1986)

A novel 42,000 dalton antigen (MB-1) expressed by mature human B cells in blood and tonsil was identified and characterized by utilizing a hybridoma monoclonal antibody. A comparison of MB-1 with other known B cell antigens suggests that the MB-1 antigen has not been previously identified. From one-and two-color immunofluorescence studies, it appears that the MB-1 antigen is found on all normal immunoglobulin (Ig)-expressing cells, but not on T cells, thymocytes, granulocytes, or platelets. Studies of malignant B cell tumors reveal that the antigen is expressed by virtually all Ig-expressing B cell tumors but only 10% of SIg- B-lineage leukemias. Data from these studies suggest that the MB-1 antigen is expressed late in B cell ontogeny before the expression of SIg.
Submicrometer Epsilon-Near-Zero Electroabsorption Modulators Enabled by High-Mobility Cadmium Oxide (2017)

Epsilon-near-zero materials provide a new path for tailoring light-matter interactions at the nanoscale. In this paper, we analyze a compact electroabsorption modulator based on epsilon-near-zero confinement in transparent conducting oxide films. The nonresonant modulator operates through field-effect carrier density tuning. We compare the performance of modulators composed of two different conducting oxides, namely, indium oxide (In2O3 ) and cadmium oxide (CdO), and show that better modulation performance is achieved when using high-mobility (i.e., low loss) epsilon-near-zero materials such as CdO. In particular, we show that nonresonant electroabsorption modulators with submicron lengths and greater than 5 dB extinction ratios may be achieved through the proper selection of high-mobility transparent conducting oxides, opening a path for device miniaturization and increased modulation depth.
Gate fault isolation and parametric characterization through the use of Atomic Force Probing (2004)

The current work is to demonstrate the power of a new class of analytical tool known as the Atomic Force Prober or AFP. The AFP is used to characterize a gate oxide breakdown both through the use of conductive or pico-current imaging and subsequent parametric characterization of the associated transistor.
Simplified dynamic deviation reduction-based Volterra model for Doherty power amplifiers (2011)

A simplified 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> -order dynamic deviation reduction-based Volterra series model is proposed for characterizing wideband multi-carrier Doherty power amplifiers. By removing several redundant terms, this model has much less complexity but maintains excellent modeling performance, compared to the full-size model. Experimental results show that both nonlinear distortion and memory effects in the Doherty PA can be almost completely removed by employing digital predistortion with proposed model, when excited by 2- and 4-carrier WCDMA signals.
NovelN6-substituted adenosine 5′-N-methyluronamides with high selectivity for human adenosine A3receptors reduce ischemic myocardial injury (2003)

We recently reported the identification of a novel human adenosine A3 receptor-selective agonist, (2S,3S,4R,5R)-3-amino-5-[6-[5-chloro-2-(3-methylisoxazol-5-ylmethoxy)benzylamino]purin-9-yl]-4-hydroxytetrahydrofuran-2-carboxylic acid methylamide (CP-608,039), with 1,260-fold selectivity for the human A3 versus human A1 receptor (DeNinno et al., J Med Chem 46: 353-355, 2003). However, because the modest (20-fold) rabbit A3 receptor selectivity of CP-608,039 precludes demonstration of A3-mediated cardioprotection in rabbit models, we identified another member of this class, (2S,3S,4R,5R)-3-amino-5-[6-(2,5-dichlorobenzylamino)purin-9-yl]-4-hydroxytetrahydrofuran-2-carboxylic acid methylamide (CP-532,903), which both retained human A3 receptor selectivity (210-fold; human A3/human A1 Ki: 23/4,800 nM) and had improved rabbit A3 receptor selectivity (90-fold; rabbit A3/rabbit A1 Ki: 23/2,000 nM). Infarct size was measured in Langendorff hearts or in vivo after 30 min of regional ischemia and 120 min of reperfusion. Five-minute perfusion with CP-532,903 before ischemia-reperfusion elicited a concentration-dependent reduction in infarct size in isolated hearts (EC50: 0.97 nM; maximum reduction in infarct size: 77%, P < 0.05 vs. control). Furthermore, administration of CP-532,903 (150 nM) at reperfusion also significantly reduced infarct size by 64% (P < 0.05 vs. control), which was not different (P > or = 0.05) from the cardioprotection provided by the same concentration of drug given before ischemia. The selective rabbit A1 receptor antagonist BWA1433 did not affect CP-532,903-dependent cardioprotection. In vivo, CP-532,903 (1 mg/kg) reduced infarct size by 50% in the absence of significant hemodynamic effects (mean arterial pressure, heart rate, rate-pressure product). CP-532,903 and CP-608,039 represent a novel class of human A3 receptor-selective agonists that may prove suitable for investigation of the clinical cardioprotective efficacy of A3 receptor activation.
The effects of dietary N‐3 and antioxidant supplementation on erythrocyte membrane fatty acid composition and fluidity in exercising horses (2006)

An enriched oral antioxidant supplementation induced changes in membrane composition, which modulated the decrease in EMF induced by exercise. Long chain n-3 fatty acid supplementation might therefore be beneficial.
Structure, expression, and T cell costimulatory activity of the murine homologue of the human B lymphocyte activation antigen B7. (1991)

Following occupancy of the T cell receptor by antigen, T cell proliferation and lymphokine production are determined by a second costimulatory signal delivered by a ligand expressed on antigen presenting cells. The human B cell activation antigen B7, which is expressed on antigen presenting cells including activated B cells and gamma interferon treated monocytes, has been shown to deliver such a costimulatory signal upon attachment to its ligand on T cells, CD28. We have cloned and sequenced the murine homologue of the human B7 gene. The predicted murine protein has 44% amino acid identity with human B7. The greatest similarity is in the Ig-V and Ig-C like domains. Murine B7 mRNA was detected in murine hematopoietic cells of B cell but not T cell origin. Cells transfected with murine B7 provided a costimulatory signal to human CD28+ T lymphocytes. These results demonstrate the costimulatory activity of murine B7 and provide evidence that the ligand attachment site is conserved between the two species.