gebhart/patrepeval huggingface dataset:
Random-priming in vitro recombination: An effective tool for directed evolution (1998)

A simple and efficient method for in vitro mutagenesis and recombination of polynucleotide sequences is reported. The method involves priming template polynucleotide(s) with random-sequence primers and extending to generate a pool of short DNA fragments which contain a controllable level of point mutations. The fragments are reassembled during cycles of denaturation, annealing and further enzyme-catalyzed DNA polymerization to produce a library of full-length sequences. Screening or selecting the expressed gene products leads to new variants with improved functions, as demonstrated by the recombination of genes encoding different thermostable subtilisins in order to obtain enzymes more stable than either parent.
Molybdenum Imido Alkylidene Metathesis Catalysts That Contain Electron-Withdrawing Biphenolates or Binaphtholates (2007)

We have prepared new Mo(NR)(CHCMe(2)Ph)(diolate) complexes (R = 2,6-i-Pr(2)C(6)H(3), 2,6-Me(2)C(6)H(3), 1-Adamantyl, or 2-CF(3)C(6)H(4)) that contain relatively electron-withdrawing binaphtholate (3,3'-bis-(9-anthracenyl), 3,3'-bispentafluorophenyl, or 3,3'-bis(3,5-bis(trifluoromethyl)phenyl) or biphenolate (3,3'-di-tert-butyl-5,5'-bistrifluoromethyl-6,6'-dimethyl-1,1'-biphenyl-2,2'-diolate) ligands. We also have prepared new monomeric Mo(NR)(CHCMe(2)Ph)(2,5-dimethylpyrrolide)(2) complexes and have treated them with biphenols or binaphthols in order to prepare several Mo(NR)(CHCMe(2)Ph)(diolate) species. In one case the new Mo(NR)(CHCMe(2)Ph)(diolate) complexes could be prepared only through reaction of a binaphthol [3,3'-bis(pentafluorophenyl)binaphthol] with a bis(2,5-dimethylpyrrolide) complex. The pyrrolide approach can be employed either to isolate catalysts on a preparative scale or to generate catalysts in situ. Several simple preliminary ring-closing metathesis reactions show that the new complexes are catalytically competent.
Structuring databases for analysis (1993)

Databases for online analytical processing (also called end-user computing) are discussed. The differences between end-user computing, which uses the multidimensional data model, and transaction processing, which uses the relational model, are examined. The differences between the two models are described. The data manipulation language and analytic functions used by end-user computer are also examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Toward Exosome-Based Therapeutics: Isolation, Heterogeneity, and Fit-for-Purpose Potency (2017)

Exosomes are defined as submicron (30-150 nm), lipid bilayer-enclosed extracellular vesicles (EVs), specifically generated by the late endosomal compartment through fusion of multivesicular bodies with the plasma membrane. Produced by almost all cells, exosomes were originally considered to represent just a mechanism for jettisoning unwanted cellular moieties. Although this may be a major function in most cells, evolution has recruited the endosomal membrane-sorting pathway to duties beyond mere garbage disposal, one of the most notable examples being its cooption by retroviruses for the generation of Trojan virions. It is, therefore, tempting to speculate that certain cell types have evolved an exosome subclass active in intracellular communication. We term this EV subclass "signalosomes" and define them as exosomes that are produced by the "signaling" cells upon specific physiological or environmental cues and harbor cargo capable of modulating the programming of recipient cells. Our recent studies have established that signalosomes released by mesenchymal stem/stromal cells (MSCs) represent the main vector of MSC immunomodulation and therapeutic action in animal models of lung disease. The efficacy of MSC-exosome treatments in a number of preclinical models of cardiovascular and pulmonary disease supports the promise of application of exosome-based therapeutics across a wide range of pathologies within the near future. However, the full realization of exosome therapeutic potential has been hampered by the absence of standardization in EV isolation, and procedures for purification of signalosomes from the main exosome population. This is mainly due to immature methodologies for exosome isolation and characterization and our incomplete understanding of the specific characteristics and molecular composition of signalosomes. In addition, difficulties in defining metrics for potency of exosome preparations and the challenges of industrial scale-up and good manufacturing practice compliance have complicated smooth and timely transition to clinical development. In this manuscript, we focus on cell culture conditions, exosome harvesting, dosage, and exosome potency, providing some empirical guidance and perspectives on the challenges in bringing exosome-based therapies to clinic.
Purification, Structural Analysis, and Function of Natural ATAC, a Cytokine Secreted by CD8+ T Cells (1997)

Recently, we identified a novel putative human cytokine expressed by activated CD8(+) T cells, which was designated ATAC (activation-induced, T cell-derived, and chemokine-related; the same molecule has been identified independently as lymphotactin and single cysteine motif-1). In this report, we provide evidence that ATAC is a secreted 93-amino acid protein that is generated from its precursor by proteolytic cleavage between Gly21 and Val22. An estimated 60% of ATAC (Val22-Gly114) is secreted as an unmodified protein with a molecular mass of 10,271.72 Da (apparent molecular mass of 12 kDa in SDS-polyacrylamide gel electrophoresis) and in which Cys32 and Cys69 are linked by a disulfide bridge. Unmodified ATAC is a cationic protein with a pI of 11.35 and is capable of binding to heparin. Some 40% of ATAC is O-glycosylated within 25 min of synthesis, giving rise to the appearance of a homogeneous 15-kDa (minor fraction) and a heterogeneous, terminally sialylated 17-19-kDa (major fraction) protein species in SDS-polyacrylamide gel electrophoresis. The secretion of all ATAC protein variants is completed within 30-40 min of synthesis. In terms of function, various ATAC protein forms were consistently ineffective in chemotaxis assays. In contrast, both purified natural ATAC and a chemically synthesized aglycosyl analog induced locomotion (chemokinesis) in purified CD4(+) and CD8(+) T cell populations at 400 ng/ml.
DVT and pulmonary embolism: Part II. Treatment and prevention. (2004)

Treatment goals for deep venous thrombosis include stopping clot propagation and preventing the recurrence of thrombus, the occurrence of pulmonary embolism, and the development of pulmonary hypertension, which can be a complication of multiple recurrent pulmonary emboli. About 30 percent of patients with deep venous thrombosis or pulmonary embolism have a thrombophilia. An extensive evaluation is suggested in patients younger than 50 years with an idiopathic episode of deep venous thrombosis, patients with recurrent thrombosis, and patients with a family history of thromboembolism. Infusion of unfractionated heparin followed by oral administration of warfarin remains the mainstay of treatment for deep venous thrombosis. Subcutaneously administered low-molecular-weight (LMW) heparin is at least as effective as unfractionated heparin given in a continuous infusion. LMW heparin is the agent of choice for treating deep venous thrombosis in pregnant women and patients with cancer. Based on validated protocols, warfarin can be started at a dosage of 5 or 10 mg per day. The intensity and duration of warfarin therapy depends on the individual patient, but treatment of at least three months usually is required. Some patients with thrombophilias require lifetime anticoagulation. Treatment for pulmonary embolism is similar to that for deep venous thrombosis. Because of the risk of hypoxemia and hemodynamic instability, in-hospital management is advised. Unfractionated heparin commonly is used, although LMW heparin is safe and effective. Thrombolysis is used in patients with massive pulmonary embolism. Subcutaneous heparin, LMW heparin, and warfarin have been approved for use in surgical prophylaxis. Elastic compression stockings are useful in patients at lowest risk for thromboembolism. Intermittent pneumatic leg compression is a useful adjunct to anticoagulation and an alternative when anticoagulation is contraindicated.
Autonomous Stimulation of Cancer Cell Plasticity by the Human NKG2D Lymphocyte Receptor Coexpressed with Its Ligands on Cancer Cells (2014)

The stimulatory NKG2D receptor on lymphocytes promotes tumor immune surveillance by targeting ligands selectively induced on cancer cells. Progressing tumors counteract by employing tactics to disable lymphocyte NKG2D. This negative dynamic is escalated as some human cancer cells co-opt expression of NKG2D, thereby complementing the presence of its ligands for autonomous stimulation of oncogenic signaling. Clinical association data imply relationships between cancer cell NKG2D and metastatic disease. Here we show that NKG2D promotes cancer cell plasticity by induction of phenotypic, molecular, and functional signatures diagnostic of the epithelial-mesenchymal transition, and of stem-like traits via induction of Sox9, a key transcriptional regulator of breast stem cell maintenance. These findings obtained with model breast tumor lines and xenotransplants were recapitulated by ex vivo cancer cells from primary invasive breast carcinomas. Thus, NKG2D may have the capacity to drive high malignancy traits underlying metastatic disease.
Vaccinia virus: an expression vector for genes from parasites (1986)

Smallpox has been eradicated by immunization with live vaccinia virus. Now, using genetic engineering, infectious vaccinia virus recombinants are being constructed which express genes from other pathogens. These viruses can stimulate specific immunological responses against the foreign antigen in vaccinated animals and can protect against disease caused by the corresponding pathogen. In this paper we describe how recombinant vaccinia viruses are constructed and illustrate the potential of this vector system for expression of genes from parasitic pathogens.
X-linked inhibitor of apoptosis positive nuclear labeling: a new independent prognostic biomarker of breast invasive ductal carcinoma (2011)

Disturbed balance of expression between XIAP and Smac probably contributed to carcinogenesis and XIAP positive nuclear labeling was a new independent prognostic biomarker of breast IDC.
Heparin sequences in the heparan sulfate chains of an endothelial cell proteoglycan. (1987)

The structure of the glycosaminoglycan chain of a heparan sulfate proteoglycan isolated from the conditioned medium of an endothelial cell line has been analyzed by using various degradative enzymes (heparitinase I, heparitinase II, heparinase, glycuronidase, sulfatases) from Flavobacterium heparinum. This proteoglycan inhibits the thromboplastin-activated pathway of coagulation; as a consequence, the catalytic conversion of prothrombin to thrombin is arrested. Heparitinase I (EC 4.2.2.8), an enzyme with specificity restricted to the heparan sulfate portion of the polysaccharide, releases fragments with the electrophoretic mobility and the structure of heparin. Conversely, an assessment of the size and distribution of the heparan sulfate regions has been provided by the use of heparinase (EC 4.2.2.7), which, by degrading the heparin sections of the chain, releases two segments that exhibit the structure of heparan sulfate. One of these segments is attached to the protein core. On the basis of these findings, the heparan sulfate chain can be defined as a copolymer containing heparin regions in its structure. The combined use of these enzymes has made it possible to establish the disaccharide sequence of parts of the glycosaminoglycan moiety of this proteoglycan.
Atomic Layer Deposition of AlO[sub x] for Thin Film Head Gap Applications (2001)

A 150-200°C atomic layer deposition (ALD) process has been developed for advanced gap and tunnel junction applications for thin films heads. The primary advantage of the ALD process is the near 100% step coverage with properties that are uniform along the sidewall. This process provides smooth pure (impurities atom %), films with excellent breakdown strength (9-10 MV/cm). The process uses trimethylaluminum (TMA) as the aluminum source and water as the oxidant. The optimal precursor/oxidant delivery methods for high breakdown strengths were found to be vapor draw for the TMA and a bubbler for the water. For both reagents, a sweep gas is used to reduce the transit time to the wafer. The ALD films are continuous and exhibit excellent insulating characteristics even down to 5-10 Å making them a potential candidate for tunnel barriers for magnetic tunnel junctions. By plasma annealing the films in situ every 25-50 Å, the as-deposited tensile stress becomes slightly compressive and the breakdown field exceeds 10 MV/cm. ALD provides a relatively low deposition rate of 0.8 Å/cycle. A small chamber volume that allows the cycle time of 5 s is the key to meeting production throughput requirements of 4-6 w for a 100 Å film. © 2001 The Electrochemical Society. All rights reserved.
CD5-Mediated Negative Regulation of Antigen Receptor-Induced Growth Signals in B-1 B Cells (1996)

A subset of B lymphocytes present primarily in the peritoneal and pleural cavities is defined by the expression of CD5 and is elevated in autoimmune diseases. Upon signaling through membrane immunoglobulin M (mIgM), splenic B lymphocytes (B-2) proliferate, whereas peritoneal B cells (B-1) undergo apoptosis. However, in CD5-deficient mice, B-1 cells responded to mIgM crosslinking by developing a resistance to apoptosis and entering the cell cycle. In wild-type B-1 cells, prevention of association between CD5 and mIgM rescued their growth response to mIgM crosslinking. Thus the B cell receptor-mediated signaling is negatively regulated by CD5 in normal B-1 cells.
Ionic Blockage of Sodium Channels in Nerve (1973)

Increasing the hydrogen ion concentration of the bathing medium reversibly depresses the sodium permeability of voltage-clamped frog nerves. The depression depends on membrane voltage: changing from pH 7 to pH 5 causes a 60% reduction in sodium permeability at +20 mV, but only a 20% reduction at +180 mV. This voltage-dependent block of sodium channels by hydrogen ions is explained by assuming that hydrogen ions enter the open sodium channel and bind there, preventing sodium ion passage. The voltage dependence arises because the binding site is assumed to lie far enough across the membrane for bound ions to be affected by part of the potential difference across the membrane. Equations are derived for the general case where the blocking ion enters the channel from either side of the membrane. For H(+) ion blockage, a simpler model, in which H(+) enters the channel only from the bathing medium, is found to be sufficient. The dissociation constant of H(+) ions from the channel site, 3.9 x 10(-6) M (pK(a) 5.4), is like that of a carboxylic acid. From the voltage dependence of the block, this acid site is about one-quarter of the way across the membrane potential from the outside. In addition to blocking as described by the model, hydrogen ions also shift the responses of sodium channel "gates" to voltage, probably by altering the surface potential of the nerve. Evidence for voltage-dependent blockage by calcium ions is also presented.
Stepping-Table Gadolinium- enhanced Digital Subtraction MR Angiography of the Aorta and Lower Extremity Arteries: Preliminary Experience (1999)

Stepping-table digital subtraction contrast material-enhanced MR angiography has high accuracy compared with catheter angiography in patients with arterio-occlusive disease of the aorta and outflow vessels. These preliminary study results suggest that this technique may ultimately provide a safe, noninvasive, and cost-effective alternative to catheter angiography.
Improved intra prediction mode-decision method (2005)

An improved intra-prediction method for AVS-M, which is developed by AVS (Audio Video Coding Standard Working Group of China) to meet the requirements of multimedia applications in next-generation mobile communications, is proposed in this paper. Utilizing the spatial and temporal correlation of the video sequences, the proposed method only processes a portion of normative 9 intra-prediction modes to decide the best mode, therefore, speeds up intra prediction with some degradation in the coding gain. Moreover, a complexity-scalable technique is presented to control the complexity of intra prediction, by which the video coder is matched to the limited computational resource of communication devices. The proposed methods are verified. The results show that the improved mode-decision method can significantly save encoding time at expense of little coding loss and the complexity-scalable technique works robustly and accurately. In addition, the proposed method also can be applied to other standards, such as H.264.
Aqueous tungsten(VI) alkyl chemistry (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAqueous tungsten(VI) alkyl chemistryIrene Feinstein-Jaffe, Steven F. Pedersen, and Richard R. SchrockCite this: J. Am. Chem. Soc. 1983, 105, 24, 7176–7177Publication Date (Print):November 1, 1983Publication History Published online1 May 2002Published inissue 1 November 1983https://pubs.acs.org/doi/10.1021/ja00362a029https://doi.org/10.1021/ja00362a029research-articleACS PublicationsRequest reuse permissionsArticle Views337Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Route for Lignin and Bio‐Oil Conversion: Dehydroxylation of Phenols into Arenes by Catalytic Tandem Reactions (2013)

Finding a workaround: The conversion of lignin into low-boiling-point arenes instead of high-boiling-point phenols could greatly facilitate conventional refinery processes. A new procedure for the depolymerization of lignin and simultaneous conversion phenols into arenes is described. The method can also be rendered as a fundamental finding for the upgrade of bio-oils to arenes under mild conditions.
Transmission line tower collapse investigation: A case study (2012)

Two adjacent 110kV self support suspension towers failed under broken conductor conditions. The conductor failed due to lightning damage and fatigue contributed to by Aeolian vibration. There were no earth wires on the structures which could prevent lightning damage and subsequent conductor breakage. The earth wires have a structural benefit of preventing a potential tower failure in excessive twisting of the tower top during broken phase conductor loading. This paper presents a methodology for the tower failure investigation using finite element modeling. The loading used under broken conductor conditions and the slenderness of members will be discussed. Recommendations for remedial strategies will be made.
Introduction to the algae: structure and reproduction (1985)

Very comprehensive text for physiology (algae) and/or limnology (freshwater biology) courses at the junior/senior/grad level.
Role of IL-4 and IFN-γ in modulation of immunity to Borrelia burgdorferi in mice (1995)

Because T cells appear to modulate the severity of murine Borrelia burgdorferi infections, we decided to examine the possible involvement of T cell-associated cytokines in disease outcome. Comparison of in vitro B. burgdorferi Ag-induced cytokine production in disease-susceptible and -resistant strains revealed striking differences; spleen cells from susceptible C3H mice produced significantly higher levels of IL-2 and IFN-gamma and lower levels of IL-4 than spleen cells from resistant BALB/c mice. Lymph node responses were even more divergent, with C3H mice producing high levels of IFN-gamma, and BALB/c mice producing little or none. This apparent Th1/Th2 cytokine imbalance was also reflected in vivo, since serum from C3H had significantly higher levels of B. burgdorferi-specific IgG2a Ab and lower levels of IgG1 Ab than serum from BALB/c mice. In vivo studies confirmed the importance of IL-4 in early control of spirochete growth, since treatment of either strain with neutralizing anti-IL-4 mAb led to increased joint swelling and higher spirochete burdens in joints compared with those in control mAb-treated mice. In contrast, IFN-gamma may hinder early control of spirochete growth in susceptible C3H mice, since treatment of mice with neutralizing anti-IFN-gamma mAb reduced both joint swelling and joint spirochete burdens compared with those in control mAb-treated mice. These studies indicate opposing roles for IL-4 and IFN-gamma in the modulation of spirochete growth and disease development in B. burgdorferi-infected mice and suggest that differential cytokine production early in infection may contribute to strain-related differences in susceptibility.
Biology and Physiology of the Osteoclast (1992)

Experimental Systems for Studying Osteoclast Biology (P. Osdoby, M. Krukowski, and P. Collin-Osdoby). Antigenic Markers of Osteoclasts (M.A. Horton and M.H. Helfrich). Acid Phosphatases (G. Andersson, B. Ek-Rylander, and C. Minkin). Ontogeny of the Osteoclast (P.J. Nijweide and R. de Grooth). Regulation of Osteoclast Development and Function (T.J. Chambers). Osteoclast Ultrastructure and Enzyme Histochemistry: Functional Implications (C.V. Gay). Systematic Factors Regulating Osteoclast Function (J.N.M. Heersche). Local Factors Regulating Osteoclast Function (G.R. Mundy). The Influence of Matrix Components on Osteoclasts (J. Glowacki). Signal Transduction Mechanisms in Osteoclasts (H.J. Donahue). Electrophysiology of Osteoclasts (S.M. SIms, M.E.M. Kelly, S.A. Arkett, and S.J. Dixon). Osteoclast Cytoskeleton and Attachment Proteins (A. Teti and A. Zambonin-Zallone). The Mechanism of Osteoclast Acidification (H.C. Blair and P.H. Schlesinger). Mechanism of Mineral Solubilization and Matrix Degradation in Osteoclastic Bone Resorption (J.-M. Delaisse and G. Vaes). Reactive Oxygen Species as Potential Mediators of Osteoclast Action (R.A. Greenwald and B.R. Rifkin). Osteoblast/Osteoclast Coupling (J.E. Puzas and M. Ishibe). Effects of Pharmacological Agents on Osteoclasts (P.H. Stern and P. Lakatos). Bisphosphonates (P.H. Schlesinger and H.C. Blair). . Mechanical Effects on Osteoclast Function (E.H. Burger). Osteopetrosis (L.K. Osier and S.C. MArks, Jr.). The Osteoclast in Paget's Disease of Bone (G. David Roodman). Index.
Current Practices and Controversies in Assisted Reproduction (2002)

15. 14. Ogedengbe OK, Giwa-Osagie OF, Ogunyemi O. Implications of pattern of tubal disease for microsurgery and in-vitro fertilisation in Lagos. Journal of the National Medical Association , 1987, 79:510–512.