gebhart/patrepeval huggingface dataset:
Formation of D-loops by the UvsX protein of T4 bacteriophage: a comparison of the reaction catalyzed in the presence or absence of gene 32 protein (1988)

The UvsX protein of T4 bacteriophage will catalyze the formation of D loops between linear single-stranded DNA (ssDNA) and homologous supercoiled double-stranded DNA (dsDNA) in the absence of T4 gene 32 protein (gp32). This reaction requires one monomer of UvsX protein per three nucleotides of ssDNA so that the ssDNA is completely covered with UvsX protein. Under these conditions, high rates of ATP hydrolysis are observed, and one-third of the products are joined paranemically. The reaction proceeds through a mechanism that creates homology-independent coaggregates of UvsX protein, dsDNA, and ssDNA. When UvsX protein is added to only 1 monomer per 8 nucleotides, but with 1 monomer of gp32 per 12 nucleotides, the rate of ATP hydrolysis is depressed, but D-loop formation is enhanced. Nearly all of the product is bound in plectonemic joints, and no coaggregated intermediates are formed. Coaggregate formation at high concentrations of UvsX protein is not inhibited by the presence of gp32; gp32 simply allows for efficient formation of D loops at such low concentrations of UvsX protein that coaggregates are not constructed. Electron microscopic visualization of the joint structures in this reaction reveals that both gp32 and UvsX protein are bound to the ssDNA. The single-stranded DNA binding (SSB) protein of Escherichia coli will substitute only partially for gp32: in the presence of SSB protein, D-loop formation can be catalyzed at one UvsX protein monomer per eight nucleotides, and it is accomplished without the formation of coaggregates, but a major portion of the product is joined paranemically.
Phase II trial of gemcitabine (G), carboplatin (C) and bexarotene (B) in patients (pts) with newly diagnosed, locally-advanced or metastatic non-small cell carcinoma of the lung (NSCLC) (2005)

7308 Background: The current standard of care for unresectable NSCLC is platinum-based chemotherapy. There is no benefit to adding together 3 or more cytotoxic agents, but adding a biologic agent may improve response rates and survival. B, a retinoic acid X-receptor agonist, is a differentiating agent with antineoplastic activity. Recent data suggests that the addition of B to platinum-based therapy may increase response rates and survival in NSCLC. Due to the poor outcome in this disease, we are studying a combination of G, C, and B as front-line therapy. Methods: Eligibility criteria includes histologically diagnosed NSCLC stage IIIB/IV; Karnofsky PS 70–100%; age ≥ 18, adequate bone marrow, renal and hepatic function, and written informed consent. Pts receive G, 1 g/m2 days 1 and 8 with C, AUC 5 (Calvert formula) on day 8. B, 400mg/m2 PO QD in divided doses is given days 1–28 of each treatment cycle. Pts may receive up to 6 cycles of chemotherapy or 2 cycles after CR achieved. Tumor restaging is performed every 2 cycles of therapy, in the absence of obvious rapid disease progression. Results: 19 pts have been enrolled; 10 males, 9 females; median age is 63.5 years (range 30–85 years). 2 pts had protocol violations (prior chemotherapy (1); small cell cancer on further pathologic evaluation (1)). A median of 2 cycles has been delivered (range 1–6). To date, the overall PR rate is 23.5% (4/17); 2 have had SD (1 progressed by cycle 4), for an overall clinical benefit rate of 35%. One is too early to evaluate. 18 pts to date are evaluable for toxicity. Thus far, the mean TTP is 68 days, and the mean OS is 142 days. The therapy has been well-tolerated with 7 pts experiencing Grade 2–3 myelosuppression (no febrile neutropenia), and 3 pts experiencing Grade 3–4 nausea and emesis. There have been no significant B-related adverse events. Conclusions: The addition of the differentiating agent B to a regimen of G and C is tolerable and active. In contrast to other studies, our early results suggest that the addition of B at this dose and schedule may add little to the clinical benefit observed with this regimen. Accrual continues in an effort to better define response rate and duration. No significant financial relationships to disclose.
Photocatalytic Hydrodefluorination: Facile Access to Partially Fluorinated Aromatics (2014)

Polyfluorinated aromatics are essential to materials science as well as the pharmaceutical and agrochemical industries and yet are often difficult to access. This Communication describes a photocatalytic hydrodefluorination approach which begins with easily accessible perfluoroarenes and selectively reduces the C-F bonds. The method allows facile access to a number of partially fluorinated arenes and takes place with unprecedented catalytic activity using a safe and inexpensive amine as the reductant.
Early Medical History of Children with Autism Spectrum Disorders (2006)

Previous studies have suggested that children with autism spectrum disorders (ASD) may have different medical histories than nonspectrum children in several areas: their reactions to vaccinations, number of ear infections, chronic gastrointestinal problems, and use of antibiotics. Furthermore, some studies have found associations between regressive autism and gastrointestinal (GI) symptoms. The present study analyzes the medical records from birth to the age of 2 years of 99 children (24 typically developing; 75 with ASD, of whom 29 had parent-reported regression). Data were coded in the following areas: frequency and purpose of pediatrician visits, frequency and type of illnesses and medications, type and chronicity of GI complaints, date of vaccinations, growth data, and whether the pediatrician noted behaviors indicative of an ASD before the age of 2 years. Children with ASD were found to have significantly more ear infections than the typically developing children as well as to use significantly more antibiotics. Typically developing children had significantly more illness-related fevers. There was a nonsignificant trend toward the ASD group having more chronic gastrointestinal problems. There were no significant differences between the groups for the age of vaccination or for number of pediatrician visits. Finally, pediatricians noted symptoms of onset of possible autism, including language delay, for 44 of the 75 children with ASD and 2 of the 24 typical children. Results are discussed in terms of needs for future research.
Very-low-operating-voltage organic light-emitting diodes using a p-doped amorphous hole injection layer (2001)

We demonstrate the use of a p-doped amorphous starburst amine, 4, 4′, 4″-tris(N, N-diphenyl- amino)triphenylamine (TDATA), doped with a very strong acceptor, tetrafluoro- tetracyano-quinodimethane by controlled coevaporation as an excellent hole injection material for organic light-emitting diodes (OLEDs). Multilayered OLEDs consisting of double hole transport layers of p-doped TDATA and triphenyl-diamine, and an emitting layer of pure 8-tris-hydroxyquinoline aluminum exhibit a very low operating voltage (3.4 V) for obtaining 100 cd/m2 even for a comparatively large (110 nm) total hole transport layer thickness.
GDP-fucose:GM1 α→2fucosyltransferase is activated in pare nchymal cells of rat liver during early stages of N-2-acetylaminofluorene induced hepatocarcinogenesis (1990)

Journal Article GDP-fucose:GM1 α→2fucosyltransferase is activated in pare nchymal cells of rat liver during early stages of N-2-acetylaminofluorene induced hepatocarcinogenesis Get access Eric H. Holmes Eric H. Holmes Pacific Northwest Research Foundation720 Broadway, Seattle, WA 98122, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Carcinogenesis, Volume 11, Issue 1, January 1990, Pages 89–94, https://doi.org/10.1093/carcin/11.1.89 Published: 01 January 1990 Article history Received: 03 July 1989 Revision received: 10 October 1989 Accepted: 11 October 1989 Published: 01 January 1990
N-(5,5-diacetoxypent-1-yl)doxorubicin: a new intensely potent doxorubicin analog (1992)

N-(5,5-Diacetoxypent-1-yl)doxorubicin (DAPDOX) (3), a new, water-soluble analogue of doxorubicin, has been synthesized by coupling doxorubicin with 5-oxopentane-1,1-diacetate in the presence of NaBH3CN. This analogue was designed to be converted to the corresponding aldehyde, N-(5-oxopent-1-yl)doxorubicin, in the presence of carboxylate hydrolases, enzymes that are ubiquitous in tissue. DAPDOX had a half-life of several days in 0.05 M phosphate or 0.05 M acetate buffer solution at pH 4.0. However, in 0.05 M phosphate buffer at pH 7.4 in the presence of 20 unit equiv of porcine liver carboxylate esterase, the half-life of DAPDOX was less than 1 min. N-(5-acetoxypent-1-yl)doxorubicin (4), which should give rise to N-(5-hydroxypent-1-yl)doxorubicin on esterase-mediated hydrolysis, and N-(pent-1-yl)doxorubicin (5), were also prepared for comparative biological studies. DAPDOX was 150 times more potent than doxorubicin at inhibiting the growth of Chinese hamster ovary (CHO) cells in culture. The compound retained the same degree of potency against a CHO subline 100-fold resistant to doxorubicin (CHO/DOX) that expressed elevated levels of P-glycoprotein. Compounds 4 and 5, on the other hand, were no more effective than doxorubicin at inhibiting the growth of CHO cells and were 4-7-fold less potent against the CHO/DOX subline. DAPDOX is representative of a new structural class of doxorubicin analogues with unique chemical and biological properties.
Characterization of recombinant human plasma lecithin: cholesterol acyltransferase (LCAT): N-linked carbohydrate structures and catalytic properties (1998)

The major N-linked carbohydrate structures were determined for recombinant human plasma lecithin:cholesterol acyltransferase (LCAT). The analysis of the structure of oligosaccharides by fast atom bombardment mass spectrometry (FAB-MS) and linkage analysis was preceded by reduction and carboxymethylation of the intact glycoproteins and digestion with trypsin and proline specific endopeptidase. The N-glycans were subsequently released from the glycopeptides by PNGase F digestion and the oligosaccharides were separated using a C18 Sep-pak cartridge. The data from the combination of FAB spectrometry and linkage analysis show that the N-linked glycans present on recombinant LCAT (rLCAT) were composed primarily of triantennary and tetraantennary structures with and without core fucosylation. A minor population of glycans (less than 5%) contained up to three repeats of N-acetyllactosamine in one or more antennae. The LCAT activities of both recombinant and circulating forms of plasma LCAT were determined using low molecular weight and lipoprotein substrates. The catalytic behavior of these two enzyme forms were found to be very similar if not identical. These findings validate the concept that the recombinant enzyme can serve as an appropriate model for structure/function studies of LCAT and provide the foundation for subsequent structural studies.
A 180 MHz 0.8 mu m BiCMOS modular memory family of DRAM and multiport SRAM (1993)

A family of modular memories with a built-in self-test interface designed using a synchronous self-timed architecture is described. This approach is ideally suited to modular memories embedded within synchronous systems due to its simple boundary specification, excellent speed/power performance, and ease of modelling. The basic port design is self-contained and extensible to any number of ports sharing access to a common-core cell array. The same design has been used to implement modular one-, two-, and four-part SRAMs and a one-port DRAM based on a four-transistor (4-T) cell. The latter provides a 45% core cell density improvement over the one-port SRAM. Nominal access and cycle times of 5.5 ns for 64 kb blocks have been shown for a 0.8 mu m BiCMOS process with no memory process enhancements. System operation at 100 MHz has been demonstrated on a broadband time-switch chip containing 96 kb of two-port SRAM.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Beyond e-Commerce: When Caterpillars Know What Butterflies Understand (2003)

Many small firms increasingly operate in markets under siege from new entrants who exploit the technologies associated with the Internet's World Wide Web (the web). In these circumstances, interpreting the operating environment is like a vu jade, the opposite of deja vu, a time in space where they have never been, have no idea what they are doing and who it is that could help them. Through the use of the story of the Caterpillar and the Butterfly, this paper considers the inherent difficulties faced by small firms considering the prospect of becoming an e-firm. When considered from an evolutionary perspective, the journey from small firm to small e-firm is not seen as one of choice, but rather one of necessity. In such markets, a race currently appears to exist between entrepreneurs exploiting the web's technologies, and the process of natural selection acting upon firms whose routines have lost favour.
A Single Component Conducting Polymer Hydrogel as a Scaffold for Tissue Engineering (2012)

Abstract Conducting polymers (CPs) have exciting potential as scaffolds for tissue engineering, typically applied in regenerative medicine applications. In particular, the electrical properties of CPs has been shown to enhance nerve and muscle cell growth and regeneration. Hydrogels are particularly suitable candidates as scaffolds for tissue engineering because of their hydrated nature, their biocompatibility, and their tissue‐like mechanical properties. This study reports the development of the first single component CP hydrogel that is shown to combine both electro‐properties and hydrogel characteristics. Poly(3‐thiopheneacetic acid) hydrogels were fabricated by covalently crosslinking the polymer with 1,1′‐carbonyldiimidazole (CDI). Their swelling behavior was assessed and shown to display remarkable swelling capabilities (swelling ratios up to 850%). The mechanical properties of the networks were characterized as a function of the crosslinking density and were found to be comparable to those of muscle tissue. Hydrogels were found to be electroactive and conductive at physiological pH. Fibroblast and myoblast cells cultured on the hydrogel substrates were shown to adhere and proliferate. This is the first time that the potential of a single component CP hydrogel has been demonstrated for cell growth, opening the way for the development of new tissue engineering scaffolds.
Dynamic modeling and learning user profile in personalized news agent (1999)

Due to the character of the original source materials and the nature of batch digitization, quality control issues may be present in this document. Please report any quality issues you encounter to digital@library.tamu.edu, referencing the URI of the item.
Oral and Dental Infections with Anaerobic Bacteria: Clinical Features, Predominant Pathogens, and Treatment (1993)

Microbial populations colonizing the teeth are a major source of pathogens responsible for oral and dental infections, including periodontal diseases, gingivitis, pericoronitis, endodontitis, peri-implantitis, and postextraction infections. Each entity has distinct clinical and microbial features. Bacterial species associated with oral infections include Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Bacteroides forsythus, Campylobacter rectus, Eubacterium species, Fusobacterium nucleatum, Eikenella corrodens, and Peptostreptococcus micros. Treponema pallidum-related spirochetes have been associated with acute necrotizing ulcerative gingivitis. Porphyromonas endodontalis appears to be specifically related to endodontic infections. Oral infections in medically compromised patients, including those with AIDS, are associated with similar species and are usually complicated by superinfection with enteric and Candida species. Isolation of species causing oral infections requires the collection of appropriate samples and the use of strictly anaerobic techniques. Rapid selective culture, immunofluorescence, and DNA probe methods have been developed for the identification of these oral species. The varied measures required in the management of oral and dental infections may include antimicrobial therapy. Accurate microbiological diagnosis, including antibiotic susceptibility testing, is indicated for cases that do not respond to therapy.
Transcriptional repression by the Rb-related protein p107. (1993)

The transcription factor DRTF1/E2F is believed to play an important role in regulating cellular proliferation because it undergoes a series of periodic interactions with proteins that are known to be important regulators of the cell cycle, including the retinoblastoma gene product (pRb) and cyclin A. Furthermore, certain viral oncogene products, such as adenovirus E1a, disrupt these DRTF1/E2F complexes by sequestering the associated proteins. p107, a protein that is structurally related to pRb, also binds to DRTF1/E2F, and in this study we investigate the functional consequences of this interaction. We show that p107 can repress E2F binding site-dependent transcription and that the adenovirus E1a protein overcomes p107-mediated transcriptional repression. Two distinct but related proteins, pRb and p107, can therefore repress transcription driven by DRTF1/E2F, whereas the E1a protein overrides the repression. We also demonstrate that the transcription repressing properties of p107 and pRb are influenced by the cell type and by differentiation, because neither protein affects transcription in F9 embryonal carcinoma (EC) cells but both do so efficiently in differentiated derivatives. In this respect, the repressing activities of pRb and p107 inversely correlate with the presence of the cellular E1a-like activity previously documented in F9 EC cells. These data suggest that p107 and pRb exert their biological activities in some but not all cell types.
A physiological approach to glaucoma management: the use of local hormones and the pharmacokinetics of prostaglandin esters. (1989)

It appears that a pragmatic approach, based entirely on the ability of a drug or procedure to reduce IOP, has thus far been used to develop modalities for the management of glaucoma. Barring serendipity, it is unlikely that this approach will produce effective new methods for the management of this ocular disorder, which presents an ever-increasing problem in an increasingly longevous and industrialized world population. Although a better understanding of the biology of aqueous humor dynamics and its pathogenesis, combined with new genetic engineering techniques, may eventually lead to the total elimination of glaucoma, that ultimate solution is unlikely to be achieved within the foreseeable future. Thus, a physiologic approach to glaucoma management must be developed, one that takes into consideration all of our recently acquired knowledge of aqueous humor dynamics and all other relevant physiologic principles. A review of currently available information suggests that from a physiologic point of view the best approach to glaucoma management, at least for the next few decades, will be based on the use of receptor-mediated, naturally occurring ocular hypotensive agents, or at least agents that closely resemble such naturally occurring autacoids. Based on the temporal and spatial limitations of the various classes of receptor-mediated autacoids and on differences in the specificity and the nature of the responses they elicit at different sites, we conclude that a physiologic approach to glaucoma management should focus on the use of topically applied local hormones or their analogs. This approach appears to be feasible in light of demonstrations that several members of one family of local hormones, the eicosanoids that are produced within ocular tissues under physiological conditions are effective ocular hypotensive agents. It has been shown that one member of this family, PGF2 alpha, in its esterified form, is an extremely potent ocular hypotensive agent in its esterified prodrug form in both normotensive and glaucomatous human eyes, yielding significant IOP reduction when topically applied in doses less than one-hundredth that of currently available glaucoma medications. Although no intraocular side effects have been noted in human eyes after topical application of PGF2 alpha-1-isopropylester in submaximal ocular hypotensive doses, such side effects as conjunctival hyperemia and foreign body sensation present a problem and a challenge.4
Plasma physics issues for inertial fusion with light ion beams (1992)

Inertial confinement fusion driven by beams of low atomic mass ions offers the potential for megajoule-class ignition experiments in the near term, gigajoule thermonuclear yields in the midterm, and economic fusion power in the longer term. The recent study by the Fusion Policy Advisory Committee noted that {open_quotes}light ion drivers may actually be closest to meeting the needs of an inertial fusion energy driver for economic power production.{close_quotes} However, the report also goes on to say that the ion beam program must still demonstrate the required beam intensity on target and resolve pulse shape and beam transport issues. The power generation, ion production, ion acceleration, focusing, and beam transport of these intense beams introduce new and challenging physics issues. The status of those issues and the progress in resolving them for the Particle Beam Fusion Accelerator II will be presented.
DNA sequence of a major human leukocyte interferon gene. (1981)

The gene for human leukocyte interferon alpha 2 (designated either LeIF A or HuIFN-alpha 2) has been isolated from a human genome library. The DNA sequence of this gene demonstrates that it lacks introns. The 3' noncoding sequences of the IFN-alpha 2 gene correspond to two types of IFN-alpha 2 cDNA clones we have isolated that have alternate sites of polyadenylylation. A comparison of seven human IFN-alpha sequences shows that they are homologous in the 5' flanking region and contain identical "TATA box" sequences. The recombinant lambda clone containing the IFN-alpha 2 gene also contains two copies of the "Alu family" repeat sequence.
Structure/Activity Relationships of 2-haloalkanoic Acids and Their Esters as Antitermitic Agents Against Formosan Subterranean Termites (Isoptera: Rhinotermitidae) (1987)

Journal Article Structure/Activity Relationships of 2-haloalkanoic Acids and Their Esters as Antitermitic Agents Against Formosan Subterranean Termites (Isoptera: Rhinotermitidae) Get access Rudolf H. Scheffrahn, Rudolf H. Scheffrahn Fort Lauderdale Research and Education Center, University of Florida-Institute of Food and Agricultural Sciences, 3205 College Avenue, Fort Lauderdale, Florida 33314 Search for other works by this author on: Oxford Academic PubMed Google Scholar Nan-Yao Su Nan-Yao Su Fort Lauderdale Research and Education Center, University of Florida-Institute of Food and Agricultural Sciences, 3205 College Avenue, Fort Lauderdale, Florida 33314 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 80, Issue 2, 1 April 1987, Pages 312–316, https://doi.org/10.1093/jee/80.2.312 Published: 01 April 1987 Article history Received: 23 June 1986 Accepted: 21 November 1986 Published: 01 April 1987
Aqueous-Phase One-Pot Synthesis of 2-Aminothiazole- or 2-Aminoselenazole-5-carboxylates from β-Keto Esters, Thiourea or Selenourea, and N-Bromo-succinimide under Supramolecular Catalysis (2007)

2-Amino-4-alkyl- and 2-amino-4-arylthiazole-5-carboxylates and their selenazole analogues were synthesized by α-halogenation of β-keto esters with N-bromosuccinimide, followed by cyclization with thiourea or selenourea, respectively, in the presence of β-cyclodextrin in water at 50 °C.