gebhart/patrepeval huggingface dataset:
Conformational Changes and Dynamics of tRNAs: Evidence from Hydrolysis Patterns (1987)

Splitting of the ribose-phosphate chain of RNA has been reported in different works dealing with mRNA (see, e.g., Berger and Birkenmeier 1979), rRNA (see, e.g., Carbon et al. 1978; Garrett and Olesen 1982), and tRNA (Vlassov et al. 1981; Garret et al. 1984; Romby et al. 1985b). In some of these reports, ribonuclease contamination has been implicated (Berger and Birkenmeier 1979); in others, different experimental conditions have allowed the search for other causes of the degradations observed. This parasite phenomenon is of small amplitude (only a small percentage of the molecules are involved) but occurs even under the mild conditions generally used in biochemical work. Crystals provide a homogeneous sample of molecules, free from ribonucleases and under controlled conditions of ionic strength, pH, and temperature. Observation of the cleavage of the backbone of crystallized tRNAs has already been reported: Brown et al. (1983) and Rubin and Sundaralingam (1983) have described...
Characterization of Functionally Important Regions of Tissue Factor by Using Monoclonal Antibodies1 (1993)

Tissue factor is a cellular membrane glycoprotein that acts as a cofactor for Factor VIIa-catalyzed activation of Factors X and IX in the extrinsic blood coagulation pathway. We prepared fourteen murine monoclonal antibodies to human tissue factor (designated MTF-1 to -14), and purified tissue factor from human placenta by immunoaffinity chromatography using the antibody-coupled Sepharose 4B. The antibodies were characterized for inhibitory activity against the activation of Factor X by a complex of Factor VIIa and purified placental tissue factor or a recombinant mutant tissue factor whose transmembrane and cytoplasmic domains were deleted. Four MTFs (MTF-6, -7, -8, and -14) markedly inhibited the cofactor activity of tissue factor by directly blocking the interaction with Factor VIIa. Three other MTFs (MTF-1, -4, and -9) moderately inhibited the cofactor activity of the mutant tissue factor, presumably by diminishing the interaction between the extracellular region of the tissue factor and phospholipids. Both groups of MTFs inhibited the cofactor activity of the mutant tissue factor in Factor X activation by Factor VIIa in the absence of phospholipids. These findings suggest that the former four MTFs recognize the binding site for Factor VIIa and the latter three MTFs recognize the site for Factor X in the extracellular region of tissue factor. These MTFs are useful to purify tissue factor by immunoaffinity chromatography and to study the structure-function relationship of tissue factor, and may be useful to establish an immunoassay of tissue factor in body fluids.
History of structural acoustics and vibrations in the Acoustical Society of America (2002)

Structural acoustics refers to the interaction of sound and structures—the response of structures to sound, the radiation of sound from vibrating structures, and the effect of the acoustic medium on the structural vibrations. Interest in these subjects increased greatly during the 1930s and 40s because of practical applications in the design of microphones and loud speakers used in telephones, radios, and electronic phonographs. The combination of electrical and mechanical systems lead to the use of electrical engineering concepts such as impedance, circuits, and electrical analogies, in the analysis of mechanical systems. In later years, much of the work dealt with various aspects of underwater structures, prompted by U.S. Navy interests. The field, which began with classical analytical mechanics applications, has progressed to new approaches, including statistical energy analysis, near-field acoustical holography, fuzzy structures, active control of vibrations, and smart materials. In recognition of these new developments, the name of the technical committee was changed in 1987 from ‘‘Shock and Vibration’’ to ‘‘Structural Acoustics and Vibration.’’
Photobehavior of alkyl halides in solution: radical, carbocation, and carbene intermediates (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotobehavior of alkyl halides in solution: radical, carbocation, and carbene intermediatesPaul J. KroppCite this: Acc. Chem. Res. 1984, 17, 4, 131–137Publication Date (Print):April 1, 1984Publication History Published online1 May 2002Published inissue 1 April 1984https://doi.org/10.1021/ar00100a003RIGHTS & PERMISSIONSArticle Views773Altmetric-Citations159LEARN 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 InReddit PDF (823 KB) Get e-Alertsclose Get e-Alerts
Cloning and Functional Characterization of a Constitutively Expressed Nitrate Transporter Gene,OsNRT1, from Rice (2000)

Elucidating how rice (Oryza sativa) takes up nitrate at the molecular level could help improve the low recovery rate (<50%) of nitrogen fertilizer in rice paddies. As a first step toward that goal, we have cloned a nitrate transporter gene from rice called OsNRT1. OsNRT1 is a new member of a growing transporter family called PTR, which consists not only of nitrate transporters from higher plants that are homologs of the Arabidopsis CHL1 (AtNRT1) protein, but also peptide transporters from a wide variety of genera including animals, plants, fungi, and bacteria. However, despite the fact that OsNRT1 shares a higher degree of sequence identity with the two peptide transporters from plants (approximately 50%) than with the nitrate transporters (approximately 40%) of the PTR family, no peptide transport activity was observed when OsNRT1 was expressed in either Xenopus oocytes or yeast. Furthermore, contrasting the dual-affinity nitrate transport activity of CHL1, OsNRT1 displayed only low-affinity nitrate transport activity in Xenopus oocytes, with a K(m) value of approximately 9 mM. Northern-blot and in situ hybridization analysis indicated that OsNRT1 is constitutively expressed in the most external layer of the root, epidermis and root hair. These data strongly indicate that OsNRT1 encodes a constitutive component of a low-affinity nitrate uptake system for rice.
Gene therapy for neurological disease (2003)

Significant advances have been made in the last 20 years in understanding the basic biology of the normal nervous system and in elucidating molecular and cellular mechanisms underlying neurological disease. This progress has generated, for the first time, a realistic possibility of treating what have historically been common and tragically untreatable diseases of the nervous system. In particular, therapeutic delivery of genes to the degenerating, injured or developmentally-deficient nervous system offers the potential to prevent cell death, induce new growth and restore function. Clinical trials of gene therapy are beginning to move forward in several neurological disorders. We have thereby begun the transition to molecular-based medicine which has the potential to alter the landscape and prognosis of neurological disease.
Tritiation of pyrimidines by HTO in the presence of aluminium chloride (1965)

Abstract Pyrimidine derivatives (pyrimidine, 4, 6‐dichloropyrimidine, uracil, cytosine and 4‐chloro‐6‐hydroxypyrimidine) were tritiated at the ring by tritiated water in the presence of aluminium chloride in carbon disulphide or in ethylene dichloride (which is also tritiated in these conditions).
Development of a New Crosslinked-HEC Fluid Loss Control Pill for Highly-Overbalanced, High-Permeability and/or High Temperature Formations (1998)

Abstract The loss of brine to the hydrocarbon formations has been one of the major concerns during well completion operations. Fluid-loss control pill scontaining sized particulates, such as CaCO3 or sized salt, have often been used. However, damage to the formations and gravel packs by the solids due to solids invasion often causes reduced production and an expensive workover. The cleanup of the carbonate pill is often ineffective, especially in long intervals, since the reaction between acid and carbonate is too fast for the acid to cover the entire zone. Therefore, a reliable viscous fluid system without solids is more desirable than a particulate system. In high-permeability reservoirs, a highly crosslinked gel is needed to achieve good fluid-loss control hydroxyethylcellulose (HEC) is known for its low residue content and difficulty to be crosslinked. A highly elastic zirconium crosslinked HEC gel is achieved by using an activator and a chelant. A delaying agent is used to adjust the timing of the crosslink process. The gel is capable of stopping fluid loss in formations of 2 darcies and above at temperatures upto 290 F. Internal and/or external breakers can be used to reduce the gelviscosity to near water consistency. P. 215
Towards virtual networks for virtual machine grid computing (2004)

Virtual machines can greatly simplify wide-area distributed computing by lowering the level of abstraction to the benefit of both resource providers and users. Networking, however, can be a challenge because remote sites are loath to provide connectivity to any machine attached to the site network by outsiders. In response, we have developed a simple and efficient layer two virtual network tool that in effect connects the virtual machine to the home network of the user, making the connectivity problem identical to that faced by the user when connecting any new machine to his own network. We describe this tool and evaluate its performance in LAN and WAN environments. Next, we describe our plans to enhance it to become an adaptive virtual network that will dynamically modify its topology and routing rules in response to the offered traffic load of the virtual machines it supports and to the load of the underlying network. We formalize the adaptation problem induced by this scheme and take initial steps to solving it. The virtual network will also be able to use underlying resource reservation mechanisms on behalf of virtual machines. Both adaptation and reservation will work with existing, unmodified applications and operating systems.
Nausea and vomiting (N and V) in bone marrow transplant (BMT) patients—an investigation of the incidence, timing, and related factors (2006)

Background: Patients receiving high dose chemotherapy (HDCT) pre-BMT are at risk of N and V from multiple causes—highly emetic conditioning chemotherapy ± Total Body Irradiation; prior chemotherapy experiences; concomittant medications such as anti-infectives, opioid analgesics, immunosuppressants which may add to N and V; regimen related toxicity such as mucositis may play a role; nasoenteric feeding (N/E) is sometimes used. Whereas evidence based antiemetic guidelines are available for standard chemotherapy, they have not yet been accepted for BMT. Information on our own BMT patients had not been collected. Aim: To investigate the incidence, timing, and factors affecting N and V in BMT patients. Methods: Patients were interviewed to obtain consent, history of previous emesis and their risk factors for emesis. HDCT started on day −7 to −2 depending on protocol, and transplant on day 0. Patients were given a diary and education on how to record N and V daily until discharge. Standard antiemetics were given during HDCT. Chemotherapy, nursing emesis scores, all medications, incidence of mucositis, and use of N/E feeding was recorded. Results: There were 21 patients, 52% male, mean age 51. Conditioning regimens included high dose melphalan, cyclophosphamide/TBI, Bu/Cy/Etoposide, and BEAM. Most patients had experienced prior CT-induced nausea (81%) and vomiting (62%). Patients did not all record N and V every day for the following reasons: too unwell (febrile, severe mucositis etc), forgot, lost interest. Eight patients (38%) had novomiting at all during this study. Incidence of vomiting of any grade peaked on day 5 (36% patients). Nausea of any grade was up to 71% on days 3 and 4. Nausea persisted in >50% of reporting patients on day 12, and in 4 patients (all receiving melphalan) on day 25. Prior chemotherapy-induced emesis was a significant predictor of at least one vomiting episode (P = .01). Other factors were not significant. Conclusions: Nausea and vomiting are unresolved toxicities in BMT. Methodology for collecting N and V information will be modified for an on-going study.
Microarray analysis of xenograft‐derived cancer cell lines representing multiple experimental models of human prostate cancer (2003)

Expression analysis of 7129 transcripts was carried out in five human prostate cancer cell lines derived from orthotopic xenografts after one to five passages in nude mice and primary cultures of human normal prostate epithelial (NPE) cells. These experiments identified a consensus class of 214 genes (43 up- and 171 downregulated transcripts), expression of which was altered at least twofold in the same direction in all the cell lines relative to NPE cells. To validate the relevance of altered expression behavior of these genes for human prostate cancer, their expression pattern was evaluated in multiple additional experimental and clinical settings. Expression of 170 of these 214 genes (79%) was altered in the same direction in vivo in experimental human prostate tumors in mice. Similarly, the expression of 151 of the 214 genes (71%) was altered in the same direction in M12 cells, a variant of an SV40 large T antigen transformed normal human prostate epithelial cell line selected for increased malignancy in vivo. In clinical samples of human prostate tumors, the changes in transcript expression levels of majority of these genes (85% of downregulated and 76% of upregulated transcripts) are consistent with alterations of their expression pattern in xenograft-derived cancer cell lines. These results imply that the expression pattern of a large class of genes is consistently altered in multiple experimental models and clinical samples of human prostate cancer and underscore the potential relevance of the xenograft models and cell lines derived from them for expression analysis studies relevant to human cancer.
Simulation of Built-in PHP Features for Precise Static Code Analysis (2014)

The World Wide Web grew rapidly during the last decades and is used by millions of people every day for online shopping, banking, networking, and other activities. Many of these websites are developed with PHP, the most popular scripting language on the Web. However, PHP code is prone to different types of critical security vulnerabilities that can lead to data leakage, server compromise, or attacks against an application's users. This problem can be addressed by analyzing the source code of the application for security vulnerabilities before the application is deployed on a web server. In this paper, we present a novel approach for the precise static analysis of PHP code to detect security vulnerabilities in web applications. As dismissed by previous work in this area, a comprehensive configuration and simulation of over 900 PHP built-in features allows us to precisely model the highly dynamic PHP language. By performing an intra- and inter-procedural data flow analysis and by creating block and function summaries, we are able to efficiently perform a backward-directed taint analysis for 20 different types of vulnerabilities. Furthermore, string analysis enables us to validate sanitization in a context-sensitive manner. Our method is the first to perform fine-grained analysis of the interaction between different types of sanitization, encoding, sources, sinks, markup contexts, and PHP settings. We implemented a prototype of our approach in a tool called RIPS. Our evaluation shows that RIPS is capable of finding severe vulnerabilities in popular real-world applications: we reported 73 previously unknown vulnerabilities in five well-known PHP applications such as phpBB, osCommerce, and the conference management software HotCRP.
Continuous in Vitro Evolution of Catalytic Function (1997)

A population of RNA molecules that catalyze the template-directed ligation of RNA substrates was made to evolve in a continuous manner in the test tube. A simple serial transfer procedure was used to achieve approximately 300 successive rounds of catalysis and selective amplification in 52 hours. During this time, the population size was maintained against an overall dilution of 3 x 10(298). Both the catalytic rate and amplification rate of the RNAs improved substantially as a consequence of mutations that accumulated during the evolution process. Continuous in vitro evolution makes it possible to maintain laboratory "cultures" of catalytic molecules that can be perpetuated indefinitely.
Would-Be Counterfactual Dependence, Binary Causation and the Causality of Absences (2012)

Metaphysics has long taken for granted that causation is a binary relation. Recently, theories have arisen which challenge this claim. Such theories claim that some metaphysical problems regarding causation can be solved by taking causation to be ternary or quaternary. I respond to an argument that a quaternary formulation of causation can help resolve the causality of absences paradox (CAP). I reject this claim and propose an alternative solution to the CAP, which I argue is both consistent with a binary formulation of causal relations and preferable to the solution which a quaternary formulation allows for.
CYP82Y1 Is N-Methylcanadine 1-Hydroxylase, a Key Noscapine Biosynthetic Enzyme in Opium Poppy (2013)

Noscapine is a phthalideisoquinoline alkaloid investigated for its potent pharmacological properties. Although structurally elucidated more than a century ago, the biosynthesis of noscapine has not been established. Radiotracer studies have shown that noscapine is derived from the protoberberine alkaloid (S)-scoulerine and has been proposed to proceed through (S)-N-methylcanadine. However, pathway intermediates involved in the conversion of N-methylcanadine to noscapine have not been identified. We report the isolation and characterization of the cytochrome P-450 CYP82Y1, which catalyzes the 1-hydroxylation of N-methylcanadine to 1-hydroxy-N-methylcanadine. Comparison of transcript and metabolite profiles of eight opium poppy chemotypes revealed four cytochrome P-450s, three from the CYP82 and one from the CYP719 families, that were tightly correlated with noscapine accumulation. Recombinant CYP82Y1 was the only enzyme that accepted (R,S)-N-methylcanadine as a substrate with strict specificity and high affinity. As expected, CYP82Y1 was abundantly expressed in opium poppy stems where noscapine accumulation is highest among plant organs. Suppression of CYP82Y1 using virus-induced gene silencing caused a significant reduction in the levels of noscapine, narcotoline, and a putative downstream secoberbine intermediate and also resulted in increased accumulation of the upstream pathway intermediates scoulerine, tetrahydrocolum-bamine, canadine, and N-methylcanadine. The combined biochemical and physiological data support the 1-hydroxylation of (S)-N-methylcanadine catalyzed by CYP82Y1 as the first committed step in the formation of noscapine in opium poppy.
Anti-CD38-blocked ricin: an immunotoxin for the treatment of multiple myeloma [see comments] (1994)

We report the development of a potent anti-CD38 immunotoxin capable of killing human myeloma and lymphoma cell lines. The immunotoxin is composed of an anti-CD38 antibody HB7 conjugated to a chemically modified ricin molecule wherein the binding sites of the B chain have been blocked by covalent attachment of affinity ligands (blocked ricin). Conjugation of blocked ricin to the HB7 antibody has minimal effect on the apparent affinity of the antibody and no effect on the ribosome-inactivating activity of the ricin A-chain moiety. Four to six logs of CD38+ tumor cell line kill was achieved at concentrations of HB7-blocked ricin in the range of 0.1 to 3 nmol/L. Low level of toxicity for normal bone marrow (BM) granulocyte-macrophage colony- forming units (CFU-GM), burst-forming units-erythroid (BFU-E), colony- forming units-granulocyte/erythroid/monocyte/macrophage (CFU-GEMM) cells was observed. Greater than two logs of CD38+ multiple myeloma cells were depleted from a 10-fold excess of normal BM mononuclear cells (BMMCs) after an exposure to HB7-blocked ricin under conditions (0.3 nmol/L) that were not very toxic for the normal BM precursors. HB7- blocked ricin was tested for its ability to inhibit protein synthesis in fresh patients' multiple myeloma cells and in normal BMMCs isolated from two healthy volunteers; tumor cells from four of five patients were 100-fold to 500-fold more sensitive to the inhibitory effect of HB7-blocked ricin than the normal BM cells. HB7 antibody does not activate normal resting peripheral blood lymphocytes, and HB7-blocked ricin is not cytotoxic toward these cells at concentrations of up to 1 nmol/L. The potent killing of antigen-bearing tumor cells coupled with a lack of effects on peripheral blood T cells or on hematopoietic progenitor cells suggests that HB7-blocked ricin may have clinical utility for the in vivo or in vitro purging of human multiple myeloma cells.
An intramolecular FRET system monitors fingers subdomain opening in Klentaq1 (2008)

A major goal of polymerase research is to determine the mechanism through which a nucleotide complementary to a templating DNA base is selected and delivered to the polymerase active site. Structural evidence suggests a large open-to-closed conformational change affecting the fingers subdomain as being crucial to the process. We previously designed a FRET system capable of measuring the rate of fingers subdomain closure in the presence of correct nucleotide. However, this FRET system was limited in that it could not directly measure the rate of fingers subdomain opening by FRET after polymerization or in the absence of DNA. Here we report the development of a new system capable of measuring both fingers subdomain closure and reopening by FRET, and show that the rate of fingers subdomain opening is limited only by the rate of polymerization. We anticipate that this system will scale down to the single molecule level, allowing measurement of fingers subdomain movements in the presence of incorrect nucleotide and in the absence of DNA.