gebhart/patrepeval huggingface dataset:
ISOLATION AND CHARACTERIZATION OF CONDITIONAL ALLELES OF BACTERIOPHAGE T4 GENES uvsX AND uvsY (1984)

The bacteriophage T4 uvsW, uvsX and uvsY gene functions are required for wild-type levels of recombination and for normal survival and mutagenesis after treatments with ultraviolet (UV) and ionizing radiations. The ability of uvsX and uvsY mutations to suppress the lethality of gene 49 mutations was used to select temperature-sensitive and amber alleles of these two genes. (uvsW mutations do not suppress gene 49 mutations.) A simple and powerful complementation test was developed to assist in assigning uvs mutations to genes. The amber alleles of uvsX and uvsY behave as simple null alleles, fully suppressing a gene 49 defect, enhancing UV killing and abolishing UV mutagenesis. However, the properties of the ts alleles of uvsX and uvsY demonstrated that suppression of a gene 49 defect, sensitivity to UV-induced inactivation and UV mutability can be partially uncoupled. These results prompt the hypothesis that radiation mutagenesis occurs during DNA chain elongation past template damage within a recombinational intermediate rather than within a conventional replication fork.
Identification of an 85-100 kDa glycoprotein as a cell surface marker for an advanced stage of urothelial differentiation: association with the inter-plaque ('hinge') area. (1992)

Although bladder cancers account for almost 5% of all human cancer deaths, little is known about the biochemistry of urothelial differentiation. We have recently identified three major protein subunits ('uroplakins') of asymmetric unit membranes (AUM), which form rigid-looking plaques covering up to 70% of the apical surface of urothelial superficial (umbrella) cells. The ordinary-looking plasma membranes that interconnect these plaques are believed to be functionally specialized, serving as flexible but durable 'hinges'. Whether these hinge membranes are biochemically unique is unknown. Using a new monoclonal antibody (AE32) we have identified an 85-100 kDa glycoprotein (UGP85) which appears to be urothelium-specific. In both normal urothelium and cultured urothelial colonies this cell surface protein is associated mainly with superficial cells, suggesting that its expression is differentiation dependent. Results from in vitro translation experiments indicated that this glycoprotein contains a core polypeptide of about 55 kDa. Using immunogold localization techniques, we showed that in cultured urothelial colonies--which are known to lack mature AUM plaques--UGP85 is distributed relatively uniformly on the apical surface of some differentiated cells. However, in superficial cells of normal urothelium UGP85 is mainly associated with the hinge areas. These results raise the possibility that UGP85 is a plasma membrane component which can be excluded, to varying extents, from the plaque region as 12 nm protein particles are assembled into a tightly packed paracrystalline AUM structure. The identification of UGP85 provides the first evidence that the hinge areas interconnecting the urothelial plaques are biochemically distinguishable from the plasma membranes of the relatively undifferentiated urothelial cells of the lower cell layers.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of 2-Enoyl Thioester Reductase from Mammals (2003)

A data base search with YBR026c/MRF1', which encodes trans-2-enoyl thioester reductase of the intramitochondrial fatty acid synthesis (FAS) type II in yeast (Torkko, J. M., Koivuranta, K. T., Miinalainen, I. J., Yagi, A. I., Schmitz, W., Kastaniotis, A. J., Airenne, T. T., Gurvitz, A., and Hiltunen, K. J. (2001) Mol. Cell. Biol. 21, 6243-6253), revealed the clone AA393871 (HsNrbf-1, nuclear receptor binding factor 1) in human EST data bank. Expression of HsNrbf-1, tagged C-terminally with green fluorescent protein, in HeLa cells, resulted in a punctated fluorescence signal, superimposable with the MitoTracker Red dye. Wild-type polypeptide was immunoisolated from the extract of bovine heart mitochondria. Recombinant HsNrbf-1p reduces trans-2-enoyl-CoA to acyl-CoA with chain length from C6 to C16 in an NADPH-dependent manner with preference to medium chain length substrate. Furthermore, expression of HsNRBF-1 in the ybr026cDelta yeast strain restored mitochondrial respiratory function allowing growth on glycerol. These findings provide evidence that Nrbf-1ps act as a mitochondrial 2-enoyl thioester reductase, and mammalian cells may possess bacterial type fatty acid synthetase (FAS type II) in mitochondria, in addition to FAS type I in the cytoplasm.
Three-dimensional structure of the "long" neurotoxin from cobra venom. (1980)

The three-dimensional structure of alpha-cobra-toxin, the "long" neurotoxin from the venom of Naja naja siamensis, has been determined at 2.8-A resolution. Crystals grown as hexagonal needles have space group P6522 with unit cell parameters a = b = 74.59 A, c = 42.89 A; one molecule per asymmetric unit. Phases were determined with a single isomorphous derivative with HgI2 by using the anomalous scattering of the single-site HgI2 molecule to resolve the phase ambiguity. The polypeptide chain folds into three major loops and one tail emerging from a globular head. The protruding long central loop (residues 21-40) is flanked on either side by two shorter loops (residues 4-13 and 44-55); the tail piece (residues 63-71) hangs behind this loop. The molecular conformation is determined by four disulfides in the head and one at the tip of the long loop, by a triple-stranded beta-pleated sheet involving this loop, and by hydrophobic interactions stabilizing the other two loops. The structure of alpha-cobratoxin is compared to that described for the "short" erabutoxin b which shows similar arrangement of structurally and functionally invariant groups.
The effect of a heat and moisture exchanger on gas flow in a Mapleson F breathing system during inhalational induction (2000)

Heat and moisture exchangers (HMEs) humidify, warm and filter inspired gas, protecting patients and apparatus during anaesthesia. Their incorporation into paediatric anaesthetic breathing systems is recommended. We experienced delays in inhalational induction whilst using a Mapleson F breathing system with an HME. We have demonstrated that the HME significantly alters gas flow within the breathing system. Approximately half of the fresh gas flow is delivered to the patient, the remainder being wasted into the expiratory limb of the breathing system. We suggest that the HME should be removed from the Mapleson F breathing system until inhalational induction is complete, or that the reservoir bag is completely occluded until an effective seal is obtained with the mask.
The Effect of Saline Iontophoresis on Skin Integrity in Human Volunteers (1996)

This study, conducted in 36 human volunteers, was an evaluation of the effects of saline iontophoresis on skin temperature, irritation, and barrier function. The major objectives were to assess the effects of low-level ionic currents, to validate the proposed methodology of assessment, and to establish reproducibility in repeated saline iontophoresis applications. This was the first of a multistage study designed to assess the safety of 24-hr saline iontophoresis episodes at selected currents and current densities. Since an iontophoresis patch challenges the skin harrier both by occluding the skin surface and by passing ionic current through the skin, the experimental protocol was designed to permit measurement of the contribution of each of these processes to the overall response. In this first stage we investigated the effect of 10 min of current delivery, at 0.1 mA/cm2 on a 1-cm2 area patch and 0.2 mA/cm2 on a 6.5-cm2 area patch compared to unpowered control patches. Twelve subjects were tested under each condition on two separate occasions to examine reproducibility of the response variable measurements. A further 12 subjects were tested once under the 0.2 mA/cm 6.5-cm2 condition. Skin irritation was evaluated via repeated measurements of transepidermal water loss, capacitance, skin temperature, skin color, and a visual scoring system, before the iontophoresis episode and after patch removal. No damage to skin harrier function in terms of skin-water loss or skin-water content was detected. Slight, subclinical, short-lasting erythema was observed for both conditions. Assessment of correlation coefficients showed highly statistically significant indications of reproducibility for all five response variables measured. The experimental design, in combination with a repeated measures analysis, provided clear separation of the occlusion and ionic current components of the iontophoretic patch challenge. Further, the repeated measures analysis gave a highly sensitive assessment of skin irritation and resolution after patch removal. We conclude that the experimental methodology is appropriate for assessing possible changes in skin integrity resulting from saline iontophoresis under similar operating conditions for longer durations and for other skin challenges from which a subclinical response is expected.
The in vivo effect of regional hyperthermia on dunning R3327 prostatic tumor (1991)

This report describes the in vivo effect of regional hyperthermia on male Copenhagen rats implanted with Dunning R3327 prostatic carcinoma. In six rats, a 22-gauge 1.5-cm needle was inserted into the tumor and heated to 46.5 degrees C for 2 hr. Two hyperthermia treatments were administered 48 hr apart. In a separate group of six rats, the needle was inserted into the tumor, but not heated. After treatment, serial measurements of tumor volume and body weight were made twice a week for 4 weeks. From the first day of measurement to day 22, the tumor size in the treated group compared to control was significantly smaller, P = 0.02. In the first 12 days following treatment, the mean value of body weight in the treated and control groups decreased 7% and 3%, respectively. Following this, body weights increased to baseline levels by the end of the study. No other side effects related to hyperthermia were observed and no immediate mortality occurred. In the control group, two rats died from lung metastasis of the prostatic carcinoma after day 22. In the treated group, no lung metastases were found and no rats died before being sacrificed on day 29. Our experiments show that local elevation of the temperature of the Dunning tumor results in the death of tumor cells; at 46.5 degrees C for 2 hr there is marked tumor damage while the rats tolerated the hyperthermia well.
Tumor Necrosis Factor Alpha and Interleukin-1β Regulate the Murine Manganese Superoxide Dismutase Gene Through a Complex Intronic Enhancer Involving C/EBP-β and NF-κB (1997)

Manganese superoxide dismutase (MnSOD), a tumor necrosis factor (TNF)-inducible reactive oxygen-scavenging enzyme, protects cells from TNF-mediated apoptosis. To understand how MnSOD is regulated, transient transfections of promoter-reporter gene constructions, in vitro DNA binding assays, and in vivo genomic footprint (IVGF) analysis were carried out on the murine MnSOD gene. The results of this analysis identified a 238-bp region of intron 2 that was responsive to TNF and interleukin-1beta (IL-1). This TNF response element (TNFRE) had the properties of a traditional enhancer element that functioned in an orientation- and position-independent manner. IVGF of the TNFRE revealed TNF- and IL-1-induced factor occupancy of sites that could bind NF-kappaB and C/EBP. The 5' portion of the TNFRE bound C/EBP-beta in vitro and was both necessary and sufficient for TNF responsiveness with the MnSOD promoter or with a heterologous promoter when in an upstream position. The 3' end of the TNFRE bound both NF-kappaB and C/EBP but was not necessary for TNF responsiveness with the MnSOD promoter. However, this 3' portion of the TNFRE was required for the TNFRE to function as a downstream enhancer with a heterologous promoter. These data functionally separate the MnSOD TNFRE into a region responsible for TNF activation and one that mediates induction when it is downstream of a promoter.
Open fixed dose trial of fluoxetine in the treatment of obsessive compulsive disorder (1990)

Abstract Twelve non‐depressed DSM‐III obsessive compulsive disorder (OCD) patients were treated with fluoxetine in a 12 week open fixed dose study. After a 2 week washout period, patients were treated with 20 mg/day of fluoxetine for 1 week. The dosage was then raised to 40 mg/day for the remainder of the study. The Yale‐Brown Obsessive Compulsive Scale (Y‐BOCS) score (mean ± SD) decreased from 25.8 ± 4.5 to 15.4 ± 7.0 ( P &lt; 0.01) and the Symptom Check List‐90‐Obsessive Compulsive Subscale (SCL‐90‐OC) score (mean ± SD) also showed a decrease from 2.4 ± 0.8 to 1.3 ± 0.9 ( P &lt; 0.005). The results suggest that fluoxetine is effective in non‐depressed OCD patients. Our results also show that a 40 mg/day dosage is effective in contrast to previous studies that used 80 mg/day. Our finding of a significant treatment reduction in the SCL‐90‐OC is also in contrast to a previous OCD study in which the SCL‐58‐OC was not significantly reduced.
Accumulation of Ricinoleic, Lesquerolic, and Densipolic Acids in Seeds of Transgenic Arabidopsis Plants That Express a Fatty Acyl Hydroxylase cDNA from Castor Bean (1997)

A cDNA encoding the oleate 12-hydroxylase from castor bean (Ricinus communis L.) has previously been shown to direct the synthesis of small amounts of ricinoleic acid (12-hydroxyoctadec-cis-9-enoic acid) in seeds of transgenic tobacco plants. Expression of the cDNA under control of the Brassica napus napin promoter in transgenic Arabidopsis thaliana plants resulted in the accumulation of up to 17% of seed fatty acids as ricinoleate and two novel fatty acids that have been identified by gas chromatography-mass spectrometry as lesquerolic (14-hydroxyeicos-cis-11-enoic acid) and densipolic (12-hydroxyoctadec-cis-9,15-dienoic acid) acids. Traces of auricolic acid were also observed. These results suggest that either the castor hydroxylase can utilize oleic acid and eicosenoic acid as substrates for ricinoleic and lesquerolic acid biosynthesis, respectively, or Arabidopsis contains an elongase that accepts ricinoleic acid as a substrate. These observations are also consistent with indirect biochemical evidence that an n-3 desaturase is capable of converting ricinoleic acid to densipolic acid. Expression of the castor hydroxylase also caused enhanced accumulation of oleic acid and a corresponding decrease in the levels of polyunsaturated fatty acids. Since the steady-state level of mRNA for the oleate-12 desaturase was not affected, it appears that the presence of the hydroxylase, directly or indirectly, causes posttranscriptional inhibition of desaturation.
Prospects for hepatitis C vaccine. (1995)

The genetic and serological heterogeneity of hepatitis C virus and reinfections will make the development of a broad spectrum effective hepatitis C vaccine difficult. Important steps are identification of neutralising antibodies; reproducible techniques for tissue culture of HCV; the application of methods used for the development of vaccines against flaviviruses and pestiviruses, and the application of gene transfer techniques.
Quantifying the cerebral metabolic rate of oxygen by combining diffuse correlation spectroscopy and time-resolved near-infrared spectroscopy (2013)

Preterm infants are highly susceptible to ischemic brain injury; consequently, continuous bedside monitoring to detect ischemia before irreversible damage occurs would improve patient outcome. In addition to monitoring cerebral blood flow (CBF), assessing the cerebral metabolic rate of oxygen (CMRO2) would be beneficial considering that metabolic thresholds can be used to evaluate tissue viability. The purpose of this study was to demonstrate that changes in absolute CMRO2 could be measured by combining diffuse correlation spectroscopy (DCS) with time-resolved near-infrared spectroscopy (TR-NIRS). Absolute CBF was determined using bolus-tracking TR-NIRS to calibrate the DCS measurements. Cerebral venous blood oxygenation (SvO2) was determined by multiwavelength TR-NIRS measurements, the accuracy of which was assessed by directly measuring the oxygenation of sagittal sinus blood. In eight newborn piglets, CMRO2 was manipulated by varying the anesthetics and by injecting sodium cyanide. No significant differences were found between the two sets of SvO2 measurements obtained by TR-NIRS or sagittal sinus blood samples and the corresponding CMRO2 measurements. Bland-Altman analysis showed a mean CMRO2 difference of 0.0268 ± 0.8340 mLO2/100 g/min between the two techniques over a range from 0.3 to 4 mL O2/100 g/min.
Purification and some properties of the protein component of tissue thromboplastin from human brain (1977)

The protein component of tissue thromboplastib (Factor III) from human brain was purified by extraction of a microsomal fraction with sodium deoxycholate, gel filtration of the extract on Sephadex G-100 and preparative polyacrylamide-gel electrophoresis in the presence of sodium dodecyl sulphate. The product, apoprotein III, was homogeneous by anayltical polyacrylamide-gel electrophoresis, and it induced monospecific antibodies in rabbits and goat as shown by immunodiffusion and immunoelectrophoresis. Amino acid- and carbohydrate-analysis data for apoprotein III are presented. The carbohydrate moiety of the protein consists of fucose, mannose, galactose, N-acetylglucosamine and N-acetylneuraminate, amounting to a total content of 6.3g/100g. The apoprotein alone had no procoagulant activity. When Factor III was reconstituted by combining the pure apoprotein with a purified lipid fraction from the deoxycholate extract of crude Factor III, a high and optimal procoagulant activity was obtained at a phospholipid/protein ratio of 1.1g/g. Phosphatidylethanolamine alone had a weak but significant ability to restore activity, whereas phosphatidylcholine and phosphatidylserine separately had almost none. Two-component mixtures were on average more effective, and three-component mixtures far more effective, than the single phospholipids. The inclusion of a small amount of phosphatidylserine was very important for high activity.
p53 domains: structure, oligomerization, and transformation. (1994)

Wild-type p53 forms tetramers and multiples of tetramers. Friedman et al. (P. N. Friedman, X. B. Chen, J. Bargonetti, and C. Prives, Proc. Natl. Acad. Sci. USA 90:3319-3323, 1993) have reported that human p53 behaves as a larger molecule during gel filtration than it does during sucrose gradient sedimentation. These differences argue that wild-type p53 has a nonglobular shape. To identify structural and oligomerization domains in p53, we have investigated the physical properties of purified segments of p53. The central, specific DNA-binding domain within murine amino acids 80 to 320 and human amino acids 83 to 323 behaves predominantly as monomers during analysis by sedimentation, gel filtration, and gel electrophoresis. This consistent behavior argues that the central region of p53 is globular in shape. Under appropriate conditions, however, this segment can form transient oligomers without apparent preference for a single oligomeric structure. This region does not enhance transformation by other oncogenes. The biological implications of transient oligomerization by this central segment, therefore, remain to be demonstrated. Like wild-type p53, the C terminus, consisting of murine amino acids 280 to 390 and human amino acids 283 to 393, behaves anomalously during gel filtration and apparently has a nonglobular shape. Within this region, murine amino acids 315 to 350 and human amino acids 323 to 355 are sufficient for assembly of stable tetramers. The finding that murine amino acids 315 to 360 enhance transformation by other oncogenes strongly supports the role of p53 tetramerization in oncogenesis. Amino acids 330 to 390 of murine p53 and amino acids 340 to 393 of human p53, which have been implicated by Sturzbecher et al. in tetramerization (H.-W. Sturzbecher, R. Brain, C. Addison, K. Rudge, M. Remm, M. Grimaldi, E. Keenan, and J. R. Jenkins, Oncogene 7:1513-1523, 1992), do not form stable tetramers under our conditions. Our findings indicate that p53 has at least two autonomous oligomerization domains: a strong tetramerization domain in its C-terminal region and a weaker oligomerization domain in the central DNA binding region of p53. Together, these domains account for the formation of tetramers and multiples of tetramers by wild-type p53. The tetramerization domain is the major determinant of the dominant negative phenotype leading to transformation by mutant p53s.
The Current Status of Heterocyclic Combinatorial Libraries (1997)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Current Status of Heterocyclic Combinatorial LibrariesAdel Nefzi, John M. Ostresh, and Richard A. HoughtenView Author Information Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121 Cite this: Chem. Rev. 1997, 97, 2, 449–472Publication Date (Web):April 1, 1997Publication History Received8 November 1996Revised22 January 1997Published online1 April 1997Published inissue 1 April 1997https://pubs.acs.org/doi/10.1021/cr960010bhttps://doi.org/10.1021/cr960010bresearch-articleACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views2722Altmetric-Citations535LEARN 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 SUBJECTS:Amines,Organic polymers,Peptides and proteins,Reaction products,Solid phase synthesis Get e-Alerts
Reliability of Computed Tomography Measurements of Paraspinal Muscle Cross-Sectional Area and Density in Patients With Chronic Low Back Pain (2003)

The reliability of the CT scan for measuring the cross-sectional area and density of the back muscles is acceptable. The authors do not know definitely whether their results can be generalized because the interobserver and intermachine reliabilities were not investigated.
Preparation and Structures of 2-Dimethylamino- 4-phenyl-1,3,2-dioxaphosphorinane-2-oxides (1994)

Both cis- and trans isomers of 2-dimethylamino-4-phenyl-1.3.2-dioxaphosphorinane-2-oxide (6, 5) were formed in a cyclization reaction of Me_2NP(O)CI_2 (4) with PhCH(OH)CH_2CH_2(OH) (3) and separated into pure forms by chromatography. The X-ray molecular structure of the slowly migrating fraction 6 has been determined to be cis (Ph and P=O group cis)^1 with the configuration of 2RS, 4SR. Accordingly, the rapidly migrating fraction 5 is the trans isomer. The 1,3,2-dioxaphosphorinane ring of 6 is chair-like with the P-end essentially flattened. The crystal structure of 6 shows that both phenyl and oxygen (p=O) are seated equatorially with Me_2N- at the axial orientation. The geometry about exocyclic N deviates considerably from planarity, the sum of the angles around N being 345.0(4)°.