gebhart/patrepeval huggingface dataset:
Nitrogen fixation genetics and regulation in a Pseudomonas stutzeri strain associated with rice (2003)

The Pseudomonas stutzeri strain A1501 (formerly known as Alcaligenes faecalis) fixes nitrogen under microaerobic conditions in the free-living state and colonizes rice endophytically. The authors characterized a region in strain A1501, corresponding to most of the nif genes and the rnf genes, involved in electron transport to nitrogenase in Rhodobacter capsulatus. The region contained three groups of genes arranged in the same order as in Azotobacter vinelandii: (1) nifB fdx ORF3 nifQ ORF5 ORF6; (2) nifLA-rnfABCDGEF-nifY2/nafY; (3) ORF13 ORF12-nifHDK-nifTY ORF1 ORF2-nifEN. Unlike in A. vinelandii, where these genes are not contiguous on the chromosome, but broken into two regions of the genome, the genes characterized here in P. stutzeri are contiguous and present on a 30 kb region in the genome of this organism. Insertion mutagenesis confirmed that most of the nif and the rnf genes in A1501 were essential for nitrogen fixation. Using lacZ fusions it was found that nif and rnf gene expression was under the control of ntrBC, nifLA and rpoN and that the rnf gene products were involved in the regulation of the nitrogen fixation process.
Lidocaine Patches Reduce Pain in Trauma Patients with Rib Fractures (2011)

Rib fracture pain is notoriously difficult to manage. The lidocaine patch is effective in other pain scenarios with an excellent safety profile. This study assesses the efficacy of lidocaine patches for treating rib fracture pain. A prospectively gathered cohort of patients with rib fracture was retrospectively analyzed for use of lidocaine patches. Patients treated with lidocaine patches were matched to control subjects treated without patches. Subjective pain reports and narcotic use before and after patch placement, or equivalent time points for control subjects, were gathered from the chart. All patients underwent long-term follow-up, including a McGill Pain Questionnaire (MPQ). Twenty-nine patients with lidocaine patches (LP) and 29 matched control subjects (C) were analyzed. During the 24 hours before patch placement, pain scores and narcotic use were similar (LP 5.3, C 4.6, P = 0.19 and LP 51, C 32 mg morphine, P = 0.17). In the 24 hours after patch placement, LP patients had a greater decrease in pain scores (LP 1.2, C 0.0, P = 0.01) with no change in narcotic use (LP -8.4, C 0.5-mg change in morphine, P = 0.25). At 60 days, LP patients had a lower MPQ pain score (LP 7.7, C 12.2, P < 0.01), although only one patient was still using a patch. There was no difference in time to return to baseline activity (LP 73, C 105 days, P = 0.16) and no adverse events. Lidocaine patches are a safe, effective adjunct for rib fracture pain. Lidocaine patches resulted in a sustained reduction in pain, outlasting the duration of therapy.
Structure-activity relation of steroid teratogens. 1. Jervine ring system (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure-activity relation of steroid teratogens. 1. Jervine ring systemDennis Brown and Richard F. KeelerCite this: J. Agric. Food Chem. 1978, 26, 3, 561–563Publication Date (Print):May 1, 1978Publication History Published online1 May 2002Published inissue 1 May 1978https://doi.org/10.1021/jf60217a063Request reuse permissionsArticle Views159Altmetric-Citations22LEARN 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 (374 KB) Get e-Alertsclose Get e-Alerts
Structure of Microcin J25, a Peptide Inhibitor of Bacterial RNA Polymerase, is a Lassoed Tail (2003)

Microcin J25 (MccJ25) is a 21-amino acid peptide inhibitor active against the DNA-dependent RNA polymerase of Gram negative bacteria. Previously, the structure of MccJ25 was reported to be a head-to-tail circle, cyclo(-G(1)GAGHVPEYF(10)VGIGTPISFY(20)G-). On the basis of biochemical studies, mass spectrometry, and NMR, we show that this structure is incorrect, and that the peptide has an extraordinary structural fold. MccJ25 contains an internal lactam linkage between the alpha-amino group of Gly1 and the gamma-carboxyl of Glu8. The tail (Tyr9-Gly21) passes through the ring (Gly1-Glu8), with Phe19 and Tyr20 straddling each side of the ring, sterically trapping the tail in a noncovalent interaction we call a lassoed tail.
Transglutaminase activity in normal and hereditary cataractous rat lens and its partial purification (1981)

Hereditary cataractous rat lenses showed significantly higher specific activity for transglutaminase than the normal lenses of comparable age. Transglutaminase activity of normal lenses was distributed predominantly in the buffer-soluble fraction. The buffer-insoluble fraction showed 14% of total activity. The cortical and nuclear fractions of the normal lens showed 43% and 57% distribution of total activity, respectively. Protein solubilizing agents enhanced the activity of the enzyme in the lens homogenate in the following order: Triton X-100 greater than Tween 20 greater than Sodium dodecyl sulfate greater than Sodium deoxycholate greater than Sodium cholate greater than NaSCN greater than KI. Transglutaminase was purified 15 fold by hydrophobic affinity chromatography employing omega-amine octylagarose matrix. The purified enzyme was activated by calcium and inactivated by iodoacetamide and upon freeze-drying. Lens crystallins served as exogenous substrate for transglutaminase, with gamma-crystallin as the most effective amine acceptor.
Macrophages contribute to the cellular uptake of von Willebrand factor and factor VIII in vivo (2008)

Von Willebrand factor (VWF) and factor VIII (FVIII) circulate in a tight noncovalent complex. At present, the cells that contribute to the removal of FVIII and VWF are of unknown identity. Here, we analyzed spleen and liver tissue sections of VWF-deficient mice infused with recombinant VWF or recombinant FVIII. This analysis revealed that both proteins were targeted to cells of macrophage origin. When applied as a complex, both proteins were codirected to the same macrophages. Chemical inactivation of macrophages using gadolinium chloride resulted in doubling of endogenous FVIII levels in VWF-null mice, and of VWF levels in wild-type mice. Moreover, the survival of infused VWF was prolonged almost 2-fold in VWF-deficient mice after gadolinium chloride treatment. VWF and FVIII also bound to primary human macrophages in in vitro tests. In addition, radiolabeled VWF bound to human THP1 macrophages in a dose-dependent, specific, and saturable manner (half-maximal binding at 0.014 mg/mL). Binding to macrophages was followed by a rapid uptake and subsequent degradation of the internalized protein. This process was also visualized using a VWF-green fluorescent protein fusion protein. In conclusion, our data strongly indicate that macrophages play a prominent role in the clearance of the VWF/FVIII complex.
Development and Evaluation of Optimized Sucrose Ester Stabilized Oleanolic Acid Nanosuspensions Prepared by Wet Ball Milling with Design of Experiments (2014)

The aim of this study was to develop optimized sucrose ester (SE) stabilized oleanolic acid (OA) nanosuspensions (NS) for enhanced delivery via wet ball milling by design of experiments (DOE). In this study, SEOA NS batches were prepared by wet ball milling method. Mean particle sizes and polydispersity indices were determined using a nanosizer. The percent encapsulation efficiency, saturation solubility and in vitro dissolution rate were obtained with analyses using HPLC. Preparation methods were optimized by DOE using the Minitab software. The in vitro bioefficacy was obtained by methyl thiazolyl tetrazolium (MTT) measurements in A549 human non small cell lung cancer cell line. The in vivo pharmacokinetics profile was determined using LC-electrospray ionization (ESI)-MS/MS. The study produced spherical SEOA NS particles (ca. 100 nm in diameter) which were found to be able to increase OA saturation solubility considerably. Optimized SEOA-GBD NS (milled at 600 rpm for 3 h, sucrose monolaurate (SEL) : sucrose monopalmitate (SEP) at 9 : 1, w/w; SE : OA at 1 : 1, w/w) was found to be physically stable over 14 d at 4°C. The NS showed much higher dissolution rate, cytotoxicity and bioavailability when compared with the free drug. Thus, the prepared OA as SE stabilized NS particles by wet ball milling enhanced the saturation solubility, in vitro dissolution rate, bioefficacy and in vivo bioavailability of OA. The use of sugar esters may also be potentially applied to other hydrophobic drugs.
Distributed constrained heuristic search (1991)

A model of decentralized problem solving, called distributed constrained heuristic search (DCHS), that provides both structure and focus in individual agent search spaces to optimize decisions in the global space, is presented. The model achieves this by integrating decentralized constraint satisfaction and heuristic search. It is a formalism suitable for describing a large set of distributed artificial intelligence problems. The notion of textures that allow agents to operate in an asynchronous concurrent manner is introduced. The use of textures coupled with distributed asynchronous backjumping, a type of distributed dependency-directed backtracking that the authors have developed, enables agents to instantiate variables in such a way as to substantially reduce backtracking. The approach has been tested experimentally in the domain of decentralized job-shop scheduling. A formulation of distributed job-shop scheduling as a DCHS and experimental results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation, mapping, and regulated expression of the gene encoding mouse C-type natriuretic peptide (1996)

Genomic sequences encoding mouse C-type natriuretic peptide (CNP) were isolated from bacteriophage libraries and characterized by restriction enzyme and sequence analysis. The mouse CNP gene (Nppc) comprised at least two exons and one intron and included several cis-regulatory elements in the 5'-flanking sequence. The deduced amino acid sequence of mouse CNP-22 was identical to other mammalian CNPs. Analysis of allele distributions in interspecific back-cross and recombinant inbred strains assigned Nppc to chromosome 1. CNP transcripts were detected by ribonuclease protection analysis in brain, ovary, and uterus, with lower levels in testes and epididymus. Uterine CNP transcripts and protein were low in sexually immature mice and adults at estrus and increased at proestrus, but similar variations in ovarian CNP expression were not statistically significant. Atrial natriuretic peptide and B-type natriuretic peptide transcripts were not detected in mouse ovary or uterus. Thus CNP gene expression is regulated by tissue-specific and inducible mechanisms in female reproductive organs. Correlations between CNP expression and uterine fluid content suggest that CNP may regulate uterine fluid balance in mice and other mammals.
The short- and long-term safety of 5-aminosalicylate products in the treatment of ulcerative colitis. (2004)

5-aminosalicylic acid agents are effective in the treatment of ulcerative colitis. Balsalazide, mesalamine, and olsalazine are alternative formulations to sulfasalazine for the delivery of 5-aminosalicylic acid. The newer compounds might be better tolerated than sulfasalazine in some patients, as long as the intolerance is not due to hypersensitivity to 5-aminosalicylic acid. Adverse events requiring the withdrawal of therapy seem to occur less frequently with balsalazide, mesalamine, and olsalazine compared with sulfasalazine. If patients are unable to tolerate any one of these three 5-aminosalicylic acid-releasing preparations, they might be able to tolerate one of the others, as long as the intolerance is not due to hypersensitivity to 5-aminosalicylic acid.
Physical and functional interaction of human cytomegalovirus DNA polymerase and its accessory protein (ICP36) expressed in insect cells (1992)

Expression of the human cytomegalovirus (HCMV) (AD169) DNA polymerase gene under the control of the polyhedrin promoter of Autographa californica nuclear polyhedrosis virus in Spodoptera frugiperda (Sf9) cells has provided a source of highly active CMV DNA polymerase. In extracts from CMV-infected cells, the CMV DNA polymerase is found strongly associated with an additional polypeptide, ICP36. This protein has been identified as the CMV homolog of the herpes simplex virus type 1 UL42 gene product and may have a similar function. We have expressed HCMV DNA polymerase and ICP36 in the same system and demonstrated that they interact to form a stable complex. Moreover, ICP36 functions to stimulate the DNA polymerase activity in a template-dependent manner. We have compared the activity of the recombinant DNA polymerase in the presence and absence of ICP36 on a number of DNA templates and measured the effect of the polymerase inhibitors phosphonoformic acid and acyclovir triphosphate.
AZD9291 in TKI EGFR resistance in non-small cell lung cancer and the new concept of phase I trials. (2016)

Epidermal growth factor receptor (EGFR) tyrosine-kinase inhibitors (TKIs) constitute the standard of care for stage IV EGFR mutated non-small cell lung cancer (NSCLC) patients initiating first-line systemic treatment. Despite the initial remarkable activity of targeted treatment in these patients rendering objective response rates (ORR) of 50-80% and progression-free survivals (PFS) of 9-12 months, most patients present disease progression during the first 12 to 24 months. Although the activity of platinum-based doublets has been shown in EGFR mutated NSCLC patients after progression to first-line TKIs, PFS is rather short. Drug development companies have more recently focused their attention on the molecular basis of EGFR TKIs acquired resistance. Secondary resistance mutations have proven to be the most frequent cause of acquired resistance. Among them, T790M mutation in exon 20 seems to be the leading responsible for that resistance. Several agents have shown preliminary preclinical and clinical activity in overcoming acquired resistance to firstline EGFR TKIs. To date, however, only AZD9291, an oral, potent, irreversible EGFR TKI that is selective for EGFR tyrosine kinase inhibitor-sensitizing mutations and the T790M resistance mutation has shown to be not only highly active but also fairly tolerable in a large cohort of patients. Here we present a critical analysis of this trial in its clinical setting and propose some future directions.
Integrative Proteomics:  Functional and Molecular Characterization of a Particular Glutamate-Related Neuregulin Isoform (2005)

Glutamate is the major excitatory neurotransmitter in the mammalian brain and is related to memory by calcium-conducting receptors. Neuregulins have emerged as long-term modulating molecules of synaptic signaling by glutamate receptors, playing a role in some cognition/memory-related disorders and moreover being part of transient functional microdomains, called lipid rafts. Here we characterize one specific isoform of neuregulin as a central biomarker for glutamate-related signaling, integrating results from in vitro and in vivo models by a differential functional and proteomic approach.
The availability of unavailable information. (1997)

Currently, developers of decision-support systems try to integrate these systems with the electronic medical record. The drawback is a limited amount of recorded medical data. System developers who face the choice between designing an integrated 'non-inquisitive' system and an integrated 'inquisitive' system need insight into the availability of information that is being missed by the support system. Therefore, we have investigated in a simulation study, the reasons why information that was being missed from the electronic medical records of patients with asthma/COPD by reviewers, had not been recorded by general practitioners. Important reasons were: the physicians had not recorded the information explicitly, they assumed the requested information to be common knowledge, and the information was available elsewhere in the electronic medical record. Also, we investigated the reasons why information that was being missed, could not be made available by the physicians. Important reasons were: the decision had been made by another decision maker, or the physician had not recorded the information at the time of the encounter. In addition to insight into the availability of missing information, system developers need to have insight into the significance of this information for the quality of the decision support, before the final choice between a non-inquisitive and an inquisitive design can be made.
Measuring health-related quality of life in patients with mild to moderate eczema and psoriasis: clinical validity, reliability and sensitivity to change of the DLQI (1999)

The aim of this study was to assess the feasibility, validity, reliability and sensitivity to change of a Spanish version of the Dermatology Life Quality Index (DLQI) in patients with mild to moderate eczema and psoriasis who were treated with topical corticosteroids. The final study sample comprised 237 patients (48% eczema). Discriminant validity was tested by comparing patients' scores with those of a random sample of the general population (n = 100), and convergent validity by analysing correlations between DLQI scores, measures of clinical severity, and domain scores on the Nottingham Health Profile (NHP). Internal consistency and test-retest reliability were tested in clinically stable patients (n = 94), and responsiveness in a clinically unstable group (n = 143) initiating treatment with topical corticosteroids. Patient scores were significantly higher than general population scores (4.3 vs. 0. 27, P < 0.001). Correlations with NHP domains ranged from 0.12 to 0. 32, and there was significant correlation with clinical measures (r = 0.26, P < 0.001). Reliability was good (Cronbach's alpha = 0.83; intraclass correlation coefficient = 0.88), and the instrument proved responsive to change (effect size for the total group of de novo patients = 0.70), though the great majority of changes occurred in items 1 and 2. The NHP Emotional Reactions and Mobility domains were more responsive than some DLQI domains. In clinical trials of treatments for mild to moderate eczema and psoriasis, it is likely that only items 1 and 2 of the DLQI will be needed, and it is probably advisable to include generic instruments alongside the DLQI.
Differences in brain serotonergic metabolism between nonbulimic and bulimic patients with anorexia nervosa (1984)

CSF concentrations of serotonin and dopamine metabolites in 16 patients with anorexia nervosa were measured before and after probenecid administration, and the patients were studied before and at intervals after weight recovery. After probenecid administration, the weight-recovered nonbulimic anorexic patients had a higher concentration of the serotonin metabolite, 5-hydroxyindoleacetic acid, than the weight-recovered bulimic patients but no significant differences in CSF homovanillic acid. This finding is consistent with evidence that suggests a role for brain serotonin metabolism in carbohydrate and mood regulation.
A low-noise low-offset capacitive sensing amplifier for a 50-/spl mu/g//spl radic/Hz monolithic CMOS MEMS accelerometer (2004)

This paper describes a CMOS capacitive sensing amplifier for a monolithic MEMS accelerometer fabricated by post-CMOS surface micromachining. This chopper stabilized amplifier employs capacitance matching with optimal transistor sizing to minimize sensor noise floor. Offsets due to sensor and circuit are reduced by ac offset calibration and dc offset cancellation based on a differential difference amplifier (DDA). Low-duty-cycle periodic reset is used to establish robust dc bias at the sensing electrodes with low noise. This work shows that continuous-time voltage sensing can achieve lower noise than switched-capacitor charge integration for sensing ultra-small capacitance changes. A prototype accelerometer integrated with this circuit achieves 50-/spl mu/g//spl radic/Hz acceleration noise floor and 0.02-aF//spl radic/Hz capacitance noise floor while chopped at 1 MHz.
Abnormal involuntary movements induced by subthalamic nucleus stimulation in parkinsonian patients (1996)

Chronic electrical subthalamic nucleus (STN) stimulation is under investigation for alleviating parkinsonian symptoms. STN alterations may carry the risk of provoking abnormal involuntary movements (AIMs). We took advantage of the reversibility of the stimulation technique to assess the possibility of inducing AIMs, using different electrical variables with or without concomitant levodopa intake. Above a given threshold voltage, stimulation could induce contralateral distal mobile AIMs or hemiballism in the off-drug condition in two patients. AIMs occurred after a latency that varied from a few minutes up to several hours after switching on the stimulator. Hemiballism immediately disappeared upon switching off the stimulator. In these patients, levodopa had never provoked that type of AIMs before surgery. Levodopa-induced AIMs were not modified by electrical stimulation, but off-phase dystonia disappeared in one patient. Stimulation of the STN induced AIMs that resembled both those observed following spontaneous lesions of the STN and levodopa-induced diphasic AIMs in parkinsonian patients. As electrical stimulation provoked AIMs and antiparkinsonian benefit occurred with different electrical variables and different timing, the mechanisms responsible for these two effects could be distinct.
Binding of tenascin‐X to decorin (2001)

Tenascin-X (TN-X) is an extracellular matrix protein whose absence results in an alteration of the mechanical properties of connective tissue. To understand the mechanisms of integration of TN-X in the extracellular matrix, overlay blot assays were performed on skin extracts. A 100 kDa molecule interacting with TN-X was identified by this method and this interaction was abolished when the extract was digested by chondroitinase. By solid-phase assays, we showed that dermatan sulfate chains of decorin bind to the heparin-binding site included within the fibronectin-type III domains 10 and 11 of TN-X. We thus postulate that the association of TN-X with collagen fibrils is mediated by decorin and contributes to the integrity of the extracellular network.